From asen at gate.sinica.edu.tw  Thu Mar  1 05:55:37 2007
From: asen at gate.sinica.edu.tw (A Sen)
Date: Thu, 1 Mar 2007 12:55:37 +0800
Subject: [Pw_forum] Selective dynamics
Message-ID: <20070301044736.M85525@gate.sinica.edu.tw>

Dear all,
???????????? Is it possible to do 'selective dynamics' with PWScf? If so, then how? By 'selective dynamics', I mean that certain atoms be allowed to move in certain directions while the others are kept fixed during structural relaxation of a semi-infinite system. 
I would greatly appreciate receiving your suggestions.
Best regards,
Arijit

 
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From ding at sissa.it  Thu Mar  1 08:08:53 2007
From: ding at sissa.it (Xunlei Ding)
Date: Thu, 01 Mar 2007 08:08:53 +0100
Subject: [Pw_forum] Selective dynamics
In-Reply-To: <20070301044736.M85525@gate.sinica.edu.tw>
References: <20070301044736.M85525@gate.sinica.edu.tw>
Message-ID: <45E67C05.6090404@sissa.it>

Dear Arijit,

In the file Doc/INPUT_PW, you can find these:

ATOMIC_POSITIONS { alat | bohr | crystal | angstrom }
in all cases except calculation = 'neb' or 'smd' :
  X 0.0  0.0  0.0  {if_pos(1) if_pos(2) if_pos(3)}
  Y 0.5  0.0  0.0
  Z 0.0  0.2  0.2
if calculation = 'neb' .OR. 'smd' :
  first_image
  X 0.0  0.0  0.0  {if_pos(1) if_pos(2) if_pos(3)}
  Y 0.5  0.0  0.0
  Z 0.0  0.2  0.2

In which,
if_pos=1: this atom in this direction can be moved,
and if_pos=0: this atom in this direction is frozen.

So you can write like this:
Au  1.0 0.5 0.5  1 1 0  (this Au atom can be moved in x,y directions and 
frozen in z direction)

Best regards,
Ding


A Sen wrote:

> Dear all,
>              Is it possible to do 'selective dynamics' with PWScf? If 
> so, then how? By 'selective dynamics', I mean that certain atoms be 
> allowed to move in certain directions while the others are kept fixed 
> during structural relaxation of a semi-infinite system.
> I would greatly appreciate receiving your suggestions.
> Best regards,
> Arijit
>


From wangjunjie1981_0 at 163.com  Thu Mar  1 09:12:09 2007
From: wangjunjie1981_0 at 163.com (wangjunjie1981_0)
Date: Thu, 1 Mar 2007 16:12:09 +0800 (CST)
Subject: [Pw_forum] error in q2r.out
Message-ID: <1161453016.459981172736729692.JavaMail.root@bj163app92.163.com>

 Dear stefano
 I have checked my files ,my qpoints list including Gamma point in scf calculation is 13 ,but the number of qpoints including Gamma point generated by kpoints.x is 12. Is this problem? symmetry operations in scf calculations is 12.digits of atomic coordinates is always  9 . in addition, I don't know whether symmetry of bravais lattice generated by kpoints.x is in info file. if it is in info file the symmetry of bravais  lattice is 24 .
at last , you say what truncation in the number of digits is and how to control it . with the input data  truncation in the number of digits can be modified. Thank you very much .
the info file is
  crystal axis:
  ( 1.0000 0.0000 0.0000)
  (-0.5000 0.8660 0.0000)
  ( 0.0000 0.0000 1.0680)
  reciprocal axis:
  ( 1.0000 0.5774 0.0000)
  ( 0.0000 1.1547 0.0000)
  ( 0.0000 0.0000 0.9363)
  Omega (in a^3 units) =   0.9249133991910384
  24  symmetry operations
  1  0  0   -1  0  0   -1  0  0    1  0  0    1  1  0    0 -1  0
  0  1  0    0 -1  0    1  1  0   -1 -1  0   -1  0  0    1  1  0
  0  0  1    0  0  1    0  0 -1    0  0 -1    0  0  1    0  0  1
  0  1  0   -1 -1  0    0 -1  0    1  1  0   -1 -1  0    0  1  0
 -1 -1  0    1  0  0   -1  0  0    0 -1  0    0  1  0    1  0  0
  0  0  1    0  0  1    0  0 -1    0  0 -1    0  0 -1    0  0 -1
 -1  0  0    1  0  0    1  0  0   -1  0  0   -1 -1  0    0  1  0
  0 -1  0    0  1  0   -1 -1  0    1  1  0    1  0  0   -1 -1  0
  0  0 -1    0  0 -1    0  0  1    0  0  1    0  0 -1    0  0 -1
  0 -1  0    1  1  0    0  1  0   -1 -1  0    1  1  0    0 -1  0
  1  1  0   -1  0  0    1  0  0    0  1  0    0 -1  0   -1  0  0
  0  0 -1    0  0 -1    0  0  1    0  0  1    0  0  1    0  0  1
  k(  1)=(  0  0  0 ) --- weight=  1 |folds in point #  0
  k(  2)=(  1  0  0 ) --- weight=  6 |folds in point #  0
  k(  3)=(  2  0  0 ) --- weight=  3 |folds in point #  0
  k(  6)=(  1  1  0 ) --- weight=  6 |folds in point #  0
  k( 17)=(  0  0  1 ) --- weight=  2 |folds in point #  0
  k( 18)=(  1  0  1 ) --- weight= 12 |folds in point #  0
  k( 19)=(  2  0  1 ) --- weight=  6 |folds in point #  0
  k( 22)=(  1  1  1 ) --- weight= 12 |folds in point #  0
  k( 33)=(  0  0  2 ) --- weight=  1 |folds in point #  0
  k( 34)=(  1  0  2 ) --- weight=  6 |folds in point #  0
  k( 35)=(  2  0  2 ) --- weight=  3 |folds in point #  0
  k( 38)=(  1  1  2 ) --- weight=  6 |folds in point #  0
the scf file is
Program PWSCF     v.2.1.5  starts ...
     Today is 28Feb2007 at 22:23: 1
     Ultrasoft (Vanderbilt) Pseudopotentials
     Current dimensions of program pwscf are:
     ntypx =10   npk =40000  lmax = 3
     nchix = 6  ndmx = 2000  nbrx =14 nqfx = 8
     bravais-lattice index     =            4
     lattice parameter (a_0)   =       6.6736  a.u.
     unit-cell volume          =     274.9038 (a.u.)^3
     number of atoms/cell      =            4
     number of atomic types    =            2
     kinetic-energy cutoff     =     110.0000  Ry
     charge density cutoff     =     400.0000  Ry
     convergence threshold     =      1.0E-08
     beta                      =       0.7000
     number of iterations used =            8  plain     mixing
     Exchange-correlation      = SLA  PW   NOGX NOGC (1400)
     iswitch =  0
     celldm(1)=   6.673595  celldm(2)=   0.000000  celldm(3)=   1.067998
     celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000
     crystal axes: (cart. coord. in units of a_0)
               a(1) = (  1.000000  0.000000  0.000000 )
               a(2) = ( -0.500000  0.866025  0.000000 )
               a(3) = (  0.000000  0.000000  1.067998 )
     reciprocal axes: (cart. coord. in units 2 pi/a_0)
               b(1) = (  1.000000  0.577350  0.000000 )
               b(2) = (  0.000000  1.154701  0.000000 )
               b(3) = (  0.000000  0.000000  0.936331 )
     PSEUDO 1 is Li         zval =  1.0   lmax= 1   lloc= 0
     (in numerical form:   433 grid points, xmin =  0.00, dx = 0.0000)
     PSEUDO 2 is N          zval =  5.0   lmax= 1   lloc= 0
     (in numerical form:   467 grid points, xmin =  0.00, dx = 0.0000)
     atomic species   valence    mass     pseudopotential
        Li             1.00     6.94120     Li( 1.00)
        N              5.00    14.00670     N ( 1.00)
     12 Sym.Ops. (with inversion)
   Cartesian axes
     site n.     atom                  positions (a_0 units)
         1           Li  tau(  1) = (   0.0000000   0.0000000   0.5339992  )
         2           Li  tau(  2) = (   0.0000000   0.5773503   0.0235199  )
         3           Li  tau(  3) = (   0.5000000   0.2886751  -0.0235199  )
         4           N   tau(  4) = (   0.0000000   0.0000000   0.0000000  )
     number of k points=   13
                       cart. coord. in units 2pi/a_0
        k(   1) = (   0.0000000   0.0000000   0.0000000), wk =   0.0312500
        k(   2) = (   0.0000000   0.0000000   0.2340828), wk =   0.0625000
        k(   3) = (   0.0000000   0.0000000  -0.4681655), wk =   0.0312500
        k(   4) = (   0.0000000   0.2886751   0.0000000), wk =   0.1875000
        k(   5) = (   0.0000000   0.2886751   0.2340828), wk =   0.1875000
        k(   6) = (   0.0000000   0.2886751  -0.4681655), wk =   0.1875000
        k(   7) = (   0.0000000  -0.5773503   0.0000000), wk =   0.0937500
        k(   8) = (   0.0000000  -0.5773503   0.2340828), wk =   0.1875000
        k(   9) = (   0.0000000  -0.5773503  -0.4681655), wk =   0.0937500
        k(  10) = (   0.2500000   0.4330127   0.0000000), wk =   0.1875000
        k(  11) = (   0.2500000   0.4330127   0.2340828), wk =   0.3750000
        k(  12) = (   0.2500000   0.4330127  -0.4681655), wk =   0.1875000
        k(  13) = (   0.0000000  -0.2886751   0.2340828), wk =   0.1875000
     G cutoff =  451.2529  (  37053 G-vectors)     FFT grid: ( 45, 45, 48)
     nbndx  =    16  nbnd   =     4  natomwfc =    36  npwx   =    5380
     nelec  =    8.00 nkb   =    16  ngl    =    1708
the file generate by kpoints.x
12
    1   0.0000000  0.0000000  0.0000000   1.00
    2   0.2500000  0.1443376  0.0000000   6.00
    3   0.5000000  0.2886751  0.0000000   3.00
    4   0.2500000  0.4330127  0.0000000   6.00
    5   0.0000000  0.0000000  0.2340828   2.00
    6   0.2500000  0.1443376  0.2340828  12.00
    7   0.5000000  0.2886751  0.2340828   6.00
    8   0.2500000  0.4330127  0.2340828  12.00
    9   0.0000000  0.0000000  0.4681655   1.00
   10   0.2500000  0.1443376  0.4681655   6.00
   11   0.5000000  0.2886751  0.4681655   3.00
   12   0.2500000  0.4330127  0.4681655   6.00
  
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From giannozz at nest.sns.it  Thu Mar  1 10:29:00 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 1 Mar 2007 10:29:00 +0100
Subject: [Pw_forum] error in q2r.out
In-Reply-To: <1161453016.459981172736729692.JavaMail.root@bj163app92.163.com>
References: <1161453016.459981172736729692.JavaMail.root@bj163app92.163.com>
Message-ID: <67FE6A24-90E4-4959-9BBA-4E4730355181@nest.sns.it>

On Mar 1, 2007, at 9:12 , wangjunjie1981_0 wrote:

> the info file is

If you want to have a small but nonzero probability of having
your problem solved, you should submit input data for pw.x,
ph.x, q2r.x

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




From giannozz at nest.sns.it  Thu Mar  1 10:33:16 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 1 Mar 2007 10:33:16 +0100
Subject: [Pw_forum] Berry Phase calculation in antimagnetic insulator
In-Reply-To: <OF63B86661.0FD48055-ON49257290.004182DB-49257290.0042EC58@mta.fujifilm.co.jp>
References: <OF63B86661.0FD48055-ON49257290.004182DB-49257290.0042EC58@mta.fujifilm.co.jp>
Message-ID: <AE6C8405-C507-4DB9-838D-A4F170C59484@nest.sns.it>

On Feb 28, 2007, at 13:11 , yukihiro_okuno at fujifilm.co.jp wrote:

> Should I set starting magnetization also in the Berry phase  
> calculation?

if the code says so, you should. It is actually not used in the  
calculation.
I think that recent versions of the code no longer require to specify a
starting magnetization if it is not needed

> By the way, in the berry phase calculation should we  set LDA+U option
> when I calculated previous scf run with LDA+U. ?

basically it is a bands structure calculation, so you should

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




From marcello.rosini at unimore.it  Thu Mar  1 12:09:30 2007
From: marcello.rosini at unimore.it (Marcello Rosini)
Date: Thu, 01 Mar 2007 12:09:30 +0100
Subject: [Pw_forum] NEB
Message-ID: <45E6B46A.70305@unimore.it>

Hi all,
I'm using espresso 3.0 for calculating the neb on a surface. I'm using
the "broyden" method as suggested by the input file explanation.
Nevertheless the suggested method is "quick-min".
My question is: since NEB calculation is quite long, what is the best
compromise between time saving and accuracy?
Thanks for any suggestion
Marcello
-- 
------------------------------------------------------------------------
*Dr. ROSINI MARCELLO*
rosini.marcello at unimo.it <mailto:rosini.marcello at unimo.it>
---------------------------------------------------
dipartimento di fisica <http://www.fisica.unimo.it>
Universit? degli studi di Modena e Reggio Emilia

via campi 213/a, 41100 Modena, Italy
tel +39 059 2055312  -  fax +39 059 2055616
------------------------------------------------------------------------



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From giannozz at nest.sns.it  Thu Mar  1 12:47:19 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 1 Mar 2007 12:47:19 +0100
Subject: [Pw_forum] NEB
In-Reply-To: <45E6B46A.70305@unimore.it>
References: <45E6B46A.70305@unimore.it>
Message-ID: <B263CB65-2E48-4BA0-AE28-88B94BD1A5CF@nest.sns.it>

On Mar 1, 2007, at 12:09 , Marcello Rosini wrote:

> I'm using espresso 3.0 for calculating the neb on a surface.
> I'm using the "broyden" method as suggested by the input
> file explanation. Nevertheless the suggested method is "quick-min".

who suggests what?

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




From degironc at sissa.it  Thu Mar  1 14:07:41 2007
From: degironc at sissa.it (degironc)
Date: Thu, 01 Mar 2007 14:07:41 +0100
Subject: [Pw_forum] error in q2r.out
In-Reply-To: <1161453016.459981172736729692.JavaMail.root@bj163app92.163.com>
References: <1161453016.459981172736729692.JavaMail.root@bj163app92.163.com>
Message-ID: <45E6D01D.5040101@sissa.it>

please read again my previous reply.
As stated there the grid you should feed to ph.x is the one augmented by 
pw.x on the basis of the crystal symmetry.
best,
stefano

wangjunjie1981_0 wrote:

> Dear stefano
> I have checked my files ,my qpoints list including Gamma point in scf 
> calculation is 13 ,but the number of qpoints including Gamma point 
> generated by kpoints.x is 12. Is this problem? symmetry operations in 
> scf calculations is 12.digits of atomic coordinates is always 9 . in 
> addition, I don't know whether symmetry of bravais lattice generated 
> by kpoints.x is in info file. if it is in info file the symmetry of 
> bravais lattice is 24 .
> at last , you say what truncation in the number of digits is and how 
> to control it . with the input data truncation in the number of digits 
> can be modified. Thank you very much .
>
> the info file is
>
> crystal axis:
> ( 1.0000 0.0000 0.0000)
> (-0.5000 0.8660 0.0000)
> ( 0.0000 0.0000 1.0680)
>
> reciprocal axis:
> ( 1.0000 0.5774 0.0000)
> ( 0.0000 1.1547 0.0000)
> ( 0.0000 0.0000 0.9363)
>
> Omega (in a^3 units) = 0.9249133991910384
>
>
> 24 symmetry operations
>
> 1 0 0 -1 0 0 -1 0 0 1 0 0 1 1 0 0 -1 0
> 0 1 0 0 -1 0 1 1 0 -1 -1 0 -1 0 0 1 1 0
> 0 0 1 0 0 1 0 0 -1 0 0 -1 0 0 1 0 0 1
>
> 0 1 0 -1 -1 0 0 -1 0 1 1 0 -1 -1 0 0 1 0
> -1 -1 0 1 0 0 -1 0 0 0 -1 0 0 1 0 1 0 0
> 0 0 1 0 0 1 0 0 -1 0 0 -1 0 0 -1 0 0 -1
>
> -1 0 0 1 0 0 1 0 0 -1 0 0 -1 -1 0 0 1 0
> 0 -1 0 0 1 0 -1 -1 0 1 1 0 1 0 0 -1 -1 0
> 0 0 -1 0 0 -1 0 0 1 0 0 1 0 0 -1 0 0 -1
>
> 0 -1 0 1 1 0 0 1 0 -1 -1 0 1 1 0 0 -1 0
> 1 1 0 -1 0 0 1 0 0 0 1 0 0 -1 0 -1 0 0
> 0 0 -1 0 0 -1 0 0 1 0 0 1 0 0 1 0 0 1
>
>
> k( 1)=( 0 0 0 ) --- weight= 1 |folds in point # 0
> k( 2)=( 1 0 0 ) --- weight= 6 |folds in point # 0
> k( 3)=( 2 0 0 ) --- weight= 3 |folds in point # 0
> k( 6)=( 1 1 0 ) --- weight= 6 |folds in point # 0
> k( 17)=( 0 0 1 ) --- weight= 2 |folds in point # 0
> k( 18)=( 1 0 1 ) --- weight= 12 |folds in point # 0
> k( 19)=( 2 0 1 ) --- weight= 6 |folds in point # 0
> k( 22)=( 1 1 1 ) --- weight= 12 |folds in point # 0
> k( 33)=( 0 0 2 ) --- weight= 1 |folds in point # 0
> k( 34)=( 1 0 2 ) --- weight= 6 |folds in point # 0
> k( 35)=( 2 0 2 ) --- weight= 3 |folds in point # 0
> k( 38)=( 1 1 2 ) --- weight= 6 |folds in point # 0
>
> the scf file is
> Program PWSCF v.2.1.5 starts ...
> Today is 28Feb2007 at 22:23: 1
>
> Ultrasoft (Vanderbilt) Pseudopotentials
>
> Current dimensions of program pwscf are:
> ntypx =10 npk =40000 lmax = 3
> nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8
>
>
> bravais-lattice index = 4
> lattice parameter (a_0) = 6.6736 a.u.
> unit-cell volume = 274.9038 (a.u.)^3
> number of atoms/cell = 4
> number of atomic types = 2
> kinetic-energy cutoff = 110.0000 Ry
> charge density cutoff = 400.0000 Ry
> convergence threshold = 1.0E-08
> beta = 0.7000
> number of iterations used = 8 plain mixing
> Exchange-correlation = SLA PW NOGX NOGC (1400)
> iswitch = 0
>
> celldm(1)= 6.673595 celldm(2)= 0.000000 celldm(3)= 1.067998
> celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
>
> crystal axes: (cart. coord. in units of a_0)
> a(1) = ( 1.000000 0.000000 0.000000 )
> a(2) = ( -0.500000 0.866025 0.000000 )
> a(3) = ( 0.000000 0.000000 1.067998 )
>
> reciprocal axes: (cart. coord. in units 2 pi/a_0)
> b(1) = ( 1.000000 0.577350 0.000000 )
> b(2) = ( 0.000000 1.154701 0.000000 )
> b(3) = ( 0.000000 0.000000 0.936331 )
>
>
> PSEUDO 1 is Li zval = 1.0 lmax= 1 lloc= 0
> (in numerical form: 433 grid points, xmin = 0.00, dx = 0.0000)
>
> PSEUDO 2 is N zval = 5.0 lmax= 1 lloc= 0
> (in numerical form: 467 grid points, xmin = 0.00, dx = 0.0000)
>
> atomic species valence mass pseudopotential
> Li 1.00 6.94120 Li( 1.00)
> N 5.00 14.00670 N ( 1.00)
>
> 12 Sym.Ops. (with inversion)
>
>
> Cartesian axes
>
> site n. atom positions (a_0 units)
> 1 Li tau( 1) = ( 0.0000000 0.0000000 0.5339992 )
> 2 Li tau( 2) = ( 0.0000000 0.5773503 0.0235199 )
> 3 Li tau( 3) = ( 0.5000000 0.2886751 -0.0235199 )
> 4 N tau( 4) = ( 0.0000000 0.0000000 0.0000000 )
>
> number of k points= 13
> cart. coord. in units 2pi/a_0
> k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0312500
> k( 2) = ( 0.0000000 0.0000000 0.2340828), wk = 0.0625000
> k( 3) = ( 0.0000000 0.0000000 -0.4681655), wk = 0.0312500
> k( 4) = ( 0.0000000 0.2886751 0.0000000), wk = 0.1875000
> k( 5) = ( 0.0000000 0.2886751 0.2340828), wk = 0.1875000
> k( 6) = ( 0.0000000 0.2886751 -0.4681655), wk = 0.1875000
> k( 7) = ( 0.0000000 -0.5773503 0.0000000), wk = 0.0937500
> k( 8) = ( 0.0000000 -0.5773503 0.2340828), wk = 0.1875000
> k( 9) = ( 0.0000000 -0.5773503 -0.4681655), wk = 0.0937500
> k( 10) = ( 0.2500000 0.4330127 0.0000000), wk = 0.1875000
> k( 11) = ( 0.2500000 0.4330127 0.2340828), wk = 0.3750000
> k( 12) = ( 0.2500000 0.4330127 -0.4681655), wk = 0.1875000
> k( 13) = ( 0.0000000 -0.2886751 0.2340828), wk = 0.1875000
>
> G cutoff = 451.2529 ( 37053 G-vectors) FFT grid: ( 45, 45, 48)
>
> nbndx = 16 nbnd = 4 natomwfc = 36 npwx = 5380
> nelec = 8.00 nkb = 16 ngl = 1708
>
> the file generate by kpoints.x
> 12
> 1 0.0000000 0.0000000 0.0000000 1.00
> 2 0.2500000 0.1443376 0.0000000 6.00
> 3 0.5000000 0.2886751 0.0000000 3.00
> 4 0.2500000 0.4330127 0.0000000 6.00
> 5 0.0000000 0.0000000 0.2340828 2.00
> 6 0.2500000 0.1443376 0.2340828 12.00
> 7 0.5000000 0.2886751 0.2340828 6.00
> 8 0.2500000 0.4330127 0.2340828 12.00
> 9 0.0000000 0.0000000 0.4681655 1.00
> 10 0.2500000 0.1443376 0.4681655 6.00
> 11 0.5000000 0.2886751 0.4681655 3.00
> 12 0.2500000 0.4330127 0.4681655 6.00
>
>
>
> ------------------------------------------------------------------------
> ??????????1.9?????????????????????? www.126.com <http://www.126.com/> 




From giannozz at nest.sns.it  Thu Mar  1 14:23:41 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 1 Mar 2007 14:23:41 +0100
Subject: [Pw_forum] phonon elph espresso 3.2
In-Reply-To: <Pine.LNX.4.58.0702221125250.24990@g32.physik.fu-berlin.de>
References: <Pine.LNX.4.58.0702221125250.24990@g32.physik.fu-berlin.de>
Message-ID: <C7571536-3132-4B41-8E82-6AB451083E0E@nest.sns.it>


On Feb 22, 2007, at 11:50 , Andrea Floris wrote:

> Sometime when one wants to perform phonon-e-ph calculation in the
> Brillouin zone BZ, it is faster to divide by hand the q's (i.e.  
> parallelizing
> by hand:), and then compute in parallel each q. That's why the option
> ldisp=.false. can be useful also in the contest of an a2F  
> calculation, in
> which by definition one needs the q's in BZ.

it works for me, if I understand correctly what you want. See the
attached input and output (1 = ldisp=.true. , 2 and 3 single q-point
calculations)

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

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From marcello.rosini at unimore.it  Thu Mar  1 14:41:01 2007
From: marcello.rosini at unimore.it (Marcello Rosini)
Date: Thu, 01 Mar 2007 14:41:01 +0100
Subject: [Pw_forum] NEB
Message-ID: <45E6D7ED.2090400@unimore.it>

from the Doc/INPUT_PW file, so which is the best compromise between time
saving and accuracy, among these methods?
Anyway I'm running some tests.

opt_scheme
               CHARACTER ( default = "quick-min" )
               specify the type of optimization scheme
               "sd"         : steepest descent
               "broyden"    : quasi-Newton Broyden's second method
(suggested)
               "quick-min"  : a minimization algorithm based on
                              molecular dynamics
               "damped-dyn" : damped molecular dynamics. See also the
                              keyword damp
               "mol-dyn"    : constant temperature molecular dynamics. See
                              also the keyword temp_req.
                              Note that, in order to perform such molecular
                              dynamics, spring forces are NOT projected
                              along the path.
               "langevin"   : finite temperature langevin dynamics of the
                              string (smd only). It is used to compute the
                              average path and the free-energy profile.
-- 
------------------------------------------------------------------------
*Dr. ROSINI MARCELLO*
rosini.marcello at unimo.it <mailto:rosini.marcello at unimo.it>
---------------------------------------------------
dipartimento di fisica <http://www.fisica.unimo.it>
Universit? degli studi di Modena e Reggio Emilia

via campi 213/a, 41100 Modena, Italy
tel +39 059 2055312  -  fax +39 059 2055616
------------------------------------------------------------------------



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From asen at gate.sinica.edu.tw  Thu Mar  1 14:42:00 2007
From: asen at gate.sinica.edu.tw (A Sen)
Date: Thu, 1 Mar 2007 21:42:00 +0800
Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1371 - 5 msgs
In-Reply-To: <20070301111001.11696.99171.Mailman@democritos.sissa.it>
References: <20070301111001.11696.99171.Mailman@democritos.sissa.it>
Message-ID: <20070301133343.M33968@gate.sinica.edu.tw>

Dear Ding,

Thank you so much for your ?helpful suggestions. I will definitely try it out.

Best regards,

Arijit?

> Message: 1 
> Date: Thu, 01 Mar 2007 08:08:53 +0100 
> From: Xunlei Ding <ding at sissa.it> 
> To: pw_forum at pwscf.org 
> Subject: Re: [Pw_forum] Selective dynamics 
> Reply-To: pw_forum at pwscf.org 
> 
> Dear Arijit, 
> 
> In the file Doc/INPUT_PW, you can find these: 
> 
> ATOMIC_POSITIONS { alat | bohr | crystal | angstrom } 
> in all cases except calculation = 'neb' or 'smd' : 
> ?X 0.0 ?0.0 ?0.0 ?{if_pos(1) if_pos(2) if_pos(3)} 
> ?Y 0.5 ?0.0 ?0.0 
> ?Z 0.0 ?0.2 ?0.2 
> if calculation = 'neb' .OR. 'smd' : 
> ?first_image 
> ?X 0.0 ?0.0 ?0.0 ?{if_pos(1) if_pos(2) if_pos(3)} 
> ?Y 0.5 ?0.0 ?0.0 
> ?Z 0.0 ?0.2 ?0.2 
> 
> In which, 
> if_pos=1: this atom in this direction can be moved, 
> and if_pos=0: this atom in this direction is frozen. 
> 
> So you can write like this: 
> Au ?1.0 0.5 0.5 ?1 1 0 ?(this Au atom can be moved in x,y directions and 
> frozen in z direction) 
> 
> Best regards, 
> Ding 
>

 
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From giannozz at nest.sns.it  Thu Mar  1 15:08:31 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 1 Mar 2007 15:08:31 +0100
Subject: [Pw_forum] phonon elph espresso 3.2
In-Reply-To: <Pine.LNX.4.58.0702221125250.24990@g32.physik.fu-berlin.de>
References: <Pine.LNX.4.58.0702221125250.24990@g32.physik.fu-berlin.de>
Message-ID: <C3717BC0-3889-40A4-8586-CF0B2BE44DF2@nest.sns.it>

On Feb 22, 2007, at 11:50 , Andrea Floris wrote:

> In any case with this meshes I get the error
>           1           2           4
>
>   0.500000000000000      -0.500000000000000       0.500000000000000
>  -0.250000000000000       0.250000000000000      -0.250000000000000
>   0.000000000000000E+000  0.000000000000000E+000  0.000000000000000E 
> +000

>      from phq_init : error #         1
>      wrong order of k points

I see: it is the option 'lnscf=.true.' that does not work as expected
(i.e. it doesn't work at all). It will be fixed very soon.

Paolo

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




From lawrence_lee_lee at yahoo.com.hk  Fri Mar  2 03:15:13 2007
From: lawrence_lee_lee at yahoo.com.hk (Lawrence Lee)
Date: Fri, 2 Mar 2007 10:15:13 +0800 (CST)
Subject: [Pw_forum] Pseudopotential problem about Mg
Message-ID: <20070302021513.63487.qmail@web54515.mail.yahoo.com>

Dear all,

I did a molecular dynamics run using pw.x on MgO, using pseudopotentials generated myself. The results turn out to be quite different from literature. I suspect that it's my pseudopotential's problem. Here below is the input file for ld1.x. Since I am green in generating pseudopotential, can anyone point out any problems in my input file, if there are any?

Lawrence.

 &input
     title='Mg',
     prefix='mg_lda_s1.5p0d0_n'
     zed=12,
     rel=1,
     beta=0.2,
     rlderiv=2.5,
     eminld=-6.0,
     emaxld=6.0,
     deld=0.02d0,
     nld=3,
     config='[Ne] 3s1.5 3p0 3d0',
     iswitch=3,
     dft='LDA',
 /
 &inputp
   pseudotype=2,
   lloc=2,
  !rcloc=1.00
   file_pseudopw='Mg_lda_s1.5p0d0_n.upf',
   nlcc=.true.,
 /
3
3S  1  0  1.50  0.00  1.90 1.90
3P  2  1  0.00  0.00  1.90 1.90
3D  3  2  0.00  0.00  1.90 1.90


 _______________________________________
 YM - ????
 ???????????????????????????????????????????
 http://messenger.yahoo.com.hk
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From kondor.jess at gmail.com  Fri Mar  2 04:43:14 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Thu, 1 Mar 2007 21:43:14 -0600
Subject: [Pw_forum] masses in vc-relax calculations
Message-ID: <1d9d5d9d0703011943h47335a83r143270ebc6aacf73@mail.gmail.com>

 Dear all,

   If I  will put all atomic masses equal to 1 for all atomic species in the
system,   will it speed up  'vc-relax' calculations? will be results
correct?

  Sincerely,
    jess
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From akohlmey at cmm.chem.upenn.edu  Fri Mar  2 06:09:16 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 2 Mar 2007 00:09:16 -0500 (EST)
Subject: [Pw_forum] Pseudopotential problem about Mg
In-Reply-To: <20070302021513.63487.qmail@web54515.mail.yahoo.com>
Message-ID: <Pine.LNX.4.44.0703020006010.12047-100000@localhost.localdomain>

On Fri, 2 Mar 2007, Lawrence Lee wrote:

LL> Dear all,
LL> 


LL> I did a molecular dynamics run using pw.x on MgO, using
LL> pseudopotentials generated myself. The results turn out to be quite
LL> different from literature. I suspect that it's my pseudopotential's
LL> problem. Here below is the input file for ld1.x. Since I am green in
LL> generating pseudopotential, can anyone point out any problems in my
LL> input file, if there are any?

Mg is a tough customer in terms of pseudopotentials.
i've been trying to get a good Mg potential on and off
for quite a while now. so it is probably better you start 
with practicing on some easier elements.

also, for MgO you'll need to include semi-core states.
a minimal pseudo will essentially be stripped off almost
all its electron density and is likely to give bad results.

cheers,
   axel.

LL> 
LL> Lawrence.
LL> 
LL>  &input
LL>      title='Mg',
LL>      prefix='mg_lda_s1.5p0d0_n'
LL>      zed=12,
LL>      rel=1,
LL>      beta=0.2,
LL>      rlderiv=2.5,
LL>      eminld=-6.0,
LL>      emaxld=6.0,
LL>      deld=0.02d0,
LL>      nld=3,
LL>      config='[Ne] 3s1.5 3p0 3d0',
LL>      iswitch=3,
LL>      dft='LDA',
LL>  /
LL>  &inputp
LL>    pseudotype=2,
LL>    lloc=2,
LL>   !rcloc=1.00
LL>    file_pseudopw='Mg_lda_s1.5p0d0_n.upf',
LL>    nlcc=.true.,
LL>  /
LL> 3
LL> 3S  1  0  1.50  0.00  1.90 1.90
LL> 3P  2  1  0.00  0.00  1.90 1.90
LL> 3D  3  2  0.00  0.00  1.90 1.90
LL> 
LL> 
LL>  _______________________________________
LL>  YM - ???u?T??
LL>  ?N???A?S???W???A?A???B?????i?H?d?U?T?????A?A???A?W?????N?????Y?????A???????????N?????C
LL>  http://messenger.yahoo.com.hk

-- 
=======================================================================
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.



From cesards at msi.umn.edu  Fri Mar  2 09:31:25 2007
From: cesards at msi.umn.edu (cesards at msi.umn.edu)
Date: Fri, 2 Mar 2007 02:31:25 -0600 (CST)
Subject: [Pw_forum] Re: masses in vc-relax calculations (Jess Kondor)
In-Reply-To: <20070302063809.23721.12823.Mailman@democritos.sissa.it>
References: <20070302063809.23721.12823.Mailman@democritos.sissa.it>
Message-ID: <49732.209.162.45.156.1172824285.squirrel@www.msi.umn.edu>

Hi Jess,

Using the same masses for all atomic species in vc-relax will usually
speed up calculations, and results will be still correct. The mass value
deos not matter, provided it is consistent with cell mass (wmass) and time
step. Consistent values will produce stable oscilations in vc-md and cell
frequencies will be in the same range as atomic ones.

Yours,

Cesar R.S. da Silva


>
>  Dear all,
>
>    If I  will put all atomic masses equal to 1 for all atomic species in
> the
> system,   will it speed up  'vc-relax' calculations? will be results
> correct?
>
>   Sincerely,
>     jess





From afloris at physik.fu-berlin.de  Fri Mar  2 10:55:22 2007
From: afloris at physik.fu-berlin.de (Andrea Floris)
Date: Fri, 2 Mar 2007 10:55:22 +0100 (CET)
Subject: [Pw_forum] phonon elph espresso 3.2
In-Reply-To: <20070302063809.23721.12823.Mailman@democritos.sissa.it>
References: <20070302063809.23721.12823.Mailman@democritos.sissa.it>
Message-ID: <Pine.LNX.4.58.0703021008460.31935@g32.physik.fu-berlin.de>

Dear Paolo and Malgorzata, thank you for your help.

Summarizing:

With ldisp=.true. (automatic q grid)
if one does the sequence of calculation
1) pw.x scf (with 'la2F=.true.')  2) pw.x scf (with la2F=.false.)  (at
k-mesh good enough for phonons, as in example07)  3) ph.x for phonon and
elph, then I don't get errors (with a sensible choice of grids:)

With ldisp=.false. (q by hand) :
if one does the sequence of calculation
1) pw.x scf (with 'la2F=.true.')  2) pw.x phonon (to diagonalize in ek
e(k+q) 3) ph.x phonon and elph, then I don't get errors.

With ldisp=.false. (q by hand) :
if one does the sequence of calculation
1) pw.x scf (with 'la2F=.true.')  2) pw.x scf (with la2F=.false.)  (at
k-mesh good enough for phonons, as in example07)  3) ph.x for phonon and
elph, then I get the error
     from phq_init : error #         1
      wrong order of k points

Then there is the example that you reported below (i.e. with
'lnscf=.true.'),
that seems to  produce the same error.
-------

Moreover: in my previous mail I said wrongly that the interpolation of the
elph
matrix elements was done in the subroutine lint. It is actually done in
PH/clinear.f90. Sorry for this.

Relative to PH/clinear.f90, I have a question:
can you confirm that
noint(1) noint(2) noint(3)...noint(nkfit) are the interpolated matrix
elements associated
respectively to the k point in crystal coordinates in this order: 000,
001, 002....010
011...100 101....nk1fit-nk2fit-nk3fit ?

ciao, grazie
Andrea



> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] phonon elph espresso 3.2
> Date: Thu, 1 Mar 2007 15:08:31 +0100
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Feb 22, 2007, at 11:50 , Andrea Floris wrote:
>
> > In any case with this meshes I get the error
> >           1           2           4
> >
> >   0.500000000000000      -0.500000000000000       0.500000000000000
> >  -0.250000000000000       0.250000000000000      -0.250000000000000
> >   0.000000000000000E+000  0.000000000000000E+000  0.000000000000000E
> > +000
>
> >      from phq_init : error #         1
> >      wrong order of k points
>
> I see: it is the option 'lnscf=.true.' that does not work as expected
> (i.e. it doesn't work at all). It will be fixed very soon.
>
> Paolo
>
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy



From baroni at sissa.it  Fri Mar  2 10:55:09 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 2 Mar 2007 10:55:09 +0100
Subject: [Pw_forum] Pseudopotential problem about Mg
In-Reply-To: <Pine.LNX.4.44.0703020006010.12047-100000@localhost.localdomain>
References: <Pine.LNX.4.44.0703020006010.12047-100000@localhost.localdomain>
Message-ID: <DA8BBA48-EED5-446D-85D0-BE72834F2B40@sissa.it>


On Mar 2, 2007, at 6:09 AM, Axel Kohlmeyer wrote:

> On Fri, 2 Mar 2007, Lawrence Lee wrote:
>
> LL> Dear all,
> LL>
>
>
> LL> I did a molecular dynamics run using pw.x on MgO, using
> LL> pseudopotentials generated myself. The results turn out to be  
> quite
> LL> different from literature. I suspect that it's my  
> pseudopotential's
> LL> problem. Here below is the input file for ld1.x. Since I am  
> green in
> LL> generating pseudopotential, can anyone point out any problems  
> in my
> LL> input file, if there are any?
>
> Mg is a tough customer in terms of pseudopotentials.
> i've been trying to get a good Mg potential on and off
> for quite a while now. so it is probably better you start
> with practicing on some easier elements.
>
> also, for MgO you'll need to include semi-core states.
> a minimal pseudo will essentially be stripped off almost
> all its electron density and is likely to give bad results.

or include non-linear core corrections at the very least (semi-core  
states may require a very large cutoff for norm-conserving PP's or  
multiple projectors for US PP's)

S.

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From marcel at physik.tu-berlin.de  Fri Mar  2 15:39:59 2007
From: marcel at physik.tu-berlin.de (Marcel Mohr)
Date: Fri, 2 Mar 2007 15:39:59 +0100 (CET)
Subject: [Pw_forum] Parallel pw compilation fftw.c warning
In-Reply-To: <49732.209.162.45.156.1172824285.squirrel@www.msi.umn.edu>
References: <20070302063809.23721.12823.Mailman@democritos.sissa.it>
 <49732.209.162.45.156.1172824285.squirrel@www.msi.umn.edu>
Message-ID: <20070302153005.H9602@rosa.physik-pool.TU-Berlin.DE>

Dear all

I just succesfully compiled pw.x with own compiled lapack, blas, fftw 
(v2.1.5 and with --enable-mpi).
During compilation of pw I get this warning:
>>>
icc -O3 -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA 
-I../include   -c fft_stick.c
fftw.c(27449): warning #188: enumerated type mixed with another type
           EXPECT_INT(dir);
           ^

fftw.c(27450): warning #188: enumerated type mixed with another type
           EXPECT_INT(type);
           ^
But the compilation finishes.

Should I use the provided fftw libs?

Regards
Marcel

________________________________________________________________________
Marcel Mohr			Institut f?r Festk?rperphysik, TU Berlin
marcel at physik.tu-berlin.de	Sekr. PN 5-4
TEL: +49-30-314 24442		Hardenbergstr. 36
FAX: +49-30-314 27705		10623 Berlin


From eyvaz_isaev at yahoo.com  Fri Mar  2 16:40:39 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 2 Mar 2007 07:40:39 -0800 (PST)
Subject: [Pw_forum] Parallel pw compilation fftw.c warning
Message-ID: <857203.42827.qm@web60316.mail.yahoo.com>

Hi Marcel,
 
fftw.c(27449): warning #188: enumerated type mixed with another type
           EXPECT_INT(dir);
           ^

fftw.c(27450): warning #188: enumerated type mixed with another type
           EXPECT_INT(type);
           ^
But the compilation finishes.

Should I use the provided fftw libs?

Yes, I think so. There are only warnings and seem to be harmless.

Bests,
Eyvaz.


Regards
Marcel

________________________________________________________________________
Marcel Mohr            Institut f?r Festk?rperphysik, TU Berlin
marcel at physik.tu-berlin.de    Sekr. PN 5-4
TEL: +49-30-314 24442        Hardenbergstr. 36
FAX: +49-30-314 27705        10623 Berlin






 
____________________________________________________________________________________
TV dinner still cooling? 
Check out "Tonight's Picks" on Yahoo! TV.
http://tv.yahoo.com/


From cao at qtp.ufl.edu  Fri Mar  2 20:55:03 2007
From: cao at qtp.ufl.edu (Chao Cao)
Date: Fri, 02 Mar 2007 14:55:03 -0500
Subject: [Pw_forum] PWSCF and PAW
Message-ID: <45E88117.3000106@qtp.ufl.edu>

Dear PWSCF users,
 Since I see there's a subdirectory in atomic_doc/ about PAW 
pseudopotential generation, and also several files about PAW in 
directory PW/, I assumed that PWSCF is capable to use PAW 
pseudopotentials. However, when I set the pseudopotential to the file 
produced in paw_gen_test/, the program fails because of "pseudopotential 
is empty or wrong". So, does that mean I can't use PAW or I have to turn 
on some secrete flags in the input file? Thanks


Best


Chao Cao


From degironc at sissa.it  Fri Mar  2 22:07:30 2007
From: degironc at sissa.it (degironc)
Date: Fri, 02 Mar 2007 22:07:30 +0100
Subject: [Pw_forum] PWSCF and PAW
In-Reply-To: <45E88117.3000106@qtp.ufl.edu>
References: <45E88117.3000106@qtp.ufl.edu>
Message-ID: <45E89212.4070903@sissa.it>

This means that PAW are under development and that so far only the 
generation of datasets is done, while the incorporation into PW is 
underway. We hope it will be available soon in the distribution.
stefano

Chao Cao wrote:

> Dear PWSCF users,
> Since I see there's a subdirectory in atomic_doc/ about PAW 
> pseudopotential generation, and also several files about PAW in 
> directory PW/, I assumed that PWSCF is capable to use PAW 
> pseudopotentials. However, when I set the pseudopotential to the file 
> produced in paw_gen_test/, the program fails because of 
> "pseudopotential is empty or wrong". So, does that mean I can't use 
> PAW or I have to turn on some secrete flags in the input file? Thanks
>
>
> Best
>
>
> Chao Cao
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum




From ghaderyan at gmail.com  Fri Mar  2 21:57:32 2007
From: ghaderyan at gmail.com (saman ghaderyan)
Date: Sat, 3 Mar 2007 00:27:32 +0330
Subject: [Pw_forum] cell parameter
Message-ID: <aa36e8060703021257s277c23b7v19820f8399ba5644@mail.gmail.com>

hi
i have some problem in definition of CELL PARAMETER and CRYSTAL AXES ,what
they related to CELLDM(1)..?
thanks.
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From akohlmey at cmm.chem.upenn.edu  Sat Mar  3 00:11:44 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 2 Mar 2007 18:11:44 -0500 (EST)
Subject: [Pw_forum] cell parameter
In-Reply-To: <aa36e8060703021257s277c23b7v19820f8399ba5644@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0703021809500.12232-100000@localhost.localdomain>

On Sat, 3 Mar 2007, saman ghaderyan wrote:

SG> hi
SG> i have some problem in definition of CELL PARAMETER and CRYSTAL AXES ,what
SG> they related to CELLDM(1)..?

there are plenty of files in the Doc directory. they explain
exactly what is going on. you may have to read through several
of them, since not everybody explains and understands everything
in the same way.

axel.

SG> thanks.
SG> 

-- 
=======================================================================
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.



From amit76.india at gmail.com  Sat Mar  3 09:22:58 2007
From: amit76.india at gmail.com (Amit Kumar)
Date: Sat, 3 Mar 2007 13:52:58 +0530
Subject: [Pw_forum] filelph
Message-ID: <aef8bbf00703030022j71cf2970md73fe606f38122@mail.gmail.com>

 Respected Users,

 It's written in the DOC file that

 filelph     file where electron-phonon matrix elements are written  ' '

 However, in the new version, if we run example 7 with filelph = 'al.elph',
we  don't get
 any al.elph file in the output directory 'results'.
 On the oherhand, in case of old version we get
 al.elph where different lambda values are written not the matrix element
 | <V (SCF) > | ^2 .

 Any useful comments will be appreciated.

 Regards,
 Amit
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From ihsanas at yahoo.com  Sat Mar  3 17:46:46 2007
From: ihsanas at yahoo.com (احسان عريقات)
Date: Sat, 3 Mar 2007 08:46:46 -0800 (PST)
Subject: [Pw_forum] plotrho
Message-ID: <734130.34603.qm@web52312.mail.yahoo.com>

Hi 
please, can you tell me what`s the meaning of 0 0.9 6
in plotrho file and how can I change it for different
atoms.
Thanks

si.rho.dat
si.rho.ps
n
0 0.09 6

Ihsan


 
____________________________________________________________________________________
Don't pick lemons.
See all the new 2007 cars at Yahoo! Autos.
http://autos.yahoo.com/new_cars.html 


From d.schmicker at yahoo.de  Sat Mar  3 18:19:33 2007
From: d.schmicker at yahoo.de (Detlef Schmicker)
Date: Sat, 03 Mar 2007 18:19:33 +0100
Subject: [Pw_forum] Using fftw wrapper for intel mkl lib?
Message-ID: <1172942373.12797.1.camel@localhost>

Hello,

did anybody manage to compile pwscf (pw.x) using the fftw-wrapper of mkl
9.0?

Would be great to get some help.

Thanks Detlef



From ihsanas at yahoo.com  Sat Mar  3 18:53:12 2007
From: ihsanas at yahoo.com (احسان عريقات)
Date: Sat, 3 Mar 2007 09:53:12 -0800 (PST)
Subject: [Pw_forum] plotrho
Message-ID: <150444.17888.qm@web52311.mail.yahoo.com>

Hi thank you Ifound all what I need to know about
plotrho from the archive
Thanks


 
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From akohlmey at cmm.chem.upenn.edu  Sat Mar  3 18:55:13 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 3 Mar 2007 12:55:13 -0500 (EST)
Subject: [Pw_forum] plotrho
In-Reply-To: <734130.34603.qm@web52312.mail.yahoo.com>
Message-ID: <Pine.LNX.4.44.0703031253180.12232-100000@localhost.localdomain>

On Sat, 3 Mar 2007, ????? ?????? wrote:

I> Hi 
I> please, can you tell me what`s the meaning of 0 0.9 6
I> in plotrho file and how can I change it for different
I> atoms.

this is the input for the plotrho.x program that you'd
normally type in interactively (its been redirected in scripts).
just run plotrho.x interactively and you'll see the meaning.

axel.

I> Thanks
I> 
I> si.rho.dat
I> si.rho.ps
I> n
I> 0 0.09 6
I> 
I> Ihsan
I> 
I> 
I>  
I> ____________________________________________________________________________________
I> Don't pick lemons.
I> See all the new 2007 cars at Yahoo! Autos.
I> http://autos.yahoo.com/new_cars.html 
I> _______________________________________________
I> Pw_forum mailing list
I> Pw_forum at pwscf.org
I> http://www.democritos.it/mailman/listinfo/pw_forum
I> 

-- 
=======================================================================
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.



From ghaderyan at gmail.com  Sat Mar  3 22:00:52 2007
From: ghaderyan at gmail.com (saman ghaderyan)
Date: Sun, 4 Mar 2007 00:30:52 +0330
Subject: [Pw_forum] thanks
Message-ID: <aa36e8060703031300q54c17b0cy3d4cec328179611c@mail.gmail.com>

dear akohlmey
thank you
but i don't understand ,why cell parameter or crystal axes used without
definition.
thans
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From akohlmey at cmm.chem.upenn.edu  Sat Mar  3 23:12:13 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 3 Mar 2007 17:12:13 -0500 (EST)
Subject: [Pw_forum] thanks
In-Reply-To: <aa36e8060703031300q54c17b0cy3d4cec328179611c@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0703031710390.2621-100000@localhost.localdomain>

On Sun, 4 Mar 2007, saman ghaderyan wrote:

SG> dear akohlmey
SG> thank you
SG> but i don't understand ,why cell parameter or crystal axes used without
SG> definition.

well, and i don't get what your problem is.
can you please be more elaborate and, e.g., give an example.

axel.

SG> thans
SG> 

-- 
=======================================================================
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.



From rui_zhi_zhang at yahoo.com  Sun Mar  4 09:31:39 2007
From: rui_zhi_zhang at yahoo.com (ruizhi zhang)
Date: Sun, 4 Mar 2007 00:31:39 -0800 (PST)
Subject: [Pw_forum] Abnormally Dielectric constant and Effective charges
Message-ID: <626465.2423.qm@web39813.mail.mud.yahoo.com>

Dear all
   
  I met a problem when I used ph.x to calculate Dielectric constant of BaTiO3. The Dielectric constants are abnormally large, and so do the effective charges. The output and input files are attached below. I have searched the forum and find someone fixed this problem by using denser k-grid. However, in my case this does not work. Even I use a 16x16x16 MP k-point, the problem also exsits. 
I also calculate effective charges of BaTiO3 using Berry Phase method, and the result is reasonable. It is not likely pseudopotentials are the problem, because Linear Response calculations of PbTiO3, BaZrO3, PbZrO3 all give reasonable results, and agree well with Berry Phase results.
   
  Really appreciate your help, thanks!
Ruizhi Zhang
  
Here are the input and output files
  bto.ph.out
.......
.......
 Dielectric constant in cartesian axis
   (  -10960.282004778       0.000000000       0.000000000 )
 (       0.000000000  -10960.282004778       0.000000000 )
 (       0.000000000       0.000000000  -10960.282004778 )
   Effective charges E-U in cartesian axis
    atom      1
 (      -30.52734        0.00000        0.00000 )
 (        0.00000      -30.52734        0.00000 )
 (        0.00000        0.00000      -30.52734 )
  atom      2
 (      -48.86837        0.00000        0.00000 )
 (        0.00000      -48.86837        0.00000 )
 (        0.00000        0.00000      -48.86837 )
  atom      3
 (       25.10465        0.00000        0.00000 )
 (        0.00000       27.75341        0.00000 )
 (        0.00000        0.00000       27.75341 )
  atom      4
 (       27.75341        0.00000        0.00000 )
 (        0.00000       27.75341        0.00000 )
 (        0.00000        0.00000       25.10465 )
  atom      5
 (       27.75341        0.00000        0.00000 )
 (        0.00000       25.10465        0.00000 )
 (        0.00000        0.00000       27.75341 )
.......
.......
  bto.scf.in
&control
    calculation  = 'scf'
    restart_mode = 'from_scratch'
    prefix = 'bto'
    pseudo_dir   = '/home/zrz/espresso-3.1.1/pseudo/'
    outdir       = '/home/zrz/phonon/bto.cub/tmp/'
 /
 &system
    ibrav=1
    celldm(1)=7.56
    nat=5
    ntyp=3
    ecutwfc=30
  /
 &electrons
    conv_thr = 1e-7
    mixing_beta=0.7
 /
&IONS
 /
ATOMIC_SPECIES
  Ba    137.33     Ba.vdb.UPF
  Ti    47.90      Ti.vdb.UPF
  O     15.9994    O.vdb.UPF
ATOMIC_POSITIONS
  Ba    0.000    0.000    0.000
  Ti    0.500    0.500    0.500
  O     0.000    0.500    0.500
  O     0.500    0.500    0.000
  O     0.500    0.000    0.500
K_POINTS {automatic}
4 4 4 0 0 0
  
bto.ph.in
phonons of bto
&inputph
  tr2_ph=1.0d-12,
  prefix='bto',
  epsil = .true.
  trans = .false.
  amass(1)=137.33,
  amass(2)=47.90,
  amass(3)=15.9996
  outdir='/home/zrz/phonon/bto.cub/tmp/',
  fildyn='bto.dyn',
 /
0.0 0.0 0.0
   

 
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From nguyenhalvt at yahoo.com  Mon Mar  5 07:04:56 2007
From: nguyenhalvt at yahoo.com (Nguyen Ngoc Ha)
Date: Sun, 4 Mar 2007 22:04:56 -0800 (PST)
Subject: [Pw_forum] Help me structure of V2O5 Crystal
Message-ID: <149774.98852.qm@web31001.mail.mud.yahoo.com>

Dear PWscf Users!
    Would you please help me structure of V2O5 crystal
or tell me where to have the structure?
    Thank you very much!

