from:"Muthu V"

[QE-users] missing f orbital - Sm atom reg

2019-08-06 Thread Muthu V

Dear All,
i use Sm.pbe-spdn-rrkjus_psl.1.0.0.UPF, downloaded from QE web page, for my
system which contains Sm atoms.
the electronic configuration of Sm contains f orbitals and the
configuration is
*1s2 |   2s2 2p6 |  3s2 3p6 3d10 |  4s2 4p6 4d10   5s2 5p6 4f6 6s2*
when gone through this potential file i could see
Valence configuration:
nl pn  l   occ   Rcut  Rcut US   E pseu
5S  1  0  2.00  1.400  1.700-3.480513
6S  2  0  1.50  1.400  1.700-0.320378
5P  2  1  6.00  1.400  1.800-1.957179
6P  3  1  0.50  1.400  1.800-0.119872
5D  3  2  1.00  1.400  2.000-0.238636
Generation configuration:
5S  1  0  2.00  1.400  1.700-3.480555
6S  2  0  1.50  1.400  1.700-0.320387
5P  2  1  6.00  1.400  1.800-1.957209
6P  3  1  0.50  1.400  1.800-0.119877
5D  3  2  1.00  1.400  2.000-0.238652
5D  3  2  0.00  1.400  2.000 2.00
...
and
 &input
   title='Sm',
   zed=62.0,
   rel=1,
   config='[Xe] 4f5.0 5d1.0 6s1.5 6p0.5',
   iswitch=3,
   dft='PBE'
 /
...
when i did PDOS calculation, i do not see any f orbital contribution.
"Valence configuration:"  and  " Generation configuration: " and the
keyword "config" in &input card are different from each other. my
question is
whether electrons f orbitals  are treated as core electron ? if yes the why
it is so ?

your explanation would be more help

best regards

Muthu Vallinayagam
PhD - student
HZDR, Germany
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[QE-users] missing f orbital - Sm atom reg

2019-08-04 Thread Muthu V

Dear Users,
i am using Sm.pbe-spdn-rrkjus_psl.1.0.0.UPF for my system which contains Sm
atoms.
the electronic configuration of Sm contains f orbitals and the
configuration is

*1s2 |   2s2 2p6 |  3s2 3p6 3d10 |  4s2 4p6 4d10   5s2 5p6 4f6 6s2*

when gone through this potential file i could see
Valence configuration:
nl pn  l   occ   Rcut  Rcut US   E pseu
5S  1  0  2.00  1.400  1.700-3.480513
6S  2  0  1.50  1.400  1.700-0.320378
5P  2  1  6.00  1.400  1.800-1.957179
6P  3  1  0.50  1.400  1.800-0.119872
5D  3  2  1.00  1.400  2.000-0.238636
Generation configuration:
5S  1  0  2.00  1.400  1.700-3.480555
6S  2  0  1.50  1.400  1.700-0.320387
5P  2  1  6.00  1.400  1.800-1.957209
6P  3  1  0.50  1.400  1.800-0.119877
5D  3  2  1.00  1.400  2.000-0.238652
5D  3  2  0.00  1.400  2.000 2.00
...
and

 &input
   title='Sm',
   zed=62.0,
   rel=1,
   config='[Xe] 4f5.0 5d1.0 6s1.5 6p0.5',
   iswitch=3,
   dft='PBE'
 /
...

here it is confusing that "Valence configuration:"  and  " Generation
configuration: " are not same. also these two do not contain f orbitals.
but  the keyword "config" in &input card contains f orbitals with
occupancy of 5 electrons.  So these three are different from one another.

but actual way of writing of electronic configuration do not involve 5d and
6s orbitals and f orbital occupancy is 6 not 5. i have done PDOS
calculation and i do not see any f orbital wave function contribution. pdos
generates only s,p, and d orbitals as seen in "Valence configuration:" .

My questions are
1. what happens to f orbitals ?
2. where it is hidden and why it is not treated explicitly ?
3. why pdos calculation not writing f orbital contribution ? ( i can
understand that  "Valence configuration:"  do not have it, but the card
"&input"  includes it with wrong occupancy)
4. what is the point one missing in understanding this potential file?

your explanation would be more help

best regards

Muthu Vallinayagam
PhD - student
HZDR, Germany
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[Pw_forum] Pseudo Potential selection with different methods

2017-11-11 Thread Muthu V

Dear QE Users,
i like to use USPP for my system. but for some element i do not find proper
PP in QE web page.
for example i want to study Mn effects in MoS2 layers for this my PP
selection is
   Mo :   Mo.pbe-spn-rrkjus_psl.0.2.UPF
S   :   S.pbe-n-rrkjus_psl.0.1.UPF
   Mn  :  Mn.pbe-sp-van.UPF
although all are USPP, these are produced with different methods RRKJ for
Mn and S and Vanderbilt method for Mn
so in QE such a combination of same Functional
exchange-correlation and different generating method is valid?
irrespective of this particular system , it is possible to follow such
combination for other system also ( in case i do not find same methods for
all elements in system )?

Just i want to be very sure about PP selection, your clarification will
help a lot

thank you 
-
  Muthu Vallinayagam
  PhD-student
  Helmholtz Zentrum Dresden Rossendorf  
-


Note: similar, not exactly, discussion about PP type follows here
http://qe-forge.org/pipermail/pw_forum/2014-February/103209.html



‌
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Re: [Pw_forum] problem with PWgui-6.0 (Tone Kokalj)

2017-03-09 Thread Muthu V

Hi Tone Kokalj. I am using Fedora 25 64 bit version in my i3 core Dell
laptop.
Looking forward to your further mails
thanks

-
Muthu V
IGCAR
Kalpakkam
India
-

On Thu, Mar 9, 2017 at 7:16 AM, Muthu V  wrote:

> Dear Tone Kokalj
> Thank you for your interest in this issue. first i test all Tk Tcl and itk
> itcl as follows in my laptop.
> ( as suggested in discussion http://qe-forge.org/
> pipermail/pw_forum/2016-May/109744.html )
>
> **
>
>
>
>
>
>
>
>
>
>
>
>
>
> *[pearl@localhost ~]$ tclsh% package require Tk 8.6.6% package require
> Tcl8.6.6% package require Itcl4.0.3% package require Iwidgets4.0.2% package
> require Itkcan't find package Itk% package require itk4.0.1 % ^C*
>
> 
> So it is clear that my system knows Itk ad itk. so i edited the 
> *lib/Guib-0.5.1/init.tcl
> *as
> ..
> package require Tk
> package require Itcl
> package require itk
> package require Iwidgets
> .
> here initial the line  package require itk was like this package require
> Itk. i changed Itk to itk.
> now in pwgui directory  just lanched pwgui from terminal as ./pwgui
>
> in terminal i can see
>
>
>
>
>
>
>
>
>
>
>
>
> *[pearl@localhost pwgui-6.0]$
> ./pwgui ==  This is PWgui
> version: 6.0 -- PWgui:
> using the system default "tclsh" interpreter PWGUI   :
> /home/pearl/qe-6.0/pwgui-6.0 GUIB engine :
> /home/pearl/qe-6.0/pwgui-6.0/lib/Guib-0.5.1*
> when i tried to open any input files in PWgui window , for example pw
> input file, i am getting this whole error message,
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
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>
>
>
> *member function "::guib::moduleObj::makeEmbedGUI" is not defined and
> cannot be autoloadedmember function "::guib::moduleObj::makeEmbedGUI" is
> not defined and cannot be autoloadedwhile executing"$obj makeEmbedGUI
> [expr {$containerWidget != "." ? $containerWidget : "" }]"(procedure
> "::guib::embedGUI" line 6)invoked from within"::guib::embedGUI
> $moduleFile $wid"(object "::gUI0" method "::guib::GUI::_newInput" body
> line 56)invoked from within"$cmd $moduleIdent $moduleName
> $moduleFile"(object "::gUI0" method "::guib::GUI::_toolbarCmd" body
> line 3)invoked from within"::gUI0 _toolbarCmd .gUI0_toolbarnew
> _newInput pw PW.X /home/pearl/qe-6.0/pwgui-6.0/modules/pw/pw.tcl"(in
> namespace inscope "::guib::GUI" script line 1)invoked from
> within"namespace inscope ::guib::GUI {::gUI0 _toolbarCmd .gUI0_toolbarnew
> _newInput pw PW.X /home/pearl/qe-6.0/pwgui-6.0/modules/pw/pw.tcl}"
> invoked from within".gUI0_toolbarnew.0 invoke"("uplevel" body line
> 1)invoked from within"uplevel #0 [list $w invoke]"(procedure
> "tk::ButtonUp" line 22)invoked from within"tk::ButtonUp
> .gUI0_toolbarnew.0"(command bound to event)*
> and in terminal i just get
> [pearl@localhost pwgui-6.0]$ ./pwgui
>
>  ==
>   This is PWgui version: 6.0
>  --
>
>
>  PWgui: using the system default "tclsh" interpreter
>
>  PWGUI   : /home/pearl/qe-6.0/pwgui-6.0
>  GUIB engine : /home/pearl/qe-6.0/pwgui-6.0/lib/Guib-0.5.1
>
> [pearl@localhost pwgui-6.0]$
>
> so to resolve this problem my guess is that i have to set enviro such that
> itk should named as Itk, but i do not how to do in case this is correct
> reason.
>
> Looking forward to your further mails
>
> thanks
>
> -
> Muthu V
> IGCAR
> Kalpakkam
> India
> -
>
> On Tue, Mar 7, 2017 at 12:00 PM,  wrote:
>
>> Re: problem with PWgui-6.0 (Tone Kokalj
>
>
>
>
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Re: [Pw_forum] problem with PWgui-6.0 (Tone Kokalj)

