[Pw_forum] Pw_forum Digest, Vol 64, Issue 34
funmi ayedun
funmiayedun at yahoo.com
Fri Oct 12 20:56:14 CEST 2012
Okay Sir,
though I know that you are always busy and your schedule is tight but please do not forget.. Have a pleasant weekend.
Greetings to your wife and Wonderful.
--- On Fri, 10/12/12, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote:
From: pw_forum-request at pwscf.org <pw_forum-request at pwscf.org>
Subject: Pw_forum Digest, Vol 64, Issue 34
To: pw_forum at pwscf.org
Date: Friday, October 12, 2012, 7:46 AM
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Today's Topics:
1. Cell optimization converges to unrealistic value
(Yury Vishnevskiy)
2. Re: Cell optimization converges to unrealistic value
(Yury Vishnevskiy)
3. Re: Test wdw1 failed (Alexandr Rzhechitskii)
4. Re: Cell optimization converges to unrealistic value
(Giuseppe Mattioli)
5. Error: At line 230 of file bands_FS.f90 (unit = 5, file =
'stdin') (Bramha Pandey)
6. Re: error : US j-average not yet implemented (Bramha Pandey)
7. assignment of spin label to electronic band (koushik pal)
----------------------------------------------------------------------
Message: 1
Date: Fri, 12 Oct 2012 12:18:22 +0200
From: Yury Vishnevskiy <YVVishnevsky at yandex.ru>
Subject: [Pw_forum] Cell optimization converges to unrealistic value
To: pw_forum at pwscf.org
Message-ID: <5077EE6E.1060409 at yandex.ru>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear QE users,
I have a problem with cell optimization for one of my objects -- Copper
phthalocyanine. It has layered structure and the distance between sheets
must be around 3.3 Angstroms according to some experimental evidences.
Using this value as an initial approximation I've started "vc-relax"
calculation with pw.x from the latest version of the QE package (5.0).
The calculation died several times after 15-20 optimization cycles with
message
"Error in routine scale_h (1):
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor."
and I restarted it using latest optimized parameters. During the
optimization the distance between layers (parameter celldm(3)) got
unrealistically small. Now it is around 0.5 Angstrom. What could be
wrong with my input (see below)?
&control
calculation = 'vc-relax' ,
restart_mode = 'from_scratch' ,
prefix = 'cuph_3d_k444' ,
verbosity = 'high' ,
/
&SYSTEM
ibrav = 6,
celldm(1) = 20.11677,
celldm(3) = 2.59367,
nat = 33,
ntyp = 4,
ecutwfc = 25 ,
tot_charge = 0.000000,
occupations = 'smearing' ,
degauss = 0.02 ,
smearing = 'gaussian' ,
nspin = 2 ,
starting_magnetization(1) = 0.0,
starting_magnetization(2) = 0.0,
starting_magnetization(3) = 0.0,
starting_magnetization(4) = 0.5,
exxdiv_treatment = 'gygi-baldereschi' ,
/
&ELECTRONS
/
&IONS
/
&CELL
cell_dofree = 'xyz' ,
/
ATOMIC_SPECIES
N 14.00700 N.pbe-van_ak.UPF
H 1.00800 H.pbe-van_ak.UPF
C 12.01100 C.pbe-van_ak.UPF
Cu 63.54600 Cu.pbe-n-van_ak.UPF
ATOMIC_POSITIONS angstrom
N -0.002404756 1.949223697 -0.000000000
N 1.949223697 -0.002404756 -0.000000000
N 2.391389529 2.391389529 0.000000000
N 8.271536989 2.397282537 -0.000000000
N 8.695607152 -0.002619412 0.000000000
N 2.397282537 8.271536989 0.000000000
N -0.002619412 8.695607152 -0.000000000
N 8.265225407 8.265225407 0.000000000
H 5.350243681 8.115613628 0.000000000
H 8.115613628 5.350243681 0.000000000
H 5.350427438 2.574913054 0.000000000
H 2.574913054 5.350427438 0.000000000
C 1.116474541 2.759541645 0.000000000
C 2.759541645 1.116474541 -0.000000000
C 9.548405832 2.763398467 -0.000000000
C 6.499236299 0.719922493 -0.000000000
C 7.893740728 1.123273203 0.000000000
C 5.329717857 1.479863666 0.000000000
C 4.155377490 0.720022335 0.000000000
C 2.763398467 9.548405832 0.000000000
C 0.719922493 6.499236299 -0.000000000
C 1.123273203 7.893740728 0.000000000
C 1.479863666 5.329717857 -0.000000000
C 0.720022335 4.155377490 -0.000000000
C 6.497591960 9.961479852 0.000000000
C 9.961479852 6.497591960 -0.000000000