Nguyen, Ngoc Ha
Hanoi University of Education
Faculty of Chemistry
Department of Physical Chemistry
Tel: Office: 04/8330842
Home: 04/7681083
Mobile: 0912129517


 
____________________________________________________________________________________
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with the Yahoo! Search weather shortcut.
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From chen_shao_hua197 at yahoo.com.tw  Mon Mar  5 08:41:05 2007
From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=)
Date: Mon, 5 Mar 2007 15:41:05 +0800 (CST)
Subject: [Pw_forum] el-ph calculation
Message-ID: <287348.402.qm@web73002.mail.tp2.yahoo.com>

Dear members,
When I did el-ph calculation as example07 steps.The
first 3 steps were fine but the last step showed the
error message below:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from readmat : error #         2
     inconsistent data

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Does anyone know what it means ?

Besr Regards
max

___________________________________________________ 
 ??????? ? ???????????????? 
 http://messenger.yahoo.com.tw/


From chen_shao_hua197 at yahoo.com.tw  Mon Mar  5 10:08:59 2007
From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=)
Date: Mon, 5 Mar 2007 17:08:59 +0800 (CST)
Subject: [Pw_forum] el-ph calculation
In-Reply-To: <287348.402.qm@web73002.mail.tp2.yahoo.com>
Message-ID: <544103.61631.qm@web73004.mail.tp2.yahoo.com>

Dear members,
Sorry ,the whole error message is

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from readmat : error #         2
1525-097 A READ statement using decimal base input
found the invalid digit 'c' in the input file.  The
program will recover by assuming a zero in its place.
1525-097 A READ statement using decimal base input
found the invalid digit 'u' in the input file.  The
program will recover by assuming a zero in its place.
1525-097 A READ statement using decimal base input
found the invalid digit 'b' in the input file.  The
program will recover by assuming a zero in its place.
1525-097 A READ statement using decimal base input
found the invalid digit 'i' in the input file.  The
program will recover by assuming a zero in its place.
1525-097 A READ statement using decimal base input
found the invalid digit 'c' in the input file.  The
program will recover by assuming a zero in its place.


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from readmat : error #         2
     inconsistent data

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

But there are no "cubic" words in my input file.
So what does it means ? Or it showed in which file ?

Best Regards
max 

--- ? ?? <chen_shao_hua197 at yahoo.com.tw> ??

> Dear members,
> When I did el-ph calculation as example07 steps.The
> first 3 steps were fine but the last step showed the
> error message below:
> 
>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from readmat : error #         2
>      inconsistent data
> 
>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> Does anyone know what it means ?
> 
> Besr Regards
> max
> 
> ___________________________________________________ 
>  ??????? ? ???????????????? 
>  http://messenger.yahoo.com.tw/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


___________________________________________________ 
 ??????? ? ???????????????? 
 http://messenger.yahoo.com.tw/


From giannozz at nest.sns.it  Mon Mar  5 10:13:26 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 5 Mar 2007 10:13:26 +0100
Subject: [Pw_forum] filelph
In-Reply-To: <aef8bbf00703030022j71cf2970md73fe606f38122@mail.gmail.com>
References: <aef8bbf00703030022j71cf2970md73fe606f38122@mail.gmail.com>
Message-ID: <C3ADEBA9-CA7F-47B2-AEF7-F66A2F0806E0@nest.sns.it>

On Mar 3, 2007, at 9:22 , Amit Kumar wrote:

>  It's written in the DOC file that
>
>  filelph     file where electron-phonon matrix elements are  
> written  ' '
>
>  However, in the new version, if we run example 7 with filelph =  
> 'al.elph',
>  we  don't get any al.elph file in the output directory 'results'.

variable 'filelph' is obsolete and no longer used. The documentation
is incorrect. Thank you for noticing this, it will be fixed in the  
next version

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




From giannozz at nest.sns.it  Mon Mar  5 10:21:45 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 5 Mar 2007 10:21:45 +0100
Subject: [Pw_forum] el-ph calculation
In-Reply-To: <544103.61631.qm@web73004.mail.tp2.yahoo.com>
References: <544103.61631.qm@web73004.mail.tp2.yahoo.com>
Message-ID: <4589D330-3D1E-44E3-AD22-C7DED7DDE939@nest.sns.it>

On Mar 5, 2007, at 10:08 , ? ?? wrote:

> But there are no "cubic" words in my input file.
> So what does it means ?

if the code finds the word "cubic", it means that it is reading
from a file that contains the word "cubic". Computer codes
don't invent words.

> Or it showed in which file ?

>>      from readmat : error #         2
>>      inconsistent data

this error occurs in subroutine "readmat", which reads the
dielectric matrix. See PH/elphon.f90, look for 'readmat'.

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




From lanhaiping at gmail.com  Mon Mar  5 10:21:03 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 5 Mar 2007 17:21:03 +0800
Subject: [Pw_forum] Help me structure of V2O5 Crystal
In-Reply-To: <149774.98852.qm@web31001.mail.mud.yahoo.com>
References: <149774.98852.qm@web31001.mail.mud.yahoo.com>
Message-ID: <c92002fa0703050121g2da69dd2g8f185f2c18b87007@mail.gmail.com>

hi, you may try to digg out http://www.cryst.ehu.es/
 or http://cst-www.nrl.navy.mil/lattice/

Regards
h.p


On 3/5/07, Nguyen Ngoc Ha <nguyenhalvt at yahoo.com> wrote:
>
> Dear PWscf Users!
>    Would you please help me structure of V2O5 crystal
> or tell me where to have the structure?
>    Thank you very much!
>
> Nguyen, Ngoc Ha
> Hanoi University of Education
> Faculty of Chemistry
> Department of Physical Chemistry
> Tel: Office: 04/8330842
> Home: 04/7681083
> Mobile: 0912129517
>
>
>
>
> ____________________________________________________________________________________
> Don't get soaked.  Take a quick peak at the forecast
> with the Yahoo! Search weather shortcut.
> http://tools.search.yahoo.com/shortcuts/#loc_weather
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
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From niuli1978 at yahoo.com.cn  Mon Mar  5 13:01:19 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Mon, 5 Mar 2007 20:01:19 +0800 (CST)
Subject: [Pw_forum] about vc-relax of graphite
Message-ID: <964803.25854.qm@web15008.mail.cnb.yahoo.com>

dear all:
  When optimizing lattice constant of the bulk graphite I met an error :
  ---------------------------------------------------
from checkallsym : error #         3
     not orthogonal operation
---------------------------------------------------
What is the reason? How to resolve it?
  any help will be appreciated
  NiuLi
=================================================
my input as follows:
  cat > graphite.vcrx.in << EOF
&CONTROL
  calculation  = "vc-relax",
  prefix       = "graphite",
  pseudo_dir   = "$PSEUDO_DIR",
  outdir       = "$TMP_DIR",
  tstress = .true. ,
  tprnfor = .true. ,
                       nstep = 65 ,
               etot_conv_thr = 1.0E-4 ,
               forc_conv_thr = 1.0D-3 ,
                          dt = 100 ,
/
&SYSTEM
    ibrav = 4, 
    celldm(1) =4.6336, 
    celldm(3)=2.7243,
    nat= 4, ntyp= 1,
    ecutwfc =40  
/
&ELECTRONS
  diagonalization = 'cg',
  conv_thr    = 1.D-9,
  mixing_beta = 0.7D0,
/
&IONS
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
&CELL
               cell_dynamics = 'damp-w',
                       press = 0.0 ,
                       wmass = 0.010 ,
 /
ATOMIC_SPECIES
 C   12.0107  C.pz-vbc.UPF
  ATOMIC_POSITIONS {crystal}
 C  0.0000000 0.0000000 0.0000000 
 C  0.0000000 0.0000000 0.5000000
 C  0.6666667 0.3333333 0.0000000
 C  0.3333333 0.6666667 0.5000000
K_POINTS automatic
4 4 4 1 1 1
  EOF
$ECHO " optimizing the lattice constant for bulk graphite...\c"
$PW_COMMAND < graphite.vcrx.in > graphite.vcrx.out
$ECHO " done"


 		
---------------------------------
 Mp3???-???????   
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From d.schmicker at yahoo.de  Mon Mar  5 13:23:24 2007
From: d.schmicker at yahoo.de (Detlef Schmicker)
Date: Mon, 05 Mar 2007 13:23:24 +0100
Subject: [Pw_forum] about vc-relax of graphite
In-Reply-To: <964803.25854.qm@web15008.mail.cnb.yahoo.com>
References: <964803.25854.qm@web15008.mail.cnb.yahoo.com>
Message-ID: <1173097404.21997.19.camel@localhost>

Hello NiuLi,

I had simelar problems. I reduced dt, and it worked.

Detlef

Am Montag, den 05.03.2007, 20:01 +0800 schrieb li niu:
> dear all:
> When optimizing lattice constant of the bulk graphite I met an error :
> ---------------------------------------------------
> from checkallsym : error #         3
>      not orthogonal operation
> ---------------------------------------------------
> What is the reason? How to resolve it?
> any help will be appreciated
> NiuLi
> =================================================
> my input as follows:
> cat > graphite.vcrx.in << EOF
> &CONTROL
>   calculation  = "vc-relax",
>   prefix       = "graphite",
>   pseudo_dir   = "$PSEUDO_DIR",
>   outdir       = "$TMP_DIR",
>   tstress = .true. ,
>   tprnfor = .true. ,
>                        nstep = 65 ,
>                etot_conv_thr = 1.0E-4 ,
>                forc_conv_thr = 1.0D-3 ,
>                           dt = 100 ,
> /
> &SYSTEM
>     ibrav = 4, 
>     celldm(1) =4.6336, 
>     celldm(3)=2.7243,
>     nat= 4, ntyp= 1,
>     ecutwfc =40  
> /
> &ELECTRONS
>   diagonalization = 'cg',
>   conv_thr    = 1.D-9,
>   mixing_beta = 0.7D0,
> /
> &IONS
>   pot_extrapolation = "second_order",
>   wfc_extrapolation = "second_order",
> /
> &CELL
>                cell_dynamics = 'damp-w',
>                        press = 0.0 ,
>                        wmass = 0.010 ,
>  /
> ATOMIC_SPECIES
>  C   12.0107  C.pz-vbc.UPF
> ATOMIC_POSITIONS {crystal}
>  C  0.0000000 0.0000000 0.0000000 
>  C  0.0000000 0.0000000 0.5000000
>  C  0.6666667 0.3333333 0.0000000
>  C  0.3333333 0.6666667 0.5000000
> K_POINTS automatic
> 4 4 4 1 1 1
> EOF
> $ECHO " optimizing the lattice constant for bulk graphite...\c"
> $PW_COMMAND < graphite.vcrx.in > graphite.vcrx.out
> $ECHO " done"
> 
> 
> ______________________________________________________________________
> Mp3???-???????  



From amit76.india at gmail.com  Mon Mar  5 13:49:01 2007
From: amit76.india at gmail.com (Amit Kumar)
Date: Mon, 5 Mar 2007 18:19:01 +0530
Subject: [Pw_forum] filelph
Message-ID: <aef8bbf00703050449l4dd3425cr1f726ee7dc5438f0@mail.gmail.com>

  Dear Paolo,

  Thank you very much  for your kind reply.

  >>>>> variable 'filelph' is obsolete and no longer used. The documentation
 is incorrect. Thank you for noticing this, it will be fixed in the
 next version

 It implies  that we can't see the individual electron-phonon
 matrix elements in new version.
 I think it's not a good decision.
 To be confirmed with my results,
  I ran an identical program of electron phonon
  calculation  using la2F flag in new the version as well as
  using the old method (scf nscf without la2F).
  Surprisingly, I'm getting different results  still using
  the identical input parameters for both case. I'm really confused and
  that's why I want to find out the exact origin of this mismatch
  by debugging the  every steps of the calculations.
  I want to write every element of the g-matrix (electron-phonon matrix).

  I have one more question.

  I'm trying to calculate the el-ph coupling for a large system with
  30 atoms per unit cell .
  So it's calculaing 30 x3 = 90 represntations  ( should take 6 months
  in a non - parallel single node computer ) before giving lambda
  values.
  So my question is,
  is it possible to run the el-ph part in parallel cluster????
  Is it possible to restart the jobs if it get killed in the mid way???
  Is it possible to calculate different reprensentations or phonon modes
separetly???

     There are  Representation #  90 ,  mode #   90
     like  this

     Atomic displacements:
     There are  90 irreducible representations

     Representation     1      1 modes - To be done

     Representation     2      1 modes - To be done

     Representation     3      1 modes - To be done

     Representation     4      1 modes - To be done

     Representation     5      1 modes - To be done

     Representation     6      1 modes - To be done

  ........
  .......
  .......   and so on.....


  It takes 2 days for a single  Representation.

  So I'll be highly obliged if you kindly give me some
  valuable suggestions to overcome this problem.

  Regards,
  Amit






 >variable 'filelph' is obsolete and no longer used. The documentation
is incorrect. Thank you for noticing this, it will be fixed in the
next version

Paolo
---
Paolo Giannozzi, Democritos and University of Udine, Italy
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From d.schmicker at yahoo.de  Mon Mar  5 16:42:40 2007
From: d.schmicker at yahoo.de (Detlef Schmicker)
Date: Mon, 05 Mar 2007 16:42:40 +0100
Subject: [Pw_forum] Using NVIDIA CUDA for blas with pwscf
Message-ID: <1173109361.5106.5.camel@localhost>

Hi,

I am looking for cheap computational power to use pwscf.

Did anybody tried to use the GPU of NVIDIA graphic cards?

The NVIDIA CUDA development kit offers blas and fft routines. But it is
quite difficult to get information on performance of these GPUs,
especially if you need much memory. 

The benchmarks show 2.4 times faster computation than with fastest
woodcrest (intel) processors.
http://rapidmind.net/sc06_hp_rapidmind_cpugpu_summary.php

Any information would be nice,

Detlef



From giannozz at nest.sns.it  Mon Mar  5 16:51:03 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 5 Mar 2007 16:51:03 +0100
Subject: [Pw_forum] Using fftw wrapper for intel mkl lib?
In-Reply-To: <1172942373.12797.1.camel@localhost>
References: <1172942373.12797.1.camel@localhost>
Message-ID: <39BF9F58-EBC8-4BDD-BD06-57C78340089F@nest.sns.it>

On Mar 3, 2007, at 18:19 , Detlef Schmicker wrote:

> did anybody manage to compile pwscf (pw.x) using the fftw-wrapper
> of mkl 9.0?

AFAIK there is no special trick to compile pw.x; just compile
for either v.2 or v.3 of FFTW and load the mkl wrappers,
provided by Intel as a separate package, to be compiled.

I heard that the FFTW v.2 wrappers work for both serial
and parallel execution, but you gain little; you gain much
more with v.3 wrappers, but they work only for the serial
case.

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




From akohlmey at cmm.chem.upenn.edu  Mon Mar  5 18:52:12 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 5 Mar 2007 12:52:12 -0500 (EST)
Subject: [Pw_forum] Using NVIDIA CUDA for blas with pwscf
In-Reply-To: <1173109361.5106.5.camel@localhost>
Message-ID: <Pine.LNX.4.44.0703051246430.18330-100000@localhost.localdomain>

On Mon, 5 Mar 2007, Detlef Schmicker wrote:

DS> Hi,
DS> 
DS> I am looking for cheap computational power to use pwscf.
DS> 
DS> Did anybody tried to use the GPU of NVIDIA graphic cards?

DS> The NVIDIA CUDA development kit offers blas and fft routines. But it is
DS> quite difficult to get information on performance of these GPUs,
DS> especially if you need much memory. 

depending on the application the performance increase can be up
to 30 (in ideal cases). i know from somebody who wrote a multithreaded
grid based simple poisson code across multiple GPUs with almost
200x speedup.

however, for BLAS/FFT the gain is less.

DS> The benchmarks show 2.4 times faster computation than with fastest
DS> woodcrest (intel) processors.
DS> http://rapidmind.net/sc06_hp_rapidmind_cpugpu_summary.php
DS> 
DS> Any information would be nice,

it is no point for pw.x and related codes, since 
the hardware does not support double precision 
operation. DP however, is _essential_.

you should not give up hope. the next generation hardware
is supposed to have double precision hardware and the API
is already there.

i'm quite curious to get my hands on that stuff, as soon
as it is available, too. :-)

cheers,
   axel.

DS> 
DS> Detlef
DS> 
DS> _______________________________________________
DS> Pw_forum mailing list
DS> Pw_forum at pwscf.org
DS> http://www.democritos.it/mailman/listinfo/pw_forum
DS> 

-- 
=======================================================================
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.



From d.schmicker at yahoo.de  Mon Mar  5 20:04:47 2007
From: d.schmicker at yahoo.de (Detlef Schmicker)
Date: Mon, 05 Mar 2007 20:04:47 +0100
Subject: [Pw_forum] Using fftw wrapper for intel mkl lib?
In-Reply-To: <39BF9F58-EBC8-4BDD-BD06-57C78340089F@nest.sns.it>
References: <1172942373.12797.1.camel@localhost>
	 <39BF9F58-EBC8-4BDD-BD06-57C78340089F@nest.sns.it>
Message-ID: <1173121488.5106.12.camel@localhost>

Dear Paolo,

thanks. I managed to link to mkl with v.2 and v.3 wrapper. Both are
working in my serial execution setup.

I could not reproduce spead up using v.3 wrapper and mkl. I have a
Pentium 4 and espresso 3.2.

Just as an information,

thanks Detlef

Am Montag, den 05.03.2007, 16:51 +0100 schrieb Paolo Giannozzi:
> On Mar 3, 2007, at 18:19 , Detlef Schmicker wrote:
> 
> > did anybody manage to compile pwscf (pw.x) using the fftw-wrapper
> > of mkl 9.0?
> 
> AFAIK there is no special trick to compile pw.x; just compile
> for either v.2 or v.3 of FFTW and load the mkl wrappers,
> provided by Intel as a separate package, to be compiled.
> 
> I heard that the FFTW v.2 wrappers work for both serial
> and parallel execution, but you gain little; you gain much
> more with v.3 wrappers, but they work only for the serial
> case.
> 
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



From mverissi at ictp.it  Mon Mar  5 21:19:38 2007
From: mverissi at ictp.it (Marcos Verissimo Alves)
Date: Mon, 5 Mar 2007 21:19:38 +0100 (CET)
Subject: [Pw_forum] Error restarting NEB calculation
In-Reply-To: <1173121488.5106.12.camel@localhost>
References: <1172942373.12797.1.camel@localhost> 
    <39BF9F58-EBC8-4BDD-BD06-57C78340089F@nest.sns.it>
    <1173121488.5106.12.camel@localhost>
Message-ID: <60966.10.107.44.32.1173125978.squirrel@webmail2.ictp.trieste.it>

Hi all,

I am trying to perform neb calculations on the system whose input and
error files are attached to this e-mail. I am trying to run this job at
cl-x in CINECA, but without success in the restart. I have tried using
version 3.0 as compiled in cineca, and the latest version with the patches
available from the espresso website, but with no success. The error seems
to be a read error in the .path file. Attached to this e-mail I am sending
the input for the lsf queue job run at cl-x using the latest version of
espresso, as well as the error and output files that come from it. Am I
doing something wrong, or is there anything that must be done for the
restart, which is not in the file?

Best regards,

Marcos

-- 
Dr. Marcos Verissimo Alves
Post-Doctoral Fellow
Condensed Matter and Statistical Physics Sector
International Centre for Theoretical Physics
Trieste, Italy

--------

I have become so addicted to vi that I try to exit OpenOffice by typing :wq!
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From akohlmey at cmm.chem.upenn.edu  Mon Mar  5 22:22:40 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 5 Mar 2007 16:22:40 -0500 (EST)
Subject: [Pw_forum] Using fftw wrapper for intel mkl lib?
In-Reply-To: <1173121488.5106.12.camel@localhost>
Message-ID: <Pine.LNX.4.44.0703051616460.11153-100000@localhost.localdomain>

On Mon, 5 Mar 2007, Detlef Schmicker wrote:

DS> Dear Paolo,
DS> 
DS> thanks. I managed to link to mkl with v.2 and v.3 wrapper. Both are
DS> working in my serial execution setup.
DS> 
DS> I could not reproduce spead up using v.3 wrapper and mkl. I have a
DS> Pentium 4 and espresso 3.2.

detlef,

please keep in mind, that speedup frequently depends
also on the number of supported grids. fftw can handle
grids with roots up to 11, and does a very decent job
at that. many other ffts only support roots up to 5,
so it might frequently happen that with fftw you can
use smaller grids, which will compensate or even overcompensate
the speedup from a faster fft. so when you compare performance,
you should check wether you have the same grids.

in the case of - for example - fftw vs. essl, it can be that 
you go from a 5% advantage of essl for an 128x128x128 grid
to a 20% deficit for an 132^3 grid (since essl has to use 144^3).
i stumbled across this with a different code, but it has
to apply to QE as well.

cheers,
   axel.


DS> 
DS> Just as an information,
DS> 
DS> thanks Detlef
DS> 
DS> Am Montag, den 05.03.2007, 16:51 +0100 schrieb Paolo Giannozzi:
DS> > On Mar 3, 2007, at 18:19 , Detlef Schmicker wrote:
DS> > 
DS> > > did anybody manage to compile pwscf (pw.x) using the fftw-wrapper
DS> > > of mkl 9.0?
DS> > 
DS> > AFAIK there is no special trick to compile pw.x; just compile
DS> > for either v.2 or v.3 of FFTW and load the mkl wrappers,
DS> > provided by Intel as a separate package, to be compiled.
DS> > 
DS> > I heard that the FFTW v.2 wrappers work for both serial
DS> > and parallel execution, but you gain little; you gain much
DS> > more with v.3 wrappers, but they work only for the serial
DS> > case.
DS> > 
DS> > Paolo
DS> > ---
DS> > Paolo Giannozzi, Democritos and University of Udine, Italy
DS> > 
DS> > 
DS> > _______________________________________________
DS> > Pw_forum mailing list
DS> > Pw_forum at pwscf.org
DS> > http://www.democritos.it/mailman/listinfo/pw_forum
DS> 
DS> _______________________________________________
DS> Pw_forum mailing list
DS> Pw_forum at pwscf.org
DS> http://www.democritos.it/mailman/listinfo/pw_forum
DS> 

-- 
=======================================================================
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.



From niuli1978 at yahoo.com.cn  Tue Mar  6 03:22:49 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Tue, 6 Mar 2007 10:22:49 +0800 (CST)
Subject: [Pw_forum] about vc-relax of graphite
Message-ID: <948599.78230.qm@web15008.mail.cnb.yahoo.com>

dear Detlef,
   
  thanks for your help.  
Reducing dt from 100 to 20, I found "Entering Dynamics;  it = " increasing .
However in all the case when P equaled about  -59 (kbar) the code stoped  and appeared 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from checkallsym : error #         3
     not orthogonal operation
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  stopping ...
  
What do you think about it ?
I want to  run the vc-relax code again using obtained new lattice constant until
the stress convergence achieved. Is it right?
  
thank you in adance
   
  Niu Li


 		
---------------------------------
 Mp3???-???????   
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From rcjhawk at gmail.com  Tue Mar  6 05:03:05 2007
From: rcjhawk at gmail.com (Mike Mehl)
Date: Mon, 5 Mar 2007 23:03:05 -0500
Subject: [Pw_forum] Help me structure of V2O5 Crystal
In-Reply-To: <c92002fa0703050121g2da69dd2g8f185f2c18b87007@mail.gmail.com>
References: <149774.98852.qm@web31001.mail.mud.yahoo.com>
	 <c92002fa0703050121g2da69dd2g8f185f2c18b87007@mail.gmail.com>
Message-ID: <6084bd70703052003r3b5a5009wa4080bfa4e9a6e6@mail.gmail.com>

Since this seems to come up often, I'd like to point out that the American
Mineralogist Crystal Structure Database (
http://rruff.geo.arizona.edu/AMS/amcsd.php) is another excellent place to
find structures, though you will have to use it in conjunction with Bilbao (
http://www.cryst.ehu.es/), and have some understanding of space groups and
Wyckoff positions.

On 3/5/07, lan haiping <lanhaiping at gmail.com> wrote:
>
> hi, you may try to digg out http://www.cryst.ehu.es/
>  or http://cst-www.nrl.navy.mil/lattice/
>
> Regards
> h.p
>
>
> On 3/5/07, Nguyen Ngoc Ha <nguyenhalvt at yahoo.com> wrote:
> >
> > Dear PWscf Users!
> >    Would you please help me structure of V2O5 crystal
> > or tell me where to have the structure?
> >    Thank you very much!
> >
> >


-- 
                                            mjm (
http://hawknotes.blogspot.com/ and http://cst-www.nrl.navy.mil/lattice/)
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From amit76.india at gmail.com  Tue Mar  6 07:29:00 2007
From: amit76.india at gmail.com (Amit Kumar)
Date: Tue, 6 Mar 2007 11:59:00 +0530
Subject: [Pw_forum] Example7
Message-ID: <aef8bbf00703052229u40c8a8ffibc52febf458e49c3@mail.gmail.com>

   Respected Users,

   I'm very much confused with the Electron-phonon output of Example 7.
   Please check it out:

    1 .  KPOINT  16 16 16 for scf.fit    and   2 2 2 for scf calculation.

    Gaussian Broadening:   0.090 Ry, ngauss=   0
    DOS =  2.674745 states/spin/Ry/Unit Cell at Ef=  8.266810 eV
    lambda( 1)=  0.1373   gamma=   15.97 GHz
    lambda( 2)=  0.1116   gamma=   12.97 GHz
    lambda( 3)=  0.0504   gamma=    6.93 GHz


    Gaussian Broadening:   0.10 Ry, ngauss=   0
    DOS =  2.674314 states/spin/Ry/Unit Cell at Ef=  8.266772 eV
    lambda( 1)=  0.1403   gamma=   16.32 GHz
    lambda( 2)=  0.1132   gamma=   13.16 GHz
    lambda( 3)=  0.0520   gamma=    7.15 GHz



  2.   KPOINT  16 16 16 for scf.fit    and   8 8 8 for scf calculation.

      Gaussian Broadening:   0.090 Ry,       ngauss=   0
      DOS =  2.673746 states/spin/Ry/Unit Cell at Ef=  8.271433 eV
      lambda( 1)=  0.0828   gamma=    8.96 GHz
      lambda( 2)=  0.1720   gamma=   26.90 GHz
      lambda( 3)=  0.1742   gamma=   27.24 GHz


     Gaussian Broadening:   0.10 Ry, ngauss=   0
     DOS =  2.674314 states/spin/Ry/Unit Cell at Ef=  8.266772 eV
     lambda( 1)=  0.0831   gamma=    8.99 GHz
     lambda( 2)=  0.1721   gamma=   26.93 GHz
     lambda( 3)=  0.1740   gamma=   27.22 GHz

     So I thought great I got  convergency so easily.
     lambda( 2)=  0.1720   gamma=   26.90 GHz
     lambda( 3)=  0.1742   gamma=   27.24 GHz

                   and

     lambda( 2)=  0.1721   gamma=   26.93 GHz
     lambda( 3)=  0.1740   gamma=   27.22 GHz

     Very excellent results.

     But. life is not  so simple. Bad luck.
     With even  more K points again results start to become worse instead of
being better.

     Please check it out :


    3.   KPOINT  32 32 32  for scf.fit    and   16 16 16  for scf
calculation.

       Gaussian Broadening:   0.090 Ry,       ngauss=   0
       DOS =  2.675256 states/spin/Ry/Unit Cell at Ef=  8.271367 eV
       lambda( 1)=  0.0799   gamma=    9.12 GHz
       lambda( 2)=  0.1703   gamma=   28.62 GHz
       lambda( 3)=  0.1705   gamma=   28.64 GHz

       Gaussian Broadening:   0.10 Ry,       ngauss=   0
       DOS =  2.674732 states/spin/Ry/Unit Cell at Ef=  8.266803 eV
       lambda( 1)=  0.0799   gamma=    9.12 GHz
       lambda( 2)=  0.1686   gamma=   28.32 GHz
       lambda( 3)=  0.1687   gamma=   28.34 GHz


   4.    KPOINT  64 64 64   for scf.fit    and   32 32 32   for scf
calculation.


        Gaussian Broadening:   0.090 Ry,       ngauss=   0
        DOS =  2.675273 states/spin/Ry/Unit Cell at Ef=  8.271375 eV
        lambda( 1)=  0.0801   gamma=    9.07 GHz
        lambda( 2)=  0.1726   gamma=   28.29 GHz
        lambda( 3)=  0.1726   gamma=   28.29 GHz


        Gaussian Broadening:   0.10 Ry,       ngauss=   0
        DOS =  2.674745 states/spin/Ry/Unit Cell at Ef=  8.266810 eV
        lambda( 1)=  0.0802   gamma=    9.08 GHz
        lambda( 2)=  0.1708   gamma=   27.99 GHz
        lambda( 3)=  0.1708   gamma=   27.99 GHz


         Would anybody tell me the reason,  Why the case (2)    ( for magic
number
         KPOINT  16 16 16 for scf.fit    and   8 8 8 for scf calculation)
is  so kind
         to us?????? How far we will go to get the converged value???
         Where can we stop????
         It's really confusing.

         Looking forward to your help.

         Regards,
         Amit
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From giannozz at nest.sns.it  Tue Mar  6 11:28:45 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 6 Mar 2007 11:28:45 +0100
Subject: [Pw_forum] Abnormally Dielectric constant and Effective charges
In-Reply-To: <626465.2423.qm@web39813.mail.mud.yahoo.com>
References: <626465.2423.qm@web39813.mail.mud.yahoo.com>
Message-ID: <66348AFC-19EF-43EE-88FE-D1D54B4182A6@nest.sns.it>

On Mar 4, 2007, at 9:31 , ruizhi zhang wrote:

> I met a problem when I used ph.x to calculate Dielectric constant  
> of BaTiO3.
> The Dielectric constants are abnormally large, and so do the  
> effective charges.

for some obscure reason the self-consistent code get stuck into a bogus
solution. As a temporary workaround, just increase the number of bands
(to 24 for instance)

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




From giannozz at nest.sns.it  Tue Mar  6 11:32:26 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 6 Mar 2007 11:32:26 +0100
Subject: [Pw_forum] about vc-relax of graphite
In-Reply-To: <948599.78230.qm@web15008.mail.cnb.yahoo.com>
References: <948599.78230.qm@web15008.mail.cnb.yahoo.com>
Message-ID: <AE983D45-B432-4167-A9F9-8B8C2E546160@nest.sns.it>

On Mar 6, 2007, at 3:22 , li niu wrote:

> Reducing dt from 100 to 20, I found "Entering Dynamics;  it = "  
> increasing .
> However in all the case when P equaled about  -59 (kbar) the code  
> stoped  and appeared
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from checkallsym : error #         3
>      not orthogonal operation
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>   stopping ...
>
> What do you think about it ?

I think that you should read what is written in the users'guide:

---
\paragraph{\texttt{pw.x} stops during variable-cell optimization
in \texttt{checkallsym} with ``not orthogonal operation'' error.}

Variable-cell optimization may occasionally break the starting
symmetry of the cell. When this happens, the run is stopped
because the number of k-points calculated for the starting
configuration may no longer be suitable. Possible solutions:
\begin{itemize}
\item start with a nonsymmetric cell
\item use a symmetry-conserving algorithm: the Wentzcovitch
algorithm \\
(\texttt{cell\_dynamics='damp-w'}) shouldn't break the symmetry.
\end{itemize}
---
---
Paolo Giannozzi, Democritos and University of Udine, Italy




From giannozz at nest.sns.it  Tue Mar  6 12:00:26 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 6 Mar 2007 12:00:26 +0100
Subject: [Pw_forum] Error restarting NEB calculation
In-Reply-To: <60966.10.107.44.32.1173125978.squirrel@webmail2.ictp.trieste.it>
References: <1172942373.12797.1.camel@localhost>  <39BF9F58-EBC8-4BDD-BD06-57C78340089F@nest.sns.it> <1173121488.5106.12.camel@localhost> <60966.10.107.44.32.1173125978.squirrel@webmail2.ictp.trieste.it>
Message-ID: <8615AED5-B33E-42E1-BE19-5EC9DD7FD861@nest.sns.it>

On Mar 5, 2007, at 21:19 , Marcos Verissimo Alves wrote:

> I am trying to perform neb calculations on the system whose input
> and error files are attached to this e-mail. I am trying to run  
> this job
> at cl-x in CINECA, but without success in the restart.

restart from an interrupted run? it may or may not work, depending
on the phase of the moon and on the mood of the operating system
when the job crashes.

> I have tried using version 3.0 as compiled in cineca, and the  
> latest version

it is very unlikely that you can read restart files produced by a  
different
version of the code

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




From mverissi at ictp.it  Tue Mar  6 14:01:59 2007
From: mverissi at ictp.it (Marcos Verissimo Alves)
Date: Tue, 6 Mar 2007 14:01:59 +0100 (CET)
Subject: [Pw_forum] Error restarting NEB calculation
In-Reply-To: <8615AED5-B33E-42E1-BE19-5EC9DD7FD861@nest.sns.it>
References: <1172942373.12797.1.camel@localhost> 
    <39BF9F58-EBC8-4BDD-BD06-57C78340089F@nest.sns.it>
    <1173121488.5106.12.camel@localhost>
    <60966.10.107.44.32.1173125978.squirrel@webmail2.ictp.trieste.it>
    <8615AED5-B33E-42E1-BE19-5EC9DD7FD861@nest.sns.it>
Message-ID: <47264.10.50.40.120.1173186119.squirrel@webmail2.ictp.trieste.it>

> restart from an interrupted run? it may or may not work, depending
> on the phase of the moon and on the mood of the operating system
> when the job crashes.

Hm... Can we control the phase of the moon, or give some prozac to the OS? :)

>
>> I have tried using version 3.0 as compiled in cineca, and the
>> latest version
>
> it is very unlikely that you can read restart files produced by a
> different version of the code

Well, I actually did not try to restart with different versions, sorry if
this seemed to be so. First I ran the job with espresso 3.0 and restarted
it with 3.0; then I downloaded the latest version, applied patches,
compiled it, ran the job from scratch and tried to restart it with the
same newly compiled version. Any suggestions to make the restart
successful? As I said, for some reason it does not read the .path file
correctly, and I cannot figure out why.

Marcos

>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-- 
Dr. Marcos Verissimo Alves
Post-Doctoral Fellow
Condensed Matter and Statistical Physics Sector
International Centre for Theoretical Physics
Trieste, Italy

--------

I have become so addicted to vi that I try to exit OpenOffice by typing :wq!



From ezadshojaee at hotmail.com  Tue Mar  6 21:14:56 2007
From: ezadshojaee at hotmail.com (Ezad Shojaee)
Date: Tue, 06 Mar 2007 20:14:56 +0000
Subject: [Pw_forum] phonon
Message-ID: <BAY101-F6098E1A12D60505DEBF1FAA7B0@phx.gbl>

hi
in the version 3.2 of the code, it shows the symbol of each mode after the 
end ( like A_2u )
i want to know that if we do the phonon calculation by a Grid, and calculate 
the dispersion curve , are we able to define the symbol of the obtained 
Gamma modes?( which is for A_1g ...)
thanx

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http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From giannozz at nest.sns.it  Wed Mar  7 15:04:20 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 7 Mar 2007 15:04:20 +0100
Subject: [Pw_forum] filelph
In-Reply-To: <aef8bbf00703050449l4dd3425cr1f726ee7dc5438f0@mail.gmail.com>
References: <aef8bbf00703050449l4dd3425cr1f726ee7dc5438f0@mail.gmail.com>
Message-ID: <F34373DA-3118-457B-B853-F4F55F23E3FE@nest.sns.it>

On Mar 5, 2007, at 13:49 , Amit Kumar wrote:

>  It implies  that we can't see the individual electron-phonon
>  matrix elements in new version.

no, it implies that results are written in a different way

>   I ran an identical program of electron phonon
>   calculation  using la2F flag in new the version as well as
>   using the old method (scf nscf without la2F).
>   Surprisingly, I'm getting different results  still using
>   the identical input parameters for both case.

in some earlier versions, a different scheme for broadening was
used in the calculation of the 'double-delta' integrals. Presently
a simple gaussian is used (ngauss=0), while Methfessel-Paxton
broadening of order one (ngauss=1) was used instead. I don't
see any good reason to use the latter instead of the former,
since all we need is a representation of the delta. This may lead
to some differences.

>   is it possible to run the el-ph part in parallel cluster????

you can run the phonon code in parallel. The el-ph part is
not parallelised but it doesn't cost much by itself

>   Is it possible to restart the jobs if it get killed in the mid  
> way???

you can, but it is a mess

>   Is it possible to calculate different reprensentations or
> phonon modes separetly?

in principle you can, but the code does not implement it

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




From ghaderyan at gmail.com  Thu Mar  8 21:53:44 2007
From: ghaderyan at gmail.com (saman ghaderyan)
Date: Fri, 9 Mar 2007 00:23:44 +0330
Subject: [Pw_forum] relaxation
Message-ID: <aa36e8060703081253l4f352ec6he3254d5961b8068e@mail.gmail.com>

hi
i run relaxation for AlAs with nat=4
Al   0.00 0.00  0.00
As  0.25 0.25  0.25
Al   0.50  0.50  0.00
As -0.25 0.25 0.25
but i don't know why these atomic position have error
thanks


From akohlmey at cmm.chem.upenn.edu  Thu Mar  8 22:10:29 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 8 Mar 2007 16:10:29 -0500 (EST)
Subject: [Pw_forum] relaxation
In-Reply-To: <aa36e8060703081253l4f352ec6he3254d5961b8068e@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0703081609591.12944-100000@localhost.localdomain>

On Fri, 9 Mar 2007, saman ghaderyan wrote:

SG> hi
SG> i run relaxation for AlAs with nat=4
SG> Al   0.00 0.00  0.00
SG> As  0.25 0.25  0.25
SG> Al   0.50  0.50  0.00
SG> As -0.25 0.25 0.25
SG> but i don't know why these atomic position have error

neither will we, unless you show us the rest of the input
and the error message.

axel.

SG> thanks
SG> _______________________________________________
SG> Pw_forum mailing list
SG> Pw_forum at pwscf.org
SG> http://www.democritos.it/mailman/listinfo/pw_forum
SG> 

-- 
=======================================================================
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.



From chen_shao_hua197 at yahoo.com.tw  Fri Mar  9 12:49:48 2007
From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=)
Date: Fri, 9 Mar 2007 19:49:48 +0800 (CST)
Subject: [Pw_forum] example07 of the QE-3.2 version
Message-ID: <417404.90462.qm@web73002.mail.tp2.yahoo.com>

Dear members,
I had run example07 of the QE-3.2 version well.
For some reason,I changed the setting  in al.elph.in

nq1=10, nq2=10, nq3=6

then I got the error message below:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from elphsum : error #         3
     q is not a vector in the dense grid

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Although I know it comes from PH/elphon.f90, 
I still can not find out what the constraint or rule
is about nq1,2,3 related to its k-point setting in
scf.in ?

I mean why nq1=4, nq2=4, nq3=4 is fine ,but 10,10,6
fail ? 
Is it relative to  k-point setting 8x8x8 in scf.in ?
What other setting  could we choose ?

Best Regards
max



___________________________________________________ 
 ??????? ? ???????????????? 
 http://messenger.yahoo.com.tw/


From amit76.india at gmail.com  Fri Mar  9 13:41:02 2007
From: amit76.india at gmail.com (Amit Kumar)
Date: Fri, 9 Mar 2007 18:11:02 +0530
Subject: [Pw_forum] Example07
Message-ID: <aef8bbf00703090441q5001bbdbo9d4840adf2c75104@mail.gmail.com>

 Dear  chen_shao_hua197 at yahoo.com.tw,

 Please perform a search in the pwscf
*archive*<http://www.democritos.it/cgi-bin/htsearch?config=&restrict=&exclude=&method=and&format=builtin-long&sort=score&words=pw_forum>
just typing  'Malgorzata'.
 You will get the answer of your question (More specifically,
 check the 3rd Message).

 Regards,
 Amit



Dear members,
I had run example07 of the QE-3.2 version well.
For some reason,I changed the setting  in al.elph.in

nq1=10, nq2=10, nq3=6

then I got the error message below:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    from elphsum : error #         3
    q is not a vector in the dense grid

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Although I know it comes from PH/elphon.f90,
I still can not find out what the constraint or rule
is about nq1,2,3 related to its k-point setting in
scf.in ?

I mean why nq1=4, nq2=4, nq3=4 is fine ,but 10,10,6
fail ?
Is it relative to  k-point setting 8x8x8 in scf.in ?
What other setting  could we choose ?

Best Regards
max
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From gaoguoying at gmail.com  Mon Mar 12 09:26:42 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Mon, 12 Mar 2007 16:26:42 +0800
Subject: [Pw_forum] question on vc-relax
Message-ID: <6234c0c60703120126p76697bdaje9d1f0cc18c1e1d6@mail.gmail.com>

Dear pw users,
     I  did the scf calculation with the optimized lattice parameters.
However, the pressure in case.scf.out file is disagreement with the
optimized pressure in case.optim.out file. In optimization process,
although G^2 is replaced by G^2 + qcutz * (1 + erf ( (G^2 -
ecfixed)/q2sigma) ), the value of the parameter "qcutz" is 0, so the
ecut energy is constant. In the scf calculation, we use the same ecut
and k-mesh with the input file of optimization. What's the reason for
this? Any answer will be appreciated.
Gao


From niuli1978 at yahoo.com.cn  Mon Mar 12 13:18:14 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Mon, 12 Mar 2007 20:18:14 +0800 (CST)
Subject: [Pw_forum] vc-relax of graphite
Message-ID: <339948.42477.qm@web15009.mail.cnb.yahoo.com>

dear Paolo,
  
When I used a symmetry-conservin algorithm,  cell_dynamics = 'damp-w' ,
I still met the same error :
-------------------------------------------------------------------------
from checkallsym : error #         3
     not orthogonal operation
------------------------------------------------------------------------
And when using  "nosym = .true.", I met a warning:
       iteration #  1     ecut=    40.00 Ry     beta=0.70
     Davidson diagonalization with overlap
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     1 eigenvalues not converged
     WARNING:     1 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     1 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     1 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     1 eigenvalues not converged
     WARNING:     1 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     1 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     1 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     WARNING:     2 eigenvalues not converged
     ethr =  1.00E-06,  avg # of iterations = 19.8
       negative rho (up, down):  0.381E-03 0.000E+00
       total cpu time spent up to now is    626.96 secs
       WARNING: integrated charge=    10.59801382, expected=    16.00000000
   -----------------------------------------------------------------------------------------------
     from electrons : error #         1
     charge is wrong
 -----------------------------------------------------------------------------------------------
       stopping ...
   
  Now I don't know how to  optimize lattice constant of the bulk graphite. 
  Please give me some help.thanks!
Niu Li
=====================================================
My input as follows:
cat > graphite.vcrx.in << EOF
&CONTROL
  calculation  = "vc-relax",
  prefix       = "graphite",
  pseudo_dir   = "$PSEUDO_DIR",
  outdir       = "$TMP_DIR",
  tstress = .true. ,
  tprnfor = .true. ,
                       nstep = 65 ,
               etot_conv_thr = 1.0E-4 ,
               forc_conv_thr = 1.0D-3 ,
                          dt = 100 ,
/
&SYSTEM
    ibrav = 4, 
    celldm(1) =4.6336, 
    celldm(3)=2.7243,
    nat= 4, ntyp= 1,
    ecutwfc =40  
/
&ELECTRONS
  diagonalization = 'cg',
  conv_thr    = 1.D-9,
  mixing_beta = 0.7D0,
/
&IONS
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
&CELL
               cell_dynamics = 'damp-w',
                       press = 0.0 ,
                       wmass = 0.010 ,
 /
ATOMIC_SPECIES
 C   12.0107  C.pz-vbc.UPF
  ATOMIC_POSITIONS {crystal}
 C  0.0000000 0.0000000 0.0000000 
 C  0.0000000 0.0000000 0.5000000
 C  0.6666667 0.3333333 0.0000000
 C  0.3333333 0.6666667 0.5000000
K_POINTS automatic
4 4 4 1 1 1
  EOF
$ECHO " optimizing the lattice constant for bulk graphite...\c"
$PW_COMMAND < graphite.vcrx.in > graphite.vcrx.out
$ECHO " done"
================================================================
   

 		
---------------------------------
????????-3.5G???20M??? 
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From iori.federico at unimore.it  Mon Mar 12 16:33:52 2007
From: iori.federico at unimore.it (Federico Iori)
Date: Mon, 12 Mar 2007 16:33:52 +0100
Subject: [Pw_forum] problem with scf and nscf calculation!!
Message-ID: <45F572E0.6060802@unimore.it>

Hi pw users!

I'm doing some calculation on metallic systems but I have several 
problems with scf and than nscf (or bands) calculation for the band 
structure calcualtion:

what happen is that the eigenvalues calculated with a SCF calculation 
and with a NSCF (PWversion =< 3.0) or BANDS (for PWversion >= 3.1)
on the same kpoints differ: the band strcture is completely different in 
the NSCF (I should say wrong,because the character of the electronic 
structure completely change) with respect the SCF calculation.
I use this smearing:

        occupations='smearing',
        smearing='gaussian',
        degauss=0.005,



Could someone suggest me something, please? ( a part to change job of 
course....)

cheers,
federico iori.



From stewart at cnf.cornell.edu  Mon Mar 12 16:44:15 2007
From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu)
Date: Mon, 12 Mar 2007 11:44:15 -0400
Subject: [Pw_forum] problem with scf and nscf calculation!!
In-Reply-To: <45F572E0.6060802@unimore.it>
References: <45F572E0.6060802@unimore.it>
Message-ID: <20070312154415.6791.qmail@mail.spidergraphics.com>

Hi Federico, 

Please provide some more information on the specific system that you are 
looking at.  If you provide us with the input files in the two cases, it 
will help in determining the problem. 

Best regards, 

Derek 


Federico Iori writes: 

> Hi pw users! 
> 
> I'm doing some calculation on metallic systems but I have several problems 
> with scf and than nscf (or bands) calculation for the band structure 
> calcualtion: 
> 
> what happen is that the eigenvalues calculated with a SCF calculation and 
> with a NSCF (PWversion =< 3.0) or BANDS (for PWversion >= 3.1)
> on the same kpoints differ: the band strcture is completely different in 
> the NSCF (I should say wrong,because the character of the electronic 
> structure completely change) with respect the SCF calculation.
> I use this smearing: 
> 
>        occupations='smearing',
>        smearing='gaussian',
>        degauss=0.005, 
> 
>  
> 
> Could someone suggest me something, please? ( a part to change job of 
> course....) 
> 
> cheers,
> federico iori. 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum 
> 
 


################################
Derek Stewart, Ph. D.
Scientific Computation Associate
250 Duffield Hall
Cornell Nanoscale Facility (CNF)
Ithaca, NY 14853
stewart (at) cnf.cornell.edu
(607) 255-2856


From iori.federico at unimore.it  Mon Mar 12 17:05:49 2007
From: iori.federico at unimore.it (Federico Iori)
Date: Mon, 12 Mar 2007 17:05:49 +0100
Subject: [Pw_forum] Re: problem with scf and nscf calculation-input!!
Message-ID: <45F57A5D.6080501@unimore.it>

My input for SCF calculation is the following:                         
Input for NSCF calculation is (and is runned after
                                                                    
                                                                    
 &CONTROL                         
 &CONTROL                                                                   
calculation='nscf' (or 'bands' also)        
        
calculation='scf'                                                   
title='scf'               
        
title='scf'                                                         
verbosity='high'          
        
verbosity='high'                                                    
restart_mode='from_scratch'
        
restart_mode='from_scratch'                                         
nstep=100                 
        
nstep=100                                                           
iprint=1                  
        
iprint=1                                                            
tprnfor=.true.            
        
tprnfor=.true.                                                      
outdir='./'               
        
outdir='./'                                                         
prefix='scf'              
        
prefix='scf'                                                        
disk_io='default'         
        
disk_io='default'                                                   
pseudo_dir='../../'       
        pseudo_dir='../'                                            
/                                 
/                                                                    
&SYSTEM                          
 &SYSTEM                                                                    
ibrav=8                   
        
ibrav=8                                                             
celldm(1)=7.1912          
        
celldm(1)=7.1912                                                    
celldm(2)=5.656914006     
        
celldm(2)=5.656914006                                               
celldm(3)=5.656914006     
        
celldm(3)=5.656914006                                               
nat=28                    
        
nat=28                                                              
ntyp=3                    
        
ntyp=3                                                              
nbnd=45                   
        
nbnd=45                                                             
ecutwfc=30.0              
        
ecutwfc=30.0                                                        
ecutrho=180.0             
        
ecutrho=180.0                                                       
nosym=.TRUE.              
        
nosym=.TRUE.                                                        
occupations='smearing',   
        
occupations='smearing',                                             
smearing='gaussian',      
        
smearing='gaussian',                                                
degauss=0.005,            
        degauss=0.005,                                              
/                                 
/                                                                    
&ELECTRONS                       
 &ELECTRONS                                                                       
diagonalization='cg'    
        
diagonalization='cg'                                                      
conv_thr=1.0d-8         
        
conv_thr=1.0d-8                                                           
mixing_mode = 'plain'   
        mixing_mode = 
'plain'                                                     
mixing_beta=0.1d0       
        mixing_beta=0.1d0                                            
/                                    
        startingpot='atomic'                                          
&IONS                               
        
startingwfc='atomic'                                                 
ion_dynamics='bfgs'          
/                                                                            
upscale=20.0                 
 &IONS                                                               
/                                    
        ion_dynamics='bfgs'                                          
ATOMIC_SPECIES                       
        
upscale=20.0                                                         
H     1.00794   001-H-gpw--campos.uspp.UPF  
/                                                                            
Si    28.0855   014-Si-gpw-n-campos.uspp.UPF
ATOMIC_SPECIES                                                               
B     10.8110   005-B-gpw-n-campos.uspp.UPF 
        H     1.00794   001-H-gpw--campos.uspp.UPF                    
ATOMIC POSITION (angstrom)                         
        Si    28.0855   014-Si-gpw-n-campos.uspp.UPF                     
......                                           
        B     10.8110    005-B-gpw-n-campos.uspp.UPF                  
K_POINTS  {crystal}                                
                                                                      
    51                                             
ATOMIC POSITION (angstrom)                                             
give manually  
......                                                                   
K_POINTS  {crystal}                                                       
  51
  give manually               
                    



From iori.federico at unimore.it  Mon Mar 12 17:08:54 2007
From: iori.federico at unimore.it (Federico Iori)
Date: Mon, 12 Mar 2007 17:08:54 +0100
Subject: [Pw_forum] Re: problem with scf and nscf calculation-input!!
Message-ID: <45F57B16.9030503@unimore.it>

My input for SCF calculation is the following:

													
  &CONTROL
         calculation='scf'
         title='scf'
         verbosity='high'
         restart_mode='from_scratch'
         nstep=100
         iprint=1
         tprnfor=.true.
         outdir='./'
         prefix='scf'
         disk_io='default'
         pseudo_dir='../'
/
  &SYSTEM
         ibrav=8
         celldm(1)=7.1912
         celldm(2)=5.656914006
         celldm(3)=5.656914006
         nat=28
         ntyp=3
         nbnd=45
         ecutwfc=30.0
         ecutrho=180.0
         nosym=.TRUE.
         occupations='smearing',
         smearing='gaussian',
         degauss=0.005,
/
  &ELECTRONS
         diagonalization='cg'
         conv_thr=1.0d-8
         mixing_mode = 'plain'
         mixing_beta=0.1d0
         startingpot='atomic'
         startingwfc='atomic'
/
  &IONS
         ion_dynamics='bfgs'
         upscale=20.0
/
ATOMIC_SPECIES
         H     1.00794   001-H-gpw--campos.uspp.UPF
         Si    28.0855   014-Si-gpw-n-campos.uspp.UPF
         B     10.8110    005-B-gpw-n-campos.uspp.UPF
       												
ATOMIC POSITION (angstrom)
......
K_POINTS  {crystal}
   51
   give manually



    Input for NSCF calculation:
(is performed after a SCF calculation made on a 16x1x1 uniform kpt grid)

  &CONTROL
         calculation='nscf' (or 'bands' also)
         title='scf'
         verbosity='high'
         restart_mode='from_scratch'
         nstep=100
         iprint=1
         tprnfor=.true.
         outdir='./'
         prefix='scf'
         disk_io='default'
         pseudo_dir='../../'
/
  &SYSTEM
         ibrav=8
         celldm(1)=7.1912
         celldm(2)=5.656914006
         celldm(3)=5.656914006
         nat=28
         ntyp=3
         nbnd=45
         ecutwfc=30.0
         ecutrho=180.0
         nosym=.TRUE.
         occupations='smearing',
         smearing='gaussian',
         degauss=0.005,
/
  &ELECTRONS
               diagonalization='cg'
               conv_thr=1.0d-8
               mixing_mode = 'plain'
               mixing_beta=0.1d0
  /
   &IONS
          ion_dynamics='bfgs'
          upscale=20.0
  /
  ATOMIC_SPECIES
          H     1.00794   001-H-gpw--campos.uspp.UPF
          Si    28.0855   014-Si-gpw-n-campos.uspp.UPF
          B     10.8110   005-B-gpw-n-campos.uspp.UPF
   ATOMIC POSITION (angstrom)
  	......
   K_POINTS  {crystal}
     51                                              	
    give manually




From conor.hogan at roma2.infn.it  Mon Mar 12 17:12:03 2007
From: conor.hogan at roma2.infn.it (Conor Hogan)
Date: Mon, 12 Mar 2007 17:12:03 +0100 (CET)
Subject: [Pw_forum] problem with scf and nscf calculation!!
In-Reply-To: <45F572E0.6060802@unimore.it>
References: <45F572E0.6060802@unimore.it>
Message-ID: <38801.141.108.248.231.1173715923.squirrel@141.108.248.231>

Hi Federico,
When doing nscf/bands calculations with later versions of PWscf, and you
want well converged states, you should set diago_full_acc = .true. ,  set
diago_thr_init to a smaller value than the default (this determines the
precision of ther nscf calculation), and usually use a few more bands than
what you need will help. The Doc/INPUT_PW for 3.2 has a fair description
of these. As for bands/nscf, I notice that bands will read efermi from
data-file.xml while nscf does not, which might mean eigenvalues are not
aligned, but this is just a guess.
cheers
Conor

On Mon, March 12, 2007 4:33 pm, Federico Iori said:
> Hi pw users!
>
> I'm doing some calculation on metallic systems but I have several
problems with scf and than nscf (or bands) calculation for the band
structure calcualtion:
>
> what happen is that the eigenvalues calculated with a SCF calculation
and with a NSCF (PWversion =< 3.0) or BANDS (for PWversion >= 3.1) on
the same kpoints differ: the band strcture is completely different in
the NSCF (I should say wrong,because the character of the electronic
structure completely change) with respect the SCF calculation.
> I use this smearing:
>
>         occupations='smearing',
>         smearing='gaussian',
>         degauss=0.005,
>
>
>
> Could someone suggest me something, please? ( a part to change job of
course....)
>
> cheers,
> federico iori.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


----

Dr. Conor Hogan                                --- -----  ---   --- 
Dipartimento di Fisica e CNR-INFM             |      :   |     :    
Universita' di Roma "Tor Vergata"             |--    :    ---  |--- Tel:
+39 06 72594908                          |      :       | :     Fax: +39
06 2023507                            ---   :    ---  :    
http://www.fisica.uniroma2.it/~cmtheo-group/  European Theoretical
                                              Spectroscopy Facility 
http://www.etsf.eu

The early bird gets the worm, but the second mouse gets the cheese. - S.
Wright

If you go through a lot of hammers each month, I don't think it
necessarily
means you're a hard worker. It may just mean that you have a lot to learn 
about proper hammer maintenance - J. Handey






From iori.federico at unimore.it  Mon Mar 12 17:39:53 2007
From: iori.federico at unimore.it (Federico Iori)
Date: Mon, 12 Mar 2007 17:39:53 +0100
Subject: [Pw_forum] problem with scf and nscf calculation!!
In-Reply-To: <38801.141.108.248.231.1173715923.squirrel@141.108.248.231>
References: <45F572E0.6060802@unimore.it> <38801.141.108.248.231.1173715923.squirrel@141.108.248.231>
Message-ID: <45F58259.5060802@unimore.it>

Thanks Conor.... I'm goning to try this now!..