2017-03-08 Thread Muthu V

Dear Tone Kokalj
Thank you for your interest in this issue. first i test all Tk Tcl and itk
itcl as follows in my laptop.
( as suggested in discussion 
http://qe-forge.org/pipermail/pw_forum/2016-May/109744.html )

**













*[pearl@localhost ~]$ tclsh% package require Tk 8.6.6% package require
Tcl8.6.6% package require Itcl4.0.3% package require Iwidgets4.0.2% package
require Itkcan't find package Itk% package require itk4.0.1 % ^C*


So it is clear that my system knows Itk ad itk. so i edited the
*lib/Guib-0.5.1/init.tcl
*as
..
package require Tk
package require Itcl
package require itk
package require Iwidgets
.
here initial the line  package require itk was like this package require
Itk. i changed Itk to itk.
now in pwgui directory  just lanched pwgui from terminal as ./pwgui

in terminal i can see












*[pearl@localhost pwgui-6.0]$
./pwgui ==  This is PWgui
version: 6.0 -- PWgui:
using the system default "tclsh" interpreter PWGUI   :
/home/pearl/qe-6.0/pwgui-6.0 GUIB engine :
/home/pearl/qe-6.0/pwgui-6.0/lib/Guib-0.5.1*
when i tried to open any input files in PWgui window , for example pw input
file, i am getting this whole error message,


























*member function "::guib::moduleObj::makeEmbedGUI" is not defined and
cannot be autoloadedmember function "::guib::moduleObj::makeEmbedGUI" is
not defined and cannot be autoloadedwhile executing"$obj makeEmbedGUI
[expr {$containerWidget != "." ? $containerWidget : "" }]"(procedure
"::guib::embedGUI" line 6)invoked from within"::guib::embedGUI
$moduleFile $wid"(object "::gUI0" method "::guib::GUI::_newInput" body
line 56)invoked from within"$cmd $moduleIdent $moduleName
$moduleFile"(object "::gUI0" method "::guib::GUI::_toolbarCmd" body
line 3)invoked from within"::gUI0 _toolbarCmd .gUI0_toolbarnew
_newInput pw PW.X /home/pearl/qe-6.0/pwgui-6.0/modules/pw/pw.tcl"(in
namespace inscope "::guib::GUI" script line 1)invoked from
within"namespace inscope ::guib::GUI {::gUI0 _toolbarCmd .gUI0_toolbarnew
_newInput pw PW.X /home/pearl/qe-6.0/pwgui-6.0/modules/pw/pw.tcl}"
invoked from within".gUI0_toolbarnew.0 invoke"("uplevel" body line
1)invoked from within"uplevel #0 [list $w invoke]"(procedure
"tk::ButtonUp" line 22)invoked from within"tk::ButtonUp
.gUI0_toolbarnew.0"(command bound to event)*
and in terminal i just get
[pearl@localhost pwgui-6.0]$ ./pwgui

 ==
  This is PWgui version: 6.0
 --


 PWgui: using the system default "tclsh" interpreter

 PWGUI   : /home/pearl/qe-6.0/pwgui-6.0
 GUIB engine : /home/pearl/qe-6.0/pwgui-6.0/lib/Guib-0.5.1

[pearl@localhost pwgui-6.0]$

so to resolve this problem my guess is that i have to set enviro such that
itk should named as Itk, but i do not how to do in case this is correct
reason.

Looking forward to your further mails

thanks

-
Muthu V
IGCAR
Kalpakkam
India
-

On Tue, Mar 7, 2017 at 12:00 PM,  wrote:

> Re: problem with PWgui-6.0 (Tone Kokalj
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[Pw_forum] problem with PWgui-6.0

2017-03-02 Thread Muthu V

Dear Users
I am trying to use PWgui-6.0. while runnning
$./pwgui
the gui appears and if i try file->new->new pw.x input

then a window with the following error is coming out

member function "::guib::moduleObj::makeEmbedGUI" is not defined and cannot
be autoloaded
member function "::guib::moduleObj::makeEmbedGUI" is not defined and cannot
be autoloaded
while executing
"$obj makeEmbedGUI [expr {$containerWidget != "." ? $containerWidget : ""
}]"
(procedure "::guib::embedGUI" line 6)
invoked from within
"::guib::embedGUI $moduleFile $wid"
(object "::gUI0" method "::guib::GUI::_newInput" body line 56)
invoked from within
"$cmd $moduleIdent $moduleName $moduleFile"
(object "::gUI0" method "::guib::GUI::_toolbarCmd" body line 3)
invoked from within
"::gUI0 _toolbarCmd .gUI0_toolbarnew _newInput pw PW.X
/home/pearl/qe-6.0/PWgui-6.0/modules/pw/pw.tcl"
(in namespace inscope "::guib::GUI" script line 1)
invoked from within
"namespace inscope ::guib::GUI {::gUI0 _toolbarCmd .gUI0_toolbarnew
_newInput pw PW.X /home/pearl/qe-6.0/PWgui-6.0/modules/pw/pw.tcl}"
invoked from within
".gUI0_toolbarnew.0 invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .gUI0_toolbarnew.0"
(command bound to event)

so here where is the problem?
i am using current versions of itcl and itk

thanks


Muthu V
IGCAR
INDIA
-
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[Pw_forum] problem with PWgui-6.0

2017-02-28 Thread Muthu V

Dear Users
I am trying to use PWgui-6.0. while runnning
$./pwgui
the gui appears and if i try file->new->new pw.x input

then a window with the following error is coming out

member function "::guib::moduleObj::makeEmbedGUI" is not defined and cannot
be autoloaded
member function "::guib::moduleObj::makeEmbedGUI" is not defined and cannot
be autoloaded
while executing
"$obj makeEmbedGUI [expr {$containerWidget != "." ? $containerWidget : ""
}]"
(procedure "::guib::embedGUI" line 6)
invoked from within
"::guib::embedGUI $moduleFile $wid"
(object "::gUI0" method "::guib::GUI::_newInput" body line 56)
invoked from within
"$cmd $moduleIdent $moduleName $moduleFile"
(object "::gUI0" method "::guib::GUI::_toolbarCmd" body line 3)
invoked from within
"::gUI0 _toolbarCmd .gUI0_toolbarnew _newInput pw PW.X
/home/pearl/qe-6.0/PWgui-6.0/modules/pw/pw.tcl"
(in namespace inscope "::guib::GUI" script line 1)
invoked from within
"namespace inscope ::guib::GUI {::gUI0 _toolbarCmd .gUI0_toolbarnew
_newInput pw PW.X /home/pearl/qe-6.0/PWgui-6.0/modules/pw/pw.tcl}"
invoked from within
".gUI0_toolbarnew.0 invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .gUI0_toolbarnew.0"
(command bound to event)

so here where is the problem?
i am using current versions of itcl and itk

thanks


Muthu V
IGCAR
INDIA
-
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Re: [Pw_forum] Pw_forum Digest, Vol 115, Issue 22

2017-02-22 Thread Muthu V

On Wed, Feb 22, 2017 at 12:00 PM,  wrote:

> Subject: Re: [Pw_forum] Understanding the calculation


Hi
Yes you have update the optimized atomic coordinates and cell parameters in
scf.in. here you can do it as follows
open output file of relaxation process in any text editor then go to the
line
Final Coordinates  Begins:
under this heading you can see the optimized atomic coordinates. then look
for celldim() at last scf calculation which will be printed  after above
line. this will give you optimized cell parameters.

or just open output file of relaxation process in xcrysden and save final
coordinate in xsf format. open this xsf file in text editor then you can
see all optimized data one by one.

still if you sense difficulties then open above xsf file in vesta software.
then use file->export data option. in popup window you can different format
in plenty of options. in this select vasp format then save it.
you can get all details in file too.


regards,

*Muthu Vallinayagam*
*JRF,*
*IGCAR, Tamil nadu*
*India*
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Re: [Pw_forum] make ph strangely stops without error in 'install' folder (Christoph Wolf (??????))

2016-08-02 Thread Muthu V

Hi Christoph
I also faced the same problem. I do not know how they made *.tar.gz files.
since QE(latest one i used 5.4.0) not able to uncompress *tar.gz and
extract *tar.gz file you have to do it youself.

you can face this issue with the following *tar.gz's

ELPA-0.3.tar.gz EPW-5.4.0.tar.gz  GWW-5.4.0.tar.gz
neb-5.4.0.tar.gzPHonon-5.4.0.tar.gz   pwcond-5.4.0.tar.gz
tddfpt-5.4.0.tar.gz   xspectra-5.4.0.tar.gz

this is way i solved it. first i uncompressed and extracted , for example,
PHonon-5.4.0.tar.gz and given the commend make all .