C 7.889717032 9.542180975 0.000000000
C 9.542180975 7.889717032 -0.000000000
C 5.330043432 9.207810550 0.000000000
C 9.207810550 5.330043432 -0.000000000
C 4.156498439 9.961968783 -0.000000000
C 9.961968783 4.156498439 0.000000000
Cu -0.017433297 -0.017433297 0.000000000
K_POINTS automatic
4 4 4 0 0 0
Thanks in advance,
sincerely,
Dr. Yury V. Vishnevskiy
Lehrstuhl f?r Anorganische Chemie und Strukturchemie
Universit?t Bielefeld
------------------------------
Message: 2
Date: Fri, 12 Oct 2012 12:40:21 +0200
From: Yury Vishnevskiy <YVVishnevsky at yandex.ru>
Subject: Re: [Pw_forum] Cell optimization converges to unrealistic
value
To: pw_forum at pwscf.org, giuseppe.mattioli at ism.cnr.it
Message-ID: <5077F395.8090501 at yandex.ru>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear Giuseppe and all others,
first of all, sorry for the duplicated message in the list. I have not
received any message to my initially registered e-mail address and was
already thinking that my question has not got into the pw_forum.
> Dear Yuri
> There are technical and physical reasons behind your unrealistic results.
> technical:
>
>> N 14.00700 N.pbe-van_ak.UPF
>> H 1.00800 H.pbe-van_ak.UPF
>> C 12.01100 C.pbe-van_ak.UPF
>> Cu 63.54600 Cu.pbe-n-van_ak.UPF
>
>> ecutwfc = 25 ,
>
>In the case of ultrasoft pseudopotential ecutrho has to be indicated,
>having a value between
>6*ecutwfc and 10*ecutwfc (convergence should be reached with respect
>to all such values, but I
>perform satisfactorily converged CuPc calculations with the same
>pseudos by using
>ecutwfc=35/ecutrho=280 cutoffs...)
Ok, I will use no less then 35 and 280 for ecutwfc and ecutrho.
>> tot_charge = 0.000000,
>> starting_magnetization(1) = 0.0,
>> starting_magnetization(2) = 0.0,
>> starting_magnetization(3) = 0.0,
>> exxdiv_treatment = 'gygi-baldereschi' ,
>
>useless keywords (in this case...). Starting_magnetization(4) = x with
>0.0 < x < 1.0 is enough to
>break the spin symmetry.
>
>> nat = 33,
>
>The copper phthalocyanine (CuPc) has 57 atoms. Have you checked the
>structure?
I calculate a _polymer_ of CuPc. The unit cell I've created contains 33
atoms, that should be correct.
>> ibrav = 6,
>> celldm(1) = 20.11677,
>> celldm(3) = 2.59367,
>
>your molecules embedded into a tetragonal cell seems to be placed at a
>z distance of about 30 A from
>its periodically repeated image... Check the exact use of the
>celldm(i) variables...
Thank you! I was not careful in reading the manual and thought that
these parameters are just lengths of vectors.
>Physical:
>
>Molecular crystals stay together because of dispersion interactions.
>As you are not using any kind
>of dispersion correction, you will never obtain meaningful results on
>lattice parameters. There is
>plenty of theoretical papers investigating the CuPc molecule. I
>suggest to start with them...
Ok, thanks for pointing on that. Now I can play with calculations further.
Sincerely,
Yura
------------------------------
Message: 3
Date: Fri, 12 Oct 2012 19:47:47 +0900
From: Alexandr Rzhechitskii <a.rzhechitskii at gmail.com>
Subject: Re: [Pw_forum] Test wdw1 failed
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
<CACQOamWRC1nS3HtVbpfziMBpnQk7Lk3FZ--LPhB-imtbDiZ9-w at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
How to do it?
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Message: 4
Date: Fri, 12 Oct 2012 12:53:26 +0200
From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
Subject: Re: [Pw_forum] Cell optimization converges to unrealistic
value
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <201210121253.26296.giuseppe.mattioli at ism.cnr.it>
Content-Type: Text/Plain; charset="iso-8859-1"
Dear Yuri
I'm not sure whether my previous answer to your previous post (identical to this one... Do not ask
two times the same question, please) reached the forum, thus I paste it below, with some corrections
wrt the previous version.