...but I still dont' understand why I cant't get the right band 
structure with the PW-3.0 version.

Infact another "strange thing" happen: when my system is semiconductor 
(all the valence states are doubly occupied)  I can get the right band 
strcuture both with the PW-3.0 and PW-3.2 calculation. BUT when my 
system become metallic (inserting a substitutional impurity) and I have 
a semi-occpudied level, the calculation for the band dont' work 
anymore........!!!
sigh!

idee???


Conor Hogan ha scritto:
> Hi Federico,
> When doing nscf/bands calculations with later versions of PWscf, and you
> want well converged states, you should set diago_full_acc = .true. ,  set
> diago_thr_init to a smaller value than the default (this determines the
> precision of ther nscf calculation), and usually use a few more bands than
> what you need will help. The Doc/INPUT_PW for 3.2 has a fair description
> of these. As for bands/nscf, I notice that bands will read efermi from
> data-file.xml while nscf does not, which might mean eigenvalues are not
> aligned, but this is just a guess.
> cheers
> Conor
>
> On Mon, March 12, 2007 4:33 pm, Federico Iori said:
>   
>> Hi pw users!
>>
>> I'm doing some calculation on metallic systems but I have several
>>     
> problems with scf and than nscf (or bands) calculation for the band
> structure calcualtion:
>   
>> what happen is that the eigenvalues calculated with a SCF calculation
>>     
> and with a NSCF (PWversion =< 3.0) or BANDS (for PWversion >= 3.1) on
> the same kpoints differ: the band strcture is completely different in
> the NSCF (I should say wrong,because the character of the electronic
> structure completely change) with respect the SCF calculation.
>   
>> I use this smearing:
>>
>>         occupations='smearing',
>>         smearing='gaussian',
>>         degauss=0.005,
>>
>>
>>
>> Could someone suggest me something, please? ( a part to change job of
>>     
> course....)
>   
>> cheers,
>> federico iori.
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>     
>
>
> ----
>
> Dr. Conor Hogan                                --- -----  ---   --- 
> Dipartimento di Fisica e CNR-INFM             |      :   |     :    
> Universita' di Roma "Tor Vergata"             |--    :    ---  |--- Tel:
> +39 06 72594908                          |      :       | :     Fax: +39
> 06 2023507                            ---   :    ---  :    
> http://www.fisica.uniroma2.it/~cmtheo-group/  European Theoretical
>                                               Spectroscopy Facility 
> http://www.etsf.eu
>
> The early bird gets the worm, but the second mouse gets the cheese. - S.
> Wright
>
> If you go through a lot of hammers each month, I don't think it
> necessarily
> means you're a hard worker. It may just mean that you have a lot to learn 
> about proper hammer maintenance - J. Handey
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>   




From lanhaiping at gmail.com  Mon Mar 12 18:13:19 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Tue, 13 Mar 2007 01:13:19 +0800
Subject: [Pw_forum] vc-relax of graphite
In-Reply-To: <339948.42477.qm@web15009.mail.cnb.yahoo.com>
References: <339948.42477.qm@web15009.mail.cnb.yahoo.com>
Message-ID: <c92002fa0703121013l2ece9f53p1c36162fa0fb5bcf@mail.gmail.com>

Dear Niu Li,
 In your input file that diagonalization is 'cg',  but warnning information
is related to 'david' scheme.  I cannot understand it ..
   another suggestion to your input setting is about kpoints. i think 4x4
mesh grids are not enough for x-y plane, and you should set  more dense...


hope help

regards.

h.p





On 3/12/07, li niu <niuli1978 at yahoo.com.cn> wrote:
>
> dear Paolo,
>
> When I used a symmetry-conservin algorithm,  cell_dynamics = 'damp-w' ,
> I still met the same error :
> -------------------------------------------------------------------------
> from checkallsym : error #         3
>      not orthogonal operation
> ------------------------------------------------------------------------
> And when using  "nosym = .true.", I met a warning:
>      iteration #  1     ecut=    40.00 Ry     beta=0.70
>      Davidson diagonalization with overlap
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     1 eigenvalues not converged
>      WARNING:     1 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     1 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     1 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     1 eigenvalues not converged
>      WARNING:     1 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     1 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     1 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      WARNING:     2 eigenvalues not converged
>      ethr =  1.00E-06,  avg # of iterations = 19.8
>      negative rho (up, down):  0.381E-03 0.000E+00
>      total cpu time spent up to now is    626.96 secs
>      WARNING: integrated charge=    10.59801382, expected=    16.00000000
>
>  -----------------------------------------------------------------------------------------------
>      from electrons : error #         1
>      charge is wrong
>
>  -----------------------------------------------------------------------------------------------
>      stopping ...
>
> Now I don't know how to  optimize lattice constant of the bulk graphite.
> Please give me some help.thanks!
> Niu Li
> =====================================================
> My input as follows:
> cat > graphite.vcrx.in << EOF
> &CONTROL
>   calculation  = "vc-relax",
>   prefix       = "graphite",
>   pseudo_dir   = "$PSEUDO_DIR",
>   outdir       = "$TMP_DIR",
>   tstress = .true. ,
>   tprnfor = .true. ,
>                        nstep = 65 ,
>                etot_conv_thr = 1.0E-4 ,
>                forc_conv_thr = 1.0D-3 ,
>                           dt = 100 ,
> /
> &SYSTEM
>     ibrav = 4,
>     celldm(1) =4.6336,
>     celldm(3)=2.7243,
>     nat= 4, ntyp= 1,
>     ecutwfc =40
> /
> &ELECTRONS
>   diagonalization = 'cg',
>   conv_thr    = 1.D-9,
>   mixing_beta = 0.7D0,
> /
> &IONS
>   pot_extrapolation = "second_order",
>   wfc_extrapolation = "second_order",
> /
> &CELL
>                cell_dynamics = 'damp-w',
>                        press = 0.0 ,
>                        wmass = 0.010 ,
>  /
> ATOMIC_SPECIES
>  C   12.0107  C.pz-vbc.UPF
> ATOMIC_POSITIONS {crystal}
>  C  0.0000000 0.0000000 0.0000000
>  C  0.0000000 0.0000000 0.5000000
>  C  0.6666667 0.3333333 0.0000000
>  C  0.3333333 0.6666667 0.5000000
> K_POINTS automatic
> 4 4 4 1 1 1
> EOF
> $ECHO " optimizing the lattice constant for bulk graphite...\c"
> $PW_COMMAND < graphite.vcrx.in > graphite.vcrx.out
> $ECHO " done"
> ================================================================
>
>
> ------------------------------
> ????????-3.5G???20M??? <http://cn.mail.yahoo.com/>
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
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From Daniele.Passerone at empa.ch  Tue Mar 13 13:04:48 2007
From: Daniele.Passerone at empa.ch (Daniele Passerone)
Date: Tue, 13 Mar 2007 13:04:48 +0100
Subject: [Pw_forum] K-Points and dipole correction
Message-ID: <45F6A172.11F0.001D.0@empa.ch>

Dear collegues,

I have a strange problem with a slab calculation with the Bengtsson
dipole correction (sawlike potential). The cell is hexagonal.


If I submit two different jobs, jobA and jobB (espresso 3.2.1 on IBM
power5 , but the same problem appears on a linux cluster) with
from_scratch scf optimization, 

*) jobA:

in &control:
    tefield=.false.,
    dipfield=.false.
and:
K_POINTS {automatic}
 5 5 1 1 1 0


*) jobB:

in &control:
    tefield=.true.,
    dipfield=.true.
 
in &system:
    edir=3,
    eamp=0.,
    emaxpos=0.45
    eopreg=0.05,

 
In the first case, I get 39 K points, 
in the second case I get 13 K points. There is no symmetry found in the
slab in both cases.
Only 10 k points are common to both cases (marked by a star, see
below).

Why? 

Probably I am missing something really fundamental here, and I would be
grateful for any help.
Thanks in advance,
Daniele Passerone

jobA:
   *      k(    1) = (   0.1000000   0.1732051   0.0000000), wk =  
0.0533333
   *     k(    2) = (   0.1000000   0.4041452   0.0000000), wk =  
0.0533333
   *     k(    3) = (   0.1000000  -0.5196152   0.0000000), wk =  
0.0533333
   *     k(    4) = (   0.1000000  -0.2886751   0.0000000), wk =  
0.0533333
   *     k(    5) = (   0.1000000  -0.0577350   0.0000000), wk =  
0.0533333
   *     k(    6) = (   0.3000000   0.5196152   0.0000000), wk =  
0.0533333
   *     k(    7) = (   0.3000000  -0.4041452   0.0000000), wk =  
0.0533333
   *     k(    8) = (   0.3000000  -0.1732051   0.0000000), wk =  
0.0533333
   *     k(    9) = (  -0.5000000  -0.8660254   0.0000000), wk =  
0.0266667
        k(   10) = (  -0.1000000   0.1732051   0.0000000), wk =  
0.0533333
        k(   11) = (   0.2000000   0.0000000   0.0000000), wk =  
0.0533333
        k(   12) = (  -0.1000000   0.4041452   0.0000000), wk =  
0.0533333
        k(   13) = (  -0.3000000   0.2886751   0.0000000), wk =  
0.0533333
        k(   14) = (   0.4000000   0.1154701   0.0000000), wk =  
0.0533333
        k(   15) = (  -0.3000000  -0.2886751   0.0000000), wk =  
0.0533333
        k(   16) = (   0.4000000  -0.1154701   0.0000000), wk =  
0.0533333
        k(   17) = (  -0.1000000  -0.5196152   0.0000000), wk =  
0.0533333
        k(   18) = (   0.5000000  -0.1732051   0.0000000), wk =  
0.0533333
        k(   19) = (  -0.4000000  -0.3464102   0.0000000), wk =  
0.0533333
        k(   20) = (   0.5000000   0.1732051   0.0000000), wk =  
0.0533333
        k(   21) = (  -0.4000000   0.3464102   0.0000000), wk =  
0.0533333
        k(   22) = (  -0.1000000  -0.2886751   0.0000000), wk =  
0.0533333
        k(   23) = (   0.3000000  -0.0577350   0.0000000), wk =  
0.0533333
        k(   24) = (  -0.2000000  -0.2309401   0.0000000), wk =  
0.0533333
   *     k(   25) = (   0.3000000   0.0577350   0.0000000), wk =  
0.0533333
        k(   26) = (  -0.2000000   0.2309401   0.0000000), wk =  
0.0533333
        k(   27) = (  -0.1000000  -0.0577350   0.0000000), wk =  
0.0533333
        k(   28) = (   0.0000000  -0.1154701   0.0000000), wk =  
0.0533333
        k(   29) = (  -0.3000000   0.5196152   0.0000000), wk =  
0.0533333
        k(   30) = (   0.6000000   0.0000000   0.0000000), wk =  
0.0533333
        k(   31) = (  -0.3000000  -0.4041452   0.0000000), wk =  
0.0533333
        k(   32) = (   0.5000000   0.0577350   0.0000000), wk =  
0.0533333
        k(   33) = (  -0.2000000  -0.4618802   0.0000000), wk =  
0.0533333
        k(   34) = (   0.5000000  -0.0577350   0.0000000), wk =  
0.0533333
        k(   35) = (  -0.2000000   0.4618802   0.0000000), wk =  
0.0533333
        k(   36) = (  -0.3000000  -0.1732051   0.0000000), wk =  
0.0533333
        k(   37) = (   0.0000000  -0.3464102   0.0000000), wk =  
0.0533333
        k(   38) = (   0.5000000  -0.8660254   0.0000000), wk =  
0.0266667
        k(   39) = (  -1.0000000   0.0000000   0.0000000), wk =  
0.0266667


jobB:
        k(    1) = (   0.1000000   0.1732051   0.0000000), wk =  
0.1600000
        k(    2) = (   0.1000000   0.4041452   0.0000000), wk =  
0.1600000
        k(    3) = (   0.1000000  -0.5196152   0.0000000), wk =  
0.1600000
        k(    4) = (   0.1000000  -0.2886751   0.0000000), wk =  
0.1600000
        k(    5) = (   0.1000000  -0.0577350   0.0000000), wk =  
0.1600000
        k(    6) = (   0.3000000   0.2886751   0.0000000), wk =  
0.1600000
        k(    7) = (   0.3000000   0.5196152   0.0000000), wk =  
0.1600000
        k(    8) = (   0.3000000  -0.4041452   0.0000000), wk =  
0.1600000
        k(    9) = (   0.3000000  -0.1732051   0.0000000), wk =  
0.1600000
        k(   10) = (   0.3000000   0.0577350   0.0000000), wk =  
0.1600000
        k(   11) = (  -0.5000000  -0.1732051   0.0000000), wk =  
0.1600000
        k(   12) = (  -0.5000000   0.0577350   0.0000000), wk =  
0.1600000
        k(   13) = (  -0.5000000  -0.8660254   0.0000000), wk =  
0.0800000




~                    


From giannozz at nest.sns.it  Tue Mar 13 14:38:35 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 13 Mar 2007 14:38:35 +0100
Subject: [Pw_forum] problem with scf and nscf calculation!!
In-Reply-To: <45F58259.5060802@unimore.it>
References: <45F572E0.6060802@unimore.it> <38801.141.108.248.231.1173715923.squirrel@141.108.248.231> <45F58259.5060802@unimore.it>
Message-ID: <CDA82C24-739F-4755-854C-4B31574D3D2B@nest.sns.it>

On Mar 12, 2007, at 17:39 , Federico Iori wrote:

> Infact another "strange thing" happen: when my system is semiconductor
> (all the valence states are doubly occupied)  I can get the right  
> band structure
> both with the PW-3.0 and PW-3.2 calculation. BUT when my system  
> become metallic (inserting a substitutional impurity) and I have a  
> semi-occupied level,
> the calculation for the band dont' work anymore........!!!

I'll believe this when I'll see this. Please provide an example - ONE
THAT CAN BE RUN - showing the above phenomenon
---
Paolo Giannozzi, Democritos and University of Udine, Italy




From giannozz at nest.sns.it  Tue Mar 13 14:47:51 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 13 Mar 2007 14:47:51 +0100
Subject: [Pw_forum] problem with scf and nscf calculation!!
In-Reply-To: <38801.141.108.248.231.1173715923.squirrel@141.108.248.231>
References: <45F572E0.6060802@unimore.it> <38801.141.108.248.231.1173715923.squirrel@141.108.248.231>
Message-ID: <DD0EA871-9271-411E-AD8C-0148B52759C8@nest.sns.it>

On Mar 12, 2007, at 17:12 , Conor Hogan wrote:

> As for bands/nscf, I notice that bands will read efermi from
> data-file.xml while nscf does not, which might mean eigenvalues
> are not aligned, but this is just a guess.

'nscf' re-calculates the Fermi energy, 'bands' doesn't, but in
some cases it is useful to have it in the output file, so it is
read from the previous scf calculation

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




From iori.federico at unimore.it  Tue Mar 13 14:57:26 2007
From: iori.federico at unimore.it (Federico Iori)
Date: Tue, 13 Mar 2007 14:57:26 +0100
Subject: [Pw_forum] problem with scf and nscf calculation!!
In-Reply-To: <DD0EA871-9271-411E-AD8C-0148B52759C8@nest.sns.it>
References: <45F572E0.6060802@unimore.it> <38801.141.108.248.231.1173715923.squirrel@141.108.248.231> <DD0EA871-9271-411E-AD8C-0148B52759C8@nest.sns.it>
Message-ID: <45F6ADC6.1060901@unimore.it>

so what should I use for a band structure calculation nscf or bands?
because in a previous mail
"what's wrong with nscf when doing bands" - 13 dec 2006 degironcoli 
suggets to use bands instead nscf....

Paolo Giannozzi ha scritto:
>
> On Mar 12, 2007, at 17:12 , Conor Hogan wrote:
>
>> As for bands/nscf, I notice that bands will read efermi from
>> data-file.xml while nscf does not, which might mean eigenvalues
>> are not aligned, but this is just a guess.
>
> 'nscf' re-calculates the Fermi energy, 'bands' doesn't, but in
> some cases it is useful to have it in the output file, so it is
> read from the previous scf calculation
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>




From giannozz at nest.sns.it  Tue Mar 13 15:01:26 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 13 Mar 2007 15:01:26 +0100
Subject: [Pw_forum] problem with scf and nscf calculation!!
In-Reply-To: <45F6ADC6.1060901@unimore.it>
References: <45F572E0.6060802@unimore.it> <38801.141.108.248.231.1173715923.squirrel@141.108.248.231> <DD0EA871-9271-411E-AD8C-0148B52759C8@nest.sns.it> <45F6ADC6.1060901@unimore.it>
Message-ID: <507E7F30-905E-4ADE-B880-9141DAAD5F7D@nest.sns.it>

On Mar 13, 2007, at 14:57 , Federico Iori wrote:

> so what should I use for a band structure calculation nscf or bands?
> because in a previous mail
> "what's wrong with nscf when doing bands" - 13 dec 2006 degironcoli
> suggests to use bands instead nscf....

if all you need is the band structure at selected k-points, use 'bands'
if you need the calculation of the electronic states and of their
occupations, for further processing, use 'nscf'

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




From sagars_daya at yahoo.co.in  Tue Mar 13 20:06:47 2007
From: sagars_daya at yahoo.co.in (Daya sagar)
Date: Tue, 13 Mar 2007 19:06:47 +0000 (GMT)
Subject: [Pw_forum] Can anyone help me with GaN p type doping
In-Reply-To: <aa36e8060703081253l4f352ec6he3254d5961b8068e@mail.gmail.com>
Message-ID: <970374.74315.qm@web8321.mail.in.yahoo.com>

Hi,

  I am working on GaN nanowires. Can anyone please let me know which material should be used as p type dopant for GaN. I tried using Mg and Si as p type dopants but they seem to create bonding between 2 Ga atoms and create bands in the energygap. 
I would be really thankful if anyone can help me solve this problem.

Thanks.

Regards,
Sagar.
saman ghaderyan <ghaderyan at gmail.com> wrote: hi
i run relaxation for AlAs with nat=4
Al   0.00 0.00  0.00
As  0.25 0.25  0.25
Al   0.50  0.50  0.00
As -0.25 0.25 0.25
but i don't know why these atomic position have error
thanks
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


 				
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From sanjeev0302 at rediffmail.com  Tue Mar 13 20:09:04 2007
From: sanjeev0302 at rediffmail.com (Sanjeev Kumar Gupta)
Date: 13 Mar 2007 19:09:04 -0000
Subject: [Pw_forum] problem with band structure calculation
Message-ID: <1173812442.S.3136.22863.webmail2.rediffmail.com.1173812944.19242@webmail.rediffmail.com>

Respected sir,After running the band.x, we got this out put band structure calculation. please suggest me.regardsProgram POST-PROC v.3.1.1 starts ...Today is 14Mar2007 at 0:31:40nbndx = 12 nbnd = 12 natomwfc = 10 npwx = 360nelec = 15.00 nkb = 21 ngl = 66%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%from punch_band : error # 29Opening filband file%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%stopping ...

=================================================
Sanjeev Kumar Gupta
Junior Research Fellow (2nd Year)
Computational Condensed Matter Physics Lab.(CCMP)
Dept. of Physics, Faculty of Science,
The M.S.University of Baroda, Vadodara - 390 002.
Ph.No: +91-265-279 5339 (O) extn: 30-25 
Mobile:    09374616019
Email: skgupta-phy at msubaroda.ac.in
URL:   skgupta.physics.googlepages.com
=================================================

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From yuwen_66 at yahoo.com  Wed Mar 14 04:26:57 2007
From: yuwen_66 at yahoo.com (W. YU)
Date: Tue, 13 Mar 2007 20:26:57 -0700 (PDT)
Subject: [Pw_forum] inequivalent atoms of the same type
Message-ID: <20070314032658.85451.qmail@web51004.mail.re2.yahoo.com>

Dear PW users,

I have a question concerning the "ntype" keyword:

In a non-magnetic case, if I have the same kind
(chemically) of atoms which occupy different symmetry
sites, say "4c" and "4e",and I made them belong to the
same "type", how will the code find the symmetry for
these two inequivalent kinds of atoms. If it cannot
differentiate between these two symmetry sites, will
this has some effect on the results?

Furthermore, in a phonon calculation, the phonon modes
are associated with different site symmetries. If the
two atoms in different symmetry sites were treated as
one kind, will the phonon modes be  different?  

I would appreciate it if anybody could explain this.

Wen Yu 


 
____________________________________________________________________________________
Be a PS3 game guru.
Get your game face on with the latest PS3 news and previews at Yahoo! Games.
http://videogames.yahoo.com/platform?platform=120121


From lanhaiping at gmail.com  Wed Mar 14 06:49:16 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Wed, 14 Mar 2007 13:49:16 +0800
Subject: [Pw_forum] Can anyone help me with GaN p type doping
In-Reply-To: <970374.74315.qm@web8321.mail.in.yahoo.com>
References: <aa36e8060703081253l4f352ec6he3254d5961b8068e@mail.gmail.com>
	 <970374.74315.qm@web8321.mail.in.yahoo.com>
Message-ID: <c92002fa0703132249u768e7d0dl9f50e87b1002ef7a@mail.gmail.com>

Hi,
for doping or charged defects system, you can refer to  Alex Zunger's work.

Regards,

h.p


On 3/14/07, Daya sagar <sagars_daya at yahoo.co.in> wrote:
>
> Hi,
>
>   I am working on GaN nanowires. Can anyone please let me know which
> material should be used as p type dopant for GaN. I tried using Mg and Si as
> p type dopants but they seem to create bonding between 2 Ga atoms and create
> bands in the energygap.
> I would be really thankful if anyone can help me solve this problem.
>
> Thanks.
>
> Regards,
> Sagar.
> *saman ghaderyan <ghaderyan at gmail.com>* wrote:
>
> hi
> i run relaxation for AlAs with nat=4
> Al 0.00 0.00 0.00
> As 0.25 0.25 0.25
> Al 0.50 0.50 0.00
> As -0.25 0.25 0.25
> but i don't know why these atomic position have error
> thanks
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>  ------------------------------
> Here's a new way to find what you're looking for - Yahoo! Answers<http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/>
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
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From yupiaofei at mail.sdu.edu.cn  Wed Mar 14 09:18:28 2007
From: yupiaofei at mail.sdu.edu.cn (yupiaofei(SDU))
Date: Wed, 14 Mar 2007 16:18:28 +0800
Subject: [Pw_forum] [Pw_forum]Problems in the generation of I pseudopotential
References: <b25d3a170612182232k38fbcce8mda3a3a136c347bd0@mail.gmail.com>  <458791C4.3070303@sissa.it> <b25d3a170612190108r29d37485l206caa0740cd8ee1@mail.gmail.com> <366523677.27614@mail.sdu.edu.cn>
Message-ID: <373860639.30754@mail.sdu.edu.cn>

I made a test to generate the I pseudopotential, but the error appeared as follows:

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from ld1_readin : error #         1
     unbound states must be empty
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
what's the wrong?

This is input file.

 &input
        title='I',
        zed=53,
        iswitch=3,
        rlderiv=2.50,
        eminld=-4.0,
        emaxld=4.0,
        deld=0.02,
        nld=5,
        config='[Kr] 4d10 5s2 5p5 ',
        dft='PW91'
 /
 &inputp
        pseudotype=3,
        lloc=2,
        rcloc=2,
        file_pseudopw='I.pw91.UPF',
        nlcc=.true.,
        rcore=1.8,
        rcloc=2.8
 /
3
4D  3 2  10.00 -0.20  2.10  2.40
5S  1 0   2.00 -0.00  3.30  3.30
5P  2 1   5.00 -0.00  3.40  3.40

&test
ecutmin=100.0,
ecutmax=200.0,
decut=20.0
/
3
4D  3 2  10.00 -0.20  2.10  2.40
5S  1 0   2.00 -0.00  3.30  3.30
5P  2 1   5.00 -0.00  3.40  3.40
 

From ding at sissa.it  Wed Mar 14 09:03:54 2007
From: ding at sissa.it (Xunlei Ding)
Date: Wed, 14 Mar 2007 09:03:54 +0100
Subject: [Pw_forum] inequivalent atoms of the same type
In-Reply-To: <20070314032658.85451.qmail@web51004.mail.re2.yahoo.com>
References: <20070314032658.85451.qmail@web51004.mail.re2.yahoo.com>
Message-ID: <45F7AC6A.8060101@sissa.it>

Dear Yu,
The "same" atom at different symmetry sites is just the same at initial 
time.
When scf calculation is done, they can be totally different.
When we set ntype=2 for the same kind (chemically) of atoms, usually in 
magnetic calculation,
we just set different initial parameters for them, such as 
starting_magnetization(i), to make the initial state close to the final 
result.

For example, we do a calculation on a meterial X (only one kine of atom 
X, with two different symmetry site X1, X2).
If the final spin state is X1: 0.5, X2:0.3, then you can set them as the 
same atom and just set starting_magnetization(1)=0.7,
and also, you can set them as two kind of atoms, and set 
starting_magnetization(1)=0.7, starting_magnetization(2)=0.9.
If the final spin state is X1: 0.5, X2:-0.3, then I think we must set 
them as two kind of atoms, and set starting_magnetization(1)=0.7, 
starting_magnetization(2)=-0.6.

Hope what I said is right.

Best,
Ding

W. YU wrote:

>Dear PW users,
>
>I have a question concerning the "ntype" keyword:
>
>In a non-magnetic case, if I have the same kind
>(chemically) of atoms which occupy different symmetry
>sites, say "4c" and "4e",and I made them belong to the
>same "type", how will the code find the symmetry for
>these two inequivalent kinds of atoms. If it cannot
>differentiate between these two symmetry sites, will
>this has some effect on the results?
>
>Furthermore, in a phonon calculation, the phonon modes
>are associated with different site symmetries. If the
>two atoms in different symmetry sites were treated as
>one kind, will the phonon modes be  different?  
>
>I would appreciate it if anybody could explain this.
>
>Wen Yu 
>
>
> 
>____________________________________________________________________________________
>Be a PS3 game guru.
>Get your game face on with the latest PS3 news and previews at Yahoo! Games.
>http://videogames.yahoo.com/platform?platform=120121
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>
>  
>


From giannozz at nest.sns.it  Wed Mar 14 09:34:41 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 14 Mar 2007 09:34:41 +0100
Subject: [Pw_forum] [Pw_forum]Problems in the generation of I pseudopotential
In-Reply-To: <373860639.30754@mail.sdu.edu.cn>
References: <b25d3a170612182232k38fbcce8mda3a3a136c347bd0@mail.gmail.com>  <458791C4.3070303@sissa.it> <b25d3a170612190108r29d37485l206caa0740cd8ee1@mail.gmail.com> <366523677.27614@mail.sdu.edu.cn> <373860639.30754@mail.sdu.edu.cn>
Message-ID: <E20BBF9F-BFE4-4C11-B32C-7807CDFEA566@nest.sns.it>

On Mar 14, 2007, at 9:18 , yupiaofei(SDU) wrote:

> I made a test to generate the I pseudopotential, but the error
> appeared as follows:
> [...]
>      unbound states must be empty
> [...]
> what's the wrong?

> 4D  3 2  10.00 -0.20  2.10  2.40

here is "the wrong", as you say. You cannot set a pseudization
energy (-0.2Ry above) for a bound state (occupancy=10).
You can set it only for unbound states.

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




From giannozz at nest.sns.it  Wed Mar 14 09:51:34 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 14 Mar 2007 09:51:34 +0100
Subject: [Pw_forum] inequivalent atoms of the same type
In-Reply-To: <20070314032658.85451.qmail@web51004.mail.re2.yahoo.com>
References: <20070314032658.85451.qmail@web51004.mail.re2.yahoo.com>
Message-ID: <7825703A-7383-4341-9195-859CE63C8EF6@nest.sns.it>

On Mar 14, 2007, at 4:26 , W. YU wrote:

> In a non-magnetic case, if I have the same kind
> (chemically) of atoms which occupy different symmetry
> sites, say "4c" and "4e",and I made them belong to the
> same "type", how will the code find the symmetry for
> these two inequivalent kinds of atoms.

the code works on the complete cell, not on the subset
of inequivalent atoms, and finds the symmetry by trying
a set of candidate symmetry operations.

> If it cannot differentiate between these two symmetry
> sites, will this has some effect on the results?

no. The code knows which atom transform into which
under which symmetry operation. Atoms belonging to
different symmetry sites will never transform into each
other.

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




From wmbmacam at lg.ehu.es  Wed Mar 14 10:54:55 2007
From: wmbmacam at lg.ehu.es (=?UTF-8?B?TWlndWVsIE1hcnTDrW5leiBDYW5hbGVz?=)
Date: Wed, 14 Mar 2007 10:54:55 +0100
Subject: [Pw_forum] Phonon crash
Message-ID: <45F7C66F.2050102@lg.ehu.es>

Dear fellows,

I have found that, when running a phonon calculation under certain 
conditions, it crashes. More concretely, on fcc systems (I haven't checked 
diamond structures) if the scf run uses a 20 20 20 monkhorst-pack grid and 
the phonon calculation uses ldisp=.true. for a 8*8*8 regular grid the 
phonon run will crash at dyn23 (q = 0.625 -0.375  0.875). The last lines of 
the phonon output are:

      Calculation of q =   0.6250 -0.3750  0.8750

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from set_kplusq : error #     32000
      too many k points
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

      stopping ...

It really puzzles me that it stops on the 23rd point, and not sooner. Maybe 
it's related to the star of q?

If I specify this point by hand, doing a nscf run and then a phonon run at 
that qpoint, it will also crash. It depends neither on the lattice 
parametre, nor the the pseudpotential (I've done it with Na LDA, Li LDA and 
Li PBE). It won't crash if I reduce the k-point grid, and it won't crash 
with the same grid on a bcc lattice.

I am using espresso-3.2.1 plus the patch that Paolo submitted to make 
-npool work with ph.x. It's been compiled with ifort 8.1 and mkl 9.0 in an 
itanium 2 machine. Any ideas?

Thanks for your comments,

Miguel

In case the input is relevant, I attach it:


# self-consistent calculation
cat > na.scf.in << EOF
  &control
     calculation='scf'
     restart_mode='from_scratch',
     tstress = .true.
     tprnfor = .true.
     prefix='na',
     pseudo_dir = '$PSEUDO_DIR/',
     outdir='$TMP_DIR/'
  /
  &system
     ibrav=  2, celldm(1) = $alat , nat=  1, ntyp= 1,
     ecutwfc = 30.0
     occupations='smearing', smearing='m-p', degauss= 0.010
  /
  &electrons
     conv_thr =  1.0d-8
     mixing_beta = 0.7
  /
ATOMIC_SPECIES
  Na  22.989768  Na.pz-n-vbc.UPF
ATOMIC_POSITIONS
  Na 0.00 0.00 0.00
K_POINTS {automatic}
  20 20 20   1 1 1
EOF
$ECHO "  running the scf calculation...\c"
$PW_COMMAND < na.scf.in > na.scf.out
$ECHO " done"

# phonon calculation
cat > na.ph.in << EOF
phonons of Na
  &inputph
   tr2_ph=1.0d-16,
   prefix='na',
   ldisp=.true.,
   nq1=8, nq2=8, nq3=8
   amass(1)=22.989768,
   outdir='$TMP_DIR/',
   fildyn='na.dyn',
  /
EOF
$ECHO "  running the phonon calculation ...\c"
$PH_COMMAND < na.ph.in > na.ph.out
$ECHO " done"


-- 
----------------------------------------
Miguel Mart?nez Canales
Dto. F?sica de la Materia Condensada
UPV/EHU
Facultad de Ciencia y Tecnolog?a
Apdo. 644
48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5437
----------------------------------------

  "If you have an apple and I have an apple and
  we exchange these apples then you and I will
  still each have one apple. But if you have an
  idea and I have an idea and we exchange these
  ideas, then each of us will have two ideas."

    George Bernard Shaw



From dalcorso at sissa.it  Wed Mar 14 11:28:19 2007
From: dalcorso at sissa.it (Andrea Dal Corso)
Date: Wed, 14 Mar 2007 11:28:19 +0100
Subject: [Pw_forum] Phonon crash
In-Reply-To: <45F7C66F.2050102@lg.ehu.es>
References: <45F7C66F.2050102@lg.ehu.es>
Message-ID: <1173868100.4009.6.camel@dhpc-5-07.sissa.it>

Presently the maximum number of k points is npk    = 40000, but you need
at least 64000 for this q point. Increasing this parameter in
Module/parameters.f90 and recompiling should work.

Andrea




On Wed, 2007-03-14 at 10:54 +0100, Miguel Mart?nez Canales wrote:
> Dear fellows,
> 
> I have found that, when running a phonon calculation under certain 
> conditions, it crashes. More concretely, on fcc systems (I haven't checked 
> diamond structures) if the scf run uses a 20 20 20 monkhorst-pack grid and 
> the phonon calculation uses ldisp=.true. for a 8*8*8 regular grid the 
> phonon run will crash at dyn23 (q = 0.625 -0.375  0.875). The last lines of 
> the phonon output are:
> 
>       Calculation of q =   0.6250 -0.3750  0.8750
> 
>  
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>       from set_kplusq : error #     32000
>       too many k points
>  
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
>       stopping ...
> 
> It really puzzles me that it stops on the 23rd point, and not sooner. Maybe 
> it's related to the star of q?
> 
> If I specify this point by hand, doing a nscf run and then a phonon run at 
> that qpoint, it will also crash. It depends neither on the lattice 
> parametre, nor the the pseudpotential (I've done it with Na LDA, Li LDA and 
> Li PBE). It won't crash if I reduce the k-point grid, and it won't crash 
> with the same grid on a bcc lattice.
> 
> I am using espresso-3.2.1 plus the patch that Paolo submitted to make 
> -npool work with ph.x. It's been compiled with ifort 8.1 and mkl 9.0 in an 
> itanium 2 machine. Any ideas?
> 
> Thanks for your comments,
> 
> Miguel
> 
> In case the input is relevant, I attach it:
> 
> 
> # self-consistent calculation
> cat > na.scf.in << EOF
>   &control
>      calculation='scf'
>      restart_mode='from_scratch',
>      tstress = .true.
>      tprnfor = .true.
>      prefix='na',
>      pseudo_dir = '$PSEUDO_DIR/',
>      outdir='$TMP_DIR/'
>   /
>   &system
>      ibrav=  2, celldm(1) = $alat , nat=  1, ntyp= 1,
>      ecutwfc = 30.0
>      occupations='smearing', smearing='m-p', degauss= 0.010
>   /
>   &electrons
>      conv_thr =  1.0d-8
>      mixing_beta = 0.7
>   /
> ATOMIC_SPECIES
>   Na  22.989768  Na.pz-n-vbc.UPF
> ATOMIC_POSITIONS
>   Na 0.00 0.00 0.00
> K_POINTS {automatic}
>   20 20 20   1 1 1
> EOF
> $ECHO "  running the scf calculation...\c"
> $PW_COMMAND < na.scf.in > na.scf.out
> $ECHO " done"
> 
> # phonon calculation
> cat > na.ph.in << EOF
> phonons of Na
>   &inputph
>    tr2_ph=1.0d-16,
>    prefix='na',
>    ldisp=.true.,
>    nq1=8, nq2=8, nq3=8
>    amass(1)=22.989768,
>    outdir='$TMP_DIR/',
>    fildyn='na.dyn',
>   /
> EOF
> $ECHO "  running the phonon calculation ...\c"
> $PH_COMMAND < na.ph.in > na.ph.out
> $ECHO " done"
> 
> 
-- 
Andrea Dal Corso                    Tel. 0039-040-3787428
SISSA, Via Beirut 2/4               Fax. 0039-040-3787528
34014 Trieste (Italy)               e-mail: dalcorso at sissa.it



From wmbmacam at lg.ehu.es  Wed Mar 14 12:01:11 2007
From: wmbmacam at lg.ehu.es (=?UTF-8?B?TWlndWVsIE1hcnTDrW5leiBDYW5hbGVz?=)
Date: Wed, 14 Mar 2007 12:01:11 +0100
Subject: [Pw_forum] Phonon crash
In-Reply-To: <1173868100.4009.6.camel@dhpc-5-07.sissa.it>
References: <45F7C66F.2050102@lg.ehu.es> <1173868100.4009.6.camel@dhpc-5-07.sissa.it>
Message-ID: <45F7D5F7.2010702@lg.ehu.es>

Thank you very much, Andrea.

Andrea Dal Corso escribi?:
> Presently the maximum number of k points is npk    = 40000, but you need
> at least 64000 for this q point. Increasing this parameter in
> Module/parameters.f90 and recompiling should work.
> 
> Andrea

-- 
----------------------------------------
Miguel Mart?nez Canales
Dto. F?sica de la Materia Condensada
UPV/EHU
Facultad de Ciencia y Tecnolog?a
Apdo. 644
48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5437
----------------------------------------

  "If you have an apple and I have an apple and
  we exchange these apples then you and I will
  still each have one apple. But if you have an
  idea and I have an idea and we exchange these
  ideas, then each of us will have two ideas."

    George Bernard Shaw



From giannozz at nest.sns.it  Wed Mar 14 13:10:13 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 14 Mar 2007 13:10:13 +0100
Subject: [Pw_forum] vc-relax of graphite
In-Reply-To: <339948.42477.qm@web15009.mail.cnb.yahoo.com>
References: <339948.42477.qm@web15009.mail.cnb.yahoo.com>
Message-ID: <19A44C98-6CE1-48B3-947A-48E53075324E@nest.sns.it>

On Mar 12, 2007, at 13:18 , li niu wrote:

> When I used a symmetry-conserving algorithm,  cell_dynamics = 'damp- 
> w' ,
> I still met the same error :
> ---------------------------------------------------------------------- 
> ---
> from checkallsym : error #         3
>      not orthogonal operation
> ---------------------------------------------------------------------- 
> --

then break the initial symmetry by displacing an atom a little bit

> And when using  "nosym = .true.", I met a warning: [...]
>      WARNING: integrated charge=    10.59801382, expected=     
> 16.00000000

you did something wrong

> Now I don't know how to  optimize lattice constant of the bulk  
> graphite.

do it the good old way: fix c to the experimental value (with DFT you
get bogus values in graphite anyway) and optimize only a. Or, if you
are really curious to see what the theoretical value of graphite look
like, choose a few volumes, optimize c/a for each of them, then do
a E(V) fit. Using variable-cell MD to find optimized lattice constants
for graphite is like using a gun to kill a mosquito

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




From naromero at gmail.com  Wed Mar 14 15:42:47 2007
From: naromero at gmail.com (Nichols A. Romero)
Date: Wed, 14 Mar 2007 10:42:47 -0400
Subject: [Pw_forum] Can anyone help me with GaN p type doping
In-Reply-To: <c92002fa0703132249u768e7d0dl9f50e87b1002ef7a@mail.gmail.com>
References: <aa36e8060703081253l4f352ec6he3254d5961b8068e@mail.gmail.com>
	 <970374.74315.qm@web8321.mail.in.yahoo.com>
	 <c92002fa0703132249u768e7d0dl9f50e87b1002ef7a@mail.gmail.com>
Message-ID: <6ac064b60703140742i626900ebla725cc05e3139077@mail.gmail.com>

Also the papers of Alan Wright and Peter Schultz at Sandia National Labs.

On 3/14/07, lan haiping <lanhaiping at gmail.com> wrote:
>
> Hi,
> for doping or charged defects system, you can refer to  Alex Zunger's
> work.
>
> Regards,
>
> h.p
>
>
> On 3/14/07, Daya sagar <sagars_daya at yahoo.co.in> wrote:
> >
> > Hi,
> >
> >   I am working on GaN nanowires. Can anyone please let me know which
> > material should be used as p type dopant for GaN. I tried using Mg and Si as
> > p type dopants but they seem to create bonding between 2 Ga atoms and create
> > bands in the energygap.
> > I would be really thankful if anyone can help me solve this problem.
> >
> > Thanks.
> >
> > Regards,
> > Sagar.
> > *saman ghaderyan < ghaderyan at gmail.com>* wrote:
> >
> > hi
> > i run relaxation for AlAs with nat=4
> > Al 0.00 0.00 0.00
> > As 0.25 0.25 0.25
> > Al 0.50 0.50 0.00
> > As -0.25 0.25 0.25
> > but i don't know why these atomic position have error
> > thanks
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >  ------------------------------
> > Here's a new way to find what you're looking for - Yahoo! Answers
> > <http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/>
> >
> >
>
>
> --
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871




-- 
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)
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From marcel at physik.tu-berlin.de  Wed Mar 14 22:00:31 2007
From: marcel at physik.tu-berlin.de (Marcel Mohr)
Date: Wed, 14 Mar 2007 22:00:31 +0100 (CET)
Subject: [Pw_forum] Access to 2nd order derivatives
In-Reply-To: <19A44C98-6CE1-48B3-947A-48E53075324E@nest.sns.it>
References: <339948.42477.qm@web15009.mail.cnb.yahoo.com>
 <19A44C98-6CE1-48B3-947A-48E53075324E@nest.sns.it>
Message-ID: <20070314214907.M33774@rosa.physik-pool.tu-berlin.de>

Dear all,

I wonder if it is possible to obtain the 2nd derivative of the total 
energy for a user defined set of atomic coordinates (not a real but 
infinetively small displacement from the ground state).
This is what must be done in ph.x but for the phonon modes, or 
displacements.

Thanks in advance
Marcel





From giannozz at nest.sns.it  Thu Mar 15 14:54:00 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 15 Mar 2007 14:54:00 +0100
Subject: [Pw_forum] K-Points and dipole correction
In-Reply-To: <45F6A172.11F0.001D.0@empa.ch>
References: <45F6A172.11F0.001D.0@empa.ch>
Message-ID: <4A4B4279-765E-4BF8-A358-DFD115AE1765@nest.sns.it>

On Mar 13, 2007, at 13:04 , Daniele Passerone wrote:

> In the first case, I get 39 K points, in the second case I get 13 K  
> points.
> There is no symmetry found in the slab in both cases.

You have a uniform grid that is not centered on the origin
but it is translated half step in the 1 and 2 directions. In
absence of an electric field, the code calculates the irreducible
grid by applying all lattice symmetries to all k-points and keeping
only those that are not found to be equivalent by a symmetry
operation of the actual crystal symmetry. This yields 39 points
in your case (no symmetry, apart the k <=> -k symmetry)

In presence of an electric field, the code should remove all
symmetries that do not leave the electric field unchanged.
A quick way to achieve this is to set internally the "nosym"
option to .true. ; for a uniform grid, however, nosym=.true.
means "take the entire uniform grid with no further processing".
This yields 13 points in your case :  the 5 5 1 grid contains 25
points, 1 is gamma and of the remaining 24 only 12 are
independent (due to the k <=> -k symmetry), so 1+12=13.
If you use a centered grid, for instance 5 5 1 0 0 0, you
get 13 points in both cases.

So there is a logic, although I am not sure it is the correct one.

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




From proffess at yandex.ru  Thu Mar 15 20:13:30 2007
From: proffess at yandex.ru (Sergey Lisenkov)
Date: Thu, 15 Mar 2007 22:13:30 +0300 (MSK)
Subject: [Pw_forum] error on XD1 platform
In-Reply-To: <Pine.LNX.4.44.0611081140000.13161-100000@localhost.localdomain>
References: <Pine.LNX.4.44.0611081140000.13161-100000@localhost.localdomain>
Message-ID: <45F99ADA.000004.28096@webmail14.yandex.ru>

 Dear All,

  I have a problem with running PW-3.2 on Cray XD1 platform. Sometimes it works, but very often it crashes. It doesn't matter which version of PGI compiler is used (6.1.1, 6.1.4 or 7.0-2). The code was linked with ACML library and FFTW from QE distribution.

 The problem always happens after several ionic steps or during scf cyles. For example, I see the following in the output file:

.....
Writing output data file XXX.save
Process 0 lost connection: exiting
mpiexec: Error: read_rai_startup_ports: Failed to read barrier entry token from rank 1 process on c645n2.

Process 38 lost connection: exiting
 ask 128 got 56  at line 863 in file /var/tmp/mpich-1.2.6/mpid/rai/raifma.cPProcess 16 lost connection: exiting


I tried several PW-versions including CVS one, but the same problem happens. Cray people don't think that it is MPICH problem. 

Did anybody see this before? Googling didn't help too much.

Thanks,
  Sergey


From ferretti.andrea at unimore.it  Fri Mar 16 00:23:50 2007
From: ferretti.andrea at unimore.it (Andrea Ferretti)
Date: Fri, 16 Mar 2007 00:23:50 +0100 (CET)
Subject: [Pw_forum] error on XD1 platform
In-Reply-To: <45F99ADA.000004.28096@webmail14.yandex.ru>
References: <Pine.LNX.4.44.0611081140000.13161-100000@localhost.localdomain>
 <45F99ADA.000004.28096@webmail14.yandex.ru>
Message-ID: <Pine.LNX.4.58.0703152354590.24524@bamboo.fisica.unimo.it>


Hi all,

>  Dear All,
>
>   I have a problem with running PW-3.2 on Cray XD1 platform. Sometimes 
it works,
>   but very often it crashes. It doesn't matter which version of PGI
>   compiler is used (6.1.1, 6.1.4 or 7.0-2). The code was linked with
>   ACML library and FFTW from QE distribution.
>

I got problems which sound similar 
running as well on a Cray XD1 machine (PGI compiler 6.0)... 
I used both espresso-3.2 and the CVS version (around one 
month ago) and while for some calculations they worked, for some others 
(particularly heavy) sometimes they worked, sometimes not. 
(and the crashes were either at the beginning of the calculation, 
either after a number of scf iterations).

first, I discovered (or better, someone told me about) the existence in 
espresso of a precompiler __XD1 flag which should be intended to fix some 
troubles in the MPI stuff (troubles with PGI, I guess)... 
I don't understand the errors you got, but since they seem to be 
somehow related to MPI, I would try to add the flag
-D__XD1 
to DFLAGS and FDFLAGS in the make.sys file

in my case however, 
when I tried with __XD1 it didn't solve my problem... 
but after some feedback from the 
administrator, it seemed it was due to some instabilities of the 
system (especially related to management of memory)

cheers
andrea


> 
>  Dear All,
> 
>   I have a problem with running PW-3.2 on Cray XD1 platform. Sometimes it works, 
>   but very often it crashes. It doesn't matter which version of PGI 
>   compiler is used (6.1.1, 6.1.4 or 7.0-2). The code was linked with 
>   ACML library and FFTW from QE distribution.
> 
>   The problem always happens after several ionic steps or during scf 
>   cyles. For example, I see the following in the output file:
> 
> .....
> Writing output data file XXX.save
> Process 0 lost connection: exiting
> mpiexec: Error: read_rai_startup_ports: Failed to read barrier entry token from rank 1 process on c645n2.
> 
> Process 38 lost connection: exiting
>  ask 128 got 56  at line 863 in file /var/tmp/mpich-1.2.6/mpid/rai/raifma.cPProcess 16 lost connection: exiting
> 
> 

--
Andrea Ferretti
National Research Center S3, CNR-INFM  ( http://s3.infm.it )
Dipartimento di Fisica, Universita' di Modena e Reggio Emilia
Via Campi 213/A I-41100 Modena, Italy
Tel:     +39 059 2055301      Fax:     +39 059 374794
Skype:   andrea_ferretti
URL:     http://www.nanoscience.unimo.it

Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html


From baroni at sissa.it  Fri Mar 16 00:27:41 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 16 Mar 2007 10:27:41 +1100
Subject: [Pw_forum] Re: Problems on ESPRESSO compilation
In-Reply-To: <OF32633743.6CAAE2C4-ON8325729F.0053F505-8325729F.0054A1BE@br.ibm.com>
References: <OF32633743.6CAAE2C4-ON8325729F.0053F505-8325729F.0054A1BE@br.ibm.com>
Message-ID: <471D48A0-3FF2-45C4-803D-CE53041984C7@sissa.it>

Dear Eduardo: many thanks for your interest in our scientific  
software. I have redirected your request to the pwscf forum  
(pw_forum at pwscf.ord) where it belongs. Please note that you need to  
subscribe to the mailing list in order to have access to it. You can  
do so from the home page of the pwscf home page (www.pwscf.org,  
bottom right of the page). Hope you will get there the assistance you  
need. Greetings - Stefano

On Mar 16, 2007, at 2:24 AM, edump at br.ibm.com wrote:

>
>    Tiao Stefano,
>
>      I tried to send this email to the support addresses, but the  
> emails came back with failure delivery reports. I hope you can help  
> me to answer this question.
>      We are trying to compile the ESPRESSO distribution version 3.2  
> on a POWER architecture running Linux on POWER. We are facing  
> problems on the compilation process. I saw on the website that  
> Linux on POWER it isn't listed on the supported architectures, is  
> there any way to do it works?
>
>     Gracie tanto,
>
> Eduardo Mattos Pacini
> System p - Product Manager Brazil
> Tel: +55 (11) 2132-3851
> T/L:  842-3851
> mail to: edump at br.ibm.com
> Investment = Innovation = Client Success

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From pnspeaks at sify.com  Fri Mar 16 08:14:46 2007
From: pnspeaks at sify.com (Prithwish Nandi)
Date: Fri, 16 Mar 2007 13:14:46 +0600 (IST)
Subject: [Pw_forum] calculation of magnetization at each atom site of a super cell
Message-ID: <1174031086.45fa4aee628e0@mail.sify.com>


 Hi,

   In PWSCF,is it possible to calculate the contribution by each atom to the total magnetization of a super cell? If it possible, how it can be done???