QE will compile PHonon and after it will give the same issue you are facing
now (next one is pwcond-5.4.0.tar.gz)

now uncompress pwcond-5.4.0.tar.gz and hit make all. QE will stop at
neb-5.4.0.tar.gz

So solution is extract the *tar.gz packages by yourself and try to install

-
Muthu V
Sri Paramakalyani College
Alwarkurichi
India
-
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[Pw_forum] Raman frquency calculation - reg.,

2016-07-30 Thread Muthu V

Dear Users

I'm trying to calculation Raman and IR  frequencies with PHonon package
included in QE. i want to know the prerequisites that i have to check ,
for
example no of KPOINT in SCF run, asr typr in madyn calculation.
Since i am getting negative value for frequecy as well as raman
intensity
for my system. can any one help in this regard ?
Thank you

==

Muthu V
Sri Paramakalyani Colege
Alwarkurichi

==
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[Pw_forum] QE creating wrong i/p file for crystal_sg option

2016-07-01 Thread Muthu V

Dear Users
I have a question regarding the usage of crystal_sg option to specify
atomic position in pw input file. I'm trying make pw i/p file for TiO2
rutile system. its space group # is 136 , Ti is at 2a  site and O is at 4e
site.so from ITA i have the following i/p data

Ti 2a (0, 0, 0) (0.5, 0.5, 0.5)
O  4e (0, 0, z) (0.5, 0.5, z+1/2) (0.5, 0.5, -z+1/2)(0,0,-z)

the z value is 0.305. so from this i have created following pw.x input file

&control
  calculation ='scf'
 restart_mode = 'from_scratch',
   prefix = 'ge'
   pseudo_dir = '/home/pearl/qe-5.4.0/pseudo/',
   outdir ='/home/pearl/qe-5.4.0/tio2/tmp/'
 /
 &system
ibrav =  6 ,
  space_group = 136,
A = 4.59373 ,
C = 2.95812 ,
  nat = 2 ,
 ntyp = 2 ,
  ecutwfc = 20.0 ,
  ecutrho = 80.0 ,
  occupations = 'smearing' ,
  degauss = 0.1 ,
 smearing = 'gaussian' ,
 /
 &electrons
 conv_thr =  1.0d-8 ,
  mixing_beta = 0.7 ,
 /
ATOMIC_SPECIES
 Ti  47.867   Ti.pz-mt_fhi.UPF
 O   16.000   O.pz-mt_fhi.UPF
ATOMIC_POSITIONS crystal_sg
Ti   2a
O4e  0.305
K_POINTS automatic
4 4 4 0 0 0

with this file i'm able to run pw.x without any error message. but the
following are my questions :

1) the atomic position written in output file by pw.x is very different
from the expected. why ?

from ge.pw.out file i have ( created by pw.x for above input file)
Cartesian axes
site n. atom  positions (alat units)
 1   Ti  tau(   1) = (   0.500   0.500   0.3219736
)
 2   Ti  tau(   2) = (   0.000   0.000   0.000
)
 3   O   tau(   3) = (   0.000   0.000   0.4475434
)
 4   O   tau(   4) = (   0.500   0.500   0.1255697
)
 5   O   tau(   5) = (   0.500   0.500   0.5183776
)
 6   O   tau(   6) = (   0.000   0.000   0.1964039
)

but the atomic positions are (in crystal unit )
 Ti0.0 0.0 0.0
 Ti0.5 0.5 0.5
  O0.30527 0.30527 0.0
  O0.69473 0.69473 0.0
  O0.19473 0.80527 0.5
  O0.80527 0.19473 0.5

my second question is

2) why QE is not giving correct atomic position if i use crystal_sg option ?

cay anyone help me in this regard. with this mail i have enclosed the
output file for the given input file
Thank you


**

*Muthu V*

*Sri Paramakalyani College*

*Alwarkurichi*


ge.scf.out
Description: chemical/gulp
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[Pw_forum] Question about volume relaxation - reg

2016-06-23 Thread Muthu V

Dear Users
In every volume relaxation run ,
 
 A final scf calculation at the relaxed structure.
 The G-vectors are recalculated for the final unit cell
 Results may differ from those at the preceding step.
 
is being printed. what i have notice is that after this a final scf is
being done with input celldm(i) and optimized atomic coordinate.but the
message leading the view that we are doing scf for optimized structure (
cell parameter + atomic coordinates ).
for example i did volume relax for 2H-MoS2. the  input celldm(i) are
celldm(1)=   5.973424 and celldm(3)=   3.889592.
the relaxed cell parameter values are
  Begin final coordinates
 CELL_PARAMETERS (alat=  5.97342433)
1.010051108   0.0   0.0
   -0.505025554   0.874729919   0.0
   -0.0  -0.0   4.288136193
but for final scf calculation QE taking celldim(i) as ( though the relaxed
celldm are different) celldm(1)=   5.973424, celldm(3)=   3.889592
Why this scf is done with optimized atomic coordinate and old celldm(i)s ?
what is the physics behind such a run?
Thank you
-
Muthu V
Sri Paramakalyani College
Alwarkurichi,India
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Re: [Pw_forum] Re: Kpoints - x coordi

2016-06-14 Thread Muthu V

Thank you D L Nguyen ( i already seen plotband.f90 document ) and Stefano.
but if you , Stefano, explain how the two directions indicated in K_POINT
section become equal ie how it is true that 1 1 0 = 0 1 0 .your explanation
would be more useful to understand.

thank you

On Mon, Jun 13, 2016 at 3:30 PM,  wrote:

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> Today's Topics:
>
>1.
> 
> Re: Kpoints - x coordinates - reg., (Duc-Long Nguyen)
>4. Re: Kpoints - x coordinates - reg., (Stefano de Gironcoli)
> --
>
> Message: 1
> Date: Sun, 12 Jun 2016 18:10:07 +0800
> From: Duc-Long Nguyen 
> Subject: Re: [Pw_forum] Kpoints - x coordinates - reg.,
> To: PWSCF Forum 
> Message-ID: <575d34ff.1000...@gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Dear Muthu,
>
> IF you take a look at the file plotband.f90 in  PP/src folder,
> specifically from line 214-241 you can see some hints:
>   dxmod=sqrt ( (k(1,n)-k(1,n-1))**2 + &
>(k(2,n)-k(2,n-1))**2 + &
>(k(3,n)-k(3,n-1))**2 )
>  
>  kx(n) = kx(n-1) +  dxmod
>
> HTH,
> Duc-Long
>
> --
> Duc-Long Nguyen
> Graduate Student, Molecular Science and Technology Program, TIGP
> Institute of Atomic and Molecular Sciences,
> Academia Sinica, Taipei 106, Taiwan
> Phone +886-979279073
>
>
>
>
> On 06/12/2016 05:29 PM, Muthu V wrote:
> > Dear QE'ions
> > I used the Si example file provided in QE/PP/examples/example01/ (ie
> > run_example) and in si.bands.out i noticed the following
> >  high-symmetry point:  0.5000 0.5000 0.5000   x coordinate   0.
> >  high-symmetry point:  0. 0. 0.   x coordinate   0.8660
> >  high-symmetry point:  0. 1. 0.   x coordinate   1.8660
> >  high-symmetry point:  1. 1. 0.   x coordinate   1.8660
> >  high-symmetry point:  0. 0. 0.   x coordinate   3.2802
> > how the three index ( ex. 0.5 0.5 0.5 and so on) is converted into one
> > point ( 0. 0.86660 1.8660 1.8660 3.2802).
> > and the meaning of1.0 1.0 0.0 K_POINT in run_example file ( used
> > in band calculation)
> > Thank you
> > 
> > *Muthu V
> > *
> > *Sri Paramakalyani College
> > *
> > *Alwarkurichi
> > *
> > *India*
> > 
> >
> >
> >
> > ___
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> > http://pwscf.org/mailman/listinfo/pw_forum
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> --
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> Message: 4
> Date: Sun, 12 Jun 2016 20:42:35 +0200
> From: Stefano de Gironcoli 
> Subject: Re: [Pw_forum] Kpoints - x coordinates - reg.,
> To: PWSCF Forum 
> Message-ID: <0e85d471-aa43-4191-85bc-14855319b...@sissa.it>
> Content-Type: text/plain; charset="us-ascii"
>
> The last number is the length of the path so far.
> 110 is equivalent to 010. Hence the path does not advance
>
> stefano
> (sent from my phone)
>
> > On 12 Jun 2016, at 11:29, Muthu V  wrote:
> >
> > Dear QE'ions
> > I used the Si example file provided in QE/PP/examples/example01/ (ie
> run_example) and in si.bands.out i noticed the following
> >  high-symmetry point:  0.5000 0.5000 0.5000   x coordinate   0.
> >  high-symmetry point:  0. 0. 0.   x coordinate   0.8660
> >  high-symmetry point:  0. 1. 0.   x coordinate   1.8660
> >  high-symmetry point:  1. 1. 0.   x coordinate   1.8660
> >  high-symmetry point:  0. 0. 0.   x coordinate   3.2802
> > how the three index ( ex. 0.5 0.5 0.5 and so on) is converted into one
> point ( 0. 0.86660 1.8660 1.8660 3.2802).
> > and the meaning of1.0 1.0 0.0 K_POINT in run_example file ( used in
> band calculation)
> > Thank you
> > 
> > Muthu V
> > Sri Paramakalyani College
> > Alwarkurichi
> > India
> > 
> >
> > ___
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> > Pw_forum@pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
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[Pw_forum] pw.x warning message : IEEE_DENORMAL - reg.,