There are several technical and physical reasons behind your unrealistic results.
Technical:
> N 14.00700 N.pbe-van_ak.UPF
> H 1.00800 H.pbe-van_ak.UPF
> C 12.01100 C.pbe-van_ak.UPF
> Cu 63.54600 Cu.pbe-n-van_ak.UPF
> ecutwfc = 25 ,
In the case of ultrasoft pseudopotential, ecutrho has to be indicated, having a value between
6*ecutwfc and 10*ecutwfc (convergence should be reached with respect to all such values, but I
perform satisfactorily converged CuPc calculations with the same pseudos by using
ecutwfc=35/ecutrho=280 cutoffs...)
> tot_charge = 0.000000,
> starting_magnetization(1) = 0.0,
> starting_magnetization(2) = 0.0,
> starting_magnetization(3) = 0.0,
> exxdiv_treatment = 'gygi-baldereschi' ,
useless keywords (in this case...). Starting_magnetization(4) = x with 0.0 < x < 1.0 is enough to
break the spin symmetry.
> nat = 33,
The copper phthalocyanine (CuPc) has 57 atoms. Your system is a sort of periodical "graphene-like"
sheet, or "graphite-like" crystal, based on CuPc.
> ibrav = 6,
> celldm(1) = 20.11677,
> celldm(3) = 2.59367,
your sheet is embedded into a tetragonal cell, and it seems to be placed at a z distance of about 30
A from its periodically repeated image... Check the exact use of the celldm(i) variables: 2.59367
means that the c parameter is 2.59367*20.11677 a.u.
Physical:
Molecular crystals or layered molecular structures stay together because of dispersion interactions.
As you are not using any kind of dispersion correction, you will never obtain meaningful results on
lattice parameters. There is plenty of theoretical papers investigating the CuPc molecule, or the
graphite packing. I suggest you to start with them...
HTH
Giuseppe
On Friday 12 October 2012 12:18:22 Yury Vishnevskiy wrote:
> Dear QE users,
> I have a problem with cell optimization for one of my objects -- Copper
> phthalocyanine. It has layered structure and the distance between sheets
> must be around 3.3 Angstroms according to some experimental evidences.
> Using this value as an initial approximation I've started "vc-relax"
> calculation with pw.x from the latest version of the QE package (5.0).
> The calculation died several times after 15-20 optimization cycles with
> message
>
> "Error in routine scale_h (1):
> Not enough space allocated for radial FFT: try restarting with a
> larger cell_factor."
>
> and I restarted it using latest optimized parameters. During the
> optimization the distance between layers (parameter celldm(3)) got
> unrealistically small. Now it is around 0.5 Angstrom. What could be
> wrong with my input (see below)?
>
> &control
> calculation = 'vc-relax' ,
> restart_mode = 'from_scratch' ,
> prefix = 'cuph_3d_k444' ,
> verbosity = 'high' ,
> /
> &SYSTEM
> ibrav = 6,
> celldm(1) = 20.11677,
> celldm(3) = 2.59367,
> nat = 33,
> ntyp = 4,
> ecutwfc = 25 ,
> tot_charge = 0.000000,
> occupations = 'smearing' ,
> degauss = 0.02 ,
> smearing = 'gaussian' ,
> nspin = 2 ,
> starting_magnetization(1) = 0.0,
> starting_magnetization(2) = 0.0,
> starting_magnetization(3) = 0.0,
> starting_magnetization(4) = 0.5,
> exxdiv_treatment = 'gygi-baldereschi' ,
> /
> &ELECTRONS
> /
> &IONS
> /
> &CELL
> cell_dofree = 'xyz' ,
> /
> ATOMIC_SPECIES
> N 14.00700 N.pbe-van_ak.UPF
> H 1.00800 H.pbe-van_ak.UPF
> C 12.01100 C.pbe-van_ak.UPF
> Cu 63.54600 Cu.pbe-n-van_ak.UPF
> ATOMIC_POSITIONS angstrom
> N -0.002404756 1.949223697 -0.000000000
> N 1.949223697 -0.002404756 -0.000000000
> N 2.391389529 2.391389529 0.000000000
> N 8.271536989 2.397282537 -0.000000000
> N 8.695607152 -0.002619412 0.000000000
> N 2.397282537 8.271536989 0.000000000
> N -0.002619412 8.695607152 -0.000000000
> N 8.265225407 8.265225407 0.000000000
> H 5.350243681 8.115613628 0.000000000
> H 8.115613628 5.350243681 0.000000000