  Prithwish Nandi
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From akohlmey at cmm.chem.upenn.edu  Fri Mar 16 11:17:56 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 16 Mar 2007 05:17:56 -0500 (EST)
Subject: [Pw_forum] calculation of magnetization at each atom site of a
 super cell
In-Reply-To: <1174031086.45fa4aee628e0@mail.sify.com>
Message-ID: <Pine.LNX.4.44.0703160515070.12027-100000@localhost.localdomain>

On Fri, 16 Mar 2007, Prithwish Nandi wrote:

PN> 
PN>  Hi,
PN> 

PN>    In PWSCF,is it possible to calculate the contribution by each
PN> atom to the total magnetization of a super cell? If it possible, how
PN> it can be done???

please always search the mailing list for whether the topic you
are interested in has already been discussed (and concluded).
in your case, e.g., 

http://www.democritos.it/pipermail/pw_forum/2006-December/005467.html

and the related thread would be appropriate.

cheers,
   axel.
PN> 
PN>   Prithwish Nandi

-- 
=======================================================================
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.



From brad.malone at gmail.com  Sat Mar 17 00:43:28 2007
From: brad.malone at gmail.com (Brad Malone)
Date: Fri, 16 Mar 2007 16:43:28 -0700
Subject: [Pw_forum] Error message with pw2wannier.x
In-Reply-To: <bf16929a0703161639v65e02e98x1a582769db4b2033@mail.gmail.com>
References: <bf16929a0703161639v65e02e98x1a582769db4b2033@mail.gmail.com>
Message-ID: <bf16929a0703161643n171fa2efq342392ef58f67bbb@mail.gmail.com>

Hi, I'm getting the following error message when I run pw2wannier.x

something wrong!
rlatt(i,j) = 1.14274218052912335  at (i,j)= 1.142740000000009
ERROR: 0032-184 MPI was not finalized in routine unknown, task 0


I'm guessing that it has something to do with comparing coordinates between
pwscf and wannier.  Wannier's .nnkp file puts the units in angstroms (even
if you specify it in atomic units in the .win file), while pwscf's dim(1)=#
takes the number in atomic units.  Are they converting and trying to compare
these two numbers to too high of a precision?  If so, how can I get around
this?

Thanks for your help!
Brad
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From marzari at MIT.EDU  Sat Mar 17 06:14:57 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sat, 17 Mar 2007 01:14:57 -0400
Subject: [Pw_forum] Error message with pw2wannier.x
In-Reply-To: <bf16929a0703161643n171fa2efq342392ef58f67bbb@mail.gmail.com>
References: <bf16929a0703161639v65e02e98x1a582769db4b2033@mail.gmail.com> <bf16929a0703161643n171fa2efq342392ef58f67bbb@mail.gmail.com>
Message-ID: <45FB7951.3070308@mit.edu>


Dear Brad,

just make sure you are not using the 1.0 version of wannier90 (that
writes the lattice  vectors to the nnkp file at a lower precision than
that used to test consistency with pwscf).

This was fixed in v1.0.1 and above. Otherwise, send us your input files
(marzari at mit.edu, mostofi at mit.edu, jry20 at cam.ac.uk).

				nicola




Brad Malone wrote:
> 
> Hi, I'm getting the following error message when I run pw2wannier.x
> 
>     something wrong!
>     rlatt(i,j) = 1.14274218052912335  at (i,j)= 1.142740000000009
>     ERROR: 0032-184 MPI was not finalized in routine unknown, task 0
> 
> 
> I'm guessing that it has something to do with comparing coordinates 
> between pwscf and wannier.  Wannier's .nnkp file puts the units in 
> angstroms (even if you specify it in atomic units in the .win file), 
> while pwscf's dim(1)=# takes the number in atomic units.  Are they 
> converting and trying to compare these two numbers to too high of a 
> precision?  If so, how can I get around this?
> 
> Thanks for your help!
> Brad


-- 
---------------------------------------------------------------------
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


From giannozz at nest.sns.it  Mon Mar 19 11:13:25 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 19 Mar 2007 11:13:25 +0100
Subject: [Pw_forum] Re: Problems on ESPRESSO compilation
In-Reply-To: <471D48A0-3FF2-45C4-803D-CE53041984C7@sissa.it>
References: <OF32633743.6CAAE2C4-ON8325729F.0053F505-8325729F.0054A1BE@br.ibm.com> <471D48A0-3FF2-45C4-803D-CE53041984C7@sissa.it>
Message-ID: <C0AEA7BF-BF6A-4C94-B6D6-E9B4168D4E24@nest.sns.it>

On Mar 16, 2007, at 24:27 , Stefano Baroni wrote:

> On Mar 16, 2007, at 2:24 AM, edump at br.ibm.com wrote:

>> We are trying to compile the ESPRESSO distribution version 3.2 on a
>> POWER architecture running Linux on POWER. We are facing problems
>> on the compilation process. I saw on the website that Linux on POWER
>> it isn't listed on the supported architectures, is there any way  
>> to do it works?

if you have a decent compiler, it will work. Try with g95.

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





From giannozz at nest.sns.it  Mon Mar 19 11:38:48 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 19 Mar 2007 11:38:48 +0100
Subject: [Pw_forum] Access to 2nd order derivatives
In-Reply-To: <20070314214907.M33774@rosa.physik-pool.tu-berlin.de>
References: <339948.42477.qm@web15009.mail.cnb.yahoo.com> <19A44C98-6CE1-48B3-947A-48E53075324E@nest.sns.it> <20070314214907.M33774@rosa.physik-pool.tu-berlin.de>
Message-ID: <85AAE15B-C485-403C-B989-FB28AC39275B@nest.sns.it>

On Mar 14, 2007, at 22:00 , Marcel Mohr wrote:

> I wonder if it is possible to obtain the 2nd derivative of the  
> total energy
> for a user defined set of atomic coordinates (not a real but  
> infinitely
> small displacement from the ground state).

in principle, it is, and once upon a time it was possible.
Now there is the 'single mode calculation' (example 02),
in which you can choose a specific displacement pattern,
but only among those automatically computed by the code.

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




From marcel at physik.tu-berlin.de  Mon Mar 19 14:06:35 2007
From: marcel at physik.tu-berlin.de (Marcel Mohr)
Date: Mon, 19 Mar 2007 14:06:35 +0100 (CET)
Subject: [Pw_forum] Access to 2nd order derivatives
In-Reply-To: <85AAE15B-C485-403C-B989-FB28AC39275B@nest.sns.it>
References: <339948.42477.qm@web15009.mail.cnb.yahoo.com>
 <19A44C98-6CE1-48B3-947A-48E53075324E@nest.sns.it>
 <20070314214907.M33774@rosa.physik-pool.tu-berlin.de>
 <85AAE15B-C485-403C-B989-FB28AC39275B@nest.sns.it>
Message-ID: <20070319133926.L43884@rosa.physik-pool.tu-berlin.de>

On Mon, 19 Mar 2007, Paolo Giannozzi wrote:

>
> On Mar 14, 2007, at 22:00 , Marcel Mohr wrote:
>
>> I wonder if it is possible to obtain the 2nd derivative of the total energy
>> for a user defined set of atomic coordinates (not a real but infinitely
>> small displacement from the ground state).
>
> in principle, it is, and once upon a time it was possible.
> Now there is the 'single mode calculation' (example 02),
> in which you can choose a specific displacement pattern,
> but only among those automatically computed by the code.
>
> P.
> ---

Thank you very much for your answer.

I summarize.
One can "move" one atom, and that in the directions x, y, and z.
The variable in pw.x modenum 3 is corresponds to a "displacement" of 
the first atom in direction z. 
ph.x computes then the dynamical matrix entries for this mode, from which 
one can make conclusions on the 2nd order derivative for the atom 3 in 
direction z. 
If I have the whole dynamical matrix I can diagonalize it and obtain 
frequencies and eigenvectors.
If there are some errors please correct me.
Otherwise thanks again.

Cheers
Marcel



From mverissi at ictp.it  Mon Mar 19 18:53:01 2007
From: mverissi at ictp.it (Marcos Verissimo Alves)
Date: Mon, 19 Mar 2007 18:53:01 +0100 (CET)
Subject: [Pw_forum] About restarting neb calculations
In-Reply-To: 
     <Pine.LNX.4.44.0703160515070.12027-100000@localhost.localdomain>
References: <1174031086.45fa4aee628e0@mail.sify.com>
    <Pine.LNX.4.44.0703160515070.12027-100000@localhost.localdomain>
Message-ID: <47619.10.50.40.120.1174326781.squirrel@webmail3.ictp.trieste.it>

Hi all,

I am performing a neb calculation using ultrasoft pseudopotentials and 24
Ry for wave functions, 240 Ry for charge density. Suppose I stop my
calculation at the end of a neb step (that is, all images had their scf
convergence and no new neb step has been started). Would it be possible to
restart this calculation using different (that is, higher) cutoff
parameters for the wave functions and/or charge density? I see that for
the scf calculations, the charge density is read from files, so I am not
sure of how to do it - that is, if this is possible at all. Would it be a
matter of simply erasing the scf files for each image, but keeping the
path history, or this would produce an error?

Best regards,

Marcos


-- 
Dr. Marcos Verissimo Alves
Post-Doctoral Fellow
Condensed Matter and Statistical Physics Sector
International Centre for Theoretical Physics
Trieste, Italy

--------

I have become so addicted to vi that I try to exit OpenOffice by typing :wq!



From ding at sissa.it  Mon Mar 19 19:19:46 2007
From: ding at sissa.it (Xunlei Ding)
Date: Mon, 19 Mar 2007 19:19:46 +0100
Subject: [Pw_forum] About restarting neb calculations
In-Reply-To: <47619.10.50.40.120.1174326781.squirrel@webmail3.ictp.trieste.it>
References: <1174031086.45fa4aee628e0@mail.sify.com>    <Pine.LNX.4.44.0703160515070.12027-100000@localhost.localdomain> <47619.10.50.40.120.1174326781.squirrel@webmail3.ictp.trieste.it>
Message-ID: <45FED442.8090503@sissa.it>

Dear Marcos,

I think you need to clear the wfc and chg files.
And, be sure to recalculate the first and last images using the high cutoff.

Best regards,
Ding

Marcos Verissimo Alves wrote:

>Hi all,
>
>I am performing a neb calculation using ultrasoft pseudopotentials and 24
>Ry for wave functions, 240 Ry for charge density. Suppose I stop my
>calculation at the end of a neb step (that is, all images had their scf
>convergence and no new neb step has been started). Would it be possible to
>restart this calculation using different (that is, higher) cutoff
>parameters for the wave functions and/or charge density? I see that for
>the scf calculations, the charge density is read from files, so I am not
>sure of how to do it - that is, if this is possible at all. Would it be a
>matter of simply erasing the scf files for each image, but keeping the
>path history, or this would produce an error?
>
>Best regards,
>
>Marcos
>
>
>  
>


From brad.malone at gmail.com  Mon Mar 19 22:48:47 2007
From: brad.malone at gmail.com (Brad Malone)
Date: Mon, 19 Mar 2007 14:48:47 -0700
Subject: [Pw_forum] Re: Re: Error message with pw2wannier.x
Message-ID: <bf16929a0703191448o1f937a2el2a48d17aa5f07efa@mail.gmail.com>

As Jonathan told me after looking at my input files, I hadn't specified the
vectors in my wannier90 input file to enough precision.  After changing that
it worked correctly.  Also, for those with similar problems, you might want
to check your conversion from angstroms to atomic units, because a
difference between that and pwSCF's conversion could also result in an error
I believe.

On 3/16/07, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote:
>
> Send Pw_forum mailing list submissions to
>         pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://www.democritos.it/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
>         pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
>         pw_forum-admin at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
>    1. calculation of magnetization at each atom site of a super cell
> (Prithwish Nandi)
>    2. Re: calculation of magnetization at each atom site of a
>        super cell (Axel Kohlmeyer)
>    3. Error message with pw2wannier.x (Brad Malone)
>    4. Re: Error message with pw2wannier.x (Nicola Marzari)
>
> --__--__--
>
> Message: 1
> To: pw_forum at pwscf.org
> Date: Fri, 16 Mar 2007 13:14:46 +0600 (IST)
> From: Prithwish Nandi <pnspeaks at sify.com>
> Subject: [Pw_forum] calculation of magnetization at each atom site of a
> super cell
> Reply-To: pw_forum at pwscf.org
>
> This message is in MIME format.
>
> ---MOQ1174031086ca5225d42e1d0d04e5a0eab2bbbc6a09
> Content-Type: text/plain
> Content-Transfer-Encoding: 8bit
>
>
> Hi,
>
>    In PWSCF,is it possible to calculate the contribution by each atom to
> the total magnetization of a super cell? If it possible, how it can be
> done???
>
>   Prithwish Nandi
> ---MOQ1174031086ca5225d42e1d0d04e5a0eab2bbbc6a09
> Content-Type: text/html
> Content-Transfer-Encoding: 8bit
>
> <pre>
> Hi,
>
>    In PWSCF,is it possible to calculate the contribution by<br>each atom
> to the total magnetization of a super cell? If it possible,<br>how it can be
> done???
>
>   Prithwish Nandi</pre>
>
> <br><br><A HREF="
> http://ads.sify.com/RealMedia/ads/click_nx.ads/mail.sify.com/sentmail at Bottom"
> target=_new>
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> </P>
>
> ---MOQ1174031086ca5225d42e1d0d04e5a0eab2bbbc6a09--
>
> --__--__--
>
> Message: 2
> Date: Fri, 16 Mar 2007 05:17:56 -0500 (EST)
> From: Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>
> To: Prithwish Nandi <pnspeaks at sify.com>
> Cc: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] calculation of magnetization at each atom site of
> a
> super cell
> Reply-To: pw_forum at pwscf.org
>
>
> On Fri, 16 Mar 2007, Prithwish Nandi wrote:
>
> PN>
> PN>  Hi,
> PN>
>
> PN>    In PWSCF,is it possible to calculate the contribution by each
> PN> atom to the total magnetization of a super cell? If it possible, how
> PN> it can be done???
>
> please always search the mailing list for whether the topic you
> are interested in has already been discussed (and concluded).
> in your case, e.g.,
>
> http://www.democritos.it/pipermail/pw_forum/2006-December/005467.html
>
> and the related thread would be appropriate.
>
> cheers,
>    axel.
> PN>
> PN>   Prithwish Nandi
>
> --
> =======================================================================
> 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.
>
>
> --__--__--
>
> Message: 3
> Date: Fri, 16 Mar 2007 16:43:28 -0700
> From: "Brad Malone" <brad.malone at gmail.com>
> To: pw_forum at pwscf.org
> Subject: [Pw_forum] Error message with pw2wannier.x
> Reply-To: pw_forum at pwscf.org
>
> ------=_Part_84959_32874074.1174088608396
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Content-Transfer-Encoding: 7bit
> Content-Disposition: inline
>
> Hi, I'm getting the following error message when I run pw2wannier.x
>
> something wrong!
> rlatt(i,j) = 1.14274218052912335  at (i,j)= 1.142740000000009
> ERROR: 0032-184 MPI was not finalized in routine unknown, task 0
>
>
> I'm guessing that it has something to do with comparing coordinates
> between
> pwscf and wannier.  Wannier's .nnkp file puts the units in angstroms (even
> if you specify it in atomic units in the .win file), while pwscf's
> dim(1)=#
> takes the number in atomic units.  Are they converting and trying to
> compare
> these two numbers to too high of a precision?  If so, how can I get around
> this?
>
> Thanks for your help!
> Brad
>
> ------=_Part_84959_32874074.1174088608396
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: 7bit
> Content-Disposition: inline
>
> <br><span class="gmail_quote"></span>Hi, I&#39;m getting the following
> error message when I run pw2wannier.x <br><br><blockquote>something
> wrong!<br>rlatt(i,j) = 1.14274218052912335&nbsp; at (i,j)=
> 1.142740000000009<br>ERROR: 0032-184 MPI was not finalized in routine
> unknown, task 0
> <br></blockquote><br>I&#39;m guessing that it has something to do with
> comparing coordinates between pwscf and wannier.&nbsp; Wannier&#39;s .nnkp
> file puts the units in angstroms (even if you specify it in atomic units in
> the .win file), while pwscf&#39;s dim(1)=# takes the number in atomic
> units.&nbsp; Are they converting and trying to compare these two numbers to
> too high of a precision?&nbsp; If so, how can I get around this?
> <br><br>Thanks for your help!<br><span class="sg">Brad<br>
> </span>
>
> ------=_Part_84959_32874074.1174088608396--
>
> --__--__--
>
> Message: 4
> Date: Sat, 17 Mar 2007 01:14:57 -0400
> From: Nicola Marzari <marzari at MIT.EDU>
> Organization: Massachusetts Institute of Technology
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Error message with pw2wannier.x
> Reply-To: pw_forum at pwscf.org
>
>
>
> Dear Brad,
>
> just make sure you are not using the 1.0 version of wannier90 (that
> writes the lattice  vectors to the nnkp file at a lower precision than
> that used to test consistency with pwscf).
>
> This was fixed in v1.0.1 and above. Otherwise, send us your input files
> (marzari at mit.edu, mostofi at mit.edu, jry20 at cam.ac.uk).
>
>                                 nicola
>
>
>
>
> Brad Malone wrote:
> >
> > Hi, I'm getting the following error message when I run pw2wannier.x
> >
> >     something wrong!
> >     rlatt(i,j) = 1.14274218052912335  at (i,j)= 1.142740000000009
> >     ERROR: 0032-184 MPI was not finalized in routine unknown, task 0
> >
> >
> > I'm guessing that it has something to do with comparing coordinates
> > between pwscf and wannier.  Wannier's .nnkp file puts the units in
> > angstroms (even if you specify it in atomic units in the .win file),
> > while pwscf's dim(1)=# takes the number in atomic units.  Are they
> > converting and trying to compare these two numbers to too high of a
> > precision?  If so, how can I get around this?
> >
> > Thanks for your help!
> > Brad
>
>
> --
> ---------------------------------------------------------------------
> 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
>
>
> --__--__--
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest
>
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From konstantin_kudin at yahoo.com  Tue Mar 20 03:37:38 2007
From: konstantin_kudin at yahoo.com (Konstantin Kudin)
Date: Mon, 19 Mar 2007 19:37:38 -0700 (PDT)
Subject: [Pw_forum] spilling parameter in Lowdin - how to assign the charge that went into Nirvana ?
Message-ID: <332663.39741.qm@web57708.mail.re3.yahoo.com>

 Hi all,

 I am encountering an issue where the charge that is missing from the
total Lowdin charge sum due to the non-zero spilling parameter is very
important for me. For example, 1% of missing charge may not sound that
bad, unfortunately, these missing charges will mostly come from the
negative ions which happen to be diffuse.

 Is there any way to assign it back ? For example, by entirely
projecting the remaining charge onto overlapping diffuse Gaussians that
would be roughly proportional to the atomic radii? Or, perhaps, there
is some other solution out there?

 Any ideas?

 Thanks!
 Kostya


 
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From jhashemifar at gmail.com  Tue Mar 20 10:20:09 2007
From: jhashemifar at gmail.com (Javad hashemifar)
Date: Tue, 20 Mar 2007 10:20:09 +0100
Subject: [Pw_forum] slow convergency in non-collinear calculations
Message-ID: <2fb18d9f0703200220w32818137l29c2553a8c3ab55@mail.gmail.com>

Dear pwscf users

I am trying to calculate the non-collinear helical magnetic ground
state of the orthorhombic CrAs. The system has "No symmetry!" and I am
using ecut=30, ecutrho=300, smearing="mp",  degauss=0.05D0,
mixing_beta=0.1, mixing_mode="local-TF", please find the input file
below. Unfortunately the system does not converge and "estimated scf
accuracy" is oscillating around ~ 0.01. I would appreciate your
comments and suggestions in this regard.

Thanks in advance
Javad Hashemifar

&CONTROL
  calculation = "scf",
  prefix      = "csMP-AFh",
  restart_mode= "from_scratch",
  tstress     = .true.,
  tprnfor     = .true.,
  pseudo_dir  = "/homes/hp0070/psps",
  outdir      = "/tmp/javad/results-pwscf/CrAs-MP/explat",
/
&SYSTEM
  ibrav       = 8,
  celldm(1)   = 10.849,
  celldm(2)   = 0.6072449074,
  celldm(3)   = 3.2514148769,
  nat         = 24,
  ntyp        = 7,
  ecutwfc     = 30.0,
  ecutrho     = 400.0,
  occupations = "smearing",
  smearing    = "mp",
  degauss     = 0.05D0,
  noncolin    = .true.
  starting_magnetization(1)=0.7,
  starting_magnetization(2)=0.7,
  starting_magnetization(3)=0.7,
  starting_magnetization(4)=0.7,
  starting_magnetization(5)=0.7,
  starting_magnetization(6)=0.7,
  angle1(1)=90.0, angle1(2)=90.0, angle1(3)=90.0
  angle1(4)=90.0, angle1(5)=90.0, angle1(6)=90.0
  angle2(1)=0.0,   angle2(3)=120.0, angle2(5)=240.0
  angle2(2)=100.0, angle2(4)=220.0, angle2(6)=340.0
/
&ELECTRONS
  electron_maxstep = 200,
  mixing_beta = 0.1,
  mixing_mode = "local-TF",
  conv_thr    = 1.0d-8,
/
ATOMIC_SPECIES
  Cr1  51.9960   Cr.pbe-sp-van.UPF
  Cr2  51.9960   Cr.pbe-sp-van.UPF
  Cr3  51.9960   Cr.pbe-sp-van.UPF
  Cr4  51.9960   Cr.pbe-sp-van.UPF
  Cr5  51.9960   Cr.pbe-sp-van.UPF
  Cr6  51.9960   Cr.pbe-sp-van.UPF
  As   74.9220   As.pbe-n-van.UPF
ATOMIC_POSITIONS  (alat)
 As    0.20000000    0.15181123    0.08670384
 Cr1   0.49000000    0.45543368    0.20592220
 Cr2   0.99000000    0.45543368    0.33598027
 As    0.70000000    0.15181123    0.45519864
 As    0.30000000    0.45543368    0.62860632
 Cr1   0.01000000    0.15181123    0.74782468
 Cr2   0.51000000    0.15181123    0.87788275
 As    0.80000000    0.45543368    0.99710112
 As    0.20000000    0.15181123    1.17050880
 Cr3   0.49000000    0.45543368    1.28972716
 Cr4   0.99000000    0.45543368    1.41978523
 As    0.70000000    0.15181123    1.53900359
 As    0.30000000    0.45543368    1.71241128
 Cr3   0.01000000    0.15181123    1.83162964
 Cr4   0.51000000    0.15181123    1.96168771
 As    0.80000000    0.45543368    2.08090607
 As    0.20000000    0.15181123    2.25431376
 Cr5   0.49000000    0.45543368    2.37353212
 Cr6   0.99000000    0.45543368    2.50359019
 As    0.70000000    0.15181123    2.62280855
 As    0.30000000    0.45543368    2.79621624
 Cr5   0.01000000    0.15181123    2.91543460
 Cr6   0.51000000    0.15181123    3.04549267
 As    0.80000000    0.45543368    3.16471103
K_POINTS (automatic)
 8  8  2    1 1 1




======================================
Seyed Javad  Hashemifar,    Ph.D.
[current:]
Tel:+49-203-3794743        Fax:+49-203-3794742
Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen
47048 Dusiburg, Germany
[permanent:]
Tel:  +98-311-3912375       Fax: +98-311-3912376
Physics Department, Isfahan University of Technology
84156 Isfahan, Iran
---------------------------------------------------------------------------


From ferretti.andrea at unimore.it  Tue Mar 20 11:31:48 2007
From: ferretti.andrea at unimore.it (Andrea Ferretti)
Date: Tue, 20 Mar 2007 11:31:48 +0100 (CET)
Subject: [Pw_forum] spilling parameter in Lowdin - how to assign the
 charge that went into Nirvana ?
In-Reply-To: <332663.39741.qm@web57708.mail.re3.yahoo.com>
References: <332663.39741.qm@web57708.mail.re3.yahoo.com>
Message-ID: <Pine.LNX.4.58.0703201058410.9375@bamboo.fisica.unimo.it>

Hi Kostya, Hi all,


>  I am encountering an issue where the charge that is missing from the
> total Lowdin charge sum due to the non-zero spilling parameter is very
> important for me. For example, 1% of missing charge may not sound that
> bad, unfortunately, these missing charges will mostly come from the
> negative ions which happen to be diffuse.
> 
>  Is there any way to assign it back ? For example, by entirely
> projecting the remaining charge onto overlapping diffuse Gaussians that
> would be roughly proportional to the atomic radii? Or, perhaps, there
> is some other solution out there?
> 

I came into the same problem, but I have not much to add in order to find 
a solution starting from Lowding orbitals...

moreover, sometime ago I went through the coefficients expressing the 
Lowding orbitals (LO's) in terms of the atomic orbitals (basically atomic 
orbitals are orthogonalized in order to setup projectors)...
I found that in some cases the resulting LO's were so much 
different from the starting atomic ones (for example I saw large 
projections of the same LO onto atomic orbitals (s-states) 
from different atoms, which was somehow counterintuitive to me)..

basically, I think that when spilling parameter becomes large the physical 
information one would like to obtain from lowding projections is hardly 
hidden...

One possible alternative approach which does not suffer the same 
problem is to use Wannier functions (especially the Marzari-Vanderbilt 
"maximally localized" WF)...
For insulators and semiconductors an exact (no spilling factor) 
partition of the total charge into localized orbitals can be obtained...   
in the same line, WF projected DOS can be obtained as well

again, this is just one possible choice (others are there for sure) and 
most of the game is played by the final localization reached by the 
Wannier functions (is this localization enough to my purposes ? ans so 
on..) 

any other suggestion ??
am I missing something ??

hope it helps

Andrea


From Xiangqian.Hu at duke.edu  Tue Mar 20 16:39:20 2007
From: Xiangqian.Hu at duke.edu (xqhu@duke.edu)
Date: Tue, 20 Mar 2007 11:39:20 -0400
Subject: [Pw_forum] Is the CG diagonalization suitable for the general matrix?
Message-ID: <017801c76b05$edacecd0$6400a8c0@HLHXQ>

Dear users,

I'm trying to implement PZ-SIC in PWSCF. In PZ-SIC, the Fock matrix is not symmetric any more. I can not use DIIS or Davidson since both of them are for the hermitian matrix. I checked CG codes. It seems that CG can be used in the gereral matrix. If you are familiar with the CG diagonalization, please tell me some details.

Thank you very much.

Best,
Xiangqian
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From konstantin_kudin at yahoo.com  Tue Mar 20 19:57:02 2007
From: konstantin_kudin at yahoo.com (Konstantin Kudin)
Date: Tue, 20 Mar 2007 11:57:02 -0700 (PDT)
Subject: [Pw_forum] cell size dependence of Wannier spreads
Message-ID: <619097.81973.qm@web57706.mail.re3.yahoo.com>

 Hi all,

 Can anyone briefly summarize how Wannier function spreads converge
with the size of the unit cell? The spreads somehow seem to be not so
well defined ...

 Thanks!
 Kostya


 
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From konstantin_kudin at yahoo.com  Tue Mar 20 20:12:23 2007
From: konstantin_kudin at yahoo.com (Konstantin Kudin)
Date: Tue, 20 Mar 2007 12:12:23 -0700 (PDT)
Subject: [Pw_forum] spilling parameter in Lowdin - how to assign the charge that went into Nirvana ?
In-Reply-To: <Pine.LNX.4.58.0703201058410.9375@bamboo.fisica.unimo.it>
Message-ID: <851319.42244.qm@web57701.mail.re3.yahoo.com>

 Andrea, thanks for the comment!

> different from the starting atomic ones (for example I saw large 
> projections of the same LO onto atomic orbitals (s-states) 
> from different atoms, which was somehow counterintuitive to me)..

 Yes, this does seem counter-intuitive. This seems to defeat the
purpose of atomic projections of LO orthonormal orbitals have bunch of
contributions from different atoms.

> For insulators and semiconductors an exact (no spilling factor) 
> partition of the total charge into localized orbitals can be
> obtained...   
> in the same line, WF projected DOS can be obtained as well

 I think the issue with WF is that they are hard to assign back to the
atoms, since now these are just electron pairs somewhere in the middle.

 For Lowdin projection the 1995 paper (link below) claimed that the
atomic basis could be optimized, I wonder if QE does that, and whether
it is done for each atom, or just for all atoms of the same type at
once.

http://dx.doi.org/10.1016/0038-1098(95)00341-X

 Kostya



 
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From marzari at MIT.EDU  Tue Mar 20 21:06:28 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 20 Mar 2007 16:06:28 -0400
Subject: [Pw_forum] cell size dependence of Wannier spreads
In-Reply-To: <619097.81973.qm@web57706.mail.re3.yahoo.com>
References: <619097.81973.qm@web57706.mail.re3.yahoo.com>
Message-ID: <46003EC4.80801@mit.edu>

Konstantin Kudin wrote:
>  Hi all,
> 
>  Can anyone briefly summarize how Wannier function spreads converge
> with the size of the unit cell? The spreads somehow seem to be not so
> well defined ...
> 
>  Thanks!
>  Kostya
> 



Hi Kostya,


the thins to keep in mind is that the r and r^2 operators
in the Wannier algorithm are calculated using a reciprocal
space representation, and that since we have only a
discrete k-point mesh, we are actually *approximating* these
operators.

This is to say that as you increase the fineness of the k-point 
sampling, not only your electronic structure becomes more accurate,
but that your approximate representation of the operators becomes
also more accurate. The "operators" converge more slowly than the
"electronic structure".

So, spreads can only be compared either for fully converged
calculations with respect to k-points, or when compatible meshes
are used (e.g. if you double the cell in one direction,
you halve the k-points).

If you are using CP, or any Gamma-only code, changing the unit cell
size also makes your spread operator different. So if you calculate 
spreads in liquid water for a 64-molecule unit cell, they will be
larger (I think) than for a 32-molecule unit cell, but for the only
reason that the operator is changing.

One fix that might work (if needed) would be to calculate the spread
explicitly in real space - i.e. the unitary matrices and the electronic
structure converge rapdily with k-point sampling, and than with the
U_mn^k you construct the MLWFs in real space, and you calculate
expliclty <r> and <r^2>. Or, you could use the extrapolation technique
used by Yudong Wu in his PhD (was a student of Roberto that worked with
me on WFs, he graduated in 2003 or so, and a copy should be around in
Princeton), in which <psi|exp(iGr)|psi> was calculated for very small G,
smaller than the smallest in your Bravais lattice.

				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


From niuli1978 at yahoo.com.cn  Wed Mar 21 04:07:19 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Wed, 21 Mar 2007 11:07:19 +0800 (CST)
Subject: [Pw_forum] vc-relax of graphite
In-Reply-To: <20070315065145.11920.61150.Mailman@democritos.sissa.it>
Message-ID: <258861.27894.qm@web15004.mail.cnb.yahoo.com>

dear Paolo,
  
Thanks for your help.
In the paper that "The phonon dispersion of graphite revised [Solid State Communication 131 (2004) 141-152] ", there is a sentence that"For a meaningful comparison of phonon frequencies obtained by different calculations( using different pseudopotentials, basis-sets,parameteriations of the exchange-correlation functional), each calculation should be performed at the respective optimized lattice constant."
So I tried to optimize lattice constant for graphite but always met errors.
You said the good old way: fix c to the experimental value and only optimize a.
How to excecute in the code?
  
Thanks in advance!
   
  Niu Li
  ==================================================
  My input as follows:
cat > graphite.vcrx.in << EOF
&CONTROL
  calculation  = "vc-relax",
  prefix       = "graphite",
  pseudo_dir   = "$PSEUDO_DIR",
  outdir       = "$TMP_DIR",
  tstress = .true. ,
  tprnfor = .true. ,
                       nstep = 65 ,
               etot_conv_thr = 1.0E-4 ,
               forc_conv_thr = 1.0D-3 ,
                          dt = 100 ,
/
&SYSTEM
    ibrav = 4, 
    celldm(1) =4.6336, 
    celldm(3)=2.7243,
    nat= 4, ntyp= 1,
    ecutwfc =40  
/
&ELECTRONS
   conv_thr    = 1.D-9,
  mixing_beta = 0.7D0,
/
&IONS
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
&CELL
               cell_dynamics = 'damp-w',
                       press = 0.0 ,
                       wmass = 0.010 ,
 /
ATOMIC_SPECIES
 C   12.0107  C.pz-vbc.UPF
  ATOMIC_POSITIONS {crystal}
 C  0.0000000 0.0000000 0.0000000 
 C  0.0000000 0.0000000 0.5000000
 C  0.6666667 0.3333333 0.0000000
 C  0.3333333 0.6666667 0.5000000
K_POINTS automatic
16 16 6 1 1 1
  EOF
$ECHO " optimizing the lattice constant for bulk graphite...\c"
$PW_COMMAND < graphite.vcrx.in > graphite.vcrx.out
$ECHO " done"




 		
---------------------------------
????????-3.5G???20M??? 
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From jin.zhang.pku at gmail.com  Wed Mar 21 04:55:36 2007
From: jin.zhang.pku at gmail.com (Jin Zhang)
Date: Wed, 21 Mar 2007 11:55:36 +0800
Subject: [Pw_forum] vc-relax of graphite
In-Reply-To: <258861.27894.qm@web15004.mail.cnb.yahoo.com>
References: <20070315065145.11920.61150.Mailman@democritos.sissa.it>
	 <258861.27894.qm@web15004.mail.cnb.yahoo.com>
Message-ID: <5d233b6a0703202055r7b677b41k7cfef6c05999a747@mail.gmail.com>

Dear Li,

Normally to otain a optimized lattice constant, you do not need to perform
vc-relax. Instead,
doing several single scf calculation with different a (around experiment
value, not too far away) but a fixed c, then fit the aquired data to get
zero-pressure a. Hope this is what you want.

Best,
Jin Zhang

On 3/21/07, li niu <niuli1978 at yahoo.com.cn> wrote:
>
> dear Paolo,
>
> Thanks for your help.
> In the paper that "The phonon dispersion of graphite revised [Solid State
> Communication 131 (2004) 141-152] ", there is a sentence that"For a
> meaningful comparison of phonon frequencies obtained by different
> calculations( using different pseudopotentials, basis-sets,parameteriations
> of the exchange-correlation functional), each calculation should be
> performed at the respective optimized lattice constant."
> So I tried to optimize lattice constant for graphite but always met
> errors.
> You said the good old way: fix c to the experimental value and only
> optimize a.
> How to excecute in the code?
>
> Thanks in advance!
>
> Niu Li
> ==================================================
> My input as follows:
> cat > graphite.vcrx.in << EOF
> &CONTROL
>   calculation  = "vc-relax",
>   prefix       = "graphite",
>   pseudo_dir   = "$PSEUDO_DIR",
>   outdir       = "$TMP_DIR",
>   tstress = .true. ,
>   tprnfor = .true. ,
>                        nstep = 65 ,
>                etot_conv_thr = 1.0E-4 ,
>                forc_conv_thr = 1.0D-3 ,
>                           dt = 100 ,
> /
> &SYSTEM
>     ibrav = 4,
>     celldm(1) =4.6336,
>     celldm(3)=2.7243,
>     nat= 4, ntyp= 1,
>     ecutwfc =40
> /
> &ELECTRONS
>    conv_thr    = 1.D-9,
>   mixing_beta = 0.7D0,
> /
> &IONS
>   pot_extrapolation = "second_order",
>   wfc_extrapolation = "second_order",
> /
> &CELL
>                cell_dynamics = 'damp-w',
>                        press = 0.0 ,
>                        wmass = 0.010 ,
>  /
> ATOMIC_SPECIES
>  C   12.0107  C.pz-vbc.UPF
> ATOMIC_POSITIONS {crystal}
>  C  0.0000000 0.0000000 0.0000000
>  C  0.0000000 0.0000000 0.5000000
>  C  0.6666667 0.3333333 0.0000000
>  C  0.3333333 0.6666667 0.5000000
> K_POINTS automatic
> 16 16 6 1 1 1
> EOF
> $ECHO " optimizing the lattice constant for bulk graphite...\c"
> $PW_COMMAND < graphite.vcrx.in > graphite.vcrx.out
> $ECHO " done"
>
>
>
>
> ------------------------------
> ????????-3.5G???20M??? <http://cn.mail.yahoo.com/>
>
>


-- 
MSc
Dept. of Physics, Peking University
Beijing, 100871, P.R.China
Phone: 86-10-62768590
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From conor.hogan at roma2.infn.it  Wed Mar 21 19:44:34 2007
From: conor.hogan at roma2.infn.it (Conor Hogan)
Date: Wed, 21 Mar 2007 19:44:34 +0100 (CET)
Subject: [Pw_forum] pp.x crashing with fixed occupations
Message-ID: <60936.141.108.248.231.1174502674.squirrel@141.108.248.231>

Dear forum,

I'm using pp.x from QE3.2 to plot the wavefunctions for a spin polarized
calculation, with smearing and with "from_input" occupations. System is
the Cray XD1 at Cineca, mpich 1.2.6 and pgf90 6.0.1. I'm forced to use
more than one processor as the system is large. Code is compiled with
D__XD1 D__PGI D__MPI.

I get the good old Cray MPI message:
Fatal Error: message truncated. ask 4 got 1168 at line 863 in file
/tmp/igorodet/rpm/BUILD/mpich-1.2.6/mpid/rai/raifma.c

usually around the point where the OCCUPATIONS section is read. Everything
works ok if smearing is used, but not if FIXED_OCCUPATIONS is true (and
hence, f_inp is present). I can work around the problem by cutting the
whole OCCUPATIONS section out and replacing it with a section from a
smearing run, but I don't know if this will cause damage later on (can
it?). Trying to reduce the MAXSZ XD1 MPI parameter in Modules/mp.f90 didnt
help.

I had problems like this before with ifort and earlier versions of pp.x,
but not yet with pgf90. The only thing I can come up with is that
f_inp(nbnd,nspin) is the only module-declared quantity allocated in
pw_restart.f90 : I tried moving the allocation to an earlier section of
the code, but then I get other MPI errors when passing e.g. lgauss at this
point (here I got lost and gave up!).

Any suggestions/workarounds?

Best regards,
Conor

----

Dr. Conor Hogan                                --- -----  ---   ---
Dipartimento di Fisica e CNR-INFM             |      :   |     :
Universita' di Roma "Tor Vergata"             |--    :    ---  |---
Tel: +39 06 72594908                          |      :       | :
Fax: +39 06 2023507                            ---   :    ---  :
http://www.fisica.uniroma2.it/~cmtheo-group/  European Theoretical
                                              Spectroscopy Facility
                                              http://www.etsf.eu

The early bird gets the worm, but the second mouse gets the cheese. - S.
Wright

If you go through a lot of hammers each month, I don't think it necessarily
means you're a hard worker. It may just mean that you have a lot to learn
about proper hammer maintenance - J. Handey


From yukihiro_okuno at fujifilm.co.jp  Thu Mar 22 01:40:37 2007
From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp)
Date: Thu, 22 Mar 2007 09:40:37 +0900
Subject: [Pw_forum] Oscillation behavior for structure optimization
Message-ID: <OF88564805.87BA509C-ON492572A6.0002FFDD-492572A6.0003B7F0@mta.fujifilm.co.jp>

Dear PWscf Users.

I'm now calculating the structure optimization for
monoclinic structure of PZT ( put a little shere stress for
tetragonal structure).

But the calculation is not conversed and the Total force
is oscillate like below, and this does not happen for tetragonal case.)

 Total force =     0.029288     Total SCF correction =     0.000028
     Total force =     0.610879     Total SCF correction =     0.000006
     Total force =     0.031826     Total SCF correction =     0.000017
     Total force =     0.017717     Total SCF correction =     0.000010
     Total force =     0.006548     Total SCF correction =     0.000009
     Total force =     0.004523     Total SCF correction =     0.000024
     Total force =     0.002241     Total SCF correction =     0.000004
     Total force =     0.001565     Total SCF correction =     0.000008
     Total force =     0.001102     Total SCF correction =     0.000005
     Total force =     0.001312     Total SCF correction =     0.000010
     Total force =     0.001605     Total SCF correction =     0.000009
     Total force =     0.001865     Total SCF correction =     0.000006
     Total force =     0.002391     Total SCF correction =     0.000005
     Total force =     0.002574     Total SCF correction =     0.000005
     Total force =     0.001872     Total SCF correction =     0.000008
     Total force =     0.001495     Total SCF correction =     0.000006
     Total force =     0.001430     Total SCF correction =     0.000005
     Total force =     0.001529     Total SCF correction =     0.000003
     Total force =     0.001736     Total SCF correction =     0.000004
     Total force =     0.002315     Total SCF correction =     0.000004
     Total force =     0.002271     Total SCF correction =     0.000008
     Total force =     0.001826     Total SCF correction =     0.000008
     Total force =     0.001623     Total SCF correction =     0.000004
     Total force =     0.001605     Total SCF correction =     0.000007
     Total force =     0.001720     Total SCF correction =     0.000006
     Total force =     0.002129     Total SCF correction =     0.000003
     Total force =     0.002290     Total SCF correction =     0.000007
     Total force =     0.002437     Total SCF correction =     0.000006
     Total force =     0.002619     Total SCF correction =     0.000006
     Total force =     0.002860     Total SCF correction =     0.000007
     Total force =     0.003199     Total SCF correction =     0.000006
     Total force =     0.003772     Total SCF correction =     0.000006


My input file is like below and how should we treat such a trouble?

 &control
    calculation  = 'relax',
    restart_mode = 'from_scratch',
    pseudo_dir   = '/home/okuno/PWSCF/espresso-3.2/pseudo/',
    outdir       = './',
    prefix='PZT'
    forc_conv_thr = 1.0D-4
 /
 &system
    ibrav=12
    celldm(1)=7.57696068724
    celldm(2)=2.09
    celldm(3)=1.00
    celldm(4)=0.00499993750117
    nat=10
    ntyp=4
    nbnd=44
    ecutwfc=60.0
    ecutrho = 600.0
    occupations = 'fixed'
    degauss=0.00
 /
 &electrons
    conv_thr = 1e-10,
    mixing_beta=0.3,
 /
&IONS
 ion_dynamics='bfgs'
 bfgs_ndim=3
 pot_extrapolation = "second_order"
 wfc_extrapolation = "second_order"
 trust_radius_min=1.0D-4
/
ATOMIC_SPECIES
  Pb  207.2     pb_ps.uspp.UPF
  Zr  91.224    zr_ps.uspp.UPF
  Ti  47.867    ti_ps.uspp.UPF
  O   15.9994   o_ps.uspp.UPF
ATOMIC_POSITIONS {crystal}
Pb 0.0 0.00000 0.0 1 1 0
Pb 0.0 0.53106 0.0 1 1 0
Zr 0.5 0.24462 0.5 1 1 0
Ti 0.5 0.74062 0.5 1 1 0
O  0.5 0.95432 0.5 1 1 0
O  0.5 0.48072 0.5 1 1 0
O  0.5 0.19090 0.0 1 1 0
O  0.0 0.19090 0.5 1 1 0
O  0.5 0.71336 0.0 1 1 0
O  0.0 0.71336 0.5 1 1 0
K_POINTS {automatic}
  6 6 6 0 0 0







,



From lanhaiping at gmail.com  Thu Mar 22 13:53:38 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Thu, 22 Mar 2007 20:53:38 +0800
Subject: [Pw_forum] calculation crash
Message-ID: <c92002fa0703220553g4890811btb90143706b299db4@mail.gmail.com>

Hi,All.
When i tried to perform a relaxation calculation with pw.x, it return a
CRASH to me with information below:
"
     task #         0
     from  fft_dlay_set  : error #         7
      inconsistent number of sticks "
I then digged forum and mannual , donot find any solution to this error .
would you please give me some hints and helps ?
the input file is  below :
 &control
    calculation='relax',
    restart_mode='from_scratch',
    prefix='ramman'
    pseudo_dir = '/home/haiping/espresso/pseudo/',
    outdir='/home/haiping/tmp/',
    etot_conv_thr =1.0D-4,
    forc_conv_thr =1.0D-3
 /
 &system
    ibrav = 12, celldm(1) = 8.4659764124291126,celldm(2)=1.00000,
        celldm(3)=0.90841517857142851,celldm(4)=-0.48439283090427787,
        nat=  12, ntyp= 3,
    ecutwfc = 32.0,ecutrho=300.0,
        occupations ='smearing',
        degauss= 0.03 ,
        smearing='mv',
 /
 &electrons
        diagonalization='david',
        mixing_mode='plain',
    mixing_beta = 0.3,
    conv_thr =  1.0d-10,
/
&IONS
        ion_dynamics='bfgs',
        pot_extrapolation='atomic',
        wfc_extrapolation='none',
 /
ATOMIC_SPECIES
 C   12.00    C.pbe-rrkjus.UPF
 N   14.00674 N.pbe-rrkjus.UPF
..................


Regards,

h.p
-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
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From naivebamboo at hotmail.com  Thu Mar 22 15:55:22 2007
From: naivebamboo at hotmail.com (naivebamboo Huang)
Date: Thu, 22 Mar 2007 10:55:22 -0400
Subject: [Pw_forum] Confused by BO/FPMD/CP
Message-ID: <BAY101-F24FBAE373722B875268BD5B66B0@phx.gbl>

Dear ESPRESSO users,
        I  am confused by the MD methods in pwscf and those in CP. I hope I 
can get some help from you and clarify my questions:
      1. Is the "MD" or "VCMD" in pwscf  (I found them in PWGUI)  BO MD 
(Born-Oppenheimer MD)?
      2. What's' fpmd'? Is it the same as Ehrenfest MD?
      3. If I want to get the energy of a serial of configures(I want to use 
MD to produce those configurations automatically), which method should I 
choose? (BO MD is better?) If the "MD" in PWSCF is actually BO MD, should I 
use pw.x or cp.x to run the MD?

Thanks

Baoling Huang

_________________________________________________________________
Watch free concerts with Pink, Rod Stewart, Oasis and more. Visit MSN 
Presents today. 
http://music.msn.com/presents?icid=ncmsnpresentstagline&ocid=T002MSN03A07001



From yinzping at gmail.com  Thu Mar 22 19:11:14 2007
From: yinzping at gmail.com (Zhiping Yin)
Date: Thu, 22 Mar 2007 10:11:14 -0800
Subject: [Pw_forum] external potential and partial wavefunctions
Message-ID: <523370bf0703221111w5fc8d0felacac05e863ef2f3d@mail.gmail.com>

Dear PWscf users,

In PWscf, one can get out the  1=total potential V_bare+V_H + V_xc
 !                                           2=local ionic potential
 !                                           3=local density of
states at e_fermi
 !                                           4=local density of
electronic entropy
 !                                           5=STM images
 !                                           6=spin polarization
(rho(up)-rho(down))
 !                                           7=|psi|^2 (See below)
 !                                           8=electron localization
function (ELF)
 !                                           9=planar average of all |psi|^2
 !                                          10=integrated local
density of states (ILDOS)
 !                                                    from emin to
emax (emin, emax in eV)
 !                                                      if emax is
not specified, emax=E_fermi
 !                                           11=the V_bare + V_H potential

I am trying to get out the external potential. However, none of the
plot number seems to be the external potential. Anyone knows how to
get it? For the wavefunction, I cannot use "vi" or  "more". What is
the format of the wavefunction file "case.wfc"?. How to project to
wavefunction to s, p, d, etc like component? Thanks very much.

Sincerely,
Zhiping Yin

-- 
Zhiping Yin
graduate student
department of physics
UC Davis


From fratesi at mater.unimib.it  Fri Mar 23 09:27:45 2007
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Fri, 23 Mar 2007 09:27:45 +0100 (CET)
Subject: [Pw_forum] external potential and partial wavefunctions
In-Reply-To: <523370bf0703221111w5fc8d0felacac05e863ef2f3d@mail.gmail.com>
References: <523370bf0703221111w5fc8d0felacac05e863ef2f3d@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0703230920420.17680@localhost.localdomain>

Dear Zhiping,

ZY> In PWscf, one can get out the  1=total potential V_bare+V_H + V_xc
ZY> !                                           2=local ionic potential

Isn't "local ionic potential" the "external potential" you are looking 
for?

ZY> I am trying to get out the external potential. However, none of the
ZY> plot number seems to be the external potential. Anyone knows how to
ZY> get it? For the wavefunction, I cannot use "vi" or  "more". What is
ZY> the format of the wavefunction file "case.wfc"?. How to project to
ZY> wavefunction to s, p, d, etc like component? Thanks very much.

pw.x wavefunction files are binary files in an internal format. They 
correspond to array "evc" in the code.
To project them, look for projwfc.x, INPUT_PROJWFC, and discussions on the 
forum like:
http://www.democritos.it/pipermail/pw_forum/2006-November/005339.html

Hope this helps.

Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy


From yinzping at gmail.com  Fri Mar 23 09:57:21 2007
From: yinzping at gmail.com (Zhiping Yin)
Date: Fri, 23 Mar 2007 00:57:21 -0800
Subject: [Pw_forum] external potential and partial wavefunctions
In-Reply-To: <Pine.LNX.4.64.0703230920420.17680@localhost.localdomain>
References: <523370bf0703221111w5fc8d0felacac05e863ef2f3d@mail.gmail.com>
	 <Pine.LNX.4.64.0703230920420.17680@localhost.localdomain>
Message-ID: <523370bf0703230157h1921191p74fda9e4fd782839@mail.gmail.com>

Dear Guido,

Thanks very much! I am not sure the exact meaning of the "local ionic
potential" in Pwscf. Can you explain it in more details?