2016-06-13 Thread Muthu V

Dear all
while o trying to use pw.x i'm getting the error message






*running the scf calculation...Note: The following floating-point
exceptions are signalling: IEEE_DENORMAL donerunning the band-structure
calculation for Si...Note: The following floating-point exceptions are
signalling: IEEE_DENORMAL done*
how to solve this floating point error


thank you


*--*

*Muthu V*

*Sri Paramakalyani College*

*Alwarkurichi, India--*
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[Pw_forum] Kpoints - x coordinates - reg.,

2016-06-12 Thread Muthu V

Dear QE'ions
I used the Si example file provided in QE/PP/examples/example01/ (ie
run_example) and in si.bands.out i noticed the following
 high-symmetry point:  0.5000 0.5000 0.5000   x coordinate   0.
 high-symmetry point:  0. 0. 0.   x coordinate   0.8660
 high-symmetry point:  0. 1. 0.   x coordinate   1.8660
 high-symmetry point:  1. 1. 0.   x coordinate   1.8660
 high-symmetry point:  0. 0. 0.   x coordinate   3.2802
how the three index ( ex. 0.5 0.5 0.5 and so on) is converted into one
point ( 0. 0.86660 1.8660 1.8660 3.2802).
and the meaning of1.0 1.0 0.0 K_POINT in run_example file ( used in
band calculation)
Thank you
----

*Muthu V*

*Sri Paramakalyani College*

*Alwarkurichi*
*India*

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[Pw_forum] problem in running pwgui-5.4.0

2016-05-07 Thread Muthu V

Dear Users
I am trying to run pwgui. but it is showing the following error. i have
checked in previous forum mails and as directed by paolo i checked for itcl
and itk. everything are upto date, but still getting this error. can you
spot out where is the problem ?
i have installed itcl and itk using yum extender and their respective
version is 4.0.3 and 4.0.1. i am using fedora 23
thank you


*---*

*Muthu V*

*Sri Paramakalyani College*

*Alwarkurichi*

[pearl@localhost PWgui-5.4.0]$ ./pwgui

 ==
  This is PWgui version: 5.4.0
 --


 PWgui: using the system default "tclsh" interpreter

 PWGUI   : /home/pearl/espresso-5.4.0/PWgui-5.4.0
 GUIB engine : /home/pearl/espresso-5.4.0/PWgui-5.4.0/lib/Guib-0.5.1

can't find package Itk
while executing
"package require Itk  "
(file "/home/pearl/espresso-5.4.0/PWgui-5.4.0/lib/Guib-0.5.1/init.tcl"
line 11)
invoked from within
"source /home/pearl/espresso-5.4.0/PWgui-5.4.0/lib/Guib-0.5.1/init.tcl"
("package ifneeded Guib 0.5.1" script)
invoked from within
"package require Guib 0.5"
(file "/home/pearl/espresso-5.4.0/PWgui-5.4.0/init.tcl" line 5)
invoked from within
"source [file join $env(PWGUI) init.tcl]"
(file "/home/pearl/espresso-5.4.0/PWgui-5.4.0/pwgui.tcl" line 62)
[pearl@localhost PWgui-5.4.0]$
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[Pw_forum] Slab config. Input file reg

2016-03-30 Thread Muthu V

Dear Users
I'm trying to make slab in vesta for TiO2 ( Rutile and anatase). for
instance to make (011) slab, just opened P1 structure  of rutile in vesta
and used the following matrix (0 -1 1;1 0 0;0 1 1) . this creates
interested slab, but the problem is as lattice parameters a  and c are
different one the crystallography angle of slab is not 90(remaining two
angles are 90, since a=b). but my target to prepare all to be 90* angles,
to simplify further calculations

I have attached the prepared rutile-011 slab( 1x1) vesta file with this
mail. I look forward to your kind suggestions and comments on to make 90*
for all angles.

Note: after creating slab i tried to rotate the unit cell but it losses the
symmetry hence it fails to attain 90*. since the beta is 114*. to make it
to 90 i can rotate it by (114-90) =24 about b axis, which( 24*) do not
includes required no of atoms to maintain the symmetry.

Thank you


*--*

*Muthu V*

*Sri Paramakalyani College*

*Alwarkurichi*

*India--*


rut-011.vesta
Description: Binary data
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[Pw_forum] PWgui problem - reg.,

2016-02-11 Thread Muthu V

Dear all
i am trying to run PWgui-5.2.1 in my Intel core-duo PC under fedora. but i
ma keep on getting the following error message.
[pearl@localhost pwgui-5.2.1]$ ./pwgui
 ==
  This is PWgui version: 5.2.1
 --
 PWgui: using the system default "tclsh" interpreter

 PWGUI   : /home/pearl/espresso-5.2.1/pwgui-5.2.1
 GUIB engine : /home/pearl/espresso-5.2.1/pwgui-5.2.1/lib/Guib-0.5.1

can't find package Itk
while executing
"package require Itk  "
(file "/home/pearl/espresso-5.2.1/pwgui-5.2.1/lib/Guib-0.5.1/init.tcl"
line 11)
invoked from within
"source /home/pearl/espresso-5.2.1/pwgui-5.2.1/lib/Guib-0.5.1/init.tcl"
("package ifneeded Guib 0.5.1" script)
invoked from within
"package require Guib 0.5"
(file "/home/pearl/espresso-5.2.1/pwgui-5.2.1/init.tcl" line 5)
invoked from within
"source [file join $env(PWGUI) init.tcl]"
(file "/home/pearl/espresso-5.2.1/pwgui-5.2.1/pwgui.tcl" line 62)

I have checked for Incr. Tcl and Tk and installed latest version of theses
packages through yumex-dnf. and the search option gives me

[pearl@localhost pwgui-5.2.1]$ whereis tcl
tcl: /usr/lib64/tcl8.6 /usr/include/tcl.h /usr/share/tcl8.6
[pearl@localhost pwgui-5.2.1]$ whereis tk
tk: /usr/lib64/tk8.6 /usr/include/tk.h /usr/share/tk8.6
/usr/share/man/mann/tk.n.gz
[pearl@localhost pwgui-5.2.1]$ whereis itcl
itcl: /usr/include/itcl.h /usr/share/man/mann/itcl.n.gz
[pearl@localhost pwgui-5.2.1]$ whereis itk
itk: /usr/include/itk.h /usr/share/man/mann/itk.n.gz
[pearl@localhost pwgui-5.2.1]$

can any one point out where is the mistake? why such error occurs even
though proper lib is available?
any suggestion will be appreciated.


*---*

*Muthu V*

*Sri Paramakalyani College*

*India---*
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[Pw_forum] PWgui installation Problem

2016-01-31 Thread Muthu V

Dear All
I am trying to run Pwgui-5.3.0 in fedora 23(64 bit) OS. my system spec are
Intel Core duo with 4Gb ram. when i hit
./pwgui
with PWgui-5.3.0 folder i am getting the following error meassage

I checked installed packages and i already have itk itcl and tk tcl in the
following path
/usr/lib64/tcl8.6/itk4.0.1
/usr/lib64/tcl8.6/itk4.0.1
/usr/lib64/tcl8.6/
/usr/lib64/tk8.6
can anyone help in shorting out the problem

[pearl@localhost PWgui-5.3.0]$ ./pwgui
 ==
  This is PWgui version: 5.3.0
 --
 PWgui: using the system default "tclsh" interpreter
 PWGUI   : /home/pearl/Downloads/PWgui-5.3.0
 GUIB engine : /home/pearl/Downloads/PWgui-5.3.0/lib/Guib-0.5.1
can't find package Itk
while executing
"package require Itk  "
(file "/home/pearl/Downloads/PWgui-5.3.0/lib/Guib-0.5.1/init.tcl" line
11)
invoked from within
"source /home/pearl/Downloads/PWgui-5.3.0/lib/Guib-0.5.1/init.tcl"
("package ifneeded Guib 0.5.1" script)
invoked from within
"package require Guib 0.5"
(file "/home/pearl/Downloads/PWgui-5.3.0/init.tcl" line 5)
invoked from within
"source [file join $env(PWGUI) init.tcl]"
(file "/home/pearl/Downloads/PWgui-5.3.0/pwgui.tcl" line 62)
[pearl@localhost PWgui-5.3.0]$

similar problem have been reported previously
https://www.mail-archive.com/pw_forum@pwscf.org/msg18098.html

Thank you

*-*




*Muthu.V  Sri Paramakalyani CollegeIndia
-*
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[Pw_forum] Error in running pw.x for band structure with free lattice reg.,

2015-06-07 Thread Muthu V

Dear All QE Users

I am trying to get band strucutre for Si crystal. i have edited the example
input file and used free lattce option (ibrav= 0 instead of ibrav= 2) with
no of atoms is 8 instead of 2.
while scf runs and gives sucessful result without any error. but when
programme enters into band calculation it shows the following error



















*Program PWSCF v.5.1.1 starts on  7Jun2015 at 20:18:34  This program is
part of the open-source Quantum ESPRESSO suite for quantum simulation
of materials; please cite "P. Giannozzi et al., J. Phys.:Condens.
Matter 21 395502 (2009);  URL http://www.quantum-espresso.org
<http://www.quantum-espresso.org>",  in publications or presentations
arising from this work. More details at
http://www.quantum-espresso.org/quote
<http://www.quantum-espresso.org/quote> Parallel version (MPI), running
on 1 processors Waiting for input... Reading input from
standard
input 
Error in routine find_bz_type (1): Wrong
ibrav 
stopping ...*

With this email i have enclosed the script file i have used. How to reslove
this problem?