Best regards,
Zhiping Yin

On 3/23/07, Guido Fratesi <fratesi at mater.unimib.it> wrote:
> Dear Zhiping,
>
> ZY> In PWscf, one can get out the  1=total potential V_bare+V_H + V_xc
> ZY> !                                           2=local ionic potential
>
> Isn't "local ionic potential" the "external potential" you are looking
> for?
>
> ZY> I am trying to get out the external potential. However, none of the
> ZY> plot number seems to be the external potential. Anyone knows how to
> ZY> get it? For the wavefunction, I cannot use "vi" or  "more". What is
> ZY> the format of the wavefunction file "case.wfc"?. How to project to
> ZY> wavefunction to s, p, d, etc like component? Thanks very much.
>
> pw.x wavefunction files are binary files in an internal format. They
> correspond to array "evc" in the code.
> To project them, look for projwfc.x, INPUT_PROJWFC, and discussions on the
> forum like:
> http://www.democritos.it/pipermail/pw_forum/2006-November/005339.html
>
> Hope this helps.
>
> Guido Fratesi
>
> Dipartimento di Scienza dei Materiali
> Universita` degli studi di Milano-Bicocca
> via Cozzi 53, 20125 Milano, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-- 
Zhiping Yin
graduate student
department of physics
UC Davis


From fratesi at mater.unimib.it  Fri Mar 23 10:34:12 2007
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Fri, 23 Mar 2007 10:34:12 +0100 (CET)
Subject: [Pw_forum] external potential and partial wavefunctions
In-Reply-To: <523370bf0703230157h1921191p74fda9e4fd782839@mail.gmail.com>
References: <523370bf0703221111w5fc8d0felacac05e863ef2f3d@mail.gmail.com> 
 <Pine.LNX.4.64.0703230920420.17680@localhost.localdomain>
 <523370bf0703230157h1921191p74fda9e4fd782839@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0703231029060.17680@localhost.localdomain>

 | Thanks very much! I am not sure the exact meaning of the "local ionic
 | potential" in Pwscf. Can you explain it in more details?

Please have a look at Vanderbilt, PRB 41, 7892 (1990)
(pw.x sums vloc for all atoms)

Pseudopotentials are explained also in modern textbooks like
Electronic Structure: Basic Theory and Practical Methods
by Richard M. Martin, published by Cambridge University Press, 2004

Regards,

Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy


From conor.hogan at roma2.infn.it  Fri Mar 23 19:14:19 2007
From: conor.hogan at roma2.infn.it (Conor Hogan)
Date: Fri, 23 Mar 2007 19:14:19 +0100 (CET)
Subject: [Pw_forum] Inconsistent pp.x and projwfc.x results?
Message-ID: <34711.141.108.248.231.1174673659.squirrel@141.108.248.231>

Dear forum,

I've discovered something strange in some of the results of the
postprocessing
codes, could be a bug (at least for this
version/machine/compiler/system!), or I'm doing something completely
strange.

Basically the character of the states produced by projwfc.x (atomic
projection) and pp.x (plotting the state directly) differ in the case I'm
studying:
system is Cobalt porphyrin, 121 electrons, spin polarized, with PBE or PZ,
and the states near the fermi level are mostly d orbitals of the Co.

projwfc.x says: (occupation in brackets; POR = molecular state)
--------------------------
band    up             down
61 (1) dxz + dyz  (0) dz2
60 (1) dxz + dyz  (1) dxz + dyz
59 (1) POR        (1) dxz + dyz
58 (1) POR        (1) dxy
57 (1) dxy        (1) POR
56 (1) POR        (1) POR
55 (1) dz2        (1) POR

pp.x says: (plotting via gopenmol)
--------------------------
band    up             down
61 (1) dxz + dyz  (0) dxz + dyz
60 (1) dxz + dyz  (1) dxz + dyz
59 (1) POR        (1) POR
58 (1) POR        (1) POR
57 (1) dxy        (1) dxy
56 (1) POR        (1) POR
55 (1) dz2        (1) dz2

Now the pp.x results appear to be unphysical (weird symmetry, degenerate
states of Co-d and molecule!). I redid the calculations using
non-collinear magnetism, and this time the results of pp.x seem fine (as
in the projwfc.x case).

These results are using smearing, but I get the same with fixed
occupations (using the trick I posted yesterday).

Any known bugs/comments/solutions?! Unfortunately the system is rather
large, so its hard to debug, but if anyone has any ideas how to localize
the problem I'd be grateful. Input files are below.

Best regards,
Conor

[PS if anyone can tell me how to get rid of my Co-localized LUMO I'd be
even happier :) ]


--- Compiling specs: ---
QE 3.2 Cray XD1 pgf90 6.0.1,
Default configure on XD1: -D__PGI -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI
-D__PARA (or also with -D__XD1 -lacml) , -fast -f8

--- projwfc.x input ---
&inputpp
  prefix = 'CoP_xy'
  outdir = './'
  ngauss = 0,
  degauss = 0.01,
  DeltaE = 0.05,
  filproj = 'projections.txt'
/
--- pp.x input ---
%inputpp
 prefix  = 'CoP_xy'
 outdir = './'
 filplot = 'CoP_xy.dat'
 plot_num= 7
 spin_component = 2,
 kpoint=1
 kband=55,
 /
 &plot
    nfile = 1
    filepp(1) = 'CoP_xy.dat'
    weight(1) = 1.0
    iflag = 3
    output_format = 4
    fileout = 'CoP_xy_2_55.opm'
    x0(1) =-0.25, x0(2)=-0.25, x0(3) = -0.15,
    e1(1) =0.5, e1(2)=0.0, e1(3) = 0.0,
    e2(1) =0.0, e2(2)=0.5, e2(3) = 0.0,
    e3(1) =0.0, e3(2)=0.0, e3(3) = 0.3,
    nx=30, ny=30, nz =30
 /
---pw.x input ---

 &control
    calculation = 'scf'
    etot_conv_thr=1.0e-4,
    prefix='CoP_xy',
    disk_io='minimal',
    wf_collect=.true.
 /
 &system
    ibrav= 8, celldm(1)=60., celldm(2) = 1.00, celldm(3) = 0.75
    nat=37, ntyp=4, nspin =2, starting_magnetization(4) = 1
    ecutwfc = 40.0, ecutrho=320.,
    occupations='smearing', smearing='gaussian' , degauss=0.01
 /
 &electrons
    conv_thr =  1.0d-7
    mixing_beta = 0.6,
 /
ATOMIC_SPECIES
 C  12.00  C.pbe-rrkjus.UPF
 N  14.00  N.pbe-rrkjus.UPF
 H   1.00  H.pbe-rrkjus.UPF
Co  58.00  Co.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
[...]
Co      0.0000000000   0.0000000000   0.0000000000 0 0 0
K_POINTS {gamma}


----

Dr. Conor Hogan                                --- -----  ---   ---
Dipartimento di Fisica e CNR-INFM             |      :   |     :
Universita' di Roma "Tor Vergata"             |--    :    ---  |---
Tel: +39 06 72594908                          |      :       | :
Fax: +39 06 2023507                            ---   :    ---  :
http://www.fisica.uniroma2.it/~cmtheo-group/  European Theoretical
                                              Spectroscopy Facility
                                              http://www.etsf.eu

The early bird gets the worm, but the second mouse gets the cheese. - S.
Wright

If you go through a lot of hammers each month, I don't think it necessarily
means you're a hard worker. It may just mean that you have a lot to learn
about proper hammer maintenance - J. Handey


From chen_shao_hua197 at yahoo.com.tw  Fri Mar 23 20:29:01 2007
From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=)
Date: Sat, 24 Mar 2007 03:29:01 +0800 (CST)
Subject: [Pw_forum] negative e-ph coupling constant lambda(q)
Message-ID: <366891.43774.qm@web73015.mail.tp2.yahoo.com>

Dear members,
The e-ph coupling constant lambda(q) should be >= 0 by
its definition.
So if we get the negative lambda(q) by example07
steps,does it mean the material structure unstable ?
(just like get negative freqency )

Best Regards
max

___________________________________________________ 
 ??????? ? ???????????????? 
 http://messenger.yahoo.com.tw/


From yinzping at gmail.com  Sat Mar 24 01:14:51 2007
From: yinzping at gmail.com (Zhiping Yin)
Date: Fri, 23 Mar 2007 16:14:51 -0800
Subject: [Pw_forum] external potential and partial wavefunctions
In-Reply-To: <Pine.LNX.4.64.0703231029060.17680@localhost.localdomain>
References: <523370bf0703221111w5fc8d0felacac05e863ef2f3d@mail.gmail.com>
	 <Pine.LNX.4.64.0703230920420.17680@localhost.localdomain>
	 <523370bf0703230157h1921191p74fda9e4fd782839@mail.gmail.com>
	 <Pine.LNX.4.64.0703231029060.17680@localhost.localdomain>
Message-ID: <523370bf0703231714i662d5f2ds6bb9cafb3e2037bc@mail.gmail.com>

Dear Guido,

Thanks very much for your kindly reply!
The external potential should contain both the local part (which
should be the local ionic potential) and the non-local part which is
V_NL. In the USPP,
V_NL=sum_ij (D_ij *|beta_i> <beta_j|
My question is: in PWscf, how to get out the non-local potential V_NL.
Where are the D_ij and |beta_i> stored?  In the paper Vanderbilt, PRB
41, 7892 (1990), the author suggested that "the pseudopotential itself
must be updated as part of the self-consistent screening process". I
wonder whether PWscf does this in the self-consistent iterations. If
yes, where are the new pseudopotentials stored? Regarding to the
non-local psedupotential, I guess, in the pp.x, the total potential
V_bare+V_H + V_xc doesn't contain the non-local part V_NL, right?  Do
the V_bare and local ionic potential refer to the same thing? Or what
does the V_bare mean here?

I am sorry for all these questions, but I really appreciate you for
your helpful responses.

Best regards,
Zhiping Yin

On 3/23/07, Guido Fratesi <fratesi at mater.unimib.it> wrote:
>  | Thanks very much! I am not sure the exact meaning of the "local ionic
>  | potential" in Pwscf. Can you explain it in more details?
>
> Please have a look at Vanderbilt, PRB 41, 7892 (1990)
> (pw.x sums vloc for all atoms)
>
> Pseudopotentials are explained also in modern textbooks like
> Electronic Structure: Basic Theory and Practical Methods
> by Richard M. Martin, published by Cambridge University Press, 2004
>
> Regards,
>
> Guido Fratesi
>
> Dipartimento di Scienza dei Materiali
> Universita` degli studi di Milano-Bicocca
> via Cozzi 53, 20125 Milano, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-- 
Zhiping Yin
graduate student
department of physics
UC Davis


From ferretti.andrea at unimore.it  Sat Mar 24 15:54:59 2007
From: ferretti.andrea at unimore.it (Andrea Ferretti)
Date: Sat, 24 Mar 2007 15:54:59 +0100 (CET)
Subject: [Pw_forum] spilling parameter in Lowdin - how to assign the
 charge that went into Nirvana ?
In-Reply-To: <851319.42244.qm@web57701.mail.re3.yahoo.com>
References: <851319.42244.qm@web57701.mail.re3.yahoo.com>
Message-ID: <Pine.LNX.4.58.0703241521310.14388@bamboo.fisica.unimo.it>

Hi Kostya,

> 
> > For insulators and semiconductors an exact (no spilling factor) 
> > partition of the total charge into localized orbitals can be
> > obtained...   
> > in the same line, WF projected DOS can be obtained as well
> 
>  I think the issue with WF is that they are hard to assign back to the
> atoms, since now these are just electron pairs somewhere in the middle.

yes...
this is the case when a covalent bond exists... but this is also the 
reason of the increasing of the spilling parameter when using Lowding 
orbitals... in a sense, electronic charge is physically in between atoms 
for covalent bonding and this is why WFs sit there
(of course, WFs does not always sit on bonds, it is equally 
standard they sit on atoms, like eg in the case of lone pairs, d-orbitals in Transition 
metals etc etc)

>  For Lowdin projection the 1995 paper (link below) claimed that the
> atomic basis could be optimized, I wonder if QE does that, and whether
> it is done for each atom, or just for all atoms of the same type at
> once.
> 
> http://dx.doi.org/10.1016/0038-1098(95)00341-X
> 

Lowding orbitals in Quantum-Espresso (at least as far as I know) are 
computed from the atomic reference states from pseudopotential data
according to:

S_ij = < i | j >      are the overlaps of atomic orbitals i and j

lowding orbitals are then obtained as
| low_i > =  R_ij  | j >

where  R = S^{-1/2} 

so I think there is no optimization (in the sense of the paper above)
but maybe I am missing something

all the best
andrea


From amit76.india at gmail.com  Sun Mar 25 19:58:12 2007
From: amit76.india at gmail.com (Amit Kumar)
Date: Sun, 25 Mar 2007 23:28:12 +0530
Subject: [Pw_forum] Aluminium EPC at X
Message-ID: <aef8bbf00703251058n608dda09o1f454714c2afe0d5@mail.gmail.com>

   Respected Users,

   I'm very much confused with the results of the electron-phonon coupling
of Aluminium
   at X-point.  You can see a large discrepancy in the results of Example
No. 7.
   I hope developers  have checked  their  results  carefully  before
keeping them on the web and
   they must have some clarification of the above anomaly.
   Someone can get some total value of lamda (say 0.38 for Al) by
manipulating some input  parameters
   in 100 ways.
   However it does not imply al the ways are correct. Sometime some correct
results might be accidental.
   So developers should check every part of the results carefully and
mention all the details in their
   published paper instead of   just giving an experimentally closed value
of  lambda.

   Check  out the discrepancy even in the example given by developers.
::::::::::::::::

   OLd version ::::

        electron-phonon interaction  ...

     Gaussian Broadening:   0.010 Ry, ngauss=   1
     DOS =  1.571147 states/spin/Ry/Unit Cell at Ef=  8.320258 eV
     double delta at Ef = 11.225648
     lambda( 1)=  0.159075   gamma=  8.614118 GHz
     lambda( 2)=  0.159075   gamma=  8.614118 GHz
     lambda( 3)=  0.003155   gamma=  0.507699 GHz
     Gaussian Broadening:   0.020 Ry, ngauss=   1
     DOS =  2.063779 states/spin/Ry/Unit Cell at Ef=  8.335249 eV
     double delta at Ef = 18.003706
     lambda( 1)=  0.227168   gamma= 16.158565 GHz
     lambda( 2)=  0.227168   gamma= 16.158565 GHz
     lambda( 3)=  0.186119   gamma= 39.344107 GHz
     Gaussian Broadening:   0.030 Ry, ngauss=   1
     DOS =  2.225322 states/spin/Ry/Unit Cell at Ef=  8.330057 eV
     double delta at Ef = 16.640984
     lambda( 1)=  0.192523   gamma= 14.766136 GHz
     lambda( 2)=  0.192523   gamma= 14.766136 GHz
     lambda( 3)=  0.205460   gamma= 46.832277 GHz
     Gaussian Broadening:   0.040 Ry, ngauss=   1
     DOS =  2.326737 states/spin/Ry/Unit Cell at Ef=  8.319465 eV
     double delta at Ef = 14.664131
     lambda( 1)=  0.176025   gamma= 14.116094 GHz
     lambda( 2)=  0.176025   gamma= 14.116094 GHz
     lambda( 3)=  0.151743   gamma= 36.164371 GHz
     Gaussian Broadening:   0.050 Ry, ngauss=   1
     DOS =  2.437502 states/spin/Ry/Unit Cell at Ef=  8.308700 eV
     double delta at Ef = 13.504805
     lambda( 1)=  0.157223   gamma= 13.208493 GHz
     lambda( 2)=  0.157223   gamma= 13.208493 GHz
     lambda( 3)=  0.127499   gamma= 31.832929 GHz
     Gaussian Broadening:   0.060 Ry, ngauss=   1
     DOS =  2.540670 states/spin/Ry/Unit Cell at Ef=  8.300510 eV
     double delta at Ef = 12.914118
     lambda( 1)=  0.139587   gamma= 12.223180 GHz
     lambda( 2)=  0.139587   gamma= 12.223180 GHz
     lambda( 3)=  0.123908   gamma= 32.245781 GHz
     Gaussian Broadening:   0.070 Ry, ngauss=   1
     DOS =  2.612585 states/spin/Ry/Unit Cell at Ef=  8.295170 eV
     double delta at Ef = 12.624523
     lambda( 1)=  0.127008   gamma= 11.436544 GHz
     lambda( 2)=  0.127008   gamma= 11.436544 GHz
     lambda( 3)=  0.124915   gamma= 33.427891 GHz
     Gaussian Broadening:   0.080 Ry, ngauss=   1
     DOS =  2.651928 states/spin/Ry/Unit Cell at Ef=  8.291972 eV
     double delta at Ef = 12.510074
     lambda( 1)=  0.119464   gamma= 10.919196 GHz
     lambda( 2)=  0.119464   gamma= 10.919196 GHz
     lambda( 3)=  0.127255   gamma= 34.566893 GHz
     Gaussian Broadening:   0.090 Ry, ngauss=   1
     DOS =  2.669093 states/spin/Ry/Unit Cell at Ef=  8.290116 eV
     double delta at Ef = 12.474088
     lambda( 1)=  0.115291   gamma= 10.605987 GHz
     lambda( 2)=  0.115291   gamma= 10.605987 GHz
     lambda( 3)=  0.130520   gamma= 35.683264 GHz
     Gaussian Broadening:   0.100 Ry, ngauss=   1
     DOS =  2.674519 states/spin/Ry/Unit Cell at Ef=  8.288962 eV
     double delta at Ef = 12.456417
     lambda( 1)=  0.112978   gamma= 10.414299 GHz
     lambda( 2)=  0.112978   gamma= 10.414299 GHz
     lambda( 3)=  0.134292   gamma= 36.789272 GHz



    And check the
    Newer  Version  :::::::::



     .     Diagonalizing the dynamical matrix

     q = (    0.000000000   0.000000000   1.000000000 )

 **************************************************************************
     omega( 1) =       6.150074 [THz] =     205.145746 [cm-1]
     omega( 2) =       6.150074 [THz] =     205.145746 [cm-1]
     omega( 3) =       9.705764 [THz] =     323.751591 [cm-1]
 **************************************************************************
     electron-phonon interaction  ...

     Gaussian Broadening:   0.010 Ry, ngauss=   0
     DOS =  2.640036 states/spin/Ry/Unit Cell at Ef=  8.292189 eV
     lambda( 1)=  0.1693   gamma=   16.15 GHz
     lambda( 2)=  0.1696   gamma=   16.18 GHz
     lambda( 3)=  0.1515   gamma=   35.98 GHz
     Gaussian Broadening:   0.020 Ry, ngauss=   0
     DOS =  2.665783 states/spin/Ry/Unit Cell at Ef=  8.295265 eV
     lambda( 1)=  0.1342   gamma=   12.92 GHz
     lambda( 2)=  0.1376   gamma=   13.25 GHz
     lambda( 3)=  0.1441   gamma=   34.55 GHz
     Gaussian Broadening:   0.030 Ry, ngauss=   0
     DOS =  2.664312 states/spin/Ry/Unit Cell at Ef=  8.294084 eV
     lambda( 1)=  0.1197   gamma=   11.51 GHz
     lambda( 2)=  0.1231   gamma=   11.85 GHz
     lambda( 3)=  0.1466   gamma=   35.14 GHz
     Gaussian Broadening:   0.040 Ry, ngauss=   0
     DOS =  2.668351 states/spin/Ry/Unit Cell at Ef=  8.290682 eV
     lambda( 1)=  0.1148   gamma=   11.06 GHz
     lambda( 2)=  0.1181   gamma=   11.39 GHz
     lambda( 3)=  0.1470   gamma=   35.28 GHz
     Gaussian Broadening:   0.050 Ry, ngauss=   0
     DOS =  2.672172 states/spin/Ry/Unit Cell at Ef=  8.286936 eV
     lambda( 1)=  0.1125   gamma=   10.85 GHz
     lambda( 2)=  0.1156   gamma=   11.16 GHz
     lambda( 3)=  0.1485   gamma=   35.71 GHz
     Gaussian Broadening:   0.060 Ry, ngauss=   0
     DOS =  2.674722 states/spin/Ry/Unit Cell at Ef=  8.283275 eV
     lambda( 1)=  0.1107   gamma=   10.70 GHz
     lambda( 2)=  0.1135   gamma=   10.96 GHz
     lambda( 3)=  0.1508   gamma=   36.29 GHz
     Gaussian Broadening:   0.070 Ry, ngauss=   0
     DOS =  2.675808 states/spin/Ry/Unit Cell at Ef=  8.279572 eV
     lambda( 1)=  0.1093   gamma=   10.57 GHz
     lambda( 2)=  0.1116   gamma=   10.78 GHz
     lambda( 3)=  0.1533   gamma=   36.91 GHz
     Gaussian Broadening:   0.080 Ry, ngauss=   0
     DOS =  2.675785 states/spin/Ry/Unit Cell at Ef=  8.275659 eV
     lambda( 1)=  0.1082   gamma=   10.46 GHz
     lambda( 2)=  0.1099   gamma=   10.63 GHz
     lambda( 3)=  0.1558   gamma=   37.51 GHz
     Gaussian Broadening:   0.090 Ry, ngauss=   0
     DOS =  2.675260 states/spin/Ry/Unit Cell at Ef=  8.271439 eV
     lambda( 1)=  0.1072   gamma=   10.36 GHz
     lambda( 2)=  0.1086   gamma=   10.49 GHz
     lambda( 3)=  0.1582   gamma=   38.07 GHz
     Gaussian Broadening:   0.100 Ry, ngauss=   0
     DOS =  2.674736 states/spin/Ry/Unit Cell at Ef=  8.266876 eV
     lambda( 1)=  0.1063   gamma=   10.27 GHz
     lambda( 2)=  0.1074   gamma=   10.37 GHz
     lambda( 3)=  0.1603   gamma=   38.57 GHz


     Number of q in the star =    3
     List of q in the star:
          1   0.000000000   0.000000000   1.000000000
          2   1.000000000   0.000000000   0.000000000
          3   0.000000000   1.000000000   0.000000000




    One can easily notice that the above 2 results are not the same.
    Moreover,  the results  are not well converged.

     Please tell me
     which value will you say the correct one????????

     Gaussian Broadening:   0.090 Ry, ngauss=   0
     DOS =  2.675260 states/spin/Ry/Unit Cell at Ef=  8.271439 eV
     lambda( 3)=  0.1582   gamma=   38.07 GHz

     Gaussian Broadening:   0.080 Ry, ngauss=   0
     DOS =  2.675785 states/spin/Ry/Unit Cell at Ef=  8.275659 eV
     lambda( 3)=  0.1558   gamma=   37.51 GHz


     The value of lambda  :   0.1470     or  0.1558   or   0.1582
      are not  the same.

     By the way,  manipulating the input parameters carefully  one can
easily get  the
     total value of lambda very close to the experimental one  in the both
version.

     Looking forward to your kind explanation.

     Regards,
     Amit
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From marzari at MIT.EDU  Sun Mar 25 20:08:57 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sun, 25 Mar 2007 14:08:57 -0400
Subject: [Pw_forum] Aluminium EPC at X
In-Reply-To: <aef8bbf00703251058n608dda09o1f454714c2afe0d5@mail.gmail.com>
References: <aef8bbf00703251058n608dda09o1f454714c2afe0d5@mail.gmail.com>
Message-ID: <4606BAB9.7010708@mit.edu>

Amit Kumar wrote:
> 
> 
>    Respected Users,
> 
>    I'm very much confused with the results of the electron-phonon 
> coupling of Aluminium
>    at X-point.  You can see a large discrepancy in the results of 
> Example  No. 7.


Hi Amit,

the example is not meant to represent a fully converged calculation -
it would take too long to run. It's really meant to give you a
framework to look for convergence yourself. This can be extremely
expensive, for electron-phonon coupling (see e.g. a discussion in the
recent Giustino PRL).


				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


From kondor.jess at gmail.com  Sun Mar 25 20:05:17 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Sun, 25 Mar 2007 13:05:17 -0500
Subject: [Pw_forum] masses and dt in vc-relax
Message-ID: <1d9d5d9d0703251105p9831ed9q7503ac1f0b549d85@mail.gmail.com>

Hi all,

 I have a question. I am performing 'vc-relax' calculations of the material
that contains quite different atomic masses. In order to speed up
calculations, I tried to find out which timestep (and atomic mass) is more
appropriate. I have chosen a test system (bulk, ~20 atoms) of that material
and tried to vary timestep at fixed atomic mass. For example, I set an
atomic mass for all species to be equal 1.0d0 and found, that dt=70.0 is the
best (fast execution) and further increasing of timestep leads to divergence
of scf cycles. So, next, for the interesting system that is bigger than test
system and has different dimension (surface) I used dt=70 and masses =
1.0However, after several ionic steps the calculations crashed due to
divergence of scf algorithm. I guess this is due to timestep value. I
decreased dt up to 50.0, but it doesn't help. So, I set atomic masses to be
equal their natural values and dt=70. Now the calculations are slow, but
stable. So, the question is, what was wrong with my settings? Does it mean
that I cannot use the settings from the small system and apply them for
bigger system?


-----------------
Regards,
   Jess
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From fratesi at mater.unimib.it  Mon Mar 26 12:25:47 2007
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Mon, 26 Mar 2007 12:25:47 +0200 (CEST)
Subject: [Pw_forum] external potential and partial wavefunctions
In-Reply-To: <523370bf0703231714i662d5f2ds6bb9cafb3e2037bc@mail.gmail.com>
References: <523370bf0703221111w5fc8d0felacac05e863ef2f3d@mail.gmail.com> 
 <Pine.LNX.4.64.0703230920420.17680@localhost.localdomain> 
 <523370bf0703230157h1921191p74fda9e4fd782839@mail.gmail.com> 
 <Pine.LNX.4.64.0703231029060.17680@localhost.localdomain>
 <523370bf0703231714i662d5f2ds6bb9cafb3e2037bc@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0703261212050.22921@localhost.localdomain>

> The external potential should contain both the local part (which
> should be the local ionic potential) and the non-local part which is
> V_NL. In the USPP,
> V_NL=sum_ij (D_ij *|beta_i> <beta_j|
> My question is: in PWscf, how to get out the non-local potential V_NL.
> Where are the D_ij and |beta_i> stored?  In the paper Vanderbilt, PRB
> 41, 7892 (1990), the author suggested that "the pseudopotential itself
> must be updated as part of the self-consistent screening process". I
> wonder whether PWscf does this in the self-consistent iterations. If
> yes, where are the new pseudopotentials stored? Regarding to the
> non-local psedupotential, I guess, in the pp.x, the total potential
> V_bare+V_H + V_xc doesn't contain the non-local part V_NL, right?  Do
> the V_bare and local ionic potential refer to the same thing? Or what
> does the V_bare mean here?

pp.x plots the LOCAL part only, possibly adding Hartree and XC 
contributions. One cannot plot as function of r a nonlocal potential.

The NL part is defined by matrix D and projectors beta. IT IS updated in 
the scf cycle by PW/newd.f90 (variable deeq):
* projectors    are read from the pseudopotential file
* D^0    (unscreened D) as well
* D = D^0 + \int V Q dr   is computed by PW/newd.f90
Look at PRB 47, 10142 (1993), Laasonen, CPMD with Vanderbilt USPP in 
particular Eq. (13) and following note discussing the screening of D.

Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy

Phone: +39 02 6448 5214
email: fratesi at mater.unimib.it


From Francesco.Stellato at roma2.infn.it  Mon Mar 26 15:11:29 2007
From: Francesco.Stellato at roma2.infn.it (Francesco.Stellato at roma2.infn.it)
Date: Mon, 26 Mar 2007 15:11:29 +0200 (CEST)
Subject: [Pw_forum] Problem with pp.x
Message-ID: <41116.141.108.250.37.1174914689.squirrel@141.108.250.37>

Hi all,

when we tried to use pp.x after scf we met some problems.

the input_pp file is:

 &inputPP
    prefix='test_scf',
    outdir='/nfs_home/home0/molcp/velia/density_test/tmp_scf/',
    filplot='try_density',
    plot_num=7,
    kpoint=1,
    kband=79,
    lsign=.false.
 /

and the error is:

p6_17713:  p4_error: net_recv read:  probable EOF on socket: 1
rm_l_1_9870: (6.535927) net_send: could not write to fd=5, errno = 32
p4_17545:  p4_error: : 14
rm_l_4_17564: (4.264369) net_send: could not write to fd=5, errno = 32
p2_1649:  p4_error: : 14
rm_l_2_1668: (5.768784) net_send: could not write to fd=5, errno = 32
rm_l_5_17587: (3.528745) net_send: could not write to fd=5, errno = 32
rm_l_7_17755: (2.025592) net_send: could not write to fd=5, errno = 32
p2_1649: (13.780259) net_send: could not write to fd=5, errno = 32
p4_17545: (16.277382) net_send: could not write to fd=5, errno = 32
p1_9851: (18.548953) net_send: could not write to fd=5, errno = 32
p7_17736: (14.036573) net_send: could not write to fd=5, errno = 32
p6_17713: (14.769242) net_send: could not write to fd=5, errno = 32
p5_17568: (15.541136) net_send: could not write to fd=5, errno = 32

the input file for scf was:

&control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='test_scf',
    pseudo_dir = '/nfs_home/home0/molcp/espresso-3.0/pseudo/',
    outdir='tmp_scf/'
 /
 &system
    ibrav=0, nat=49, ntyp=5,
    nspin=1, nelec=159, nbnd=81,
    ecutwfc = 25.0, ecutrho = 200.0,
    occupations='from_input',
 /
 &electrons
    conv_thr =  1.0d-8,
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 C 12.01  C.pbe-rrkjus.UPF
 O 16.00  O.pbe-rrkjus.UPF
 N 14.01  N.pbe-rrkjus.UPF
 H 1.008  H.pbe-rrkjus.UPF
 Cu 63.54  Cu.pbe-d-rrkjus.UPF

ATOMIC_POSITIONS (angstrom)
H       13.048687135   5.346355322  10.977653086
C       12.566026597   6.326557370  10.966654622
H       12.411939015   6.654972557  12.004703275
H       13.240233934   7.047671386  10.481292067
C       11.251268793   6.204321534  10.219807284
O       10.870503680   5.139817746   9.711378941
N       10.508279932   7.341627200  10.153392499
H       10.851799312   8.265237196  10.439529139
C        9.278246390   7.384349378   9.393813447
H        9.390166625   6.713273454   8.528580432
C        8.069794071   6.889457087  10.241899349
H        8.452434666   6.441223687  11.168663227
H        7.457148193   7.759903727  10.528292424
C        7.219242223   5.888154094   9.549722730
N        6.680207486   6.104487363   8.289881371
C        5.993892227   5.011604056   7.963046398
H        5.458543361   4.858246263   7.032113723
N        6.072888857   4.106104365   8.964225756
H        5.649053164   3.186481812   8.963350003
C        6.845546044   4.638194209   9.974120387
H        7.098059531   4.073833804  10.862019564
C        9.068891453   8.830345900   8.908954804
O        9.749104797   9.746612790   9.437564822
N        8.152316580   8.997905139   7.950115018
C        7.995132917  10.328115369   7.382632331
H        8.968541449  10.801161043   7.171030809
H        7.496932087  11.025703602   8.078116333
C        7.185380471  10.297996368   6.087270636
O        6.952243927  11.329734586   5.422211538
N        6.752704598   9.067220941   5.756130388
C        5.932520964   8.876366609   4.588150955
H        6.496222695   9.012344672   3.641362293
H        5.095690122   9.601959120   4.536164452
C        5.387009510   7.461243923   4.631981063
O        5.720175774   6.662380948   5.537036403
N        4.501529641   7.071815577   3.690779473
H        4.285677746   7.691196720   2.914894886
C        3.992181275   5.721050851   3.682877910
H        3.093615439   5.672165591   3.049867744
H        3.688195251   5.457860111   4.707536993
C        5.024189371   4.691823890   3.178605788
O        6.021166121   5.008436877   2.538427033
N        4.700692577   3.405556878   3.489957243
H        3.896777355   3.165643506   4.057750735
H        5.318127309   2.659025040   3.187038428
Cu       7.014314620   7.623849931   7.009113480
O        8.796334955   6.287066861   5.780335454
H        9.736719137   6.325259373   6.039985386
H        8.774144625   6.615269176   4.860974877

CELL_PARAMETERS
28.400705 0.000000 0.000000
0.000000 25.825008 0.000000
0.000000 0.000000 27.283877

K_POINTS {Gamma}

OCCUPATIONS
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0
0.0


maybe some inconsistencies between scf and pp input files?
Thanks,

Velia e Francesco



--------------------------------------------------

Dr. Francesco Stellato
Dip. di Fisica
Universit? di Roma Tor Vergata
Via della Ricerca Scientifica, 1
I-00133 Rome Italy

Email: francesco.stellato at roma2.infn.it





--------------------------------------------------

Dr. Francesco Stellato
Dip. di Fisica
Universit? di Roma Tor Vergata
Via della Ricerca Scientifica, 1
I-00133 Rome Italy

Email: francesco.stellato at roma2.infn.it


From degironc at sissa.it  Mon Mar 26 16:05:17 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 26 Mar 2007 16:05:17 +0200 (CEST)
Subject: [Pw_forum] Problem with pp.x
In-Reply-To: <41116.141.108.250.37.1174914689.squirrel@141.108.250.37>
References: <41116.141.108.250.37.1174914689.squirrel@141.108.250.37>
Message-ID: <Pine.LNX.4.64.0703261604020.4929@shannon-02.sissa.it>

Are you using the same location for outdir in the two runs ?
It's not evidently so from your input.
stefano

On Mon, 26 Mar 2007, Francesco.Stellato at roma2.infn.it wrote:

> Hi all,
>
> when we tried to use pp.x after scf we met some problems.
>
> the input_pp file is:
>
> &inputPP
>    prefix='test_scf',
>    outdir='/nfs_home/home0/molcp/velia/density_test/tmp_scf/',
>    filplot='try_density',
>    plot_num=7,
>    kpoint=1,
>    kband=79,
>    lsign=.false.
> /
>
> and the error is:
>
> p6_17713:  p4_error: net_recv read:  probable EOF on socket: 1
> rm_l_1_9870: (6.535927) net_send: could not write to fd=5, errno = 32
> p4_17545:  p4_error: : 14
> rm_l_4_17564: (4.264369) net_send: could not write to fd=5, errno = 32
> p2_1649:  p4_error: : 14
> rm_l_2_1668: (5.768784) net_send: could not write to fd=5, errno = 32
> rm_l_5_17587: (3.528745) net_send: could not write to fd=5, errno = 32
> rm_l_7_17755: (2.025592) net_send: could not write to fd=5, errno = 32
> p2_1649: (13.780259) net_send: could not write to fd=5, errno = 32
> p4_17545: (16.277382) net_send: could not write to fd=5, errno = 32
> p1_9851: (18.548953) net_send: could not write to fd=5, errno = 32
> p7_17736: (14.036573) net_send: could not write to fd=5, errno = 32
> p6_17713: (14.769242) net_send: could not write to fd=5, errno = 32
> p5_17568: (15.541136) net_send: could not write to fd=5, errno = 32
>
> the input file for scf was:
>
> &control
>    calculation='scf'
>    restart_mode='from_scratch',
>    prefix='test_scf',
>    pseudo_dir = '/nfs_home/home0/molcp/espresso-3.0/pseudo/',
>    outdir='tmp_scf/'
> /
> &system
>    ibrav=0, nat=49, ntyp=5,
>    nspin=1, nelec=159, nbnd=81,
>    ecutwfc = 25.0, ecutrho = 200.0,
>    occupations='from_input',
> /
> &electrons
>    conv_thr =  1.0d-8,
>    mixing_beta = 0.7
> /
> ATOMIC_SPECIES
> C 12.01  C.pbe-rrkjus.UPF
> O 16.00  O.pbe-rrkjus.UPF
> N 14.01  N.pbe-rrkjus.UPF
> H 1.008  H.pbe-rrkjus.UPF
> Cu 63.54  Cu.pbe-d-rrkjus.UPF
>
> ATOMIC_POSITIONS (angstrom)
> H       13.048687135   5.346355322  10.977653086
> C       12.566026597   6.326557370  10.966654622
> H       12.411939015   6.654972557  12.004703275
> H       13.240233934   7.047671386  10.481292067
> C       11.251268793   6.204321534  10.219807284
> O       10.870503680   5.139817746   9.711378941
> N       10.508279932   7.341627200  10.153392499
> H       10.851799312   8.265237196  10.439529139
> C        9.278246390   7.384349378   9.393813447
> H        9.390166625   6.713273454   8.528580432
> C        8.069794071   6.889457087  10.241899349
> H        8.452434666   6.441223687  11.168663227
> H        7.457148193   7.759903727  10.528292424
> C        7.219242223   5.888154094   9.549722730
> N        6.680207486   6.104487363   8.289881371
> C        5.993892227   5.011604056   7.963046398
> H        5.458543361   4.858246263   7.032113723
> N        6.072888857   4.106104365   8.964225756
> H        5.649053164   3.186481812   8.963350003
> C        6.845546044   4.638194209   9.974120387
> H        7.098059531   4.073833804  10.862019564
> C        9.068891453   8.830345900   8.908954804
> O        9.749104797   9.746612790   9.437564822
> N        8.152316580   8.997905139   7.950115018
> C        7.995132917  10.328115369   7.382632331
> H        8.968541449  10.801161043   7.171030809
> H        7.496932087  11.025703602   8.078116333
> C        7.185380471  10.297996368   6.087270636
> O        6.952243927  11.329734586   5.422211538
> N        6.752704598   9.067220941   5.756130388
> C        5.932520964   8.876366609   4.588150955
> H        6.496222695   9.012344672   3.641362293
> H        5.095690122   9.601959120   4.536164452
> C        5.387009510   7.461243923   4.631981063
> O        5.720175774   6.662380948   5.537036403
> N        4.501529641   7.071815577   3.690779473
> H        4.285677746   7.691196720   2.914894886
> C        3.992181275   5.721050851   3.682877910
> H        3.093615439   5.672165591   3.049867744
> H        3.688195251   5.457860111   4.707536993
> C        5.024189371   4.691823890   3.178605788
> O        6.021166121   5.008436877   2.538427033
> N        4.700692577   3.405556878   3.489957243
> H        3.896777355   3.165643506   4.057750735
> H        5.318127309   2.659025040   3.187038428
> Cu       7.014314620   7.623849931   7.009113480
> O        8.796334955   6.287066861   5.780335454
> H        9.736719137   6.325259373   6.039985386
> H        8.774144625   6.615269176   4.860974877
>
> CELL_PARAMETERS
> 28.400705 0.000000 0.000000
> 0.000000 25.825008 0.000000
> 0.000000 0.000000 27.283877
>
> K_POINTS {Gamma}
>
> OCCUPATIONS
> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0
> 0.0
>
>
> maybe some inconsistencies between scf and pp input files?
> Thanks,
>
> Velia e Francesco
>
>
>
> --------------------------------------------------
>
> Dr. Francesco Stellato
> Dip. di Fisica
> Universit? di Roma Tor Vergata
> Via della Ricerca Scientifica, 1
> I-00133 Rome Italy
>
> Email: francesco.stellato at roma2.infn.it
>
>
>
>
>
> --------------------------------------------------
>
> Dr. Francesco Stellato
> Dip. di Fisica
> Universit? di Roma Tor Vergata
> Via della Ricerca Scientifica, 1
> I-00133 Rome Italy
>
> Email: francesco.stellato at roma2.infn.it
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From velia.minicozzi at roma2.infn.it  Mon Mar 26 16:38:48 2007
From: velia.minicozzi at roma2.infn.it (Velia Minicozzi)
Date: Mon, 26 Mar 2007 16:38:48 +0200 (CEST)
Subject: [Pw_forum] Problem with pp.x
In-Reply-To: <Pine.LNX.4.64.0703261604020.4929@shannon-02.sissa.it>
References: <41116.141.108.250.37.1174914689.squirrel@141.108.250.37>
    <Pine.LNX.4.64.0703261604020.4929@shannon-02.sissa.it>
Message-ID: <52936.141.108.253.74.1174919928.squirrel@141.108.253.74>

Yes, it is the same location because the file scf.in is in
/nfs_home/home0/molcp/velia/density_test
and writes in subdir tmp_scf/

in pp.in we only wrote the total path for outdir.

So, I don't think this is the problem.

velia

On Mon, March 26, 2007 4:05 pm, Stefano de Gironcoli said:
> Are you using the same location for outdir in the two runs ?
> It's not evidently so from your input.
> stefano
>
> On Mon, 26 Mar 2007, Francesco.Stellato at roma2.infn.it wrote:
>
>> Hi all,
>>
>> when we tried to use pp.x after scf we met some problems.
>>
>> the input_pp file is:
>>
>> &inputPP
>>    prefix='test_scf',
>>    outdir='/nfs_home/home0/molcp/velia/density_test/tmp_scf/',
>>    filplot='try_density',
>>    plot_num=7,
>>    kpoint=1,
>>    kband=79,
>>    lsign=.false.
>> /
>>
>> and the error is:
>>
>> p6_17713:  p4_error: net_recv read:  probable EOF on socket: 1
>> rm_l_1_9870: (6.535927) net_send: could not write to fd=5, errno = 32
>> p4_17545:  p4_error: : 14
>> rm_l_4_17564: (4.264369) net_send: could not write to fd=5, errno = 32
>> p2_1649:  p4_error: : 14
>> rm_l_2_1668: (5.768784) net_send: could not write to fd=5, errno = 32
>> rm_l_5_17587: (3.528745) net_send: could not write to fd=5, errno = 32
>> rm_l_7_17755: (2.025592) net_send: could not write to fd=5, errno = 32
>> p2_1649: (13.780259) net_send: could not write to fd=5, errno = 32
>> p4_17545: (16.277382) net_send: could not write to fd=5, errno = 32
>> p1_9851: (18.548953) net_send: could not write to fd=5, errno = 32
>> p7_17736: (14.036573) net_send: could not write to fd=5, errno = 32
>> p6_17713: (14.769242) net_send: could not write to fd=5, errno = 32
>> p5_17568: (15.541136) net_send: could not write to fd=5, errno = 32
>>
>> the input file for scf was:
>>
>> &control
>>    calculation='scf'
>>    restart_mode='from_scratch',
>>    prefix='test_scf',
>>    pseudo_dir = '/nfs_home/home0/molcp/espresso-3.0/pseudo/',
>>    outdir='tmp_scf/'
>> /
>> &system
>>    ibrav=0, nat=49, ntyp=5,
>>    nspin=1, nelec=159, nbnd=81,
>>    ecutwfc = 25.0, ecutrho = 200.0,
>>    occupations='from_input',
>> /
>> &electrons
>>    conv_thr =  1.0d-8,
>>    mixing_beta = 0.7
>> /
>> ATOMIC_SPECIES
>> C 12.01  C.pbe-rrkjus.UPF
>> O 16.00  O.pbe-rrkjus.UPF
>> N 14.01  N.pbe-rrkjus.UPF
>> H 1.008  H.pbe-rrkjus.UPF
>> Cu 63.54  Cu.pbe-d-rrkjus.UPF
>>
>> ATOMIC_POSITIONS (angstrom)
>> H       13.048687135   5.346355322  10.977653086
>> C       12.566026597   6.326557370  10.966654622
>> H       12.411939015   6.654972557  12.004703275
>> H       13.240233934   7.047671386  10.481292067
>> C       11.251268793   6.204321534  10.219807284
>> O       10.870503680   5.139817746   9.711378941
>> N       10.508279932   7.341627200  10.153392499
>> H       10.851799312   8.265237196  10.439529139
>> C        9.278246390   7.384349378   9.393813447
>> H        9.390166625   6.713273454   8.528580432
>> C        8.069794071   6.889457087  10.241899349
>> H        8.452434666   6.441223687  11.168663227
>> H        7.457148193   7.759903727  10.528292424
>> C        7.219242223   5.888154094   9.549722730
>> N        6.680207486   6.104487363   8.289881371
>> C        5.993892227   5.011604056   7.963046398
>> H        5.458543361   4.858246263   7.032113723
>> N        6.072888857   4.106104365   8.964225756
>> H        5.649053164   3.186481812   8.963350003
>> C        6.845546044   4.638194209   9.974120387
>> H        7.098059531   4.073833804  10.862019564
>> C        9.068891453   8.830345900   8.908954804
>> O        9.749104797   9.746612790   9.437564822
>> N        8.152316580   8.997905139   7.950115018
>> C        7.995132917  10.328115369   7.382632331
>> H        8.968541449  10.801161043   7.171030809
>> H        7.496932087  11.025703602   8.078116333
>> C        7.185380471  10.297996368   6.087270636
>> O        6.952243927  11.329734586   5.422211538
>> N        6.752704598   9.067220941   5.756130388
>> C        5.932520964   8.876366609   4.588150955
>> H        6.496222695   9.012344672   3.641362293
>> H        5.095690122   9.601959120   4.536164452
>> C        5.387009510   7.461243923   4.631981063
>> O        5.720175774   6.662380948   5.537036403
>> N        4.501529641   7.071815577   3.690779473
>> H        4.285677746   7.691196720   2.914894886
>> C        3.992181275   5.721050851   3.682877910
>> H        3.093615439   5.672165591   3.049867744
>> H        3.688195251   5.457860111   4.707536993
>> C        5.024189371   4.691823890   3.178605788
>> O        6.021166121   5.008436877   2.538427033
>> N        4.700692577   3.405556878   3.489957243
>> H        3.896777355   3.165643506   4.057750735
>> H        5.318127309   2.659025040   3.187038428
>> Cu       7.014314620   7.623849931   7.009113480
>> O        8.796334955   6.287066861   5.780335454
>> H        9.736719137   6.325259373   6.039985386
>> H        8.774144625   6.615269176   4.860974877
>>
>> CELL_PARAMETERS
>> 28.400705 0.000000 0.000000
>> 0.000000 25.825008 0.000000
>> 0.000000 0.000000 27.283877
>>
>> K_POINTS {Gamma}
>>
>> OCCUPATIONS
>> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
>> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
>> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
>> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
>> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
>> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
>> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
>> 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 1.0
>> 0.0
>>
>>
>> maybe some inconsistencies between scf and pp input files?
>> Thanks,
>>
>> Velia e Francesco
>>
>>
>>
>> --------------------------------------------------
>>
>> Dr. Francesco Stellato
>> Dip. di Fisica
>> Universit? di Roma Tor Vergata
>> Via della Ricerca Scientifica, 1
>> I-00133 Rome Italy
>>
>> Email: francesco.stellato at roma2.infn.it
>>
>>
>>
>>
>>
>> --------------------------------------------------
>>
>> Dr. Francesco Stellato
>> Dip. di Fisica
>> Universit? di Roma Tor Vergata
>> Via della Ricerca Scientifica, 1
>> I-00133 Rome Italy
>>
>> Email: francesco.stellato at roma2.infn.it
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>


*********************************
Velia Minicozzi
Department of Physics
University of Rome "Tor Vergata"
Via della Ricerca Scientifica, 1
00133 Rome - Italy
tel. +39 06 72594554
fax. +39 06 2023507
*********************************


From cao at qtp.ufl.edu  Tue Mar 27 01:03:11 2007
From: cao at qtp.ufl.edu (Chao Cao)
Date: Mon, 26 Mar 2007 19:03:11 -0400
Subject: [Pw_forum] Does anyone have RRKJ uspp for Cr?
Message-ID: <4608512F.6000100@qtp.ufl.edu>

As title. I have tried to generate the pseudopotential myself, but it 
seems to be way too complicated. It kept complaining about stuff like:


             integrated core pseudo-charge :   5.66
     from compute phi : info #        -1
     negative determinant

         1 ld=   0.518427 f2ae  0.606247 faenor  0.141808

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from gener_pseudo : error #         1
     too many nodes
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...


Thanks a lot.

Chao Cao


From yaoxinxin at mail.sdu.edu.cn  Tue Mar 27 03:39:07 2007
From: yaoxinxin at mail.sdu.edu.cn (=?gb2312?B?0qbQwtDA?=)
Date: Tue, 27 Mar 2007 09:39:07 +0800
Subject: [Pw_forum] projwfc.x
Message-ID: <374959547.28501@mail.sdu.edu.cn>

Dear users:
  I got a problem when using projwfc.x .
  At first, I calculated "vc-relax" for Ge62Mn2 system. Then I did the
post-process dos.x and projwfc.x . For two different structures--two Mn atoms at
nearest or farthest distances, the scale of output of dos.x is approximate to each
other , and the maximum dos is about 30. But the scale of output of projwfc.x is
significantly different. For the farthest distance structure, the maximum dos of
Mn3d is about 15, which seems to be reasonable, whearas for 
the nearest distance structure, the maximum dos of Mn3d is only about 0.1 . Why
did this happen?

Best regards.

Xinxin Yao




From rui_zhi_zhang at yahoo.com  Tue Mar 27 05:22:32 2007
From: rui_zhi_zhang at yahoo.com (ruizhi zhang)
Date: Mon, 26 Mar 2007 20:22:32 -0700 (PDT)
Subject: [Pw_forum] Oscillation behavior for structure optimization
In-Reply-To: <OF88564805.87BA509C-ON492572A6.0002FFDD-492572A6.0003B7F0@mta.fujifilm.co.jp>
Message-ID: <334670.14963.qm@web39801.mail.mud.yahoo.com>

hi okuno
   
  I can not slove your problem because I am a beginer as you are. But I have another way to get a monoclinic phase PZT. The input&outfile are attached below. By the way, I do not think it is correct to fix z-coordinate, because you perhaps will not get a 'groud state'.
  Hope this helps
   
  Best regards
  ruizhi

   
  INPUT:
   &control
    calculation  = 'relax'
    restart_mode = 'from_scratch'
    prefix = 'pzt.mono.rl'
    pseudo_dir   = '/'
    outdir       = '/'
 /
 &system
    ibrav=0
    celldm(1)=7.73
    nat=20
    ntyp=4
    ecutwfc=30.0
    occupations = 'fixed'
 /
 &electrons
    conv_thr = 1e-8,
    mixing_beta=0.3,
 /
 &IONS
   /
ATOMIC_SPECIES
  Pb    207.2      Pb.vdb.UPF
  Ti    47.867     Ti.vdb.UPF
  Zr    91.22      Zr.vdb.UPF
  O     15.9994    O.vdb.UPF
ATOMIC_POSITIONS
Pb      0.0     0.0     0.0
Zr      0.485   0.485   0.47
O       0.0     0.5     0.5
O       0.5     0.0     0.5
O       0.5     0.5     0.0
Pb      0.0     1.0     0.0
Ti      0.485   1.485   0.47
O       0.0     1.5     0.5
O       0.5     1.0     0.5
O       0.5     1.5     0.0
Pb      0.0     0.0     1.0
Ti      0.485   0.485   1.47
O       0.0     0.5     1.5
O       0.5     0.0     1.5
O       0.5     0.5     1.0
Pb      0.0     1.0     1.0
Zr      0.485   1.485   1.47
O       0.0     1.5     1.5
O       0.5     1.0     1.5
O       0.5     1.5     1.0
K_POINTS {automatic}
  4 2 2 0 0 0
CELL_PARAMETERS
      1  0  0
      0  2  0
      0  0  2

  OUTPUT,this is a monoclinic phase PZT
  ATOMIC_POSITIONS (alat)
Pb      -0.074746117  -0.054391084  -0.052737416
Zr       0.475968064   0.476554616   0.469572490
O       -0.002812771   0.540060157   0.546351440
O        0.538456743  -0.005360148   0.524405291
O        0.538229142   0.529414476  -0.011303199
Pb      -0.060631754   0.929474660  -0.080635128
Ti       0.461835759   1.468464184   0.467563250
O        0.029392570   1.525039365   0.520132029
O        0.532671091   1.026126063   0.530617774
O        0.531637274   1.534617711   0.026033468
Pb      -0.060631754  -0.070525340   0.919364872
Ti       0.461835759   0.468464184   1.467563250
O        0.029392570   0.525039365   1.520132029
O        0.532671091   0.026126063   1.530617774
O        0.531637274   0.534617711   1.026033468
Pb      -0.074746117   0.945608916   0.947262584
Zr       0.475968064   1.476554616   1.469572490
O       -0.002812771   1.540060157   1.546351440
O        0.538456743   0.994639852   1.524405291
O        0.538229142   1.529414476   0.988696801

   
  
yukihiro_okuno at fujifilm.co.jp wrote:
  
Dear PWscf Users.

I'm now calculating the structure optimization for
monoclinic structure of PZT ( put a little shere stress for
tetragonal structure).