Thank you



*-----*

*Muthu V  *





*Madurai Kamaraj University Madurai Tamil
NaduIndia-*


si
Description: Binary data
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[Pw_forum] calculation of specific capacitance - reg.,

2015-02-13 Thread Muthu V

Dear All

I like to do specific capacitance analysis to support some experimental
results with theoretical calculation. is it possible with DFT simulation,
if yes then how to do using QE

thank you in advance



*
*Muthu.V  Madurai Kamaraj Universit**y*

*
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[Pw_forum] wf_collect - question - reg.,

2014-12-23 Thread Muthu V

Dear Users

I did not use "wf_collect" option  in scf run and now i have four wf file(
I used four core processor). is it possible to combine them into single
file by doing any other run?

Thank you

**Muthu.V*

*Project Fellow  Madurai Kamaraj Universit**y*

*
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[Pw_forum] Help on bulk modulus calculation of an orthorhombic LaFeO3 system

2014-10-04 Thread Muthu V

Hello Isaac

you can use ev.x to do birch-muruganan fit and using this you can find bulk
modulus value


*

*Muthu.V?Project Fellow?  Madurai Kamaraj Universit**y*

*
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[Pw_forum] running example si example file for band structure - reg.,

2014-07-25 Thread Muthu V

Dear QE'ians

recently i installed QE-5.1 in my PC. everything went fine. i successfully
got o/p for si run_example file which is in espresso/PP/examples/example01/
folder.

i changed celldm(1) for si to A,B,C and cosAB, cosAC, cosBC values.  as
celldm(1) =10.2 so A = 5.3976=B=C and cosAB=cosBC=cosAC=0


i problem is. when i try with celldm(1) the run script runs well. but if i
chage celldm(1) to  a,b,c, cosAb,cosAC,cosBC values the i got the following
error message.

slave2 at slave2-CN:~/espresso-5.1/PP/examples/example01$ ./si

/home/slave2/espresso-5.1/PP/examples/example01 : starting

This example shows how to use pw.x and postprocessing codes to make a
contour plot in the [110] plane of the charge density for Si, and to
plot the band structure of Si.

  executables directory: /home/slave2/espresso-5.1/bin
  pseudo directory:  /home/slave2/espresso-5.1/pseudo
  temporary directory:   /home/slave2/espresso-5.1/tempdir
  checking that needed directories and files exist... done

  running pw.x as: /home/slave2/espresso-5.1/bin/pw.x  -nk 1 -nd 1
-nb 1 -nt 1
  running pp.x as: /home/slave2/espresso-5.1/bin/pp.x  -nk 1 -nd 1
-nb 1 -nt 1
  running plotrho.x as:  /home/slave2/espresso-5.1/bin/plotrho.x
  running bands.x as:  /home/slave2/espresso-5.1/bin/bands.x  -nk 1 -nd
1 -nb 1 -nt 1
  running plotband.x as: /home/slave2/espresso-5.1/bin/plotband.x

  running the scf calculation... done
  running pp.x to do a 2-d plot of the charge density... done
  running plotrho.x to generate rho.ps... done

  running pp.x to do another 2-d plot of the charge density... done
  generating si.charge.png... done
  generating contour plot of the charge si.contour.ps... done


*  running the band-structure calculation for Si...application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 0Error condition encountered during
test: exit status = 1*
Aborting
slave2 at slave2-CN:~/espresso-5.1/PP/examples/example01$


ple fine the si.band.out and CRASH report i attached. in this file the
error message printed as
 task # 0
 from latgen : error # 2
 wrong celldm(1)

can any one help to resolve this problem. whether band.x accept only
celldm(i)'s?

thank you in advance.


*
*Muthu.V  Madurai Kamaraj Universit**y*

*
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[Pw_forum] Installing QE-5.0.3 with ifort- iotk error- reg.,

2014-06-11 Thread Muthu V

Dear QE users

I tried to install QE-5.0.3 using ifort and icc compliers. the following is
message printed during compilation

*slave2 at slave2:~/espresso-5.0.3$ ./configure F77=ifort F90=ifort
MPIF90=ifort CC=icc BLAS_LIBS="/opt/intel/mkl/lib/intel64/"
LAPACK_LIBS="/opt/intel/mkl/lib/intel64/
/opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64/"
FFT_LIB="/opt/intel/mkl/lib/intel64/" *


checking build system type... x86_64-unknown-linux-gnu
checking architecture... x86_64
checking for ifort... ifort
configure: WARNING: using cross tools not prefixed with host triplet
checking whether the Fortran compiler works... yes
checking for Fortran compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... yes
checking for suffix of object files... o
checking whether we are using the GNU Fortran compiler... no
checking whether ifort accepts -g... yes
checking for Fortran flag to compile .f90 files... none
checking for ifort... ifort
checking whether we are using the GNU Fortran compiler... no
checking whether ifort accepts -g... yes
checking version of ifort... ifort 14.0.3.174
setting F90... ifort
setting MPIF90... ifort
checking whether we are using the GNU C compiler... yes
checking whether icc accepts -g... yes
checking for icc option to accept ISO C89... none needed
setting CC... icc
checking how to run the C preprocessor... icc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of int *... 8
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for struct mallinfo.arena... yes
checking whether we are using the GNU Fortran 77 compiler... no
checking whether ifort accepts -g... yes
setting F77... ifort
using F90... ifort
setting FFLAGS... -O2 -assume byterecl -g -traceback -par-report0
-vec-report0
setting F90FLAGS... $(FFLAGS) -nomodule
setting FFLAGS_NOOPT... -O0 -assume byterecl -g -traceback
setting FFLAGS_NOMAIN... -nofor_main
setting CFLAGS... -O3
setting CPP... cpp
setting CPPFLAGS... -P -traditional
setting LD... ifort
setting LDFLAGS...
setting AR... ar
setting ARFLAGS... ruv
checking whether make sets $(MAKE)... yes
checking whether Fortran files must be preprocessed... no
checking how to get verbose linking output from ifort... -v
checking for Fortran 77 libraries of ifort...
-L/opt/intel/composer_xe_2013_sp1.3.174/compiler/lib/intel64
-L/usr/lib/gcc/x86_64-linux-gnu/4.7/
-L/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu/
-L/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../lib/
-L/lib/x86_64-linux-gnu/ -L/lib/../lib64 -L/lib/../lib/
-L/usr/lib/x86_64-linux-gnu/ -L/usr/lib/../lib/
-L/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../ -L/lib64 -L/lib/ -L/usr/lib
-lifport -lifcore -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no
extra underscore
setting BLAS_LIBS... /opt/intel/mkl/lib/intel64/
setting LAPACK_LIBS... /opt/intel/mkl/lib/intel64/
/opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64/
checking for library containing dfftw_execute_dft... -lfftw3
setting FFT_LIBS... -lfftw3
setting MASS_LIBS...
checking for library containing mpi_init... -lmpi
setting MPI_LIBS... -lmpi
checking for library containing mpi_init... (cached) -lmpi



*checking for library containing pdgemr2d... nochecking for library
containing pdgemr2d... nochecking for library containing pdgemr2d...
nochecking for library containing pdgemr2d... no*
setting DFLAGS... -D__INTEL -D__FFTW3 -D__MPI -D__PARA
setting IFLAGS... -I../include
setting FDFLAGS... $(DFLAGS)
checking for ranlib... ranlib
setting RANLIB... ranlib
checking for wget... wget -O
setting WGET... wget -O
configure: creating ./config.status
config.status: creating include/fft_defs.h
config.status: creating make.sys
config.status: creating configure.msg
config.status: creating install/make_wannier90.sys
config.status: creating install/make_blas.inc
config.status: creating install/make_lapack.inc
config.status: creating include/c_defs.h
config.status: include/c_defs.h is unchanged

ESPRESSO can take advantage of several optimized numerical libraries
(essl, fftw, mkl...).  This configure script attempts to find them,
but may fail if they have been installed in non-standard locations.
If a required library is not found, the local copy will be compiled.