But the calculation is not conversed and the Total force
is oscillate like below, and this does not happen for tetragonal case.)

Total force = 0.029288 Total SCF correction = 0.000028
Total force = 0.610879 Total SCF correction = 0.000006
Total force = 0.031826 Total SCF correction = 0.000017
Total force = 0.017717 Total SCF correction = 0.000010
Total force = 0.006548 Total SCF correction = 0.000009
Total force = 0.004523 Total SCF correction = 0.000024
Total force = 0.002241 Total SCF correction = 0.000004
Total force = 0.001565 Total SCF correction = 0.000008
Total force = 0.001102 Total SCF correction = 0.000005
Total force = 0.001312 Total SCF correction = 0.000010
Total force = 0.001605 Total SCF correction = 0.000009
Total force = 0.001865 Total SCF correction = 0.000006
Total force = 0.002391 Total SCF correction = 0.000005
Total force = 0.002574 Total SCF correction = 0.000005
Total force = 0.001872 Total SCF correction = 0.000008
Total force = 0.001495 Total SCF correction = 0.000006
Total force = 0.001430 Total SCF correction = 0.000005
Total force = 0.001529 Total SCF correction = 0.000003
Total force = 0.001736 Total SCF correction = 0.000004
Total force = 0.002315 Total SCF correction = 0.000004
Total force = 0.002271 Total SCF correction = 0.000008
Total force = 0.001826 Total SCF correction = 0.000008
Total force = 0.001623 Total SCF correction = 0.000004
Total force = 0.001605 Total SCF correction = 0.000007
Total force = 0.001720 Total SCF correction = 0.000006
Total force = 0.002129 Total SCF correction = 0.000003
Total force = 0.002290 Total SCF correction = 0.000007
Total force = 0.002437 Total SCF correction = 0.000006
Total force = 0.002619 Total SCF correction = 0.000006
Total force = 0.002860 Total SCF correction = 0.000007
Total force = 0.003199 Total SCF correction = 0.000006
Total force = 0.003772 Total SCF correction = 0.000006


My input file is like below and how should we treat such a trouble?

&control
calculation = 'relax',
restart_mode = 'from_scratch',
pseudo_dir = '/home/okuno/PWSCF/espresso-3.2/pseudo/',
outdir = './',
prefix='PZT'
forc_conv_thr = 1.0D-4
/
&system
ibrav=12
celldm(1)=7.57696068724
celldm(2)=2.09
celldm(3)=1.00
celldm(4)=0.00499993750117
nat=10
ntyp=4
nbnd=44
ecutwfc=60.0
ecutrho = 600.0
occupations = 'fixed'
degauss=0.00
/
&electrons
conv_thr = 1e-10,
mixing_beta=0.3,
/
&IONS
ion_dynamics='bfgs'
bfgs_ndim=3
pot_extrapolation = "second_order"
wfc_extrapolation = "second_order"
trust_radius_min=1.0D-4
/
ATOMIC_SPECIES
Pb 207.2 pb_ps.uspp.UPF
Zr 91.224 zr_ps.uspp.UPF
Ti 47.867 ti_ps.uspp.UPF
O 15.9994 o_ps.uspp.UPF
ATOMIC_POSITIONS {crystal}
Pb 0.0 0.00000 0.0 1 1 0
Pb 0.0 0.53106 0.0 1 1 0
Zr 0.5 0.24462 0.5 1 1 0
Ti 0.5 0.74062 0.5 1 1 0
O 0.5 0.95432 0.5 1 1 0
O 0.5 0.48072 0.5 1 1 0
O 0.5 0.19090 0.0 1 1 0
O 0.0 0.19090 0.5 1 1 0
O 0.5 0.71336 0.0 1 1 0
O 0.0 0.71336 0.5 1 1 0
K_POINTS {automatic}
6 6 6 0 0 0







,

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From degironc at sissa.it  Tue Mar 27 08:29:27 2007
From: degironc at sissa.it (degironc)
Date: Tue, 27 Mar 2007 08:29:27 +0200
Subject: [Pw_forum] Does anyone have RRKJ uspp for Cr?
In-Reply-To: <4608512F.6000100@qtp.ufl.edu>
References: <4608512F.6000100@qtp.ufl.edu>
Message-ID: <4608B9C7.5040907@sissa.it>

I don't have any..
I hope this info from the adomic_doc/INPUT_LD1 file might be useful:
       rho0 = charge at the origin: when the Rabe-Rappe-Kaxiras-Joannopoulos
             method with 3 Bessel functions fails, specifying rho0 > 0
             may allow to override the problem (using 4 Bessel functions)
             Typical values are in the order of 0.01-0.02       (default 
0.0)
 
best, stefano

Chao Cao wrote:

> As title. I have tried to generate the pseudopotential myself, but it 
> seems to be way too complicated. It kept complaining about stuff like:
>
>
>             integrated core pseudo-charge :   5.66
>     from compute phi : info #        -1
>     negative determinant
>
>         1 ld=   0.518427 f2ae  0.606247 faenor  0.141808
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
>
>     from gener_pseudo : error #         1
>     too many nodes
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
>
>
>     stopping ...
>
>
> Thanks a lot.
>
> Chao Cao
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum




From marzari at MIT.EDU  Tue Mar 27 09:32:12 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 27 Mar 2007 03:32:12 -0400
Subject: [Pw_forum] Does anyone have RRKJ uspp for Cr?
In-Reply-To: <4608B9C7.5040907@sissa.it>
References: <4608512F.6000100@qtp.ufl.edu> <4608B9C7.5040907@sissa.it>
Message-ID: <4608C87C.7060508@mit.edu>


Another possibility is to generate a Cr using David Vanderbilt
code: http://www.physics.rutgers.edu/~dhv/uspp/ , and then convert it
to UPF format.

There is an input file there for a PW91 Cr that looks good.

				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


From giannozz at nest.sns.it  Tue Mar 27 09:43:18 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 27 Mar 2007 09:43:18 +0200
Subject: [Pw_forum] Problem with pp.x
In-Reply-To: <41116.141.108.250.37.1174914689.squirrel@141.108.250.37>
References: <41116.141.108.250.37.1174914689.squirrel@141.108.250.37>
Message-ID: <70BB7889-9B07-46E0-A078-84022D86F3F6@nest.sns.it>

On Mar 26, 2007, at 15:11 , Francesco.Stellato at roma2.infn.it wrote:

>     outdir='/nfs_home/home0/molcp/velia/density_test/tmp_scf/'

do not write to nfs-mounted file system: it is a recipe for disaster

> p6_17713:  p4_error: net_recv read:  probable EOF on socket: 1
> rm_l_1_9870: (6.535927) net_send: could not write to fd=5, errno = 32

it looks like an error while writing to unit 5. Errors like this,
occurring in system library calls, are impossible to pinpoint
unless one finds under which exact circumstances it occurs,
whether it is reproducible or not, and so on and so forth.
They are more often a sign of problems with mpi or the
filesystem or both rather than in the code itself

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




From giannozz at nest.sns.it  Tue Mar 27 10:03:04 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 27 Mar 2007 10:03:04 +0200
Subject: [Pw_forum] masses and dt in vc-relax
In-Reply-To: <1d9d5d9d0703251105p9831ed9q7503ac1f0b549d85@mail.gmail.com>
References: <1d9d5d9d0703251105p9831ed9q7503ac1f0b549d85@mail.gmail.com>
Message-ID: <FE785C57-A512-41C6-B192-18C94E346C49@nest.sns.it>

On Mar 25, 2007, at 20:05 , Jess Kondor wrote:

> Does it mean that I cannot use the settings from the small system
> and apply them for bigger system?

larger systems typically have more convergence problems than
small systems, so they might need a smaller time step

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




From giannozz at nest.sns.it  Tue Mar 27 10:07:24 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 27 Mar 2007 10:07:24 +0200
Subject: [Pw_forum] Aluminium EPC at X
In-Reply-To: <aef8bbf00703251058n608dda09o1f454714c2afe0d5@mail.gmail.com>
References: <aef8bbf00703251058n608dda09o1f454714c2afe0d5@mail.gmail.com>
Message-ID: <DA6AEC28-6697-4787-89B9-5C030B240A30@nest.sns.it>

On Mar 25, 2007, at 19:58 , Amit Kumar wrote:

> I'm very much confused with the results of the electron-phonon  
> coupling
> of Aluminium  at X-point.  You can see a large discrepancy in the  
> results
> of Example  No. 7.

>    Old version ::::
>       Gaussian Broadening:   0.010 Ry, ngauss=   1
> [...]
>     Newer  Version  :::::::::
>       Gaussian Broadening:   0.010 Ry, ngauss=   0

would you mind reading the answer that you get before
asking new questions, or more exactly, the same question?
---
Paolo Giannozzi, Democritos and University of Udine, Italy




From giannozz at nest.sns.it  Tue Mar 27 10:10:10 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 27 Mar 2007 10:10:10 +0200
Subject: [Pw_forum] spilling parameter in Lowdin - how to assign the charge that went into Nirvana ?
In-Reply-To: <Pine.LNX.4.58.0703241521310.14388@bamboo.fisica.unimo.it>
References: <851319.42244.qm@web57701.mail.re3.yahoo.com> <Pine.LNX.4.58.0703241521310.14388@bamboo.fisica.unimo.it>
Message-ID: <2A0AF24D-13E9-4EC1-8CD6-EA9763C6666E@nest.sns.it>

On Mar 24, 2007, at 15:54 , Andrea Ferretti wrote:

> Lowding orbitals in Quantum-Espresso (at least as far as I know) are
> computed from the atomic reference states from pseudopotential data
> according to:
>
> S_ij = < i | j >      are the overlaps of atomic orbitals i and j
>
> lowding orbitals are then obtained as
> | low_i > =  R_ij  | j >
>
> where  R = S^{-1/2}
>
> so I think there is no optimization (in the sense of the paper above)
> but maybe I am missing something

no, you aren't missing anything: the atomic basis is not optimized

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




From ezadshojaee at hotmail.com  Tue Mar 27 12:25:49 2007
From: ezadshojaee at hotmail.com (Ezad Shojaee)
Date: Tue, 27 Mar 2007 10:25:49 +0000
Subject: [Pw_forum] grid without symmtrical problem
Message-ID: <BAY101-F11B0C2EADB3F39FE5963EBAA6E0@phx.gbl>

hi
is it possible to define a grid with non-equal numbers for ph.x not to have 
problem with q2r.x ? because i tried sample 221 and q2r.x  gave symmetrical 
error;  while there was no error with 222 sample.
is there a way what is it?
thanx

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From hyello25 at gmail.com  Tue Mar 27 13:39:36 2007
From: hyello25 at gmail.com (hyello25 Qgrui)
Date: Tue, 27 Mar 2007 19:39:36 +0800
Subject: [Pw_forum] (no subject)
Message-ID: <a44e04ef0703270439s95d18abpd769b9226136cb35@mail.gmail.com>

hyello25 at gmail.com
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From degironc at sissa.it  Tue Mar 27 15:14:28 2007
From: degironc at sissa.it (degironc)
Date: Tue, 27 Mar 2007 15:14:28 +0200
Subject: [Pw_forum] grid without symmtrical problem
In-Reply-To: <BAY101-F11B0C2EADB3F39FE5963EBAA6E0@phx.gbl>
References: <BAY101-F11B0C2EADB3F39FE5963EBAA6E0@phx.gbl>
Message-ID: <460918B4.70800@sissa.it>

The grid should have the symmetry of your system.
Therefore it depends on the system.
stefano

Ezad Shojaee wrote:

> hi
> is it possible to define a grid with non-equal numbers for ph.x not to 
> have problem with q2r.x ? because i tried sample 221 and q2r.x  gave 
> symmetrical error;  while there was no error with 222 sample.
> is there a way what is it?
> thanx
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's 
> FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum




From giannozz at nest.sns.it  Tue Mar 27 15:21:53 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 27 Mar 2007 15:21:53 +0200
Subject: [Pw_forum] Inconsistent pp.x and projwfc.x results?
In-Reply-To: <34711.141.108.248.231.1174673659.squirrel@141.108.248.231>
References: <34711.141.108.248.231.1174673659.squirrel@141.108.248.231>
Message-ID: <0B9C96EE-8FAF-4665-B862-52E580870400@nest.sns.it>

On Mar 23, 2007, at 19:14 , Conor Hogan wrote:

> Basically the character of the states produced by projwfc.x (atomic
> projection) and pp.x (plotting the state directly) differ in the  
> case I'm
> studying

one thing to try is to re-do the calculation using k=(0,0,0)
instead of 'Gamma tricks'. It should work in both cases,
but who knows. If this is the problem, it should show up
even in much smaller calculations

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




From giannozz at nest.sns.it  Tue Mar 27 15:39:26 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 27 Mar 2007 15:39:26 +0200
Subject: [Pw_forum] calculation crash
In-Reply-To: <c92002fa0703220553g4890811btb90143706b299db4@mail.gmail.com>
References: <c92002fa0703220553g4890811btb90143706b299db4@mail.gmail.com>
Message-ID: <E17E4A92-23DF-427C-8709-92B462DD48ED@nest.sns.it>

On Mar 22, 2007, at 13:53 , lan haiping wrote:

>      from  fft_dlay_set  : error #         7
>       inconsistent number of sticks

very strange. Try to run the job in serial execution and see
what happens

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




From giannozz at nest.sns.it  Tue Mar 27 16:19:50 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 27 Mar 2007 16:19:50 +0200
Subject: [Pw_forum] Is the CG diagonalization suitable for the general matrix?
In-Reply-To: <017801c76b05$edacecd0$6400a8c0@HLHXQ>
References: <017801c76b05$edacecd0$6400a8c0@HLHXQ>
Message-ID: <397E416C-4473-4C3D-90A3-52C6CBA022E7@nest.sns.it>


On Mar 20, 2007, at 16:39 , xqhu at duke.edu wrote:

> I'm trying to implement PZ-SIC in PWSCF.

good luck!

> In PZ-SIC, the Fock matrix is not symmetric any more.
> I can not use DIIS or Davidson since both of them are
> for the hermitian matrix. I checked CG codes. It seems
> that CG can be used in the general matrix. If you are familiar
> with the CG diagonalization, please tell me some details.

all I know is written here

Paolo

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



From baroni at sissa.it  Tue Mar 27 18:03:30 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 28 Mar 2007 00:03:30 +0800
Subject: [Pw_forum] Is the CG diagonalization suitable for the general matrix?
In-Reply-To: <397E416C-4473-4C3D-90A3-52C6CBA022E7@nest.sns.it>
References: <017801c76b05$edacecd0$6400a8c0@HLHXQ> <397E416C-4473-4C3D-90A3-52C6CBA022E7@nest.sns.it>
Message-ID: <CAF3381C-EE70-4282-8EE0-97A32DA3725A@sissa.it>

You may also want to check Scuseria's paper on TDDFT (journal of  
Chemical Physics, Vol.109, No.19, 8218-8224, 1998), where a variant  
of the Davidson's method for which applies to non-hermitean matrices  
is presented. Stefano

On Mar 27, 2007, at 10:19 PM, Paolo Giannozzi wrote:

>
> On Mar 20, 2007, at 16:39 , xqhu at duke.edu wrote:
>
>> I'm trying to implement PZ-SIC in PWSCF.
>
> good luck!
>
>> In PZ-SIC, the Fock matrix is not symmetric any more.
>> I can not use DIIS or Davidson since both of them are
>> for the hermitian matrix. I checked CG codes. It seems
>> that CG can be used in the general matrix. If you are familiar
>> with the CG diagonalization, please tell me some details.
>
> all I know is written here
>
> Paolo
>
> <diago.tex>
> <diago_us.tex>
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From chen_shao_hua197 at yahoo.com.tw  Tue Mar 27 19:47:32 2007
From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=)
Date: Wed, 28 Mar 2007 01:47:32 +0800 (CST)
Subject: [Pw_forum] warings in scf.out
Message-ID: <520917.61184.qm@web73009.mail.tp2.yahoo.com>

Dear members,

In scf.out , it shows some waring as below:


     Ultrasoft (Vanderbilt) Pseudopotentials

     Current dimensions of program pwscf are:

     ntypx = 10   npk = 40000  lmax =  3
     nchix =  6  ndmx =  2000  nbrx = 14  nqfx =  8
     warning: symmetry operation #  2 not allowed.  
fractional translation:
       0.3333333 -0.3333333 -0.5000000  in crystal
coordinates
     warning: symmetry operation #  5 not allowed.  
fractional translation:
       0.3333333 -0.3333333 -0.5000000  in crystal
coordinates
     warning: symmetry operation #  6 not allowed.  
fractional translation:
       0.3333333 -0.3333333 -0.5000000  in crystal
coordinates
     warning: symmetry operation # 15 not allowed.  
fractional translation:
       0.3333333 -0.3333333 -0.5000000  in crystal
coordinates


How to solve these warings ?

The cell structure in "scf.in" is
 ibrav =4 , celldm(1) =6.261,celldm(3) = 1.61,
          nat = 4,  ntyp = 2, ecutwfc = 30.0,

ATOMIC_POSITIONS  {crystal}
in       0.000000000   0.000000000  -0.000355437
in       0.666666667   0.333333333   0.499644563
n        0.000000000   0.000000000   0.377862274
n        0.666666667   0.333333333   0.877862274
K_POINTS {automatic}
6 6 4 0 0 0

Best Regards
max


___________________________________________________ 
 ??????? ? ???????????????? 
 http://messenger.yahoo.com.tw/


From cao at qtp.ufl.edu  Tue Mar 27 20:05:27 2007
From: cao at qtp.ufl.edu (Chao Cao)
Date: Tue, 27 Mar 2007 14:05:27 -0400
Subject: [Pw_forum] Does anyone have RRKJ uspp for Cr?
In-Reply-To: <4608C87C.7060508@mit.edu>
References: <4608512F.6000100@qtp.ufl.edu> <4608B9C7.5040907@sissa.it> <4608C87C.7060508@mit.edu>
Message-ID: <46095CE7.3030708@qtp.ufl.edu>

Thanks for both reply from Nicola and Degironc. However, I am not quite 
confident in mixing Vanderbilt pp with RRKJ pp (is it justifiable?). I'm 
going to try the rho0 thing, and if it doesn't work out I'll probably 
just use Vanderbilt pp instead. Thanks again for both suggestions.

Best,


Chao Cao
Nicola Marzari wrote:
>
>
> Another possibility is to generate a Cr using David Vanderbilt
> code: http://www.physics.rutgers.edu/~dhv/uspp/ , and then convert it
> to UPF format.
>
> There is an input file there for a PW91 Cr that looks good.
>
>                 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
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



From marzari at MIT.EDU  Tue Mar 27 20:19:19 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 27 Mar 2007 14:19:19 -0400
Subject: [Pw_forum] Does anyone have RRKJ uspp for Cr?
In-Reply-To: <46095CE7.3030708@qtp.ufl.edu>
References: <4608512F.6000100@qtp.ufl.edu> <4608B9C7.5040907@sissa.it> <4608C87C.7060508@mit.edu> <46095CE7.3030708@qtp.ufl.edu>
Message-ID: <46096027.9050200@mit.edu>

Chao Cao wrote:
> Thanks for both reply from Nicola and Degironc. However, I am not quite 
> confident in mixing Vanderbilt pp with RRKJ pp (is it justifiable?). I'm 
> going to try the rho0 thing, and if it doesn't work out I'll probably 
> just use Vanderbilt pp instead. Thanks again for both suggestions.
> 
> Best,
> 
> 
> Chao Cao


Hi - there are absolutely no problems and no side effects in
mixing "Vanderbilt" ultrasoft PPs and "RRKJ" ultrasoft ones (RRKJ in
the pwscf sense, i.e. ultrasoft psp generated not from the real
atom, but from a RRKJ pseudoatom). It would also be fine to mix 
ultrasoft with norm-conserving pseudopotentials (e.g.
Troullier-Martins, RRKJ, Von-Barth-Car, Bachelet-Hamann-Schluter...), 
and even with plain local potentials (not that many that are any good,
a part from H...).

The code complains only if different exchange-correlation potentials
have been used in the generation of the atomic pseudopotentials, since 
then it wouldn't know wich xc to use for the calculation, and because
you shouldn't mix-n-match xc.


				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


From ghaderyan at gmail.com  Tue Mar 27 23:27:21 2007
From: ghaderyan at gmail.com (saman ghaderyan)
Date: Wed, 28 Mar 2007 00:57:21 +0330
Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1399 - 12 msgs
In-Reply-To: <20070327142102.17603.20338.Mailman@democritos.sissa.it>
References: <20070327142102.17603.20338.Mailman@democritos.sissa.it>
Message-ID: <aa36e8060703271427i10ceefbar8b7542a92bd838f2@mail.gmail.com>

hi
how i can plot phonon frequency for deferent q-victor (example 6).
thanks



On 3/27/07, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote:
> Send Pw_forum mailing list submissions to
> 	pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.democritos.it/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
> 	pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
> 	pw_forum-admin at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
>    1. Re: Does anyone have RRKJ uspp for Cr? (degironc)
>    2. Re: Does anyone have RRKJ uspp for Cr? (Nicola Marzari)
>    3. Re: Problem with pp.x (Paolo Giannozzi)
>    4. Re: masses and dt in vc-relax (Paolo Giannozzi)
>    5. Re: Aluminium EPC at X (Paolo Giannozzi)
>    6. Re: spilling parameter in Lowdin - how to assign the charge that went
> into Nirvana ? (Paolo Giannozzi)
>    7. grid without symmtrical problem (Ezad Shojaee)
>    8. (no subject) (hyello25 Qgrui)
>    9. Re: grid without symmtrical problem (degironc)
>   10. Re: Inconsistent pp.x and projwfc.x results? (Paolo Giannozzi)
>   11. Re: calculation crash (Paolo Giannozzi)
>   12. Re: Is the CG diagonalization suitable for the general matrix? (Paolo
> Giannozzi)
>
> --__--__--
>
> Message: 1
> Date: Tue, 27 Mar 2007 08:29:27 +0200
> From: degironc <degironc at sissa.it>
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Does anyone have RRKJ uspp for Cr?
> Reply-To: pw_forum at pwscf.org
>
> I don't have any..
> I hope this info from the adomic_doc/INPUT_LD1 file might be useful:
>        rho0 = charge at the origin: when the Rabe-Rappe-Kaxiras-Joannopoulos
>              method with 3 Bessel functions fails, specifying rho0 > 0
>              may allow to override the problem (using 4 Bessel functions)
>              Typical values are in the order of 0.01-0.02       (default
> 0.0)
>
> best, stefano
>
> Chao Cao wrote:
>
> > As title. I have tried to generate the pseudopotential myself, but it
> > seems to be way too complicated. It kept complaining about stuff like:
> >
> >
> >             integrated core pseudo-charge :   5.66
> >     from compute phi : info #        -1
> >     negative determinant
> >
> >         1 ld=   0.518427 f2ae  0.606247 faenor  0.141808
> >
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >     from gener_pseudo : error #         1
> >     too many nodes
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >
> >     stopping ...
> >
> >
> > Thanks a lot.
> >
> > Chao Cao
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --__--__--
>
> Message: 2
> Date: Tue, 27 Mar 2007 03:32:12 -0400
> From: Nicola Marzari <marzari at MIT.EDU>
> Organization: Massachusetts Institute of Technology
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Does anyone have RRKJ uspp for Cr?
> Reply-To: pw_forum at pwscf.org
>
>
>
> Another possibility is to generate a Cr using David Vanderbilt
> code: http://www.physics.rutgers.edu/~dhv/uspp/ , and then convert it
> to UPF format.
>
> There is an input file there for a PW91 Cr that looks good.
>
> 				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
>
> --__--__--
>
> Message: 3
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] Problem with pp.x
> Date: Tue, 27 Mar 2007 09:43:18 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 26, 2007, at 15:11 , Francesco.Stellato at roma2.infn.it wrote:
>
> >     outdir='/nfs_home/home0/molcp/velia/density_test/tmp_scf/'
>
> do not write to nfs-mounted file system: it is a recipe for disaster
>
> > p6_17713:  p4_error: net_recv read:  probable EOF on socket: 1
> > rm_l_1_9870: (6.535927) net_send: could not write to fd=5, errno = 32
>
> it looks like an error while writing to unit 5. Errors like this,
> occurring in system library calls, are impossible to pinpoint
> unless one finds under which exact circumstances it occurs,
> whether it is reproducible or not, and so on and so forth.
> They are more often a sign of problems with mpi or the
> filesystem or both rather than in the code itself
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 4
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] masses and dt in vc-relax
> Date: Tue, 27 Mar 2007 10:03:04 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 25, 2007, at 20:05 , Jess Kondor wrote:
>
> > Does it mean that I cannot use the settings from the small system
> > and apply them for bigger system?
>
> larger systems typically have more convergence problems than
> small systems, so they might need a smaller time step
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 5
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] Aluminium EPC at X
> Date: Tue, 27 Mar 2007 10:07:24 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 25, 2007, at 19:58 , Amit Kumar wrote:
>
> > I'm very much confused with the results of the electron-phonon
> > coupling
> > of Aluminium  at X-point.  You can see a large discrepancy in the
> > results
> > of Example  No. 7.
>
> >    Old version ::::
> >       Gaussian Broadening:   0.010 Ry, ngauss=   1
> > [...]
> >     Newer  Version  :::::::::
> >       Gaussian Broadening:   0.010 Ry, ngauss=   0
>
> would you mind reading the answer that you get before
> asking new questions, or more exactly, the same question?
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 6
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] spilling parameter in Lowdin - how to assign the
> charge that went into Nirvana ?
> Date: Tue, 27 Mar 2007 10:10:10 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 24, 2007, at 15:54 , Andrea Ferretti wrote:
>
> > Lowding orbitals in Quantum-Espresso (at least as far as I know) are
> > computed from the atomic reference states from pseudopotential data
> > according to:
> >
> > S_ij = < i | j >      are the overlaps of atomic orbitals i and j
> >
> > lowding orbitals are then obtained as
> > | low_i > =  R_ij  | j >
> >
> > where  R = S^{-1/2}
> >
> > so I think there is no optimization (in the sense of the paper above)
> > but maybe I am missing something
>
> no, you aren't missing anything: the atomic basis is not optimized
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 7
> From: "Ezad Shojaee" <ezadshojaee at hotmail.com>
> To: Pw_forum at pwscf.org
> Date: Tue, 27 Mar 2007 10:25:49 +0000
> Subject: [Pw_forum] grid without symmtrical problem
> Reply-To: pw_forum at pwscf.org
>
> hi
> is it possible to define a grid with non-equal numbers for ph.x not to have
> problem with q2r.x ? because i tried sample 221 and q2r.x  gave symmetrical
> error;  while there was no error with 222 sample.
> is there a way what is it?
> thanx
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE!
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
>
> --__--__--
>
> Message: 8
> Date: Tue, 27 Mar 2007 19:39:36 +0800
> From: "hyello25 Qgrui" <hyello25 at gmail.com>
> To: pw_forum at pwscf.org
> Subject: [Pw_forum] (no subject)
> Reply-To: pw_forum at pwscf.org
>
> ------=_Part_4479_6415940.1174995576279
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Content-Transfer-Encoding: 7bit
> Content-Disposition: inline
>
> hyello25 at gmail.com
>
> ------=_Part_4479_6415940.1174995576279
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: 7bit
> Content-Disposition: inline
>
> <a href="mailto:hyello25 at gmail.com">hyello25 at gmail.com</a>
>
> ------=_Part_4479_6415940.1174995576279--
>
> --__--__--
>
> Message: 9
> Date: Tue, 27 Mar 2007 15:14:28 +0200
> From: degironc <degironc at sissa.it>
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] grid without symmtrical problem
> Reply-To: pw_forum at pwscf.org
>
> The grid should have the symmetry of your system.
> Therefore it depends on the system.
> stefano
>
> Ezad Shojaee wrote:
>
> > hi
> > is it possible to define a grid with non-equal numbers for ph.x not to
> > have problem with q2r.x ? because i tried sample 221 and q2r.x  gave
> > symmetrical error;  while there was no error with 222 sample.
> > is there a way what is it?
> > thanx
> >
> > _________________________________________________________________
> > Express yourself instantly with MSN Messenger! Download today it's
> > FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --__--__--
>
> Message: 10
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] Inconsistent pp.x and projwfc.x results?
> Date: Tue, 27 Mar 2007 15:21:53 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 23, 2007, at 19:14 , Conor Hogan wrote:
>
> > Basically the character of the states produced by projwfc.x (atomic
> > projection) and pp.x (plotting the state directly) differ in the
> > case I'm
> > studying
>
> one thing to try is to re-do the calculation using k=(0,0,0)
> instead of 'Gamma tricks'. It should work in both cases,
> but who knows. If this is the problem, it should show up
> even in much smaller calculations
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 11
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] calculation crash
> Date: Tue, 27 Mar 2007 15:39:26 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 22, 2007, at 13:53 , lan haiping wrote:
>
> >      from  fft_dlay_set  : error #         7
> >       inconsistent number of sticks
>
> very strange. Try to run the job in serial execution and see
> what happens
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 12
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] Is the CG diagonalization suitable for the general
> matrix?
> Date: Tue, 27 Mar 2007 16:19:50 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> --Apple-Mail-1--870504716
> Content-Transfer-Encoding: 7bit
> Content-Type: text/plain;
> 	charset=US-ASCII;
> 	format=flowed
>
>
> On Mar 20, 2007, at 16:39 , xqhu at duke.edu wrote:
>
> > I'm trying to implement PZ-SIC in PWSCF.
>
> good luck!
>
> > In PZ-SIC, the Fock matrix is not symmetric any more.
> > I can not use DIIS or Davidson since both of them are
> > for the hermitian matrix. I checked CG codes. It seems
> > that CG can be used in the general matrix. If you are familiar
> > with the CG diagonalization, please tell me some details.
>
> all I know is written here
>
> Paolo
>
>
> --Apple-Mail-1--870504716
> Content-Transfer-Encoding: 7bit
> Content-Type: application/octet-stream;
> 	x-unix-mode=0644;
> 	name=diago.tex
> Content-Disposition: attachment;
> 	filename=diago.tex
>
> \documentstyle[11pt]{report}
> \pagestyle{empty}
> \textwidth = 16 cm
> \textheight = 24 cm
> \topmargin =  0.0 cm
> \oddsidemargin = 0.0 cm
> \begin{document}
>
> {\bf Poor-man conjugate-gradient single-band diagonalisation}.
>
> \par\noindent
> The problem: minimize
> \begin{equation}
> f_j={1\over 2} <\psi_j|H|\psi_j>
> \end{equation}
> under the constraints that
> \begin{equation}
> <\psi_j|\psi_j>=1, \qquad <\psi_j|\psi_k>=0,\quad k<j
> \end{equation}
> This is equivalent to solve the Euler-Lagrange problem of minimising
> \begin{equation}
> \widetilde f_j={1\over 2} <\psi_j|H|\psi_j> -
>   \epsilon_j (<\psi_j|\psi_j>-1) -
>   \sum_{k<j} \lambda_{jk} <\psi_j|\psi_k>
> \end{equation}
> {\bf First step.}
> For any given index $j$ we assume a starting trial eigenvector
> $|\psi^0_j>$ such that
> \begin{equation}
> <\psi^0_j|\psi^0_j>=1,\qquad <\psi^0_j|\psi_k>=0, \quad k<j
> \end{equation}
> The gradient $|g^0_j>$ is
> \begin{equation}
> |g^0_j>=H|\psi^0_j> - \epsilon^0_j |\psi^0_j> -
>        \sum_{k<j} \lambda^0_{jk}|\psi_k>
> \end{equation}
> where
> \begin{equation}
> \lambda^0_{jk} = <\psi_k|(H-\epsilon^0_j)|\psi^0_j>
> \end{equation}
> ensures that $<g^0_j|\psi_k>=0$, while
> \begin{equation}
> \epsilon^0_j = <\psi^0_j|H|\psi^0_j>
> \end{equation}
> ensures that $<g^0_j|\psi^0_j>=0$.
> Let us consider the conjugate direction $|h^0_j>=|g^0_j>$ and the
> normalized direction $|\widetilde h^0_j>$:
> \begin{equation}
> |\widetilde h^0_j> = {|h^0_j>\over <h^0_j|h^0_j>^{1/2}}
> \end{equation}
> By construction
> \begin{equation}
> <\widetilde h^0_j|\widetilde h^0_j>=1,  \quad
> <\widetilde h^0_j|\psi^0_j>=0,  \quad
> <\widetilde h^0_j|\psi_k>=0  \quad
> \end{equation}
> Consider the vector
> \begin{equation}
> |\psi^1_j(\theta)>= \cos\theta |\psi^0_j> + \sin\theta|\widetilde h^0_j>
> \end{equation}
> By construction,
> \begin{equation}
> <\psi^1_j(\theta)|\psi^1_j(\theta)>=1, \qquad
> <\psi^1_j(\theta)|\psi_k>=0,\quad k<j
> \end{equation}
> We look for the value of $\theta$ that minimises
> \begin{equation}
> \epsilon^1_j(\theta) = <\psi^1_j(\theta)|H|\psi^1_j(\theta)>
> \end{equation}
> The solution is
> \begin{equation}
> \theta^0_j={1\over 2}
> \mbox{arctag}\left({a^0_j\over\epsilon^0_j-b^0_j}\right)
> \end{equation}
> where
> \begin{equation}
> a^0_j=< \psi^0_j|H|\widetilde h^0_j> + c.c., \quad
> b^0_j=< \widetilde h^0_j|H|\widetilde h^0_j>
> \end{equation}
> and
> \begin{equation}
> \epsilon^1_j = {\epsilon^0_j+b^0_j - \sqrt{(\epsilon^0_j-b^0_j)^2
>                                      +(a^0_j)^2}\over 2}
> \end{equation}
>
> {\bf Following steps.} We construct the new gradient
> $|g^n_j>$ as above and the new conjugate direction
> $|h^n_j>$ as in the conjugate gradient method. We define
> \begin{equation}
> |u^n_j>=|g^n_j>+\gamma^{n-1}|h^{n-1}_j>
> \end{equation}
> \begin{equation}
> \gamma^{n-1}={<g^n_j|g^n_j>\over<g^{n-1}_j|g^{n-1}_j>}
> \quad\mbox{or}\quad
> \gamma^{n-1}={<g^n_j-g^{n-1}|g^n_j>\over<g^{n-1}_j|g^{n-1}_j>}
> \end{equation}
> (left: Fletcher-Reeves, right: Polak-Ribi\`ere). By construction,
> \begin{equation}
> <g^n_j|\psi_k>=0 \longrightarrow <u^n_j|\psi_k>=0
> \end{equation}
> but
> \begin{equation}
> \beta^n_j= <u^n_j|\psi^n_j>=\gamma^{n-1}_j<h^{n-1}_j|\psi^n_j>
>                 =\gamma^{n-1}_j\sin\theta^{n-1}_j
>                      <h^{n-1}_j|\widetilde h^{n-1}_j> \neq 0
> \end{equation}
> so that explicit orthogonalization of $|\psi^n_j>$ to $|u^n_j>$ is
> needed (it is a consequence of the constraint of unitary norm):
> \begin{equation}
> |h^n_j>=|u^n_j> - \beta^n_j |\psi^n_j>
> \end{equation}
> Then one proceeds as above.
>
> \par\bigskip
> {\bf Preconditioning.} We define a (diagonal) preconditioning matrix
> $P$ and auxiliary functions $|y>$ :
> \begin{equation}
> |y_j>=P^{-1}|\psi_j>
> \end{equation}
> One has to solve the equivalent problem of minimizing
> \begin{equation}
> f_j={1\over 2} <y_j|(PHP)|y_j>
> \end{equation}
> under the constraints that
> \begin{equation}
> <y_j|P^2|y_j>=1, \qquad <y_j|P|\psi_k>=0,\quad k<j
> \end{equation}
> Let us consider only the first constraint. The problem is equivalent
> to the minimisation of
> \begin{equation}
> \widetilde f_j={1\over 2} <y_j|(PHP)|y_j> -
>                \widetilde\epsilon_j (<y_j|P^2|y_j>-1)
> \end{equation}
> The gradient $|g_j>$ is now given by
> \begin{equation}
> |g_j>=(PHP)|y_j> - \widetilde\epsilon_j P^2|y_j>
> \end{equation}
> where
> \begin{equation}
> \widetilde\epsilon_j = {<y_j| P^2 (PHP)|y_j> \over <y_j| P^2 P^2| y_j>}
> \end{equation}
> ensures that
> \begin{equation}
> <g_j|P^2|y_j> = 0
> \end{equation}
> The second set of constraints is accounted for in a different way. We
> want that
> \begin{equation}
> <g_j|P|\psi_k> = 0
> \end{equation}
> This is obtained by orthogonalizing $|Pg_j>$ to $|\psi_k>$:
> \begin{equation}
> |Pg_j>=P(PHP)|y_j> - \widetilde\epsilon_j P^3|y_j>
>      - \sum_{k<j}\lambda_{jk}|\psi_k>
> \end{equation}
> where
> \begin{equation}
> \lambda_{jk} = <\psi_k|P(PHP)-P\widetilde\epsilon_j P^3|y_j>
> \end{equation}
> The reason for the different treatment of the second set of
> constraints is that $<\psi_k|P^2|\psi_l>\neq 0$.
>
> {\bf Modified preconditioned algorithm}. Starting from an initial
> guess $|\psi^0_j>$ (where $<\psi_k|\psi^0_j>=0$,
> $<\psi^0_j|\psi^0_j>=1$), one searches for new vector as:
> \begin{equation}
> |\psi^n_j(\theta)>= \cos\theta |\psi^{n-1}_j> +
>                     \sin\theta |P\widetilde h^{n-1}_j>
> \end{equation}
> where
> \begin{equation}
> |P\widetilde h^n_j> = {|Ph^n_j>\over <Ph^n_j|Ph^n_j>^{1/2}}
> \end{equation}
> and $|Ph^n_j>$ is the conjugate gradient. We define
> \begin{equation}
> |Pu^n_j>=|Pg^n_j>+\gamma^{n-1}|Ph^{n-1}_j>,
> \end{equation}
> \begin{equation}
> \gamma^{n-1}={<Pg^n_j|P^{-2}|Pg^n_j>\over<Pg^{n-1}_j|P^{-2}|Pg^{n-1}_j>}
> \quad\mbox{or}\quad
> \gamma^{n-1}={<Pg^n_j-Pg^{n-1}|P^{-2}|Pg^n_j> \over
>               <Pg^{n-1}_j|P^{-2}|Pg^{n-1}_j>}
> \end{equation}
> with $\gamma^{-1}=0$.
> The gradient $|Pg^n_j>$ is given by
> \begin{equation}
> |Pg_j>=P^2H|\psi_j> - \widetilde\epsilon_j P^2|\psi_j>-
>        \sum_{k<j}\lambda_{jk}|\psi_k>
> \end{equation}
> where
> \begin{equation}
> \lambda_{jk} = <\psi^n_k|P^2H-\widetilde\epsilon^n_j P^2|\psi^n_j>,\qquad
> \widetilde\epsilon_j = {<\psi^n_j| P^2 H|\psi^n_j> \over <\psi^n_j|
> P^2| \psi^n_j>}
> \end{equation}
> $|Pg^n_j>$ is by construction orthogonal to both
> $|\psi_k>$ and $|\psi^n_j>$, but $|Pu^n_j>$ is not
> orthogonal to $|\psi^n_j>$ for $n>0$:
> \begin{equation}
> \beta^n_j= <Pu^n_j|\psi^n_j>=\gamma^{n-1}_j<Ph^{n-1}_j|\psi^n_j>
>                             =\gamma^{n-1}_j\sin\theta^{n-1}_j
>                             <Ph^{n-1}_j|\widetilde Ph^{n-1}_j> \neq 0
> \end{equation}
> The conjugate direction $|Ph^n_j>$ is obtained from orthogonalization
> of $|Pu^n_j>$ to $|\psi^n_j>$:
> \begin{equation}
> |Ph^n_j>=|Pu^n_j> - \beta^n_j |\psi^n_j>
> \end{equation}
>
> {\bf Remarks}.
>
> -- Only $P^2$ (or $P^{-2}$) is actually used. A simple choice for
> $P^2$ is
> \begin{equation}
> P^2({\bf G},{\bf G}') = {2m \over
>                          \hbar^2({\bf k+G})^2}\delta_{\bf GG}'
> \end{equation}
>
> -- $\widetilde\epsilon^n_j$ will eventually converge to the real
> eigenvalue $\epsilon_j$ but in the preconditioned case they are not
> the same
>
> -- The algorithm is quite the same for hermitian Hamiltonians.
> $\theta$ and $\gamma$ are still real quantities, $beta$ and $\lambda$
> are no longer real.
>
> \newpage
>
> {\bf Conjugate-Gradient solution of linear systems}
>
> First problem: minimise the functional
> \begin{equation}
> f={1\over 2} <\delta\psi|A|\delta\psi> - {1\over 2}(<b|\delta\psi>+h.c.)
> \end{equation}
> under the constraint
> \begin{equation}
> <\psi|\delta\psi> = 0
> \end{equation}
> that is
> \begin{equation}
> \widetilde f = {1\over 2} <\delta\psi|A|\delta\psi>
>              - <b|\delta\psi>
>              - \lambda <\psi|\delta\psi>
> \end{equation}
> The gradient $|g>$ is
> \begin{equation}
> |g> = A|\delta\psi> - |b> -\lambda |\psi>
> \end{equation}
> By imposing that $<g|\psi>=0$ one gets
> \begin{equation}
> \lambda = <\psi|A|\delta\psi>-<\psi|b>
> \end{equation}
>
>
>
> \end{document}
>
> --Apple-Mail-1--870504716
> Content-Transfer-Encoding: 7bit
> Content-Type: application/octet-stream;
> 	x-unix-mode=0644;
> 	name=diago_us.tex
> Content-Disposition: attachment;
> 	filename=diago_us.tex
>
> \documentstyle[11pt]{report}
> \pagestyle{empty}
> \textwidth = 16 cm
> \textheight = 25 cm
> \topmargin =  -1.0 cm
> \oddsidemargin = 0.0 cm
> \begin{document}
> {\bf Generalized problem}.
>
> \par\noindent
> The problem: minimize
> \begin{equation}
> f_j={1\over 2} <\psi_j|H|\psi_j>
> \end{equation}
> under the constraints:
> \begin{equation}
> <\psi_j|S|\psi_j>=1, \qquad <\psi_j|S|\psi_k>=0,\quad k<j
> \end{equation}
> %The alghoritm used to solve the problem is exactly the same as the one
> %used for "normal" constrains, apart from
> %the insertion of the S matrix in the right places.
> %
> % l'algoritmo e` lo stesso perche` appunto era gia` implementato con il
> % precondizionamento che tiene conto degli accorgimenti particolari da
> % fare sull'ortogonalizzazione, pero` la scrittura di questa prima parte
> % non e` vero che e` la stessa del caso senza overlap
> %
> %
> {\bf bisogna fare come per il problema con il precondizionamento perche`
> $<\psi^0_j|{\bf S^2}|\psi_k> \ne 0$ }
> ...This is equivalent to solve the Euler-Lagrange problem of minimising
> \begin{equation}
> \widetilde f_j={1\over 2} <\psi_j|H|\psi_j> -
>   \epsilon_j (<\psi_j|S|\psi_j>-1) -
>   \sum_{k<j} \lambda_{jk} <\psi_j|S|\psi_k>
> \end{equation}
> If we consider the gradient of the expression above we have:
> \begin{equation}\label{prima}
> |g_j>=H|\psi_j> - \epsilon_j S|\psi_j> -
>        \sum_{k<j} \lambda_{jk} S|\psi_k>
> \end{equation}
> but we are not able to find a simple expression for $\epsilon_j$ and
> $\lambda_{jk}$ in order to have $<g_j|S|\psi_k>=0$ because
> $<\psi_j|S^2|\psi_k> \ne 0$.  \\
> So we use a slightly different approach:
> we firstly consider only the first constraint. The problem is
> equivalent to the minimization of
>
> \begin{equation}
> \widetilde f_j={1\over 2} <\psi_j|H|\psi_j> -
>   \epsilon_j (<\psi_j|S|\psi_j>-1)
> \end{equation}
> {\bf First step.}
> For any given index $j$ we assume a starting vector
> $|\psi^0_j>$ such that
> \begin{equation}
> <\psi^0_j|S|\psi^0_j>=1,\qquad <\psi^0_j|S|\psi_k>=0, \quad k<j
> \end{equation}
> The gradient $|g^0_j>$ is
> \begin{equation}
> |g^0_j>=H|\psi^0_j> - \epsilon^{0^*}_j S|\psi^0_j>
> \end{equation}
> where
> \begin{equation}
> \epsilon^{0^*}_j = { <\psi^0_j|SH|\psi^0_j> \over <\psi^0_j|S^2|\psi^0_j>}
> \end{equation}
> ensures that $<g^0_j|S|\psi^0_j>=0$. We also define:
> \begin{equation}
> \epsilon^{0}_j = <\psi^0_j|H|\psi^0_j>
> \end{equation}
> which is an approximation for the true eigenvalue $\epsilon_j$ of H.
> The second set of constraints is accounted requiring that
> \begin{equation}
> <g^0_j|S|\psi_k>=0
> \end{equation}
> This is obtained by an explicit Gram-Shmidt orthogonalization, with the
> overlap matrix S, of $|g^0_j>$
> to $|\psi_k>, k<j $
> \begin{equation} \label{seconda}
> |g^0_j> = H|\psi^0_j> - \epsilon^{0^*}_j S|\psi^0_j> -
> \sum_{k<j}\lambda^0_{kj} |\psi_k>
> \end{equation}
> where
> \begin{equation}
> \lambda^0_{kj}=<g^0_j|S|\psi_k>
> \end{equation}
> Note that equation \ref{seconda} is very much different from equation
> \ref{prima}, the last term of the right hand side is
> $ \sum_{k<j}\lambda^0_{kj} |\psi_k> $ instead of
> $\sum_{k<j}\lambda^0_{kj} S|\psi_k>$.\\
> Now: let us consider the conjugate direction $|h^0_j>=|g^0_j>$ and the
> normalized direction $|\widetilde h^0_j>$:
> \begin{equation}
> |\widetilde h^0_j> = {|h^0_j>\over <h^0_j|S|h^0_j>^{1/2}}
> \end{equation}
> By construction
> \begin{equation}
> <\widetilde h^0_j|S|\widetilde h^0_j>=1,  \quad
> <\widetilde h^0_j|S|\psi^0_j>=0,  \quad
> <\widetilde h^0_j|S|\psi_k>=0  \quad
> \end{equation}
> Consider the vector
> \begin{equation}
> |\psi^1_j(\theta)>= \cos\theta |\psi^0_j> + \sin\theta|\widetilde h^0_j>
> \end{equation}
> By construction,
> \begin{equation}
> <\psi^1_j(\theta)|S|\psi^1_j(\theta)>=1, \qquad
> <\psi^1_j(\theta)|S|\psi_k>=0,\quad k<j
> \end{equation}
> We look for the value of $\theta$ that minimizes
> \begin{equation}
> \epsilon^1_j(\theta) = <\psi^1_j(\theta)|H|\psi^1_j(\theta)>
> \end{equation}
> The solution is
> \begin{equation}
> \theta^0_j={1\over 2}
> \mbox{arctag}\left({a^0_j\over\epsilon^0_j-b^0_j}\right)
> \end{equation}
> where
> \begin{equation}
> a^0_j=< \psi^0_j|H|\widetilde h^0_j> + c.c., \quad
> b^0_j=< \widetilde h^0_j|H|\widetilde h^0_j>
> \end{equation}
> and
> \begin{equation}
> \epsilon^1_j = {\epsilon^0_j+b^0_j - \sqrt{(\epsilon^0_j-b^0_j)^2
>                                      +(a^0_j)^2}\over 2}
> \end{equation}
> which is a new approximation for $\epsilon_j$.\\
> {\bf Following steps.} We construct the new gradient
> $|g^n_j>$ as above and the new conjugate direction
> $|h^n_j>$ as in the conjugate gradient method. We define
> \begin{equation}
> |u^n_j>=|g^n_j>+\gamma^{n-1}_j|h^{n-1}_j>
> \end{equation}
> \begin{equation}
> \gamma^{n-1}_j={<g^n_j|S|g^n_j>\over<g^{n-1}_j|S|g^{n-1}_j>}
> \simeq{<g^n_j-g^{n-1}_j|S|g^n_j>\over<g^{n-1}_j|S|g^{n-1}_j>}
> \end{equation}
> By construction,
> \begin{equation}
> <g^n_j|S|\psi_k>=0 \longrightarrow <u^n_j|S|\psi_k>=0
> \end{equation}
> but
> \begin{equation}
> \beta^n_j= <u^n_j|S|\psi^n_j>=\gamma^{n-1}_j<h^{n-1}_j|S|\psi^n_j>
>                 =\gamma^{n-1}_j\sin\theta^{n-1}_j
>                      <h^{n-1}_j|S|\widetilde h^{n-1}_j> \neq 0
> \end{equation}
> so that explicit orthogonalization of $|\psi^n_j>$ to $|u^n_j>$ is
> needed (it is a consequence of the constraint of unitary norm):
> \begin{equation}
> |h^n_j>=|u^n_j> - \beta^n_j |\psi^n_j>
> \end{equation}
> Then one proceeds as above, finds $\epsilon^n_j$ and check if
> $\epsilon^n_j - \epsilon^{n-1}_j < tol$, where $tol$ is a small number
> which defines the precision of $\epsilon_j$.
> \par\bigskip
> {\bf Preconditioning.} We define a (diagonal) preconditioning matrix
> $P$ and auxiliary functions $|y>$ :
> \begin{equation}
> |y_j>=P^{-1}|\psi_j>
> \end{equation}
> One has to solve the equivalent problem of minimizing
> \begin{equation}
> f_j={1\over 2} <y_j|(PHP)|y_j>
> \end{equation}
> under the constraints that
> \begin{equation}
> <y_j|(PSP)|y_j>=1, \qquad <y_j|PS|\psi_k>=0,\quad k<j
> \end{equation}
> Again we firstly consider only the first constraint. The problem is
> equivalent
> to the minimization of
> \begin{equation}
> \widetilde f_j={1\over 2} <y_j|(PHP)|y_j> -
>                \widetilde\epsilon_j (<y_j|(PSP)|y_j>-1)
> \end{equation}
> The gradient $|g_j>$ is now given by
> \begin{equation}
> |g_j>=(PHP)|y_j> - \widetilde\epsilon_j(PSP)|y_j>
> \end{equation}
> where
> \begin{equation}
> \widetilde\epsilon_j = {<y_j|(PSP)(PHP)|y_j> \over <y_j|(PSP)^2| y_j>}
> \end{equation}
> ensures that
> \begin{equation}
> <g_j|(PSP)|y_j> = 0
> \end{equation}
> Now we have to care about the second set of constraints. We want that
> \begin{equation}
> <g_j|PS|\psi_k> = 0
> \end{equation}
> And again this is obtained by orthogonalizing, with the overlap matrix $S$,
> $|Pg_j>$ to $|\psi_k> ,k<j$:
> \begin{equation}
> |Pg^0_j> = |Pg^0_j> - \sum_{k<j} <g^0_j|PS|\psi_k>|\psi_k>
> \end{equation}
>
> {\bf Modified preconditioned algorithm}. Starting from an initial
> guess $|\psi^0_j>$ (where $<\psi_k|S|\psi^0_j>=0$,
> $<\psi^0_j|S|\psi^0_j>=1$), one searches for new vector as:
> \begin{equation}
> |\psi^n_j(\theta)>= \cos\theta |\psi^{n-1}_j> +
>                     \sin\theta |P\widetilde h^{n-1}_j>
> \end{equation}
> where
> \begin{equation}
> |P\widetilde h^n_j> = {|Ph^n_j>\over <Ph^n_j|S|Ph^n_j>^{1/2}}
> \end{equation}
> and $|Ph^n_j>$ is the conjugate gradient. We define
> \begin{equation}
> |Pu^n_j>=|Pg^n_j>+\gamma^{n-1}_j|Ph^{n-1}_j>,
> \end{equation}
> \begin{equation}
> \gamma^{n-1}_j={<Pg^n_j|P^{-2}S|Pg^n_j>
> \over<Pg^{n-1}_j|P^{-2}S|Pg^{n-1}_j>}
> \simeq{<Pg^n_j-Pg^{n-1}_j|P^{-2}S|Pg^n_j>
> \over<Pg^{n-1}_j|P^{-2}S|Pg^{n-1}_j>}
> \end{equation}
> with $\gamma^{-1}_j=0$.
> The gradient $|Pg^n_j>$ is given by
> \begin{equation}
> |Pg^n_j>=P^2H|\psi^n_j> - \widetilde\epsilon^n_j SP^2|\psi^n_j>-
>        \sum_{k<j}\lambda_{jk}^n|\psi_k>
> \end{equation}
> where
> \begin{equation}
> \lambda_{jk}^n = <\psi_k|S(P^2H-\widetilde\epsilon^n_j SP^2)|\psi^n_j>,
> \qquad
> \widetilde\epsilon_j^n = {<\psi^n_j| SP^2 H|\psi^n_j> \over <\psi^n_j|
> S^2P^2| \psi^n_j>}
> \end{equation}
> $|Pu^n_j>$ is by construction orthogonal to
> $|\psi_k>$ but not to  $|\psi^n_j>$:
> \begin{equation}
> \beta^n_j= <Pu^n_j|S|\psi^n_j>=
> \gamma^{n-1}_j<Ph^{n-1}_j|S|\psi^n_j>
>                             =\gamma^{n-1}_j\sin\theta^{n-1}_j
>                             <Ph^{n-1}_j|S|Ph^{n-1}_j> \neq 0
> \end{equation}
> One gets the conjugate direction $|Ph^n_j>$ from
> \begin{equation}
> |Ph^n_j>=|Pu^n_j> - \beta^n_j |\psi^n_j>
> \end{equation}
> Note that only $P^2$ (or $P^{-2}$) is actually used.
>
> \end{document}
>
>
> --Apple-Mail-1--870504716
> Content-Transfer-Encoding: 7bit
> Content-Type: text/plain;
> 	charset=US-ASCII;
> 	format=flowed
>
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --Apple-Mail-1--870504716--
>
>
> --__--__--
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest
>


From akohlmey at cmm.chem.upenn.edu  Tue Mar 27 23:35:04 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 27 Mar 2007 16:35:04 -0500 (EST)
Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1399 - 12 msgs
In-Reply-To: <aa36e8060703271427i10ceefbar8b7542a92bd838f2@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0703271630550.666-100000@localhost.localdomain>

saman,

before anybody will answer your question. please take the time
and read http://www.catb.org/~esr/faqs/smart-questions.html
and then promise to _never_ _ever_ post a question to a mailing
list by replying to a digest _and_ needlessly quoting the whole(!)
digest, yet not using a proper subject line.

thanks,
  axel.