The following libraries have been found:
  BLAS_LIBS=/opt/intel/mkl/lib/intel64/
  LAPACK_LIBS=/opt/intel/mkl/lib/intel64/
/opt

[Pw_forum] Using Intel Fortran, C++ complier- parallel, serial versions - reg.,

2014-06-04 Thread Muthu V

Dear users
usually i install QE by installing FFTW lib and Fortran complier.
everything goes fine with serial and parallel installation of QE.

but i heard that  using intel C++, fortran (ifort, icc ) compliers for
intel core(i am using intel i5 core)  improves performance so i decided to
install above two for this i used *Intel? Parallel Studio XE 2013 for Linux*

intel non-commerial package which includes C++,  fortran compliers and  mkl
lib.

Here i faced problem in configuring QE. i did this without installing *mpich2.
*all process goes fine no problem i got serial version QE. but if i try with*
mpich2, *pre-installed before QE configuration, i got the following error
message and configuration stops.

slave2 at slave2:~/espresso-5.0.1$ ./configure
checking build system type... x86_64-unknown-linux-gnu
checking architecture... x86_64
checking for ifort... ifort
configure: WARNING: using cross tools not prefixed with host triplet
checking whether the Fortran compiler works... yes
checking for Fortran compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... yes
checking for suffix of object files... o
checking whether we are using the GNU Fortran compiler... no
checking whether ifort accepts -g... yes
checking for Fortran flag to compile .f90 files... none
checking for mpif90... mpif90
checking whether we are using the GNU Fortran compiler... no
checking whether mpif90 accepts -g... no
checking version of mpif90... unknown, assuming gfortran

*configure: WARNING: parallel compiler mpif90 uses gfortran, but serial
compiler ifort was detectedconfigure: WARNING: assuming F90=gfortran,
discarding ifort*
setting F90... gfortran
setting MPIF90... mpif90
checking for cc... cc
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
setting CC... cc
checking how to run the C preprocessor... cc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of int *... 8
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for struct mallinfo.arena... yes
checking for gfortran... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether  accepts -g... no
setting F77...
using F90... gfortran
setting FFLAGS... -O3 -g
setting F90FLAGS... $(FFLAGS) -x f95-cpp-input
setting FFLAGS_NOOPT... -O0 -g
setting CFLAGS... -O3
setting CPP... cpp
setting CPPFLAGS... -P -traditional
setting LD... mpif90
setting LDFLAGS... -g
setting AR... ar
setting ARFLAGS... ruv
checking whether make sets $(MAKE)... yes
checking whether Fortran files must be preprocessed... no
checking how to get verbose linking output from ... configure: WARNING:
compilation failed

checking for Fortran 77 libraries of ...
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... configure: error: in
`/home/slave2/espresso-5.0.1':
configure: error: cannot compile a simple Fortran program
See `config.log' for more details.
slave2 at slave2:~/espresso-5.0.1$

 anybody can help me in fixing this issue. ie i want icc, ifort complier (
as these improves performance) along with parallel version QE ie with
mpich2 ( which requires gfortran complier, according to error message )

any help will be appreciated
thank you in advance
*__*

?Muthu.V
Project Fellow
School of Physics
Madurai Kamaraj University
India
*__?*
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[Pw_forum] Graphene_fixed calculation

2014-05-27 Thread Muthu V

Dr. Siddheshwar chopra

you can use unit cell of graphene for SC modeling. view UC in xceysden then
hit shift+n. in upcoming pup up window you can design SC.
other software supporting such  designing are Avogadro, VESTA

*


*Muthu.V  ?Project FellowDept. of Theoretical Physics?Madurai Kamaraj
Universit**y*

*
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[Pw_forum] Reply to: negatives frequencies phonon calculation

2014-05-08 Thread Muthu V

Hello ZAARI

I am also face the same problem in calculation el-ph coupling constant for
Hesuler systems
i tried in the following ways ( though problem still remain anyway for your
system one may solve this problem)

1. check whether your getting -ve frequency in ph.x run
2. increse k point grid in scf and nscf runs ( but 2x2x2 is enough in
epsilon,
 i think )
3. reduce  tr2_ph in el-ph calculation (ph.x)



?
**


*Muthu.V  ?Project FellowDept. of Theoretical Physics?Madurai Kamaraj
Universit*


*?y India*
**
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[Pw_forum] parallel computing -reg.

2014-04-16 Thread Muthu V

Dear all QE users

  thank you Dr. Axel Kohlmeyer for your valuable hint and
suggestions. after your reply in pw forum I checked bit configuration of
Operating system in my 3 pcs. out of three , two were in 64bit and one was
in 32bit. so i changed 32bit to 64bit.
  After this again I tried to run programmes. but still i got the
same problem.then I installed liblapack not only in  master node but also
in all nodes. finally my programme went smoothly in my Beowulf cluster (
with 3 pcs).

thank you

*_*

*??*


*Muthu.V?Project Assistant Dept. of Theoretical Physics?Madurai Kamaraj
Universit**y*

*__*
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[Pw_forum] parallel computing -reg.,

2014-04-03 Thread Muthu V

Dear all

I have constructed Beowulf type cluster with 3PCs ( i5 processor ) . I
tried to run SCF calculation for graphene with the following comment

*mpirun  --hostfile /home/physics/hosts  -np  12
/home/physics/espresso-5.0.1/bin/pw.x  -npool  12
http://grap.pw.in> > grap.pw.out*

but i received the following error message.

*/home/physics/espresso-5.0.1/bin/pw.x: error while loading shared
libraries: liblapack.so.3: cannot open shared object file: No such file or
directory*

  I checked in /user/lib directory with the comment * find liblapack** i
got the following list.





*physics at master:/usr/lib$ find
liblapack*liblapack.a
liblapack.soliblapack.so.3
liblapack.so.3gf*

so i conformed having liblapack.so.3. i searched in net but i could not get
any appropriate post. i request to help to resolve this issue
any help will be appreciated

Note: for reference i have attached my graphene input file




*Muthu.V  ?Project Fellow Dept. of Theoretical Physics?Madurai Kamaraj
Universit**y*
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[Pw_forum] "STO Structure breaking - reg."

2014-03-09 Thread Muthu V

Dear All

i thank Ari P Seitsonen, xirainbow, Paolo Giannozzi for your kind reply.

i did same calculation with Ecut = 100Ry and 8x8x8 k-point mesh. but i got
the same result as previous.so my convergence test seems to be correct.
As Paolo mentioned i expanded 3 units in each direction i retrieved initial
structure with all atoms. but i have one confusion.

Why i can't get initial structure with relaxed unit cell coordinates. ( one
reason might be duo to symmetry breaking in HSTO compared to STO)

Attached is output file for vc-relax calculation with Ecut =100 and  K
point mesh = 8x8x8

Thank you

*_*



*Muthu.V  Project FellowSchool of Physics Madurai Kamaraj University*
*, India*


*__*
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[Pw_forum] STO Structure breaking - reg.,

2014-03-05 Thread Muthu V

Dear all

I want to study H hydrogen uptake in SrTiO3 (STO). i did preliminary
convergence test for STO  and added atomic Hydrogen to STO Unit cell and
then carried out variable volume relaxation.*  below i attached Xcrysden
view of input file and Output file*. i do not know why the basic structure
is breaking. with this mail i have attached input file for reference.  i
request to point wrong  usage tags or mis valued tags. any suggestion will
be appreciated .

 &CONTROL
   title = 'hsto' ,
 calculation = 'vc-relax' ,
restart_mode = 'from_scratch' ,
  wf_collect = .false. ,
  outdir = '//' ,
  pseudo_dir = '//' ,
  prefix = 'hsto' ,
   etot_conv_thr = 1.0D-7 ,
   forc_conv_thr = 1.0D-6 ,
 tstress = .true. ,
 tprnfor = .true. ,
 /
 &SYSTEM
   ibrav = 1,
   A = 3.905 ,
   B = 3.905 ,
   C = 3.905 ,
   cosAB = 0 ,
   cosAC = 0 ,
   cosBC = 0 ,
 nat = 6,
ntyp = 4,
 ecutwfc = 25 ,
 ecutrho = 100 ,
   nosym = .true. ,
force_symmorphic = .true. ,
use_all_frac = .true. ,
 occupations = 'smearing' ,
 degauss = 0.001 ,
smearing = 'gaussian' ,
exxdiv_treatment = 'none' ,
 /
 &ELECTRONS
electron_maxstep = 700,
conv_thr = 1.0D-12 ,
 startingpot = 'atomic' ,
 startingwfc = 'atomic' ,
 mixing_mode = 'plain' ,
 mixing_beta = 0.3 ,
 diagonalization = 'david' ,
 /
 &IONS
ion_dynamics = 'bfgs' ,
   ion_positions = 'from_input' ,
 phase_space = 'full' ,
   pot_extrapolation = 'atomic' ,
   wfc_extrapolation = 'first_order' ,
 /
 &CELL
   cell_dynamics = 'bfgs' ,
 cell_factor = 2 ,
 cell_dofree = 'all' ,
 /
ATOMIC_SPECIES
   Sr   87.62000  Sr.pw-mt_fhi.UPF
   Ti   47.88000  Ti.pw-mt_fhi.UPF
O   16.0  O.pw-mt_fhi.UPF
H1.00800  H.pz-mt_fhi.UPF
ATOMIC_POSITIONS crystal
   Sr  0.00.00.01  1  1
   Ti  0.50.50.51  1  1
O  0.00.50.51  1  1
O  0.50.00.51  1  1
O  0.50.50.01  1  1
H  0.1808610000.1808610000.51  1  1
K_POINTS automatic
  2 2 2   0 0 0

and final step of output file
.
 End of BFGS Geometry Optimization
Begin final coordinates
 new unit-cell volume =256.15080 a.u.^3 (37.95763 Ang^3 )