On Wed, 28 Mar 2007, saman ghaderyan wrote:

SG> hi
SG> how i can plot phonon frequency for deferent q-victor (example 6).
SG> thanks
SG> 



-- 
=======================================================================
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.



From baroni at sissa.it  Wed Mar 28 03:28:05 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 28 Mar 2007 09:28:05 +0800
Subject: [Pw_forum] warings in scf.out
In-Reply-To: <520917.61184.qm@web73009.mail.tp2.yahoo.com>
References: <520917.61184.qm@web73009.mail.tp2.yahoo.com>
Message-ID: <380A6B14-DEAD-4CAD-BEB5-6BA0A956BA77@sissa.it>

Dear Max: this issue has been discussed zillions of times in this  
forum, and I think it is even well documented in the manuals. Please,  
search "fractional translation" in the forum archive, and I am sure  
you'll find lots of hints. Cheers - SB

On Mar 28, 2007, at 1:47 AM, ? ?? wrote:

> Dear members,
>
> In scf.out , it shows some waring as below:
>
>
>      Ultrasoft (Vanderbilt) Pseudopotentials
>
>      Current dimensions of program pwscf are:
>
>      ntypx = 10   npk = 40000  lmax =  3
>      nchix =  6  ndmx =  2000  nbrx = 14  nqfx =  8
>      warning: symmetry operation #  2 not allowed.
> fractional translation:
>        0.3333333 -0.3333333 -0.5000000  in crystal
> coordinates
>      warning: symmetry operation #  5 not allowed.
> fractional translation:
>        0.3333333 -0.3333333 -0.5000000  in crystal
> coordinates
>      warning: symmetry operation #  6 not allowed.
> fractional translation:
>        0.3333333 -0.3333333 -0.5000000  in crystal
> coordinates
>      warning: symmetry operation # 15 not allowed.
> fractional translation:
>        0.3333333 -0.3333333 -0.5000000  in crystal
> coordinates
>
>
> How to solve these warings ?
>
> The cell structure in "scf.in" is
>  ibrav =4 , celldm(1) =6.261,celldm(3) = 1.61,
>           nat = 4,  ntyp = 2, ecutwfc = 30.0,
>
> ATOMIC_POSITIONS  {crystal}
> in       0.000000000   0.000000000  -0.000355437
> in       0.666666667   0.333333333   0.499644563
> n        0.000000000   0.000000000   0.377862274
> n        0.666666667   0.333333333   0.877862274
> K_POINTS {automatic}
> 6 6 4 0 0 0
>
> Best Regards
> max
>
>
> ___________________________________________________
>  ??????? ? ????????????????
>  http://messenger.yahoo.com.tw/
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center -  
Trieste
[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

Please, if possible, don't  send me MS Word or PowerPoint attachments
Why? See:  http://www.gnu.org/philosophy/no-word-attachments.html



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From ezadshojaee at hotmail.com  Wed Mar 28 08:28:04 2007
From: ezadshojaee at hotmail.com (Ezad Shojaee)
Date: Wed, 28 Mar 2007 06:28:04 +0000
Subject: [Pw_forum] grid without symmetrical problem
Message-ID: <BAY101-F33521BD67CC2AF82078BBAA6D0@phx.gbl>

hi
yes, the grid must have the symmetries of the system,  i have tried some 
grids & non of them had the symmetries needed, how should i find the 
suitable grid according to my system not to have the error at the end of the 
phonon calculation?! is there any formal way?
thanx

_________________________________________________________________
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From ezadshojaee at hotmail.com  Wed Mar 28 08:30:00 2007
From: ezadshojaee at hotmail.com (Ezad Shojaee)
Date: Wed, 28 Mar 2007 06:30:00 +0000
Subject: [Pw_forum] grid without symmetrical problem
Message-ID: <BAY101-F284910AC53B5B392E9A9F6AA6D0@phx.gbl>

hi
yes, the grid must have the symmetries of the system,  i have tried some 
grids & non of them had the symmetries needed, how should i find the 
suitable grid according to my system not to have the error at the end of the 
phonon calculation?! is there any formal way?
thanx

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From yukihiro_okuno at fujifilm.co.jp  Thu Mar 29 07:53:20 2007
From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp)
Date: Thu, 29 Mar 2007 14:53:20 +0900
Subject: [Pw_forum] Segmentation fault in Berry Phase calculation
Message-ID: <OF2356FD23.375AAEEC-ON492572AD.001F32A0-492572AD.0020595B@mta.fujifilm.co.jp>

Dear PWScf Users.

I'm now calculationg Berry Phase of PZT with shear stress (
so the structure of crystal is monoclinic) in order to
get piezoelectric coefficient e15.

But when I do the Berry Phase calculation, calculation was crushed
with segmentation fault.

Why such a problem occurs?
Are there any need to correct  memory allocation in the program ?

My enviroment is

compiler Intel FCC 8.1
OS         linux FedoraCore
math lib  mkl721


My input file is as follow
(with the stress = 0 case)

:scf calculation


&control
    calculation  = 'scf',
    restart_mode = 'from_scratch',
    pseudo_dir   = '/home/okuno/PWSCF/espresso-3.2/pseudo/',
    outdir       = './',
    prefix='PZT'
 /
 &system
    ibrav=12
    celldm(1)=7.57696068724
    celldm(2)=2.09
    celldm(3)=1.00
    celldm(4)=0.00
    nat=10
    ntyp=4
    nbnd=44
    ecutwfc=60.0
    ecutrho = 600.0
    occupations = 'fixed'
    degauss=0.00
 /
 &electrons
    conv_thr = 1e-10,
    mixing_beta=0.3,
 /
ATOMIC_SPECIES
  Pb  207.2     pb_ps.uspp.UPF
  Zr  91.224    zr_ps.uspp.UPF
  Ti  47.867    ti_ps.uspp.UPF
  O   15.9994   o_ps.uspp.UPF
ATOMIC_POSITIONS {crystal}
Pb       0.000000000   0.006012264   0.000000000
Pb       0.000000000   0.537853199   0.000000000
Zr       0.500000000   0.244190014   0.500000000
Ti       0.500000000   0.740640879   0.500000000
O        0.500000000   0.951075914   0.500000000
O        0.500000000   0.478306726   0.500000000
O        0.500000000   0.189000664   0.000000000
O        0.000000000   0.189000664   0.500000000
O        0.500000000   0.711889837   0.000000000
O        0.000000000   0.711889837   0.500000000
K_POINTS {automatic}
  6 6 6 0 0 0


For berry phase calculation.

&control
    calculation  = 'nscf'
    restart_mode = 'from_scratch'
    pseudo_dir   = '/home/okuno/PWSCF/espresso-3.2/pseudo/'
    outdir       = './'
    lberry  = .true.
    gdir = 2
    nppstr = 10
    prefix = 'PZT'
 /
 &system
    ibrav=12
    celldm(1)=7.57696068724
    celldm(2)=2.09
    celldm(3)=1.00
    celldm(4)=0.00
    nat=10
    ntyp=4
    nbnd=44
    ecutwfc=60.0
    ecutrho = 600.0
    occupations = 'fixed'
    degauss=0.00
 /
 &electrons
    conv_thr = 1e-8,
    mixing_beta=0.3,
 /
ATOMIC_SPECIES
  Pb  207.2     pb_ps.uspp.UPF
  Zr  91.224    zr_ps.uspp.UPF
  Ti  47.867    ti_ps.uspp.UPF
  O   15.9994   o_ps.uspp.UPF
ATOMIC_POSITIONS {crystal}
Pb       0.000000000   0.006012264   0.000000000
Pb       0.000000000   0.537853199   0.000000000
Zr       0.500000000   0.244190014   0.500000000
Ti       0.500000000   0.740640879   0.500000000
O        0.500000000   0.951075914   0.500000000
O        0.500000000   0.478306726   0.500000000
O        0.500000000   0.189000664   0.000000000
O        0.000000000   0.189000664   0.500000000
O        0.500000000   0.711889837   0.000000000
O        0.000000000   0.711889837   0.500000000
K_POINTS {automatic}
  6 6 6 0 0 0






From niuli1978 at yahoo.com.cn  Thu Mar 29 09:02:20 2007
From: niuli1978 at yahoo.com.cn (li niu)
Date: Thu, 29 Mar 2007 15:02:20 +0800 (CST)
Subject: [Pw_forum] how to obtain a optimized lattice constant
Message-ID: <165580.44735.qm@web15006.mail.cnb.yahoo.com>

Dear all,
   I  have several questions on how to obtain a optimized lattice constant. I took the diamond as an  example, 
  when: C.blyp-mt.UPF
           ecutrho = 4*ecutwfc
           a = 6.74 (experimental value)
          K_POINTS AUTOMATIC  8 8 8 1 1 1
1.I did several scf and phonon calculations with different ecutwfc from 40 to 80 Ry and found a convergence of the calculated frequencies at 55 Ry (or 60).[Is it right?]
  ====================================================
ecutwfc       total energy           P=              frequency( gamma point)
--------------------------------------------------------------------------------------------------
40 Ry           -22.54608438 Ry      -324.91          1364.516269 [cm-1]
---------------------------------------------------------------------------------------------------
45             -22.58756098         P= -198.59      1356.978995 [cm-1]
---------------------------------------------------------------------------------------------
46             -22.59358560 Ry      P= -177.09       1350.238444 [cm-1]
-------------------------------------------------------------------------------------------------
48             -22.60333041         P= -139.82       1331.376654  (-11)
---------------------------------------------------------------------------------------------
49             -22.60713824 Ry      P= -124.22       1320.862623    (-9)
-------------------------------------------------------------------------------------------------
50             -22.61073198            -108.78       1311.304111     (9)
-------------------------------------------------------------------------------------------------
51             -22.61399076 Ry      P=  -94.25       1302.308894 [cm-1] (8)
-------------------------------------------------------------------------------------------------
52             -22.61688998 Ry       P=  -80.83      1294.840278 [cm-1] (4)
-----------------------------------------------------------------------------------------------------
53             -22.61953601 Ry      P=  -67.95       1290.058731 [cm-1] (5) 
-----------------------------------------------------------------------------------------------------
54            -22.62200281          P=  -55.48       1285.954996 [cm-1]  (2)
------------------------------------------------------------------------------------------------------
55            -22.62410759 Ry        P=  -44.35       1283.736877 [cm-1] (1)
-------------------------------------------------------------------------------------------------------
56            -22.62623466           P=  -32.75       1282.451118 [cm-1] (0)
-------------------------------------------------------------------------
57            -22.62815534 Ry         P=  -21.82       1282.144868 [cm-1]  (0) 
-------------------------------------------------------------------------
58            -22.62986744 Ry         P=  -11.70       1282.755051 [cm-1]  (0)
-------------------------------------------------------------------------
59             -22.63154997 Ry        P=   -1.37        1284.145461 [cm-1] (-2)
---------------------------------------------------------------------------
60          -22.63297919 Ry         P=    7.72       1285.831946 [cm-1]  (-1)
----------------------------------------------------------------------------------------------
62            -22.63565052 Ry         P=   25.81       1289.073779 [cm-1]  (-4)
----------------------------------------------------------------------------------------------------
65         warning: symmetry operation #  5 not allowed.
           -22.63882875 Ry          P=   49.83         1290.953300 [cm-1]
-----------------------------------------------------------------------------------------
70        warning: symmetry operation #  5 not allowed.  
          -22.64202864             P=   78.96         1295.485613 [cm-1]
---------------------------------------------------------------------------------------------
80        warning: symmetry operation #  5 not allowed. 
           -22.64415626 Ry         P=  101.58         1293.336207 [cm-1]
======================================================
  2. Then I did several calculations with different a (around experiment value)
when ecutwfc equal to 60 Ry. The results are follows.
   
  ecutwfc = 60
-------------------------------------------------------------------------------------------------------
  a         total energy                            frequency(experimental:1332)
6.74        -22.63297919 Ry         P=    7.72       1285.831946 [cm-1] 
6.75        -22.63324360 Ry         P=  -11.28       1279.754275 [cm-1]
6.76        -22.63347229 Ry         P=  -29.78       1274.313572 [cm-1]
6.80        -22.63386503 Ry         P= -101.36       1252.534320 [cm-1]
6.85        -22.63347988 Ry         P= -183.28       1226.237110 [cm-1]
-----------------------------------------------------------------------------------------------------
  3. The potential energy surface is then fitted by the murnaghan equation (ev.x),
and its mininum provides the theoetical precictions for the ground state equilibrium
lattice constant.
--------------------------------------------------------------------------------------------------------
# equation of state: murnaghan.        chisq = 0.1134D-10
# a0 =  6.80  k0 = 3746 kbar,  dk0 = 14.50  d2k0 =  0.000  emin =  -22.63387
--------------------------------------------------------------------------------------------------------
  4. In the end, I obtained optimized lattice constant is 6.8 when the energy cutoff is 60 Ry. In this case the phonon frequency of gamma piont equals to 1252 cm-1 but experimental is 1332 cm-1 and the stress-tensor is -101 kbar but not is 0.
  
My questions are:
(1)Is it right to choose the energy cutoff like this? 
(2) Why the stress-tensor is so large?
(3) How should I do to obtain the correct optimized parameters?
   
  I'm puzzled by these questions all the times so I hope that you can help me.
   
  Thanks in advance!
   
  Bset!
  Niu Liu

========================================================
# self-consistent calculation
cat >diamond.scf.in << EOF
 &control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='diamond',
    pseudo_dir = '$PSEUDO_DIR/',
    outdir='$TMP_DIR/'
    tstress = .true. ,
    tprnfor = .true. ,
 /
 &system    
    ibrav=  2, celldm(1) =6.74, nat=  2, ntyp= 1,
    ecutwfc =60,    
 /
 &electrons
    conv_thr =  1.0d-9
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 C   12.0107  C.blyp-mt.UPF
ATOMIC_POSITIONS
 C  0.00 0.00 0.00 
 C  0.25 0.25 0.25 
K_POINTS AUTOMATIC
8 8 8 1 1 1
  EOF
$ECHO "  running the scf calculation...\c"
$PW_COMMAND < diamond.scf.in > diamond.scf.out
$ECHO " done"
  # phonon calculation at G
cat >diamond.phG.in << EOF
phonons of C at Gamma
 &inputph
  tr2_ph=1.0d-14,
  epsil=.true.,
  prefix='diamond',
  fildyn='diamond_g.dyn',
  amass(1)=12.0107,
  outdir='$TMP_DIR/'
 /
0.0 0.0 0.0
EOF
$ECHO "  running the phonon calculation at Gamma...\c"
$PH_COMMAND < diamond.phG.in > diamond.phG.out
$ECHO " done"
  $ECHO
$ECHO "$EXAMPLE_DIR: done"
================================================

 		
---------------------------------
????????-3.5G???20M??? 
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From hyello25 at gmail.com  Thu Mar 29 10:06:25 2007
From: hyello25 at gmail.com (hyello25 Qgrui)
Date: Thu, 29 Mar 2007 16:06:25 +0800
Subject: [Pw_forum] how to use fqha.x in pwtools
Message-ID: <a44e04ef0703290106u3e07bce7l697de48d2bc69021@mail.gmail.com>

    Hi,
     I am a freshman to use Pwscf. I don't konw how to use the 'fqha.x' and
how
 to write the input file for this command.  And I am confused about which is
 the 'dos' file that fqha.x reads? In the example08 ,is the file ni.dos ?
  Need your help. thanks
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From iori.federico at unimore.it  Thu Mar 29 10:32:12 2007
From: iori.federico at unimore.it (Federico Iori)
Date: Thu, 29 Mar 2007 10:32:12 +0200
Subject: [Pw_forum] Question on chdens and  Xcrysden
Message-ID: <460B798C.5030100@unimore.it>

'Morning to everybody!

I have some trouble about the postprocessing in pp.x, and maybe some of 
you could give me some nice idea about:

I use to calculate |PSI|2 for some of the state(of interest!) of my 
system, so HOMO, HOMO-1, LUMO etc...
with pp.x
and next to  plot them again with pp.x in order to achieve the right 
input format for Xcrysden.
I do this for each separate state I calculate with pp.x (here the input 
file, that works!..):

first step (pp.x @ pw_3.2)

&inputpp
 prefix = 'scf'
 outdir = '${DIR_SCRATCH}'
 filplot= '${DIR_SCRATCH}PSI2.0${STATE}'
 plot_num=7
 kpoint = 1
 kband = ${STATE}
/
STATE = number of orbital I want to plot....

next plot part:

&inputpp
/
&plot
  nfile=1 ,
  filepp(1)='PSI2.0${STATE}' ,
  weight(1)=1.0 ,
  iflag=3 ,
  output_format=5 ,
  x0= 0.0 0.0 0.0 ,
  fileout='./PSI2_0${STATE}.xsf'
/

finally my question:

instead having for each state one corresponding file.xf ("HOMO.xsf" and 
"LUMO.xsf" for example) and  to plot HOMO and LUMO separately for the 
same system with Xcrysden, is there the possibility to obtain only one 
file.xsf in order to plot the HOMO and LUMO on the same structure with 
Xcrysden??

Have I been too unclear?

Nevertheless, thanks in advance!
cheers!


-- 
Federico Iori - PhD Student -

INFM-S3 and Dipartimento di Fisica
Universit? degli Studi di Modena e Reggio Emilia
via Campi, 213/A - 41100 Modena - Italia
www.s3.infm.it
www.fisica.unimo.it

phone: +39 59 2055283
#1 fax n?:  +39 059 37 47 94
#2 fax n?:  +39 059 205 5651 
email: iori.federico at unimore.it




From jin.zhang.pku at gmail.com  Thu Mar 29 10:51:02 2007
From: jin.zhang.pku at gmail.com (Jin Zhang)
Date: Thu, 29 Mar 2007 16:51:02 +0800
Subject: [Pw_forum] Question on chdens and Xcrysden
In-Reply-To: <460B798C.5030100@unimore.it>
References: <460B798C.5030100@unimore.it>
Message-ID: <5d233b6a0703290151l6aa7b96ci299c9fe96a1b5ff5@mail.gmail.com>

Dear Iori,

I am not familiar with your problem. But I have plotted Wannier functions
using xCrysden's surf grid. You may want to check xCrysden's website for the
format of 3D data grid. Once you get it, editing xsf itself is pretty
trivial and straight forward.

Good luck!
Jin Zhang
On 3/29/07, Federico Iori <iori.federico at unimore.it> wrote:
>
> 'Morning to everybody!
>
> I have some trouble about the postprocessing in pp.x, and maybe some of
> you could give me some nice idea about:
>
> I use to calculate |PSI|2 for some of the state(of interest!) of my
> system, so HOMO, HOMO-1, LUMO etc...
> with pp.x
> and next to  plot them again with pp.x in order to achieve the right
> input format for Xcrysden.
> I do this for each separate state I calculate with pp.x (here the input
> file, that works!..):
>
> first step (pp.x @ pw_3.2)
>
> &inputpp
> prefix = 'scf'
> outdir = '${DIR_SCRATCH}'
> filplot= '${DIR_SCRATCH}PSI2.0${STATE}'
> plot_num=7
> kpoint = 1
> kband = ${STATE}
> /
> STATE = number of orbital I want to plot....
>
> next plot part:
>
> &inputpp
> /
> &plot
> nfile=1 ,
> filepp(1)='PSI2.0${STATE}' ,
> weight(1)=1.0 ,
> iflag=3 ,
> output_format=5 ,
> x0= 0.0 0.0 0.0 ,
> fileout='./PSI2_0${STATE}.xsf'
> /
>
> finally my question:
>
> instead having for each state one corresponding file.xf ("HOMO.xsf" and
> "LUMO.xsf" for example) and  to plot HOMO and LUMO separately for the
> same system with Xcrysden, is there the possibility to obtain only one
> file.xsf in order to plot the HOMO and LUMO on the same structure with
> Xcrysden??
>
> Have I been too unclear?
>
> Nevertheless, thanks in advance!
> cheers!
>
>
> --
> Federico Iori - PhD Student -
>
> INFM-S3 and Dipartimento di Fisica
> Universit? degli Studi di Modena e Reggio Emilia
> via Campi, 213/A - 41100 Modena - Italia
> www.s3.infm.it
> www.fisica.unimo.it
>
> phone: +39 59 2055283
> #1 fax n?:  +39 059 37 47 94
> #2 fax n?:  +39 059 205 5651
> email: iori.federico at unimore.it
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
MSc
Dept. of Physics, Peking University
Beijing, 100871, P.R.China
Phone: 86-10-62768590
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From eyvaz_isaev at yahoo.com  Thu Mar 29 11:54:46 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 29 Mar 2007 02:54:46 -0700 (PDT)
Subject: [Pw_forum] how to use fqha.x in pwtools
Message-ID: <492256.75702.qm@web60324.mail.yahoo.com>

Hi,

Try to find QHA code sent to the forum approximately a month ago. The dos file in exapmle08 is 
electronic DOS, but not phonon DOS.

Bests,
Eyvaz.

----- Original Message ----
From: hyello25 Qgrui <hyello25 at gmail.com>
To: pw_forum <pw_forum at pwscf.org>
Sent: Thursday, March 29, 2007 12:06:25 PM
Subject: [Pw_forum] how to use fqha.x in pwtools

    Hi,
     I am a freshman to use Pwscf. I don't konw how to use the 'fqha.x' and how
 to write the input file for this command.  And I am confused about which is
 the 'dos' file that 
fqha.x reads? In the example08 ,is the file ni.dos ?


  Need your help. thanks







 
____________________________________________________________________________________
Looking for earth-friendly autos? 
Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center.
http://autos.yahoo.com/green_center/
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From eyvaz_isaev at yahoo.com  Thu Mar 29 12:07:26 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 29 Mar 2007 03:07:26 -0700 (PDT)
Subject: [Pw_forum] Segmentation fault in Berry Phase calculation
Message-ID: <245175.81616.qm@web60317.mail.yahoo.com>

Hi,

Most likely, you have insufficient memory. 
Try reduce ecutwfc down to 30 Ry, and ecutrho to 360 Ry.  Usually ultrasoft pseudopotentials are 
optimized for the cutoff energy around 30Ry.  Just for test case try 2x2x2 k-mesh.
Are you running a serial (single CPU) or parallel  job?

Bests,
Eyvaz.

----- Original Message ----
From: "yukihiro_okuno at fujifilm.co.jp" <yukihiro_okuno at fujifilm.co.jp>
To: pw_forum at pwscf.org
Sent: Thursday, March 29, 2007 9:53:20 AM
Subject: [Pw_forum] Segmentation fault in Berry Phase calculation


Dear PWScf Users.

I'm now calculationg Berry Phase of PZT with shear stress (
so the structure of crystal is monoclinic) in order to
get piezoelectric coefficient e15.

But when I do the Berry Phase calculation, calculation was crushed
with segmentation fault.

Why such a problem occurs?
Are there any need to correct  memory allocation in the program ?

My enviroment is

compiler Intel FCC 8.1
OS         linux FedoraCore
math lib  mkl721


My input file is as follow
(with the stress = 0 case)

:scf calculation


&control
    calculation  = 'scf',
    restart_mode = 'from_scratch',
    pseudo_dir   = '/home/okuno/PWSCF/espresso-3.2/pseudo/',
    outdir       = './',
    prefix='PZT'
 /
 &system
    ibrav=12
    celldm(1)=7.57696068724
    celldm(2)=2.09
    celldm(3)=1.00
    celldm(4)=0.00
    nat=10
    ntyp=4
    nbnd=44
    ecutwfc=60.0
    ecutrho = 600.0
    occupations = 'fixed'
    degauss=0.00
 /
 &electrons
    conv_thr = 1e-10,
    mixing_beta=0.3,
 /
ATOMIC_SPECIES
  Pb  207.2     pb_ps.uspp.UPF
  Zr  91.224    zr_ps.uspp.UPF
  Ti  47.867    ti_ps.uspp.UPF
  O   15.9994   o_ps.uspp.UPF
ATOMIC_POSITIONS {crystal}
Pb       0.000000000   0.006012264   0.000000000
Pb       0.000000000   0.537853199   0.000000000
Zr       0.500000000   0.244190014   0.500000000
Ti       0.500000000   0.740640879   0.500000000
O        0.500000000   0.951075914   0.500000000
O        0.500000000   0.478306726   0.500000000
O        0.500000000   0.189000664   0.000000000
O        0.000000000   0.189000664   0.500000000
O        0.500000000   0.711889837   0.000000000
O        0.000000000   0.711889837   0.500000000
K_POINTS {automatic}
  6 6 6 0 0 0


For berry phase calculation.

&control
    calculation  = 'nscf'
    restart_mode = 'from_scratch'
    pseudo_dir   = '/home/okuno/PWSCF/espresso-3.2/pseudo/'
    outdir       = './'
    lberry  = .true.
    gdir = 2
    nppstr = 10
    prefix = 'PZT'
 /
 &system
    ibrav=12
    celldm(1)=7.57696068724
    celldm(2)=2.09
    celldm(3)=1.00
    celldm(4)=0.00
    nat=10
    ntyp=4
    nbnd=44
    ecutwfc=60.0
    ecutrho = 600.0
    occupations = 'fixed'
    degauss=0.00
 /
 &electrons
    conv_thr = 1e-8,
    mixing_beta=0.3,
 /
ATOMIC_SPECIES
  Pb  207.2     pb_ps.uspp.UPF
  Zr  91.224    zr_ps.uspp.UPF
  Ti  47.867    ti_ps.uspp.UPF
  O   15.9994   o_ps.uspp.UPF
ATOMIC_POSITIONS {crystal}
Pb       0.000000000   0.006012264   0.000000000
Pb       0.000000000   0.537853199   0.000000000
Zr       0.500000000   0.244190014   0.500000000
Ti       0.500000000   0.740640879   0.500000000
O        0.500000000   0.951075914   0.500000000
O        0.500000000   0.478306726   0.500000000
O        0.500000000   0.189000664   0.000000000
O        0.000000000   0.189000664   0.500000000
O        0.500000000   0.711889837   0.000000000
O        0.000000000   0.711889837   0.500000000
K_POINTS {automatic}
  6 6 6 0 0 0




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





 
____________________________________________________________________________________
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From naromero at gmail.com  Thu Mar 29 15:16:01 2007
From: naromero at gmail.com (Nichols A. Romero)
Date: Thu, 29 Mar 2007 09:16:01 -0400
Subject: [Pw_forum] how to obtain a optimized lattice constant
In-Reply-To: <165580.44735.qm@web15006.mail.cnb.yahoo.com>
References: <165580.44735.qm@web15006.mail.cnb.yahoo.com>
Message-ID: <6ac064b60703290616q1b387e62vd275c3d86a996863@mail.gmail.com>

Dear Niu,

Have you searched the mail postings for a similar topic?

Go to
www.pwscf.org

On the right hand panel, click on "Search Archive" under USERS FORUM. Search
for
"pw_forum lattice constant"

Do not know too much about phonon calculations, but in general they are much
more
delicate than a total energy calculations + structural minimization.

Please note that the stress tensor converges much slower than than the total
energy.
For example, for a norm-conserving pseudopotential. If your energy is
converged at 40 Ry,
the stress tensor may not converged (+/- 3 kbar) until you get to 80 Ry.

On 3/29/07, li niu <niuli1978 at yahoo.com.cn> wrote:
>
> Dear all,
>  I  have several questions on how to obtain a optimized lattice constant.
> I took the diamond as an  example,
>   when: C.blyp-mt.UPF
>            ecutrho = 4*ecutwfc
>            a = 6.74 (experimental value)
>           K_POINTS AUTOMATIC  8 8 8 1 1 1
> 1.I did several scf and phonon calculations with different ecutwfc from 40
> to 80 Ry and found a convergence of the calculated frequencies at 55 Ry (or
> 60).[Is it right?]
> ====================================================
> ecutwfc       total energy           P=              frequency( gamma
> point)
>
> --------------------------------------------------------------------------------------------------
> 40 Ry           -22.54608438 Ry      -324.91          1364.516269 [cm-1]
>
> ---------------------------------------------------------------------------------------------------
> 45             -22.58756098         P= -198.59      1356.978995 [cm-1]
>
> ---------------------------------------------------------------------------------------------
> 46             -22.59358560 Ry      P= -177.09       1350.238444 [cm-1]
>
> -------------------------------------------------------------------------------------------------
> 48             -22.60333041         P= -139.82       1331.376654  (-11)
>
> ---------------------------------------------------------------------------------------------
> 49             -22.60713824 Ry      P= -124.22       1320.862623    (-9)
>
> -------------------------------------------------------------------------------------------------
> 50             -22.61073198            -108.78       1311.304111     (9)
>
> -------------------------------------------------------------------------------------------------
> 51             -22.61399076 Ry      P=  -94.25       1302.308894 [cm-1]
> (8)
>
> -------------------------------------------------------------------------------------------------
> 52             -22.61688998 Ry       P=  -80.83      1294.840278 [cm-1]
> (4)
>
> -----------------------------------------------------------------------------------------------------
> 53             -22.61953601 Ry      P=  -67.95       1290.058731 [cm-1]
> (5)
>
> -----------------------------------------------------------------------------------------------------
> 54            -22.62200281          P=  -55.48       1285.954996 [cm-1]
> (2)
>
> ------------------------------------------------------------------------------------------------------
> 55            -22.62410759 Ry        P=  -44.35       1283.736877 [cm-1]
> (1)
>
> -------------------------------------------------------------------------------------------------------
> 56            -22.62623466           P=  -32.75       1282.451118 [cm-1]
> (0)
> -------------------------------------------------------------------------
> 57            -22.62815534 Ry         P=  -21.82       1282.144868 [cm-1]
> (0)
> -------------------------------------------------------------------------
> 58            -22.62986744 Ry         P=  -11.70       1282.755051 [cm-1]
> (0)
> -------------------------------------------------------------------------
> 59             -22.63154997 Ry        P=   -1.37        1284.145461 [cm-1]
> (-2)
>
> ---------------------------------------------------------------------------
> 60          -22.63297919 Ry         P=    7.72       1285.831946 [cm-1]
> (-1)
>
> ----------------------------------------------------------------------------------------------
> 62            -22.63565052 Ry         P=   25.81       1289.073779 [cm-1]
> (-4)
>
> ----------------------------------------------------------------------------------------------------
> 65         warning: symmetry operation #  5 not allowed.
>            -22.63882875 Ry          P=   49.83         1290.953300 [cm-1]
>
> -----------------------------------------------------------------------------------------
> 70        warning: symmetry operation #  5 not allowed.
>           -22.64202864             P=   78.96         1295.485613 [cm-1]
>
> ---------------------------------------------------------------------------------------------
> 80        warning: symmetry operation #  5 not allowed.
>            -22.64415626 Ry         P=  101.58         1293.336207 [cm-1]
> ======================================================
> 2. Then I did several calculations with different a (around experiment
> value)
> when ecutwfc equal to 60 Ry. The results are follows.
>
> ecutwfc = 60
>
> -------------------------------------------------------------------------------------------------------
>   a         total energy
> frequency(experimental:1332)
> 6.74        -22.63297919 Ry         P=    7.72       1285.831946 [cm-1]
> 6.75        -22.63324360 Ry         P=  -11.28       1279.754275 [cm-1]
> 6.76        -22.63347229 Ry         P=  -29.78       1274.313572 [cm-1]
> 6.80        -22.63386503 Ry         P= -101.36       1252.534320 [cm-1]
> 6.85        -22.63347988 Ry         P= -183.28       1226.237110 [cm-1]
>
> -----------------------------------------------------------------------------------------------------
> 3. The potential energy surface is then fitted by the murnaghan equation (
> ev.x),
> and its mininum provides the theoetical precictions for the ground state
> equilibrium
> lattice constant.
>
> --------------------------------------------------------------------------------------------------------
> # equation of state: murnaghan.        chisq = 0.1134D-10
> # a0 =  6.80  k0 = 3746 kbar,  dk0 = 14.50  d2k0 =  0.000  emin =  -
> 22.63387
>
> --------------------------------------------------------------------------------------------------------
> 4. In the end, I obtained optimized lattice constant is 6.8 when the
> energy cutoff is 60 Ry. In this case the phonon frequency of gamma piont
> equals to 1252 cm-1 but experimental is 1332 cm-1 and the stress-tensor is
> -101 kbar but not is 0.
>
> My questions are:
> (1)Is it right to choose the energy cutoff like this?
> (2) Why the stress-tensor is so large?
> (3) How should I do to obtain the correct optimized parameters?
>
> I'm puzzled by these questions all the times so I hope that you can help
> me.
>
> Thanks in advance!
>
> Bset!
> Niu Liu
>
> ========================================================
> # self-consistent calculation
> cat >diamond.scf.in << EOF
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     prefix='diamond',
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/'
>     tstress = .true. ,
>     tprnfor = .true. ,
>  /
>  &system
>     ibrav=  2, celldm(1) =6.74, nat=  2, ntyp= 1,
>     ecutwfc =60,
>  /
>  &electrons
>     conv_thr =  1.0d-9
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  C   12.0107  C.blyp-mt.UPF
> ATOMIC_POSITIONS
>  C  0.00 0.00 0.00
>  C  0.25 0.25 0.25
> K_POINTS AUTOMATIC
> 8 8 8 1 1 1
> EOF
> $ECHO "  running the scf calculation...\c"
> $PW_COMMAND < diamond.scf.in > diamond.scf.out
> $ECHO " done"
> # phonon calculation at G
> cat >diamond.phG.in << EOF
> phonons of C at Gamma
>  &inputph
>   tr2_ph=1.0d-14,
>   epsil=.true.,
>   prefix='diamond',
>   fildyn='diamond_g.dyn',
>   amass(1)=12.0107,
>   outdir='$TMP_DIR/'
>  /
> 0.0 0.0 0.0
> EOF
> $ECHO "  running the phonon calculation at Gamma...\c"
> $PH_COMMAND < diamond.phG.in > diamond.phG.out
> $ECHO " done"
> $ECHO
> $ECHO "$EXAMPLE_DIR: done"
> ================================================
>
> ------------------------------
> ????????-3.5G???20M??? <http://cn.mail.yahoo.com>
>
>


-- 
Nichols A. Romero, Ph.D.
1613 Denise Dr. Apt. D
Forest Hill, MD 21050
443-567-8328 (C)
410-306-0709 (O)
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From akohlmey at cmm.chem.upenn.edu  Thu Mar 29 17:55:18 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 29 Mar 2007 10:55:18 -0500 (EST)
Subject: [Pw_forum] Segmentation fault in Berry Phase calculation
In-Reply-To: <OF2356FD23.375AAEEC-ON492572AD.001F32A0-492572AD.0020595B@mta.fujifilm.co.jp>
Message-ID: <Pine.LNX.4.44.0703291053470.666-100000@localhost.localdomain>

On Thu, 29 Mar 2007 yukihiro_okuno at fujifilm.co.jp wrote:

YO> 
YO> Dear PWScf Users.
YO> 
YO> I'm now calculationg Berry Phase of PZT with shear stress (
YO> so the structure of crystal is monoclinic) in order to
YO> get piezoelectric coefficient e15.
YO> 
YO> But when I do the Berry Phase calculation, calculation was crushed
YO> with segmentation fault.
YO> 
YO> Why such a problem occurs?
YO> Are there any need to correct  memory allocation in the program ?
YO> 
YO> My enviroment is
YO> 
YO> compiler Intel FCC 8.1
YO> OS         linux FedoraCore
YO> math lib  mkl721

please check your stack size.
if you use intel fortran version 8.x and later,
you may need to increase the default stack size
(try to run the job after doing: ulimit -s unlimited)

if you run in parallel, you may have to ask your
sysadmin to change the defaults.

cheers,
   axel.


YO> 
YO> 
YO> My input file is as follow
YO> (with the stress = 0 case)
YO> 
YO> :scf calculation
YO> 
YO> 
YO> &control
YO>     calculation  = 'scf',
YO>     restart_mode = 'from_scratch',
YO>     pseudo_dir   = '/home/okuno/PWSCF/espresso-3.2/pseudo/',
YO>     outdir       = './',
YO>     prefix='PZT'
YO>  /
YO>  &system
YO>     ibrav=12
YO>     celldm(1)=7.57696068724
YO>     celldm(2)=2.09
YO>     celldm(3)=1.00
YO>     celldm(4)=0.00
YO>     nat=10
YO>     ntyp=4
YO>     nbnd=44
YO>     ecutwfc=60.0
YO>     ecutrho = 600.0
YO>     occupations = 'fixed'
YO>     degauss=0.00
YO>  /
YO>  &electrons
YO>     conv_thr = 1e-10,
YO>     mixing_beta=0.3,
YO>  /
YO> ATOMIC_SPECIES
YO>   Pb  207.2     pb_ps.uspp.UPF
YO>   Zr  91.224    zr_ps.uspp.UPF
YO>   Ti  47.867    ti_ps.uspp.UPF
YO>   O   15.9994   o_ps.uspp.UPF
YO> ATOMIC_POSITIONS {crystal}
YO> Pb       0.000000000   0.006012264   0.000000000
YO> Pb       0.000000000   0.537853199   0.000000000
YO> Zr       0.500000000   0.244190014   0.500000000
YO> Ti       0.500000000   0.740640879   0.500000000
YO> O        0.500000000   0.951075914   0.500000000
YO> O        0.500000000   0.478306726   0.500000000
YO> O        0.500000000   0.189000664   0.000000000
YO> O        0.000000000   0.189000664   0.500000000
YO> O        0.500000000   0.711889837   0.000000000
YO> O        0.000000000   0.711889837   0.500000000
YO> K_POINTS {automatic}
YO>   6 6 6 0 0 0
YO> 
YO> 
YO> For berry phase calculation.
YO> 
YO> &control
YO>     calculation  = 'nscf'
YO>     restart_mode = 'from_scratch'
YO>     pseudo_dir   = '/home/okuno/PWSCF/espresso-3.2/pseudo/'
YO>     outdir       = './'
YO>     lberry  = .true.
YO>     gdir = 2
YO>     nppstr = 10
YO>     prefix = 'PZT'
YO>  /
YO>  &system
YO>     ibrav=12
YO>     celldm(1)=7.57696068724
YO>     celldm(2)=2.09
YO>     celldm(3)=1.00
YO>     celldm(4)=0.00
YO>     nat=10
YO>     ntyp=4
YO>     nbnd=44
YO>     ecutwfc=60.0
YO>     ecutrho = 600.0
YO>     occupations = 'fixed'
YO>     degauss=0.00
YO>  /
YO>  &electrons
YO>     conv_thr = 1e-8,
YO>     mixing_beta=0.3,
YO>  /
YO> ATOMIC_SPECIES
YO>   Pb  207.2     pb_ps.uspp.UPF
YO>   Zr  91.224    zr_ps.uspp.UPF
YO>   Ti  47.867    ti_ps.uspp.UPF
YO>   O   15.9994   o_ps.uspp.UPF
YO> ATOMIC_POSITIONS {crystal}
YO> Pb       0.000000000   0.006012264   0.000000000
YO> Pb       0.000000000   0.537853199   0.000000000
YO> Zr       0.500000000   0.244190014   0.500000000
YO> Ti       0.500000000   0.740640879   0.500000000
YO> O        0.500000000   0.951075914   0.500000000
YO> O        0.500000000   0.478306726   0.500000000
YO> O        0.500000000   0.189000664   0.000000000
YO> O        0.000000000   0.189000664   0.500000000
YO> O        0.500000000   0.711889837   0.000000000
YO> O        0.000000000   0.711889837   0.500000000
YO> K_POINTS {automatic}
YO>   6 6 6 0 0 0
YO> 
YO> 
YO> 
YO> 
YO> _______________________________________________
YO> Pw_forum mailing list
YO> Pw_forum at pwscf.org
YO> http://www.democritos.it/mailman/listinfo/pw_forum
YO> 

-- 
=======================================================================
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.



From eyvaz_isaev at yahoo.com  Thu Mar 29 20:21:10 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Thu, 29 Mar 2007 11:21:10 -0700 (PDT)
Subject: [Pw_forum]  Strange behaviour of QE3.2 on a cluster
Message-ID: <691155.46719.qm@web60322.mail.yahoo.com>

Dear all, 

I have a very stupid situation running QE 3.2 CVS on IA64 based Linux cluster for phonon calculations for a bct lattice. 
The problem is that for 2 different, but almost identical jobs QE  behaves in a different way. Due to a queueing (and time) problem I started these two jobs using two different accounts.   For the first user its behaviour is OK, i.e. phonon calculations start and create  dynamical matrices  for several q-points. But for another user using the same binaries and on the same cluster it calculates phonons  only for the first (Gamma) point, then starts for nscf calculations  for the next q-point  (I see  last two lines "Band Structure Calculation" and "Davidson diagonalization ....." ), and then nothing happens for a long time.
The difference for these two calculations is only different c/a . 
Of course, I had to do the same test for the second user as for the first  (unfortunately, there is a queue problem) before sending the message,   but I can not explain such a kind strange  behaviour of the code. Very likely, it is connected to the cluster, because there is another Linux cluster where I am using QE 3.2, and it works well. 

Do you have an idea   how to fix this problem?

Very bests,
Eyvaz.




 
____________________________________________________________________________________
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From yaoxinxin at mail.sdu.edu.cn  Fri Mar 30 10:55:24 2007
From: yaoxinxin at mail.sdu.edu.cn (yaoxinxin)
Date: Fri, 30 Mar 2007 16:55:24 +0800
Subject: [Pw_forum] symmetry operations in vc-relax
Message-ID: <375244924.11575@mail.sdu.edu.cn>

Hi,
   I did vc-relax calculations and got some problems. 
   In the namelist &system, I set nosym=.false. . After one scf calculation, I got
an error as follows:

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from checkallsym : error #         1
     some of the original symmetry operations not satisfied 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

  In the vc-relax calculation, the position of atoms are inevitably changed. Of
course, some symmetries are lost. How could I set parameters to avoid this error?

Thank you!

Xinxin Yao




From eyvaz_isaev at yahoo.com  Fri Mar 30 11:51:19 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 30 Mar 2007 02:51:19 -0700 (PDT)
Subject: [Pw_forum] symmetry operations in vc-relax
Message-ID: <791307.51712.qm@web60316.mail.yahoo.com>

Hi,

Try  nosym=.true. (i.e. no symmetry is considered). Keyword nosym=.false. makes available all symmetry operations  specific for a crystal you consider. 

Bests,
Eyvaz.

----- Original Message ----
From: yaoxinxin <yaoxinxin at mail.sdu.edu.cn>
To: pw_forum at pwscf.org
Sent: Friday, March 30, 2007 12:55:24 PM
Subject: [Pw_forum] symmetry operations in vc-relax

Hi,
   I did vc-relax calculations and got some problems. 
   In the namelist &system, I set nosym=.false. . After one scf calculation, I got
an error as follows:

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from checkallsym : error #         1
     some of the original symmetry operations not satisfied 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

  In the vc-relax calculation, the position of atoms are inevitably changed. Of
course, some symmetries are lost. How could I set parameters to avoid this error?

Thank you!

Xinxin Yao


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





 
____________________________________________________________________________________
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Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains.
http://farechase.yahoo.com/promo-generic-14795097


From gilles.hug at onera.fr  Fri Mar 30 14:36:12 2007
From: gilles.hug at onera.fr (Gilles Hug)
Date: Fri, 30 Mar 2007 14:36:12 +0200
Subject: [Pw_forum] intel mac - compilation with ifort/icc and not gcc
Message-ID: <B3A79CE4-DA2C-44FD-BA36-55F96E934F3B@onera.fr>

Dear Espressonists,

I am new here and trying to compile Espresso with Intel Ifort, icc  
and MKL on a Mac with Intel procs.

When I configure i get :

> --------------------------------------------------------------------
> configure: success

So I assume this part went ok.

Then I try make all
I get this message :

> end module iotk_base
> i686-apple-darwin8-gcc-4.0.1: c: No such file or directory
> i686-apple-darwin8-gcc-4.0.1: iotk_base.F90: No such file or directory
> i686-apple-darwin8-gcc-4.0.1: no input files
> make[2]: *** [iotk_base.o] Error 1
> make[1]: *** [libiotk.a] Error 2
make: *** [libiotk] Error 2

I don't understand why gcc comes in the play here since it does not  
appear in any makefile. I tried to configure with the make_sys.mac  
file provided by the post of Matteo Cococcioni but it ends up with  
the same result.

Any help appreciated,
Thanks
Gilles



From giannozz at nest.sns.it  Fri Mar 30 14:53:43 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 30 Mar 2007 14:53:43 +0200
Subject: [Pw_forum] intel mac - compilation with ifort/icc and not gcc
In-Reply-To: <B3A79CE4-DA2C-44FD-BA36-55F96E934F3B@onera.fr>
References: <B3A79CE4-DA2C-44FD-BA36-55F96E934F3B@onera.fr>
Message-ID: <600FD0D2-D24B-4403-8B05-9380E25AE48E@nest.sns.it>

On Mar 30, 2007, at 14:36 , Gilles Hug wrote:

> I am new here and trying to compile Espresso

which version?
---
Paolo Giannozzi, Democritos and University of Udine, Italy




From matteo at umn.edu  Fri Mar 30 16:20:31 2007
From: matteo at umn.edu (Matteo Cococcioni)
Date: 30 Mar 2007 09:20:31 -0500
Subject: [Pw_forum] intel mac - compilation with ifort/icc and not gcc
In-Reply-To: <B3A79CE4-DA2C-44FD-BA36-55F96E934F3B@onera.fr>
References: <B3A79CE4-DA2C-44FD-BA36-55F96E934F3B@onera.fr>
Message-ID: <Prayer.1.0.16.0703300920310.20839@wm2.tc.umn.edu>

Dear Gilles,

I remember (I haven't compiled on my mac in while) that I had to download 
gcc as well and install it before compiling. From your error message I'm 
not sure you did that. I don't remember what package I downloaded but you 
probably can find many (go to a mac-specific website).

Hope this helps,

Matteo



On Mar 30 2007, Gilles Hug wrote:

>Dear Espressonists,
>
>I am new here and trying to compile Espresso with Intel Ifort, icc  
>and MKL on a Mac with Intel procs.
>
>When I configure i get :
>
>> --------------------------------------------------------------------
>> configure: success
>
>So I assume this part went ok.
>
>Then I try make all
>I get this message :
>
>> end module iotk_base
>> i686-apple-darwin8-gcc-4.0.1: c: No such file or directory
>> i686-apple-darwin8-gcc-4.0.1: iotk_base.F90: No such file or directory
>> i686-apple-darwin8-gcc-4.0.1: no input files
>> make[2]: *** [iotk_base.o] Error 1
>> make[1]: *** [libiotk.a] Error 2
>make: *** [libiotk] Error 2
>
>I don't understand why gcc comes in the play here since it does not  
>appear in any makefile. I tried to configure with the make_sys.mac  
>file provided by the post of Matteo Cococcioni but it ends up with  
>the same result.
>
>Any help appreciated,
>Thanks
>Gilles
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Matteo Cococcioni
Department of Chemical Engineering and Materials Science
University of Minnesota
151 Amundson Hall
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



From eyvaz_isaev at yahoo.com  Fri Mar 30 19:00:20 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 30 Mar 2007 10:00:20 -0700 (PDT)
Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1399 - 12 msgs
Message-ID: <310992.85641.qm@web60319.mail.yahoo.com>

Hi Saman,

Please find bands_3.f and a Gnuplot script sent to the forum approximately 1.5 months ago. 
Any questions, let me know.

Bests,
Eyvaz.


----- Original Message ----
From: saman ghaderyan <ghaderyan at gmail.com>
To: pw_forum at pwscf.org
Sent: Wednesday, March 28, 2007 1:27:21 AM
Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1399 - 12 msgs

hi
how i can plot phonon frequency for deferent q-victor (example 6).
thanks



On 3/27/07, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote:
> Send Pw_forum mailing list submissions to
>     pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>     http://www.democritos.it/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
>     pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
>     pw_forum-admin at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
>    1. Re: Does anyone have RRKJ uspp for Cr? (degironc)
>    2. Re: Does anyone have RRKJ uspp for Cr? (Nicola Marzari)
>    3. Re: Problem with pp.x (Paolo Giannozzi)
>    4. Re: masses and dt in vc-relax (Paolo Giannozzi)
>    5. Re: Aluminium EPC at X (Paolo Giannozzi)
>    6. Re: spilling parameter in Lowdin - how to assign the charge that went
> into Nirvana ? (Paolo Giannozzi)
>    7. grid without symmtrical problem (Ezad Shojaee)
>    8. (no subject) (hyello25 Qgrui)
>    9. Re: grid without symmtrical problem (degironc)
>   10. Re: Inconsistent pp.x and projwfc.x results? (Paolo Giannozzi)
>   11. Re: calculation crash (Paolo Giannozzi)
>   12. Re: Is the CG diagonalization suitable for the general matrix? (Paolo
> Giannozzi)
>
> --__--__--
>
> Message: 1
> Date: Tue, 27 Mar 2007 08:29:27 +0200
> From: degironc <degironc at sissa.it>
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Does anyone have RRKJ uspp for Cr?
> Reply-To: pw_forum at pwscf.org
>
> I don't have any..
> I hope this info from the adomic_doc/INPUT_LD1 file might be useful:
>        rho0 = charge at the origin: when the Rabe-Rappe-Kaxiras-Joannopoulos
>              method with 3 Bessel functions fails, specifying rho0 > 0
>              may allow to override the problem (using 4 Bessel functions)
>              Typical values are in the order of 0.01-0.02       (default
> 0.0)
>
> best, stefano
>
> Chao Cao wrote:
>
> > As title. I have tried to generate the pseudopotential myself, but it
> > seems to be way too complicated. It kept complaining about stuff like:
> >
> >
> >             integrated core pseudo-charge :   5.66
> >     from compute phi : info #        -1
> >     negative determinant
> >
> >         1 ld=   0.518427 f2ae  0.606247 faenor  0.141808
> >
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >     from gener_pseudo : error #         1
> >     too many nodes
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >
> >     stopping ...
> >
> >
> > Thanks a lot.
> >
> > Chao Cao
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --__--__--
>
> Message: 2
> Date: Tue, 27 Mar 2007 03:32:12 -0400
> From: Nicola Marzari <marzari at MIT.EDU>
> Organization: Massachusetts Institute of Technology
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Does anyone have RRKJ uspp for Cr?
> Reply-To: pw_forum at pwscf.org
>
>
>
> Another possibility is to generate a Cr using David Vanderbilt
> code: http://www.physics.rutgers.edu/~dhv/uspp/ , and then convert it
> to UPF format.
>
> There is an input file there for a PW91 Cr that looks good.
>
>                 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
>
> --__--__--
>
> Message: 3
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] Problem with pp.x
> Date: Tue, 27 Mar 2007 09:43:18 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 26, 2007, at 15:11 , Francesco.Stellato at roma2.infn.it wrote:
>
> >     outdir='/nfs_home/home0/molcp/velia/density_test/tmp_scf/'
>
> do not write to nfs-mounted file system: it is a recipe for disaster
>
> > p6_17713:  p4_error: net_recv read:  probable EOF on socket: 1
> > rm_l_1_9870: (6.535927) net_send: could not write to fd=5, errno = 32
>
> it looks like an error while writing to unit 5. Errors like this,
> occurring in system library calls, are impossible to pinpoint
> unless one finds under which exact circumstances it occurs,
> whether it is reproducible or not, and so on and so forth.
> They are more often a sign of problems with mpi or the
> filesystem or both rather than in the code itself
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 4
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] masses and dt in vc-relax
> Date: Tue, 27 Mar 2007 10:03:04 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 25, 2007, at 20:05 , Jess Kondor wrote:
>
> > Does it mean that I cannot use the settings from the small system
> > and apply them for bigger system?
>
> larger systems typically have more convergence problems than
> small systems, so they might need a smaller time step
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 5
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] Aluminium EPC at X
> Date: Tue, 27 Mar 2007 10:07:24 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 25, 2007, at 19:58 , Amit Kumar wrote:
>
> > I'm very much confused with the results of the electron-phonon
> > coupling
> > of Aluminium  at X-point.  You can see a large discrepancy in the
> > results
> > of Example  No. 7.
>
> >    Old version ::::
> >       Gaussian Broadening:   0.010 Ry, ngauss=   1
> > [...]
> >     Newer  Version  :::::::::
> >       Gaussian Broadening:   0.010 Ry, ngauss=   0
>
> would you mind reading the answer that you get before
> asking new questions, or more exactly, the same question?
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 6
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] spilling parameter in Lowdin - how to assign the
> charge that went into Nirvana ?
> Date: Tue, 27 Mar 2007 10:10:10 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 24, 2007, at 15:54 , Andrea Ferretti wrote:
>
> > Lowding orbitals in Quantum-Espresso (at least as far as I know) are
> > computed from the atomic reference states from pseudopotential data
> > according to:
> >
> > S_ij = < i | j >      are the overlaps of atomic orbitals i and j
> >
> > lowding orbitals are then obtained as
> > | low_i > =  R_ij  | j >
> >
> > where  R = S^{-1/2}
> >
> > so I think there is no optimization (in the sense of the paper above)
> > but maybe I am missing something
>
> no, you aren't missing anything: the atomic basis is not optimized
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 7
> From: "Ezad Shojaee" <ezadshojaee at hotmail.com>
> To: Pw_forum at pwscf.org
> Date: Tue, 27 Mar 2007 10:25:49 +0000
> Subject: [Pw_forum] grid without symmtrical problem
> Reply-To: pw_forum at pwscf.org
>
> hi
> is it possible to define a grid with non-equal numbers for ph.x not to have
> problem with q2r.x ? because i tried sample 221 and q2r.x  gave symmetrical
> error;  while there was no error with 222 sample.
> is there a way what is it?
> thanx
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE!
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
>
>
> --__--__--
>
> Message: 8
> Date: Tue, 27 Mar 2007 19:39:36 +0800
> From: "hyello25 Qgrui" <hyello25 at gmail.com>
> To: pw_forum at pwscf.org
> Subject: [Pw_forum] (no subject)
> Reply-To: pw_forum at pwscf.org
>
> ------=_Part_4479_6415940.1174995576279
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Content-Transfer-Encoding: 7bit
> Content-Disposition: inline
>
> hyello25 at gmail.com
>
> ------=_Part_4479_6415940.1174995576279
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: 7bit
> Content-Disposition: inline
>
> <a href="mailto:hyello25 at gmail.com">hyello25 at gmail.com</a>
>
> ------=_Part_4479_6415940.1174995576279--
>
> --__--__--
>
> Message: 9
> Date: Tue, 27 Mar 2007 15:14:28 +0200
> From: degironc <degironc at sissa.it>
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] grid without symmtrical problem
> Reply-To: pw_forum at pwscf.org
>
> The grid should have the symmetry of your system.
> Therefore it depends on the system.
> stefano
>
> Ezad Shojaee wrote:
>
> > hi
> > is it possible to define a grid with non-equal numbers for ph.x not to
> > have problem with q2r.x ? because i tried sample 221 and q2r.x  gave
> > symmetrical error;  while there was no error with 222 sample.
> > is there a way what is it?
> > thanx
> >
> > _________________________________________________________________
> > Express yourself instantly with MSN Messenger! Download today it's
> > FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --__--__--
>
> Message: 10
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] Inconsistent pp.x and projwfc.x results?
> Date: Tue, 27 Mar 2007 15:21:53 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 23, 2007, at 19:14 , Conor Hogan wrote:
>
> > Basically the character of the states produced by projwfc.x (atomic
> > projection) and pp.x (plotting the state directly) differ in the
> > case I'm
> > studying
>
> one thing to try is to re-do the calculation using k=(0,0,0)
> instead of 'Gamma tricks'. It should work in both cases,
> but who knows. If this is the problem, it should show up
> even in much smaller calculations
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 11
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] calculation crash
> Date: Tue, 27 Mar 2007 15:39:26 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> On Mar 22, 2007, at 13:53 , lan haiping wrote:
>
> >      from  fft_dlay_set  : error #         7
> >       inconsistent number of sticks
>
> very strange. Try to run the job in serial execution and see
> what happens
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --__--__--
>
> Message: 12
> From: Paolo Giannozzi <giannozz at nest.sns.it>
> Subject: Re: [Pw_forum] Is the CG diagonalization suitable for the general
> matrix?
> Date: Tue, 27 Mar 2007 16:19:50 +0200
> To: pw_forum at pwscf.org
> Reply-To: pw_forum at pwscf.org
>
>
> --Apple-Mail-1--870504716
> Content-Transfer-Encoding: 7bit
> Content-Type: text/plain;
>     charset=US-ASCII;
>     format=flowed
>
>
> On Mar 20, 2007, at 16:39 , xqhu at duke.edu wrote:
>
> > I'm trying to implement PZ-SIC in PWSCF.
>
> good luck!
>
> > In PZ-SIC, the Fock matrix is not symmetric any more.
> > I can not use DIIS or Davidson since both of them are
> > for the hermitian matrix. I checked CG codes. It seems
> > that CG can be used in the general matrix. If you are familiar
> > with the CG diagonalization, please tell me some details.
>
> all I know is written here
>
> Paolo
>
>
> --Apple-Mail-1--870504716
> Content-Transfer-Encoding: 7bit
> Content-Type: application/octet-stream;
>     x-unix-mode=0644;
>     name=diago.tex
> Content-Disposition: attachment;
>     filename=diago.tex
>
> \documentstyle[11pt]{report}
> \pagestyle{empty}
> \textwidth = 16 cm
> \textheight = 24 cm
> \topmargin =  0.0 cm
> \oddsidemargin = 0.0 cm
> \begin{document}
>
> {\bf Poor-man conjugate-gradient single-band diagonalisation}.
>
> \par\noindent
> The problem: minimize
> \begin{equation}
> f_j={1\over 2} <\psi_j|H|\psi_j>
> \end{equation}
> under the constraints that
> \begin{equation}
> <\psi_j|\psi_j>=1, \qquad <\psi_j|\psi_k>=0,\quad k<j
> \end{equation}
> This is equivalent to solve the Euler-Lagrange problem of minimising
> \begin{equation}
> \widetilde f_j={1\over 2} <\psi_j|H|\psi_j> -
>   \epsilon_j (<\psi_j|\psi_j>-1) -
>   \sum_{k<j} \lambda_{jk} <\psi_j|\psi_k>
> \end{equation}
> {\bf First step.}
> For any given index $j$ we assume a starting trial eigenvector
> $|\psi^0_j>$ such that
> \begin{equation}
> <\psi^0_j|\psi^0_j>=1,\qquad <\psi^0_j|\psi_k>=0, \quad k<j
> \end{equation}
> The gradient $|g^0_j>$ is
> \begin{equation}
> |g^0_j>=H|\psi^0_j> - \epsilon^0_j |\psi^0_j> -
>        \sum_{k<j} \lambda^0_{jk}|\psi_k>
> \end{equation}
> where
> \begin{equation}
> \lambda^0_{jk} = <\psi_k|(H-\epsilon^0_j)|\psi^0_j>
> \end{equation}
> ensures that $<g^0_j|\psi_k>=0$, while
> \begin{equation}
> \epsilon^0_j = <\psi^0_j|H|\psi^0_j>
> \end{equation}
> ensures that $<g^0_j|\psi^0_j>=0$.
> Let us consider the conjugate direction $|h^0_j>=|g^0_j>$ and the
> normalized direction $|\widetilde h^0_j>$:
> \begin{equation}
> |\widetilde h^0_j> = {|h^0_j>\over <h^0_j|h^0_j>^{1/2}}
> \end{equation}
> By construction
> \begin{equation}
> <\widetilde h^0_j|\widetilde h^0_j>=1,  \quad
> <\widetilde h^0_j|\psi^0_j>=0,  \quad
> <\widetilde h^0_j|\psi_k>=0  \quad
> \end{equation}
> Consider the vector
> \begin{equation}
> |\psi^1_j(\theta)>= \cos\theta |\psi^0_j> + \sin\theta|\widetilde h^0_j>
> \end{equation}
> By construction,
> \begin{equation}
> <\psi^1_j(\theta)|\psi^1_j(\theta)>=1, \qquad
> <\psi^1_j(\theta)|\psi_k>=0,\quad k<j
> \end{equation}
> We look for the value of $\theta$ that minimises
> \begin{equation}
> \epsilon^1_j(\theta) = <\psi^1_j(\theta)|H|\psi^1_j(\theta)>
> \end{equation}
> The solution is
> \begin{equation}
> \theta^0_j={1\over 2}
> \mbox{arctag}\left({a^0_j\over\epsilon^0_j-b^0_j}\right)
> \end{equation}
> where
> \begin{equation}
> a^0_j=< \psi^0_j|H|\widetilde h^0_j> + c.c., \quad
> b^0_j=< \widetilde h^0_j|H|\widetilde h^0_j>
> \end{equation}
> and
> \begin{equation}
> \epsilon^1_j = {\epsilon^0_j+b^0_j - \sqrt{(\epsilon^0_j-b^0_j)^2
>                                      +(a^0_j)^2}\over 2}
> \end{equation}
>
> {\bf Following steps.} We construct the new gradient
> $|g^n_j>$ as above and the new conjugate direction
> $|h^n_j>$ as in the conjugate gradient method. We define
> \begin{equation}
> |u^n_j>=|g^n_j>+\gamma^{n-1}|h^{n-1}_j>
> \end{equation}
> \begin{equation}
> \gamma^{n-1}={<g^n_j|g^n_j>\over<g^{n-1}_j|g^{n-1}_j>}
> \quad\mbox{or}\quad
> \gamma^{n-1}={<g^n_j-g^{n-1}|g^n_j>\over<g^{n-1}_j|g^{n-1}_j>}
> \end{equation}
> (left: Fletcher-Reeves, right: Polak-Ribi\`ere). By construction,
> \begin{equation}
> <g^n_j|\psi_k>=0 \longrightarrow <u^n_j|\psi_k>=0
> \end{equation}
> but
> \begin{equation}
> \beta^n_j= <u^n_j|\psi^n_j>=\gamma^{n-1}_j<h^{n-1}_j|\psi^n_j>
>                 =\gamma^{n-1}_j\sin\theta^{n-1}_j
>                      <h^{n-1}_j|\widetilde h^{n-1}_j> \neq 0
> \end{equation}
> so that explicit orthogonalization of $|\psi^n_j>$ to $|u^n_j>$ is
> needed (it is a consequence of the constraint of unitary norm):
> \begin{equation}
> |h^n_j>=|u^n_j> - \beta^n_j |\psi^n_j>
> \end{equation}
> Then one proceeds as above.
>
> \par\bigskip
> {\bf Preconditioning.} We define a (diagonal) preconditioning matrix
> $P$ and auxiliary functions $|y>$ :
> \begin{equation}
> |y_j>=P^{-1}|\psi_j>
> \end{equation}
> One has to solve the equivalent problem of minimizing
> \begin{equation}
> f_j={1\over 2} <y_j|(PHP)|y_j>
> \end{equation}
> under the constraints that
> \begin{equation}
> <y_j|P^2|y_j>=1, \qquad <y_j|P|\psi_k>=0,\quad k<j
> \end{equation}
> Let us consider only the first constraint. The problem is equivalent
> to the minimisation of
> \begin{equation}
> \widetilde f_j={1\over 2} <y_j|(PHP)|y_j> -
>                \widetilde\epsilon_j (<y_j|P^2|y_j>-1)
> \end{equation}
> The gradient $|g_j>$ is now given by
> \begin{equation}
> |g_j>=(PHP)|y_j> - \widetilde\epsilon_j P^2|y_j>
> \end{equation}
> where
> \begin{equation}
> \widetilde\epsilon_j = {<y_j| P^2 (PHP)|y_j> \over <y_j| P^2 P^2| y_j>}
> \end{equation}
> ensures that
> \begin{equation}
> <g_j|P^2|y_j> = 0
> \end{equation}
> The second set of constraints is accounted for in a different way. We
> want that
> \begin{equation}
> <g_j|P|\psi_k> = 0
> \end{equation}
> This is obtained by orthogonalizing $|Pg_j>$ to $|\psi_k>$:
> \begin{equation}
> |Pg_j>=P(PHP)|y_j> - \widetilde\epsilon_j P^3|y_j>
>      - \sum_{k<j}\lambda_{jk}|\psi_k>
> \end{equation}
> where
> \begin{equation}
> \lambda_{jk} = <\psi_k|P(PHP)-P\widetilde\epsilon_j P^3|y_j>
> \end{equation}
> The reason for the different treatment of the second set of
> constraints is that $<\psi_k|P^2|\psi_l>\neq 0$.
>
> {\bf Modified preconditioned algorithm}. Starting from an initial
> guess $|\psi^0_j>$ (where $<\psi_k|\psi^0_j>=0$,
> $<\psi^0_j|\psi^0_j>=1$), one searches for new vector as:
> \begin{equation}
> |\psi^n_j(\theta)>= \cos\theta |\psi^{n-1}_j> +
>                     \sin\theta |P\widetilde h^{n-1}_j>
> \end{equation}
> where
> \begin{equation}
> |P\widetilde h^n_j> = {|Ph^n_j>\over <Ph^n_j|Ph^n_j>^{1/2}}
> \end{equation}
> and $|Ph^n_j>$ is the conjugate gradient. We define
> \begin{equation}
> |Pu^n_j>=|Pg^n_j>+\gamma^{n-1}|Ph^{n-1}_j>,
> \end{equation}
> \begin{equation}
> \gamma^{n-1}={<Pg^n_j|P^{-2}|Pg^n_j>\over<Pg^{n-1}_j|P^{-2}|Pg^{n-1}_j>}
> \quad\mbox{or}\quad
> \gamma^{n-1}={<Pg^n_j-Pg^{n-1}|P^{-2}|Pg^n_j> \over
>               <Pg^{n-1}_j|P^{-2}|Pg^{n-1}_j>}
> \end{equation}
> with $\gamma^{-1}=0$.
> The gradient $|Pg^n_j>$ is given by
> \begin{equation}
> |Pg_j>=P^2H|\psi_j> - \widetilde\epsilon_j P^2|\psi_j>-
>        \sum_{k<j}\lambda_{jk}|\psi_k>
> \end{equation}
> where
> \begin{equation}
> \lambda_{jk} = <\psi^n_k|P^2H-\widetilde\epsilon^n_j P^2|\psi^n_j>,\qquad
> \widetilde\epsilon_j = {<\psi^n_j| P^2 H|\psi^n_j> \over <\psi^n_j|
> P^2| \psi^n_j>}
> \end{equation}
> $|Pg^n_j>$ is by construction orthogonal to both
> $|\psi_k>$ and $|\psi^n_j>$, but $|Pu^n_j>$ is not
> orthogonal to $|\psi^n_j>$ for $n>0$:
> \begin{equation}
> \beta^n_j= <Pu^n_j|\psi^n_j>=\gamma^{n-1}_j<Ph^{n-1}_j|\psi^n_j>
>                             =\gamma^{n-1}_j\sin\theta^{n-1}_j
>                             <Ph^{n-1}_j|\widetilde Ph^{n-1}_j> \neq 0
> \end{equation}
> The conjugate direction $|Ph^n_j>$ is obtained from orthogonalization
> of $|Pu^n_j>$ to $|\psi^n_j>$:
> \begin{equation}
> |Ph^n_j>=|Pu^n_j> - \beta^n_j |\psi^n_j>
> \end{equation}
>
> {\bf Remarks}.
>
> -- Only $P^2$ (or $P^{-2}$) is actually used. A simple choice for
> $P^2$ is
> \begin{equation}
> P^2({\bf G},{\bf G}') = {2m \over
>                          \hbar^2({\bf k+G})^2}\delta_{\bf GG}'
> \end{equation}
>
> -- $\widetilde\epsilon^n_j$ will eventually converge to the real
> eigenvalue $\epsilon_j$ but in the preconditioned case they are not
> the same
>
> -- The algorithm is quite the same for hermitian Hamiltonians.
> $\theta$ and $\gamma$ are still real quantities, $beta$ and $\lambda$
> are no longer real.
>
> \newpage
>
> {\bf Conjugate-Gradient solution of linear systems}
>
> First problem: minimise the functional
> \begin{equation}
> f={1\over 2} <\delta\psi|A|\delta\psi> - {1\over 2}(<b|\delta\psi>+h.c.)
> \end{equation}
> under the constraint
> \begin{equation}
> <\psi|\delta\psi> = 0
> \end{equation}
> that is
> \begin{equation}
> \widetilde f = {1\over 2} <\delta\psi|A|\delta\psi>
>              - <b|\delta\psi>
>              - \lambda <\psi|\delta\psi>
> \end{equation}
> The gradient $|g>$ is
> \begin{equation}
> |g> = A|\delta\psi> - |b> -\lambda |\psi>
> \end{equation}
> By imposing that $<g|\psi>=0$ one gets
> \begin{equation}
> \lambda = <\psi|A|\delta\psi>-<\psi|b>
> \end{equation}
>
>
>
> \end{document}
>
> --Apple-Mail-1--870504716
> Content-Transfer-Encoding: 7bit
> Content-Type: application/octet-stream;
>     x-unix-mode=0644;
>     name=diago_us.tex
> Content-Disposition: attachment;
>     filename=diago_us.tex
>
> \documentstyle[11pt]{report}
> \pagestyle{empty}
> \textwidth = 16 cm
> \textheight = 25 cm
> \topmargin =  -1.0 cm
> \oddsidemargin = 0.0 cm
> \begin{document}
> {\bf Generalized problem}.
>
> \par\noindent
> The problem: minimize
> \begin{equation}
> f_j={1\over 2} <\psi_j|H|\psi_j>
> \end{equation}
> under the constraints:
> \begin{equation}
> <\psi_j|S|\psi_j>=1, \qquad <\psi_j|S|\psi_k>=0,\quad k<j
> \end{equation}
> %The alghoritm used to solve the problem is exactly the same as the one
> %used for "normal" constrains, apart from
> %the insertion of the S matrix in the right places.
> %
> % l'algoritmo e` lo stesso perche` appunto era gia` implementato con il
> % precondizionamento che tiene conto degli accorgimenti particolari da
> % fare sull'ortogonalizzazione, pero` la scrittura di questa prima parte
> % non e` vero che e` la stessa del caso senza overlap
> %
> %
> {\bf bisogna fare come per il problema con il precondizionamento perche`
> $<\psi^0_j|{\bf S^2}|\psi_k> \ne 0$ }
> ...This is equivalent to solve the Euler-Lagrange problem of minimising
> \begin{equation}
> \widetilde f_j={1\over 2} <\psi_j|H|\psi_j> -
>   \epsilon_j (<\psi_j|S|\psi_j>-1) -
>   \sum_{k<j} \lambda_{jk} <\psi_j|S|\psi_k>
> \end{equation}
> If we consider the gradient of the expression above we have:
> \begin{equation}\label{prima}
> |g_j>=H|\psi_j> - \epsilon_j S|\psi_j> -
>        \sum_{k<j} \lambda_{jk} S|\psi_k>
> \end{equation}
> but we are not able to find a simple expression for $\epsilon_j$ and
> $\lambda_{jk}$ in order to have $<g_j|S|\psi_k>=0$ because
> $<\psi_j|S^2|\psi_k> \ne 0$.  \\
> So we use a slightly different approach:
> we firstly consider only the first constraint. The problem is
> equivalent to the minimization of
>
> \begin{equation}
> \widetilde f_j={1\over 2} <\psi_j|H|\psi_j> -
>   \epsilon_j (<\psi_j|S|\psi_j>-1)
> \end{equation}
> {\bf First step.}
> For any given index $j$ we assume a starting vector
> $|\psi^0_j>$ such that
> \begin{equation}
> <\psi^0_j|S|\psi^0_j>=1,\qquad <\psi^0_j|S|\psi_k>=0, \quad k<j
> \end{equation}
> The gradient $|g^0_j>$ is
> \begin{equation}
> |g^0_j>=H|\psi^0_j> - \epsilon^{0^*}_j S|\psi^0_j>
> \end{equation}
> where
> \begin{equation}
> \epsilon^{0^*}_j = { <\psi^0_j|SH|\psi^0_j> \over <\psi^0_j|S^2|\psi^0_j>}
> \end{equation}
> ensures that $<g^0_j|S|\psi^0_j>=0$. We also define:
> \begin{equation}
> \epsilon^{0}_j = <\psi^0_j|H|\psi^0_j>
> \end{equation}
> which is an approximation for the true eigenvalue $\epsilon_j$ of H.
> The second set of constraints is accounted requiring that
> \begin{equation}
> <g^0_j|S|\psi_k>=0
> \end{equation}
> This is obtained by an explicit Gram-Shmidt orthogonalization, with the
> overlap matrix S, of $|g^0_j>$
> to $|\psi_k>, k<j $
> \begin{equation} \label{seconda}
> |g^0_j> = H|\psi^0_j> - \epsilon^{0^*}_j S|\psi^0_j> -
> \sum_{k<j}\lambda^0_{kj} |\psi_k>
> \end{equation}
> where
> \begin{equation}
> \lambda^0_{kj}=<g^0_j|S|\psi_k>
> \end{equation}
> Note that equation \ref{seconda} is very much different from equation
> \ref{prima}, the last term of the right hand side is
> $ \sum_{k<j}\lambda^0_{kj} |\psi_k> $ instead of
> $\sum_{k<j}\lambda^0_{kj} S|\psi_k>$.\\
> Now: let us consider the conjugate direction $|h^0_j>=|g^0_j>$ and the
> normalized direction $|\widetilde h^0_j>$:
> \begin{equation}
> |\widetilde h^0_j> = {|h^0_j>\over <h^0_j|S|h^0_j>^{1/2}}
> \end{equation}
> By construction
> \begin{equation}
> <\widetilde h^0_j|S|\widetilde h^0_j>=1,  \quad
> <\widetilde h^0_j|S|\psi^0_j>=0,  \quad
> <\widetilde h^0_j|S|\psi_k>=0  \quad
> \end{equation}
> Consider the vector
> \begin{equation}
> |\psi^1_j(\theta)>= \cos\theta |\psi^0_j> + \sin\theta|\widetilde h^0_j>
> \end{equation}
> By construction,
> \begin{equation}
> <\psi^1_j(\theta)|S|\psi^1_j(\theta)>=1, \qquad
> <\psi^1_j(\theta)|S|\psi_k>=0,\quad k<j
> \end{equation}
> We look for the value of $\theta$ that minimizes
> \begin{equation}
> \epsilon^1_j(\theta) = <\psi^1_j(\theta)|H|\psi^1_j(\theta)>
> \end{equation}
> The solution is
> \begin{equation}
> \theta^0_j={1\over 2}
> \mbox{arctag}\left({a^0_j\over\epsilon^0_j-b^0_j}\right)
> \end{equation}
> where
> \begin{equation}
> a^0_j=< \psi^0_j|H|\widetilde h^0_j> + c.c., \quad
> b^0_j=< \widetilde h^0_j|H|\widetilde h^0_j>
> \end{equation}
> and
> \begin{equation}
> \epsilon^1_j = {\epsilon^0_j+b^0_j - \sqrt{(\epsilon^0_j-b^0_j)^2
>                                      +(a^0_j)^2}\over 2}
> \end{equation}
> which is a new approximation for $\epsilon_j$.\\
> {\bf Following steps.} We construct the new gradient
> $|g^n_j>$ as above and the new conjugate direction
> $|h^n_j>$ as in the conjugate gradient method. We define
> \begin{equation}
> |u^n_j>=|g^n_j>+\gamma^{n-1}_j|h^{n-1}_j>
> \end{equation}
> \begin{equation}
> \gamma^{n-1}_j={<g^n_j|S|g^n_j>\over<g^{n-1}_j|S|g^{n-1}_j>}
> \simeq{<g^n_j-g^{n-1}_j|S|g^n_j>\over<g^{n-1}_j|S|g^{n-1}_j>}
> \end{equation}
> By construction,
> \begin{equation}
> <g^n_j|S|\psi_k>=0 \longrightarrow <u^n_j|S|\psi_k>=0
> \end{equation}
> but
> \begin{equation}
> \beta^n_j= <u^n_j|S|\psi^n_j>=\gamma^{n-1}_j<h^{n-1}_j|S|\psi^n_j>
>                 =\gamma^{n-1}_j\sin\theta^{n-1}_j
>                      <h^{n-1}_j|S|\widetilde h^{n-1}_j> \neq 0
> \end{equation}
> so that explicit orthogonalization of $|\psi^n_j>$ to $|u^n_j>$ is
> needed (it is a consequence of the constraint of unitary norm):
> \begin{equation}
> |h^n_j>=|u^n_j> - \beta^n_j |\psi^n_j>
> \end{equation}
> Then one proceeds as above, finds $\epsilon^n_j$ and check if
> $\epsilon^n_j - \epsilon^{n-1}_j < tol$, where $tol$ is a small number
> which defines the precision of $\epsilon_j$.
> \par\bigskip
> {\bf Preconditioning.} We define a (diagonal) preconditioning matrix
> $P$ and auxiliary functions $|y>$ :
> \begin{equation}
> |y_j>=P^{-1}|\psi_j>
> \end{equation}
> One has to solve the equivalent problem of minimizing
> \begin{equation}
> f_j={1\over 2} <y_j|(PHP)|y_j>
> \end{equation}
> under the constraints that
> \begin{equation}
> <y_j|(PSP)|y_j>=1, \qquad <y_j|PS|\psi_k>=0,\quad k<j
> \end{equation}
> Again we firstly consider only the first constraint. The problem is
> equivalent
> to the minimization of
> \begin{equation}
> \widetilde f_j={1\over 2} <y_j|(PHP)|y_j> -
>                \widetilde\epsilon_j (<y_j|(PSP)|y_j>-1)
> \end{equation}
> The gradient $|g_j>$ is now given by
> \begin{equation}
> |g_j>=(PHP)|y_j> - \widetilde\epsilon_j(PSP)|y_j>
> \end{equation}
> where
> \begin{equation}
> \widetilde\epsilon_j = {<y_j|(PSP)(PHP)|y_j> \over <y_j|(PSP)^2| y_j>}
> \end{equation}
> ensures that
> \begin{equation}
> <g_j|(PSP)|y_j> = 0
> \end{equation}
> Now we have to care about the second set of constraints. We want that
> \begin{equation}
> <g_j|PS|\psi_k> = 0
> \end{equation}
> And again this is obtained by orthogonalizing, with the overlap matrix $S$,
> $|Pg_j>$ to $|\psi_k> ,k<j$:
> \begin{equation}
> |Pg^0_j> = |Pg^0_j> - \sum_{k<j} <g^0_j|PS|\psi_k>|\psi_k>
> \end{equation}
>
> {\bf Modified preconditioned algorithm}. Starting from an initial
> guess $|\psi^0_j>$ (where $<\psi_k|S|\psi^0_j>=0$,
> $<\psi^0_j|S|\psi^0_j>=1$), one searches for new vector as:
> \begin{equation}
> |\psi^n_j(\theta)>= \cos\theta |\psi^{n-1}_j> +
>                     \sin\theta |P\widetilde h^{n-1}_j>
> \end{equation}
> where
> \begin{equation}
> |P\widetilde h^n_j> = {|Ph^n_j>\over <Ph^n_j|S|Ph^n_j>^{1/2}}
> \end{equation}
> and $|Ph^n_j>$ is the conjugate gradient. We define
> \begin{equation}
> |Pu^n_j>=|Pg^n_j>+\gamma^{n-1}_j|Ph^{n-1}_j>,
> \end{equation}
> \begin{equation}
> \gamma^{n-1}_j={<Pg^n_j|P^{-2}S|Pg^n_j>
> \over<Pg^{n-1}_j|P^{-2}S|Pg^{n-1}_j>}
> \simeq{<Pg^n_j-Pg^{n-1}_j|P^{-2}S|Pg^n_j>
> \over<Pg^{n-1}_j|P^{-2}S|Pg^{n-1}_j>}
> \end{equation}
> with $\gamma^{-1}_j=0$.
> The gradient $|Pg^n_j>$ is given by
> \begin{equation}
> |Pg^n_j>=P^2H|\psi^n_j> - \widetilde\epsilon^n_j SP^2|\psi^n_j>-
>        \sum_{k<j}\lambda_{jk}^n|\psi_k>
> \end{equation}
> where
> \begin{equation}
> \lambda_{jk}^n = <\psi_k|S(P^2H-\widetilde\epsilon^n_j SP^2)|\psi^n_j>,
> \qquad
> \widetilde\epsilon_j^n = {<\psi^n_j| SP^2 H|\psi^n_j> \over <\psi^n_j|
> S^2P^2| \psi^n_j>}
> \end{equation}
> $|Pu^n_j>$ is by construction orthogonal to
> $|\psi_k>$ but not to  $|\psi^n_j>$:
> \begin{equation}
> \beta^n_j= <Pu^n_j|S|\psi^n_j>=
> \gamma^{n-1}_j<Ph^{n-1}_j|S|\psi^n_j>
>                             =\gamma^{n-1}_j\sin\theta^{n-1}_j
>                             <Ph^{n-1}_j|S|Ph^{n-1}_j> \neq 0
> \end{equation}
> One gets the conjugate direction $|Ph^n_j>$ from
> \begin{equation}
> |Ph^n_j>=|Pu^n_j> - \beta^n_j |\psi^n_j>
> \end{equation}
> Note that only $P^2$ (or $P^{-2}$) is actually used.
>
> \end{document}
>
>
> --Apple-Mail-1--870504716
> Content-Transfer-Encoding: 7bit
> Content-Type: text/plain;
>     charset=US-ASCII;
>     format=flowed
>
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
> --Apple-Mail-1--870504716--
>
>
> --__--__--
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest
>
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____________________________________________________________________________________
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From akohlmey at cmm.chem.upenn.edu  Fri Mar 30 19:23:52 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 30 Mar 2007 12:23:52 -0500 (EST)
Subject: please don't reply to digests.  Re: [Pw_forum] Re: Pw_forum digest,
 Vol 1 #1399 - 12 msgs
In-Reply-To: <310992.85641.qm@web60319.mail.yahoo.com>
Message-ID: <Pine.LNX.4.44.0703301219370.666-100000@localhost.localdomain>

On Fri, 30 Mar 2007, Eyvaz Isaev wrote:

dear eyvaz,

_please_ have mercy on people with limited bandwidth or
that read e-mails through wireless devices and do _not_
quote lengthy parts of a mail that have _no_ relevance
to what you are writing. especially, in this case,
where the original was a pointless reply to begin with.

thanks,
   axel.


EI> Hi Saman,
EI> 
EI> Please find bands_3.f and a Gnuplot script sent to the forum approximately 1.5 months ago. 
EI> Any questions, let me know.
EI> 
EI> Bests,
EI> Eyvaz.
EI> 
EI> 
EI> ----- Original Message ----
EI> From: saman ghaderyan <ghaderyan at gmail.com>
EI> To: pw_forum at pwscf.org
EI> Sent: Wednesday, March 28, 2007 1:27:21 AM
EI> Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1399 - 12 msgs
EI> 
EI> hi
EI> how i can plot phonon frequency for deferent q-victor (example 6).
EI> thanks
EI> 
EI> 
EI> 
EI> On 3/27/07, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote:
EI> > Send Pw_forum mailing list submissions to
EI> >     pw_forum at pwscf.org
EI> >
EI> > To subscribe or unsubscribe via the World Wide Web, visit
EI> >     http://www.democritos.it/mailman/listinfo/pw_forum
EI> > or, via email, send a message with subject or body 'help' to
EI> >     pw_forum-request at pwscf.org
EI> >
EI> > You can reach the person managing the list at
EI> >     pw_forum-admin at pwscf.org
EI> >

[...]

-- 
=======================================================================
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.



From amit76.india at gmail.com  Fri Mar 30 21:05:04 2007
From: amit76.india at gmail.com (Amit Kumar)
Date: Sat, 31 Mar 2007 00:35:04 +0530
Subject: [Pw_forum] EPC of Al at X
Message-ID: <aef8bbf00703301205x27bccbf4q3ba71a02e4871027@mail.gmail.com>

>>>>>>>>
 would you mind reading the answer that you get before
asking new questions, or more exactly, the same question?


 Dear Paolo,
 I read your every answer very carefully.
 My question was not the same.
 I agree that Methfessel-Paxton  or Gaussian broadening  might change  the
absolute
 value of Lambda little bit.
 However,
 last time I wanted to say that electron-phonon matrix elements are not
 converged using 32x32x32 k-point  grid.  I know  achieving convergency is
very
 slow and painful. But I was very surprised to see the value of averaged
'lambda' in the
 example 's out put directrory.  How come  it's so close to the
experimental value
 even for  very  low  el-ph broadening (0.01 Ryd).

 Please check it once.

  Electron-phonon coupling constant, lambda

 Broadening   0.0100 lambda       0.3845 dos_el   1.8818
 Broadening   0.0200 lambda       0.3744 dos_el   2.2498
 Broadening   0.0300 lambda       0.3447 dos_el   2.3960
 Broadening   0.0400 lambda       0.3446 dos_el   2.5079
 Broadening   0.0500 lambda       0.3515 dos_el   2.5896
 Broadening   0.0600 lambda       0.3555 dos_el   2.6381
 Broadening   0.0700 lambda       0.3551 dos_el   2.6616
 Broadening   0.0800 lambda       0.3516 dos_el   2.6709
 Broadening   0.0900 lambda       0.3463 dos_el   2.6737
 Broadening   0.1000 lambda       0.3405 dos_el   2.6743


 When individual matrix elements are not well converged (Please see my last
mail)
 then how come lambda value is so  good    even for   small broadening and
 small  nq value (4 4 4)????  Many things confuse me lot -----

 Which dos_el   or  Fermi energy or  double delta integral are
acceptable???

 Sometime with increasing  k-point grid we did not get better convergence
---
 it seems the value changes very slowly with increasing K-point.
 We can't take arbitrary large k-point  grid (millions of K-points) because
it  demands large
 disk space and very long computational time.


 Do you think the following numbers are converged???????

 . Gaussian Broadening:   0.010 Ry, ngauss=   0
     DOS =  1.881758 states/spin/Ry/Unit Cell at Ef=  8.327154 eV
     lambda( 1)=  0.0253   gamma=    0.92 GHz
     lambda( 2)=  0.0291   gamma=    1.05 GHz
     lambda( 3)=  0.0403   gamma=    6.35 GHz
     Gaussian Broadening:   0.020 Ry, ngauss=   0
     DOS =  2.249756 states/spin/Ry/Unit Cell at Ef=  8.324326 eV
     lambda( 1)=  0.0699   gamma=    3.02 GHz
     lambda( 2)=  0.0781   gamma=    3.37 GHz
     lambda( 3)=  0.1272   gamma=   24.01 GHz
     Gaussian Broadening:   0.030 Ry, ngauss=   0
     DOS =  2.396042 states/spin/Ry/Unit Cell at Ef=  8.311302 eV
     lambda( 1)=  0.0799   gamma=    3.67 GHz
     lambda( 2)=  0.0856   gamma=    3.93 GHz
     lambda( 3)=  0.1515   gamma=   30.44 GHz
     Gaussian Broadening:   0.040 Ry, ngauss=   0
     DOS =  2.507879 states/spin/Ry/Unit Cell at Ef=  8.299961 eV
     lambda( 1)=  0.0851   gamma=    4.10 GHz
     lambda( 2)=  0.0885   gamma=    4.26 GHz
     lambda( 3)=  0.1599   gamma=   33.63 GHz
     Gaussian Broadening:   0.050 Ry, ngauss=   0
     DOS =  2.589584 states/spin/Ry/Unit Cell at Ef=  8.291558 eV
     lambda( 1)=  0.0881   gamma=    4.38 GHz
     lambda( 2)=  0.0901   gamma=    4.48 GHz
     lambda( 3)=  0.1645   gamma=   35.73 GHz
     Gaussian Broadening:   0.060 Ry, ngauss=   0
     DOS =  2.638140 states/spin/Ry/Unit Cell at Ef=  8.285378 eV
     lambda( 1)=  0.0887   gamma=    4.49 GHz
     lambda( 2)=  0.0900   gamma=    4.56 GHz
     lambda( 3)=  0.1673   gamma=   37.02 GHz
     Gaussian Broadening:   0.070 Ry, ngauss=   0
     DOS =  2.661607 states/spin/Ry/Unit Cell at Ef=  8.280404 eV
     lambda( 1)=  0.0876   gamma=    4.47 GHz
     lambda( 2)=  0.0883   gamma=    4.51 GHz
     lambda( 3)=  0.1695   gamma=   37.82 GHz
     Gaussian Broadening:   0.080 Ry, ngauss=   0
     DOS =  2.670887 states/spin/Ry/Unit Cell at Ef=  8.275903 eV
     lambda( 1)=  0.0856   gamma=    4.39 GHz
     lambda( 2)=  0.0859   gamma=    4.40 GHz
     lambda( 3)=  0.1717   gamma=   38.47 GHz
     Gaussian Broadening:   0.090 Ry, ngauss=   0
     DOS =  2.673746 states/spin/Ry/Unit Cell at Ef=  8.271433 eV
     lambda( 1)=  0.0834   gamma=    4.28 GHz
     lambda( 2)=  0.0834   gamma=    4.28 GHz
     lambda( 3)=  0.1744   gamma=   39.10 GHz
     Gaussian Broadening:   0.100 Ry, ngauss=   0
     DOS =  2.674314 states/spin/Ry/Unit Cell at Ef=  8.266772 eV
     lambda( 1)=  0.0813   gamma=    4.17 GHz
     lambda( 2)=  0.0811   gamma=    4.16 GHz
     lambda( 3)=  0.1773   gamma=   39.76 GHz

     and so on ..........................

     It keeps on incresaing forever even with a very large K-point grid.

     Then how come averaged 'lamda' value is so closed to the experimental
value
     even with  small Gaussian broadennig and  small K-point grids (like 16
16 16) ???????

     Is it accidental??????

 Should  we take large value of nq like  nq1=32, nq2=32, nq3=32
 like large value of nk for better results?????????

 Sometime  even  in total energy calculatiion  we may get accidental
convergence.
 In MIT lecture notes, it's written that

 You do need to be careful though. It is possible to get "false" or
"accidental"
 convergence as well. That is, your energy at a 2x2x2 k-grid may be the same
as
 the energy at a 8x8x8 k-grid, but the energy at a 4x4x4 might be very
different
 from both of these. In this case, you aren't really converged at a 2x2x2
k-grid.


 Is it possible to calculate EPC for arbitrary q -point like
 0.13579         0.3474     0.83765  ???????????

 Looking forward to your valuable suggestions.


 With best regards,
 Amit

 P.S.  Dear Nicola, Thank you very much for  your  useful  reference.
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From amit76.india at gmail.com  Fri Mar 30 21:15:58 2007
From: amit76.india at gmail.com (Amit Kumar)
Date: Sat, 31 Mar 2007 00:45:58 +0530
Subject: [Pw_forum] EPC of Aluminium at X
Message-ID: <aef8bbf00703301215r44af2da6o83fd919e73740bf6@mail.gmail.com>

>
> >>>>>>>>
>  would you mind reading the answer that you get before
> asking new questions, or more exactly, the same question?
>
>
>  Dear Paolo,
>  I read your every answer very carefully.
>  My question was not the same.
>  I agree that Methfessel-Paxton  or Gaussian broadening  might change  the
> absolute
>  value of Lambda little bit.
>  However,
>  last time I wanted to say that electron-phonon matrix elements are not
>  converged using 32x32x32 k-point  grid.  I know  achieving convergency is
> very
>  slow and painful. But I was very surprised to see the value of averaged
> 'lambda' in the
>  example 's out put directrory.  How come  it's so close to the
> experimental value
>  even for  very  low  el-ph broadening (0.01 Ryd).
>
>  Please check it once.
>
>   Electron-phonon coupling constant, lambda
>
>  Broadening   0.0100 lambda       0.3845 dos_el   1.8818
>  Broadening   0.0200 lambda       0.3744 dos_el   2.2498
>  Broadening   0.0300 lambda       0.3447 dos_el   2.3960
>  Broadening   0.0400 lambda       0.3446 dos_el   2.5079
>  Broadening   0.0500 lambda       0.3515 dos_el   2.5896
>  Broadening   0.0600 lambda       0.3555 dos_el   2.6381
>  Broadening   0.0700 lambda       0.3551 dos_el   2.6616
>  Broadening   0.0800 lambda       0.3516 dos_el   2.6709
>  Broadening   0.0900 lambda       0.3463 dos_el   2.6737
>  Broadening   0.1000 lambda       0.3405 dos_el   2.6743
>
>
>  When individual matrix elements are not well converged (Please see my
> last mail)
>  then how come lambda value is so  good    even for   small broadening and
>
>  small  nq value (4 4 4)????  Many things confuse me lot -----
>
>  Which dos_el   or  Fermi energy or  double delta integral are
> acceptable???
>
>  Sometime with increasing  k-point grid we did not get better convergence
> ---
>  it seems the value changes very slowly with increasing K-point.
>  We can't take arbitrary large k-point  grid (millions of K-points)
> because it  demands large
>  disk space and very long computational time.
>
>
>  Do you think the following numbers are converged???????
>
>  . Gaussian Broadening:   0.010 Ry, ngauss=   0
>      DOS =  1.881758 states/spin/Ry/Unit Cell at Ef=  8.327154 eV
>      lambda( 1)=  0.0253   gamma=    0.92 GHz
>      lambda( 2)=  0.0291   gamma=    1.05 GHz
>      lambda( 3)=  0.0403   gamma=    6.35 GHz
>      Gaussian Broadening:   0.020 Ry, ngauss=   0
>      DOS =  2.249756 states/spin/Ry/Unit Cell at Ef=  8.324326 eV
>      lambda( 1)=  0.0699   gamma=    3.02 GHz
>      lambda( 2)=  0.0781   gamma=    3.37 GHz
>      lambda( 3)=  0.1272   gamma=   24.01 GHz
>      Gaussian Broadening:   0.030 Ry, ngauss=   0
>      DOS =  2.396042 states/spin/Ry/Unit Cell at Ef=  8.311302 eV
>      lambda( 1)=  0.0799   gamma=    3.67 GHz
>      lambda( 2)=  0.0856   gamma=    3.93 GHz
>      lambda( 3)=  0.1515   gamma=   30.44 GHz
>      Gaussian Broadening:   0.040 Ry, ngauss=   0
>      DOS =  2.507879 states/spin/Ry/Unit Cell at Ef=  8.299961 eV
>      lambda( 1)=  0.0851   gamma=    4.10 GHz
>      lambda( 2)=  0.0885   gamma=    4.26 GHz
>      lambda( 3)=  0.1599   gamma=   33.63 GHz
>      Gaussian Broadening:   0.050 Ry, ngauss=   0
>      DOS =  2.589584 states/spin/Ry/Unit Cell at Ef=  8.291558 eV
>      lambda( 1)=  0.0881   gamma=    4.38 GHz
>      lambda( 2)=  0.0901   gamma=    4.48 GHz
>      lambda( 3)=  0.1645   gamma=   35.73 GHz
>      Gaussian Broadening:   0.060 Ry, ngauss=   0
>      DOS =  2.638140 states/spin/Ry/Unit Cell at Ef=  8.285378 eV
>      lambda( 1)=  0.0887   gamma=    4.49 GHz
>      lambda( 2)=  0.0900   gamma=    4.56 GHz
>      lambda( 3)=  0.1673   gamma=   37.02 GHz
>      Gaussian Broadening:   0.070 Ry, ngauss=   0
>      DOS =  2.661607 states/spin/Ry/Unit Cell at Ef=  8.280404 eV
>      lambda( 1)=  0.0876   gamma=    4.47 GHz
>      lambda( 2)=  0.0883   gamma=    4.51 GHz
>      lambda( 3)=  0.1695   gamma=   37.82 GHz
>      Gaussian Broadening:   0.080 Ry, ngauss=   0
>      DOS =  2.670887 states/spin/Ry/Unit Cell at Ef=  8.275903 eV
>      lambda( 1)=  0.0856   gamma=    4.39 GHz
>      lambda( 2)=  0.0859   gamma=    4.40 GHz
>      lambda( 3)=  0.1717   gamma=   38.47 GHz
>      Gaussian Broadening:   0.090 Ry, ngauss=   0
>      DOS =  2.673746 states/spin/Ry/Unit Cell at Ef=  8.271433 eV
>      lambda( 1)=  0.0834   gamma=    4.28 GHz
>      lambda( 2)=  0.0834   gamma=    4.28 GHz
>      lambda( 3)=  0.1744   gamma=   39.10 GHz
>      Gaussian Broadening:   0.100 Ry, ngauss=   0
>      DOS =  2.674314 states/spin/Ry/Unit Cell at Ef=  8.266772 eV
>      lambda( 1)=  0.0813   gamma=    4.17 GHz
>      lambda( 2)=  0.0811   gamma=    4.16 GHz
>      lambda( 3)=  0.1773   gamma=   39.76 GHz
>
>      and so on ..........................
>
>      It keeps on incresaing forever even with a very large K-point grid.
>
>      Then how come averaged 'lamda' value is so closed to the experimental
> value
>      even with  small Gaussian broadennig and  small K-point grids (like
> 16 16 16) ???????
>
>      Is it accidental??????
>
>  Should  we take large value of nq like  nq1=32, nq2=32, nq3=32
>  like large value of nk for better results?????????
>
>  Sometime  even  in total energy calculatiion  we may get accidental
> convergence.
>  In MIT lecture notes, it's written that
>
>  You do need to be careful though. It is possible to get "false" or
> "accidental"
>  convergence as well. That is, your energy at a 2x2x2 k-grid may be the
> same as
>  the energy at a 8x8x8 k-grid, but the energy at a 4x4x4 might be very
> different
>  from both of these. In this case, you aren't really converged at a 2x2x2
> k-grid.
>
>
>  Is it possible to calculate EPC for arbitrary q -point like
>  0.13579         0.3474     0.83765  ???????????
>
>  Looking forward to your valuable suggestions.
>
>
>  With best regards,
>  Amit
>
>  P.S.  Dear Nicola, Thank you very much for  your  useful  reference.
>
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From ghaderyan at gmail.com  Fri Mar 30 23:46:14 2007
From: ghaderyan at gmail.com (saman ghaderyan)
Date: Sat, 31 Mar 2007 01:16:14 +0330
Subject: [Pw_forum] thanks
Message-ID: <aa36e8060703301446s1106e893lb5ed13c3bf711968@mail.gmail.com>

hi
thanks
i am reading your helping now
but my problem is when i have matdyn files in a lot of q_vectors
how i plot them together .
thanks again
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From marzari at MIT.EDU  Sat Mar 31 19:44:09 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Sat, 31 Mar 2007 13:44:09 -0400
Subject: [Pw_forum] thanks
In-Reply-To: <aa36e8060703301446s1106e893lb5ed13c3bf711968@mail.gmail.com>
References: <aa36e8060703301446s1106e893lb5ed13c3bf711968@mail.gmail.com>
Message-ID: <460E9DE9.2050901@mit.edu>

saman ghaderyan wrote:
> hi
> thanks
> i am reading your helping now
> but my problem is when i have matdyn files in a lot of q_vectors
> how i plot them together .
> thanks again


You get the dynamical matrices on a uniform mesh of q vectors,
FFT in real space to get the real space interatomic force
constants, you apply translational sum rules, and transform back
with a regular Fourier transfrom at any arbitrary q. Diagonalize
at that q, and you have the w_{n,q} phonon dispersion.

If system has a FCC Bravais lattice (e.g. Silicon) it is convential
to plot them from L to Gamma to X to K to X, or permutations.

				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


From gilles.hug at onera.fr  Sat Mar 31 22:02:02 2007
From: gilles.hug at onera.fr (Gilles Hug)
Date: Sat, 31 Mar 2007 22:02:02 +0200
Subject: [Pw_forum] intel mac - compilation with ifort/icc and not gcc
In-Reply-To: <600FD0D2-D24B-4403-8B05-9380E25AE48E@nest.sns.it>
References: <B3A79CE4-DA2C-44FD-BA36-55F96E934F3B@onera.fr> <600FD0D2-D24B-4403-8B05-9380E25AE48E@nest.sns.it>
Message-ID: <3D0BD08B-A526-43FD-9879-EC5A39684A62@onera.fr>

Le 30 mars 07 ? 14:53, Paolo Giannozzi a ?crit :

>
> On Mar 30, 2007, at 14:36 , Gilles Hug wrote:
>
>> I am new here and trying to compile Espresso
>
> which version?

This is espresso-3.2

G



From gilles.hug at onera.fr  Sat Mar 31 22:04:23 2007
From: gilles.hug at onera.fr (Gilles Hug)
Date: Sat, 31 Mar 2007 22:04:23 +0200
Subject: [Pw_forum] intel mac - compilation with ifort/icc and not gcc
In-Reply-To: <Prayer.1.0.16.0703300920310.20839@wm2.tc.umn.edu>
References: <B3A79CE4-DA2C-44FD-BA36-55F96E934F3B@onera.fr> <Prayer.1.0.16.0703300920310.20839@wm2.tc.umn.edu>
Message-ID: <F6854A30-CB0A-453B-981B-F7D318B6638D@onera.fr>

Le 30 mars 07 ? 16:20, Matteo Cococcioni a ?crit :

>
> Dear Gilles,
>
> I remember (I haven't compiled on my mac in while) that I had to  
> download gcc as well and install it before compiling. From your  
> error message I'm not sure you did that. I don't remember what  
> package I downloaded but you probably can find many (go to a mac- 
> specific website).
>

Dear Mateo,
I think gcc is automatically installed with XCode & dev tools.
 > gcc
i686-apple-darwin8-gcc-4.0.1: no input files
 > which gcc
/usr/bin/gcc

Does espresso search gcc in some other directory?
Cheers
Gilles