CELL_PARAMETERS (alat=  7.37938055)
   0.870870969   0.012033131   0.00822
   0.012033035   0.870875788   0.00824
   0.00373   0.00373   0.840637748

ATOMIC_POSITIONS (crystal)
Sr  -0.023090315  -0.023090076  -0.00036
Ti   0.536760793   0.536756648   0.51056
O0.025340380   0.502299235   0.50334
O0.502299364   0.025344838   0.50335
O0.445274884   0.445274408  -0.01291
H0.194275894   0.194275947   0.49602
End final coordinates


*_*



*Muthu.V  Madurai Kamaraj University__*
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[Pw_forum] Xcrysden charge plot - reg.,

2014-01-31 Thread Muthu V

Dear QE'ians

i drawn charge density plot using .xsf (for charge density)  file. i have
two questions  regarding plotting with xcrysden

1.   xcrysden do well. but i want to display atom only at the interested
point in crystal not all atoms in whole crystal. i do not have crystal.xx
package and i
  want to delete unwanted atom. can i do this in xcrysden (without
crystal package) ? ( since with out this package of the options in xcrysden
are inactive
  for e.g *"AdvGeom,Properties"*

2.   at starting window if i load .xsf (charge density file)file , xcrysden
shows opening with which gives details of the file along with multiplying
factor. if
  change this value nothing happens except changes in lower and higher
rendering value of charge. what is the use of multiplying factor?

3.   i want to plot for specific bands in that in band structure. QE gives
me options for this. but by changing the  lowest and highest rendered value
i can get
  different plot. what they mean?  is this correspond to charge plot
for different bands?

dear qe users your help will be appreciated

thank you



*_*
*Muthu.V*
*Project Fellow*
*School of Physics*
*Madurai Kamaraj University*
*Mandurai, Tamil Nadu*
*India*

*__*
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[Pw_forum] band structure of Si unit cell and supercer

2014-01-22 Thread Muthu V

Dear QE users


i have run band structure calculation for Si unit cell and 2x2x2
super-cell. as far as i know the both band structure should be same since
2x2x2 super-cell is = simply repeating unit cell in space twice all
direction.

but here i have different band structures and do not know why this occurs.
below i attached input of Si unit & 2x2x2 supercell.

*input for Si 2x2x2 supercell*
# self-consistent calculation
cat > si.scf.in << EOF
 &control
calculation='scf'
restart_mode='from_scratch',
prefix='si'
pseudo_dir = '/home/physics/Desktop/espresso-5.0.1/pseudo/',
outdir='/home/physics/tmp/'
 /
 &system
  ibrav = 2,
   A = 10.7952 ,
   B = 10.7952 ,
   C = 10.7952 ,
   cosAB = 0 ,
   cosAC = 0 ,
   cosBC = 0 ,
 nat = 16,
ntyp = 1,
 ecutwfc = 18.0 ,
 ecutrho = 72 ,
 occupations = 'smearing' ,
 degauss = 0.01 ,
smearing = 'gaussian' ,

/
 &ELECTRONS
conv_thr =  1.0d-6,
mixing_beta = 0.3,
 /
ATOMIC_SPECIES
   Si   28.08600  Si.pz-mt_fhi.UPF
ATOMIC_POSITIONS angstrom
   Si  0.00.00.0
   Si  1.3494013501.3494013501.349401350
   Si -2.6988027002.6988027000.0
   Si -1.3494013504.0482040501.349401350
   Si  0.02.6988027002.698802700
   Si  1.3494013504.0482040504.048204050
   Si -2.6988027005.3976054002.698802700
   Si -1.3494013506.7470067504.048204050
   Si -2.6988027000.02.698802700
   Si -1.3494013501.3494013504.048204050
   Si -5.3976054002.6988027002.698802700
   Si -4.0482040504.0482040504.048204050
   Si -2.6988027002.6988027005.397605400
   Si -1.3494013504.0482040506.747006750
   Si -5.3976054005.3976054005.397605400
   Si -4.0482040506.7470067506.747006750
K_POINTS automatic
2 2 2 0 0 0
EOF

# band structure calculation along high-symmetry lines
cat > si.band.in << EOF
 &control
calculation='bands'
pseudo_dir = '/home/physics/Desktop/espresso-5.0.1/pseudo/',
outdir='/home/physics/tmp/',
prefix='si'
 /
 &system
  ibrav = 2,
   A = 10.7952 ,
   B = 10.7952 ,
   C = 10.7952 ,
   cosAB = 0 ,
   cosAC = 0 ,
   cosBC = 0 ,
 nat = 16,
ntyp = 1,
 ecutwfc = 18.0 ,
 ecutrho = 72 ,
 occupations = 'smearing' ,
 degauss = 0.01 ,
smearing = 'gaussian' ,
nbnd = 50,
 /
  &ELECTRONS
conv_thr = 1.0d-6 ,
 mixing_beta = 0.3 ,
 /
ATOMIC_SPECIES
   Si   28.08600  Si.pz-mt_fhi.UPF
ATOMIC_POSITIONS angstrom
   Si  0.00.00.0
   Si  1.3494013501.3494013501.349401350
   Si -2.6988027002.6988027000.0
   Si -1.3494013504.0482040501.349401350
   Si  0.02.6988027002.698802700
   Si  1.3494013504.0482040504.048204050
   Si -2.6988027005.3976054002.698802700
   Si -1.3494013506.7470067504.048204050
   Si -2.6988027000.02.698802700
   Si -1.3494013501.3494013504.048204050
   Si -5.3976054002.6988027002.698802700
   Si -4.0482040504.0482040504.048204050
   Si -2.6988027002.6988027005.397605400
   Si -1.3494013504.0482040506.747006750
   Si -5.3976054005.3976054005.397605400
   Si -4.0482040506.7470067506.747006750
K_POINTS
 36
   0.5 0.5 0.5  1
   0.4 0.4 0.4  2
   0.3 0.3 0.3  3
   0.2 0.2 0.2  4
   0.1 0.1 0.1  5
   0.0 0.0 0.0  6
   0.0 0.0 0.1  7
   0.0 0.0 0.2  8
   0.0 0.0 0.3  9
   0.0 0.0 0.4 10
   0.0 0.0 0.5 11
   0.0 0.0 0.6 12
   0.0 0.0 0.7 13
   0.0 0.0 0.8 14
   0.0 0.0 0.9 15
   0.0 0.0 1.0 16
   0.0 0.1 1.0 17
   0.0 0.2 1.0 18
   0.0 0.3 1.0 19
   0.0 0.4 1.0 20
   0.0 0.5 1.0 21
   0.0 0.6 1.0 22
   0.0 0.7 1.0 23
   0.0 0.8 1.0 24
   0.0 0.9 1.0 25
   0.0 1.0 1.0 26
   0.0 0.9 0.9 27
   0.0 0.8 0.8 28
   0.0 0.7 0.7 29
   0.0 0.6 0.6 30
   0.0 0.5 0.5 31
   0.0 0.4 0.4 32
   0.0 0.3 0.3 33
   0.0 0.2 0.2 34
   0.0 0.1 0.1 35
   0.0 0.0 0.0 36
EOF

*Si Unitcell:*
# self-consistent calculation
cat > si.scf.in << EOF
 &control
calculation='scf'
restart_mode='from_scratch',
prefix='si'
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
 /
 &system
ibrav= 2,
A = 5.397,
B =5.397,
C = 5.397,
cosAB = 0 ,
cosAC = 0 ,
cosBC = 0 , nat=

[Pw_forum] forming super cell - reg.,

2014-01-22 Thread Muthu V

Dear QE users

i want to create supercell of Si and iO2 from their unitcell. i searched
and there are some topics on this issue in this forum

*Tone Kokalj* tone.kokalj at ijs.si

*Wed Mar 21 11:24:27 CET 2012*

nut it still not working for both Si and TiO2. can anyone help in this
regard. ie how to get atomic coordinates of super cell build using xcrysden.

thank you

*_*



*Muthu.VMadurai Kamaraj University__*
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[Pw_forum] magnetic Moment calculation

2014-01-09 Thread Muthu V

Dear QE Users

  i plane to calculate magnetic moment for SrTiO3 and TiO2. but i don?t
know how to do this. i searched it qe forum and after that i tried to scf
run for TiO2 system without  and with magnetic field. but i don?t know
whether this is correct or

 can you help me in this reg.,  ie where i can get details about it

Thank you

*_*



*Muthu.VMadurai Kamaraj University__*
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[Pw_forum] Plotband.x Error

2013-11-13 Thread Muthu V

hello
JdGa The Pro

i can you send your input file

*_*



*Muthu.VMadurai Kamaraj University__*
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[Pw_forum] Re to Re: band structure drawing reg.,

2013-10-18 Thread Muthu V

thank you Bramha Pandy for your suggestion .

*_
**
Muthu.V
Madurai Kamaraj University
__
*
**
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[Pw_forum] band structure drawing reg.,

2013-10-18 Thread Muthu V

Dear QE Friends

This question may be irritating ( i apology for it if it is so). in usually
band structure calculation i get it without any problem. but in the band
diagram i do not see the k vector symbols like X,M,G(Gamma) in x axis and
in y axis it do not have any label except numbers to represent energy. i
have gone through post processing and plot.x files i do not know where i
have to correct or add commends.

i request all for your valuable suggestion.

thank you
*_
**
Muthu.V
Madurai Kamaraj University
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*
**
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[Pw_forum] rutile.dynGxx- reg.,

2013-10-17 Thread Muthu V

Dear QE  Friends

i did some calculations on phonon dispersion spectrum for tio2. while i was
gone through q2r.out file i noticed that
*reading force constants from file rutile.dynG1 *sentence and gone back to
rutile.dynG1 file. but i found it is doubt to understand without any basic
idea about it. i found some queries, pointed out below, but i need
something more than this about the structure of the file. meaning of each
and every letters.
*Asked by: Denny Jackson* denny.jackson at gmail.com

*Wed Aug 26 22:47:56 CEST 2009**
*
*Replied by:* *Stefano Baroni* baroni at sissa.it

*Thu Aug 27 13:41:17 CEST 2009*

where can i find the such description?
i thank in advance.

*copy of rutile.dynG1 file:*
Dynamical matrix file

  36  6  8.6795121  1.000  0.6440235  0.000  0.000
0.000
   1  'Ti  '43639.950313293208
   2  'O   '14583.107874116360
   3  'N   '12766.599499546741
11  0.000  0.000  0.000
21  0.500  0.500  0.3220118
32  0.3053000  0.3053000  0.000
42  0.6947000  0.6947000  0.000
53  0.1947000  0.8053000  0.3220118
63  0.8053000  0.1947000  0.3220118

 Dynamical  Matrix in cartesian axes

 q = (0.0   0.0   0.0 )

11
  0.25781241  0.   -0.06316295  0.0.  0.
 -0.06316295  0.0.25781241  0.0.  0.
  0.  0.0.  0.0.25202771  0.
12
 -0.04646516  0.   -0.07155401  0.0.  0.
 -0.07155401  0.   -0.04646516  0.0.  0.
  0.  0.0.  0.   -0.02398728  0.
xxx

 Dielectric Tensor:

686.203143355029-85.917073797734  0.
-85.917073797734686.203143355029  0.
  0.  0.342.625962907908

 Effective Charges E-U: Z_{alpha}{s,beta}

 atom #1
 12.691270414187  4.281938314436  0.
  4.281938314436 12.691270414187  0.
  0.  0.  8.547647213524
 atom #2
 -7.184223609054 -5.615972707426  0.
 -5.615972707426 -7.184223609054  0.
  0.  0.  3.255196675680
 atom #3
  2.078878897165  1.094949477197  0.
  1.094949477197  2.078878897165  0.
  0.  0. -0.620577263710
 atom #4
  2.078878897165  1.094949477197  0.
  1.094949477197  2.078878897165  0.
  0.  0. -0.620577263710
 atom #5
 -4.751230586840 -0.614251742701  0.
 -0.614251742701 -4.751230586840  0.
  0.  0. -5.459389033205
 atom #6
 -4.751230586840 -0.614251742701  0.
 -0.614251742701 -4.751230586840  0.
  0.  0. -5.459389033205

 Effective Charges U-E: Z_{s,alpha}{beta}

 atom #1
  0.126916859529E+02  0.428231649887E+01  0.E+00
  0.428231649887E+01  0.126916859529E+02  0.E+00
  0.E+00  0.E+00  0.854662318603E+01
 atom #2
 -0.718403575583E+01 -0.561690445757E+01  0.E+00
 -0.561690445757E+01 -0.718403575583E+01  0.E+00
  0.E+00  0.E+00  0.325513014546E+01
 atom #3
  0.207779719692E+01  0.109423636156E+01  0.E+00
  0.109423636156E+01  0.207779719692E+01  0.E+00
  0.E+00  0.E+00 -0.620537883158E+00
 atom #4
  0.207779719692E+01  0.109423636156E+01  0.E+00
  0.109423636156E+01  0.207779719692E+01  0.E+00
  0.E+00  0.E+00 -0.620537883158E+00
 atom #5
 -0.475079928391E+01 -0.613744966194E+00  0.E+00
 -0.613744966194E+00 -0.475079928391E+01  0.E+00
  0.E+00  0.E+00 -0.545903108538E+01
 atom #6
 -0.475079928391E+01 -0.613744966194E+00  0.E+00
 -0.613744966194E+00 -0.475079928391E+01  0.E+00
  0

[Pw_forum] Suggested cutoff for wfc and rho - reg.,

2013-10-11 Thread Muthu V

Deal QE Users

I have the following Pseudo Potential files for Ti.  in all file  what i
observed is
Suggested minimum cutoff for wavefunctions : 0 Ry
Suggested minimum cutoff for charge density:  0 Ry
why these values are zero?
then for calculation what value for wfc and rho is reliable? (if i want to
use any of these)
*List of Pseudo potential files *

Ti.blyp-sp-hgh.UPF Ti.blyp-sp-van_ak.UPF   Ti.bp-sp-van_ak.UPF
Ti.pbe-mt_fhi.UPF  Ti.pbe-sp-van_ak.UPF Ti.pw91-nsp-van.UPF
Ti.pw-mt_fhi.UPFTi.pz-hgh.UPF Ti.pw91-sp-van_ak.UPF

Ti.pz-mt_fhi.UPF Ti.pz-sp-van.UPFTi.pz-sp-van_ak.UPF

thank you
*_
**
Muthu.V
Madurai Kamaraj University
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[Pw_forum] Activation - BANDS.X and DOS.X -

2013-07-01 Thread Muthu V

Hi everyone

currently i am using PWgui - 5.0.2 software. in this i can not run BANDS.X
and DOS.X.
if i make BANDS.X ( and DOS.X) file the all option n RUN menu are inactive.
i do not know how to make these active

How to make these options active?

Thank you

*_
**
Muthu.V
Madurai Kamaraj University
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[Pw_forum] Hi all

2013-06-29 Thread Muthu V

I am Muthu.v.  I'm new to quantum espresso and currently try to use full
utility of PWgui-5.0.2. i have installed espresso-5.0.1 in Ubuntu.

But in PWgui- 5.0.2 i can not run Band.x and Dos.x. while i open new Pw.x
file all options in PWgui are active but if i open either Bands.x or Dos.x
the RUN option is not so that i could not run the program.*

*
i request you 
all to help me in this regards 
*
_
**
Muthu.V

Project Assistant

Madurai Kamaraj University
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[Pw_forum] Debugging BAND.X in PWGUI - 5.0.2 - reg.,

2013-03-17 Thread MUTHU V

 i use  espresso- 5.0.1 with aid of PWGUI-5.0.2 software. in this package i
can run PW.X files. but if I try for other format( NEB.X BANDS.X and
DOS.X). the RUN menu is not active so that I couldn't run these formats for
my system.
*(*
for example consider in BAND.X window
In the* VIEW* menu *"structure with  XCrysDen " *is inactive and in *RUN
* menu all four are inactive * ( run calculation , run calculation &
configure, run calculation +XCrysDen's Display, run calculation & configure
+XCrysDen's Display)*
  *
)*

I request you to help to make all thinks are possible to run in my package.
or
simply, please help me to debug the errors in order to make ( NEB.X BANDS.X
and DOS.X) active?

thank you for considering my request

-- 
*Muthu.V**
Research Scholar
Madurai Kamaraj University*
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[Pw_forum] Debugging BAND.X regarding mail.

2013-03-14 Thread MUTHU V

 i use  espresso- 5.0.1 with aid of PWGUI-5.0.2 software. in this package i
can run PW.X files. but if I try for other format( NEB.X BANDS.X and
DOS.X). the RUN menu is not active so that I couldn't run these formats for
my system.
*(*
for example consider in BAND.X window
In the* VIEW* menu *"structure with  XCrysDen " *is inactive and in *RUN
* menu all four are inactive * ( run calculation , run calculation &
configure, run calculation +XCrysDen's Display, run calculation & configure
+XCrysDen's Display)*
*)*

I request you to help to make all thinks are possible to run in my package.
or
simply, please help me to debug the errors in order to make ( NEB.X BANDS.X
and DOS.X) active?


thank you for considering my request

-- 
*Muthu.V**
Madurai Kamaraj University*
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