> H 5.350427438 2.574913054 0.000000000
> H 2.574913054 5.350427438 0.000000000
> C 1.116474541 2.759541645 0.000000000
> C 2.759541645 1.116474541 -0.000000000
> C 9.548405832 2.763398467 -0.000000000
> C 6.499236299 0.719922493 -0.000000000
> C 7.893740728 1.123273203 0.000000000
> C 5.329717857 1.479863666 0.000000000
> C 4.155377490 0.720022335 0.000000000
> C 2.763398467 9.548405832 0.000000000
> C 0.719922493 6.499236299 -0.000000000
> C 1.123273203 7.893740728 0.000000000
> C 1.479863666 5.329717857 -0.000000000
> C 0.720022335 4.155377490 -0.000000000
> C 6.497591960 9.961479852 0.000000000
> C 9.961479852 6.497591960 -0.000000000
> C 7.889717032 9.542180975 0.000000000
> C 9.542180975 7.889717032 -0.000000000
> C 5.330043432 9.207810550 0.000000000
> C 9.207810550 5.330043432 -0.000000000
> C 4.156498439 9.961968783 -0.000000000
> C 9.961968783 4.156498439 0.000000000
> Cu -0.017433297 -0.017433297 0.000000000
> K_POINTS automatic
> 4 4 4 0 0 0
>
>
> Thanks in advance,
> sincerely,
> Dr. Yury V. Vishnevskiy
> Lehrstuhl f?r Anorganische Chemie und Strukturchemie
> Universit?t Bielefeld
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM)
Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>
------------------------------
Message: 5
Date: Fri, 12 Oct 2012 16:36:23 +0530
From: Bramha Pandey <pandey.bramha at gmail.com>
Subject: [Pw_forum] Error: At line 230 of file bands_FS.f90 (unit = 5,
file = 'stdin')
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
<CAC2dNGEaXWDWi+rjS0KJkrLO3GhGa=a2Tg+pFUKaTg925wLGPA at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear All Developres and usres,
I was running the example02 in PP directory of espresso-5.0.1.This example
shows how to calculate the Density of States (DOS) and
how to plot the Fermi Surface of Ni . I am able to do first job but got the
error for the Fermi Surface calculation of Ni.
Error::::
Fermi Surface plot Spin-Polarized case... running the scf calculation
spin-polarization ... done
running the Fermi Surface calculation ... done
At line 230 of file bands_FS.f90 (unit = 5, file = 'stdin')
Fortran runtime error: Bad real number in item 1 of list input
mv: cannot stat `Bands_FS_up.bxsf': No such file or directory
mv: cannot stat `Bands_FS_down.bxsf': No such file or directory
The same problems occurs for the non spin-polarized case of Fermi surface
calculation of Ni.
Please help me to get rid of this error.
Thanks in advanced for your kind help.
--
Thanks and Regards
Bramha Prasad Pandey
Ph.D Student Indian School of Mines(ISM)
Dhanbad, INDIA.
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Message: 6
Date: Fri, 12 Oct 2012 16:37:40 +0530
From: Bramha Pandey <pandey.bramha at gmail.com>
Subject: Re: [Pw_forum] error : US j-average not yet implemented
To: dalcorso at sissa.it, PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
<CAC2dNGEALo6D7nw_7kCJ9d+Lzb8xn+TkTJYg8GGqMUBWwxiScw at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Thank you very much Dear Prof Andrea for your kind help. it works.
On Fri, Oct 12, 2012 at 12:30 AM, Andrea Dal Corso <dalcorso at sissa.it>wrote:
>
>
>
> On Thu, 2012-10-11 at 22:14 +0530, Bramha Pandey wrote:
> > Dear all
> > i want to use the 'Ga.rel-pbe-dn-kjpaw.UPF' and
> > 'As.rel-pbe-n-kjpaw.UPF' for the ZB-GaAs syatem.
> > It is giving the following error:::
> > I am using espresso-5.0.1 in serial version with ubuntu-12.04.
> >
> > Error in routine setup (1):
> > US j-average not yet implemented
> >
>
> These are fully relativistic PPs. You have to use them with
> lspinorb=.true..
>
>
> Andrea
>
>
> >
> > This error is also the same for the full relativistic ultrasoft
> > pseudopotential 'Ga.rel-pbe-dn-rrkjus.UPF' and
> > 'As.rel-pbe-n-rrkjus.UPF'.
> >
> > Any comment is appreciable in this regards.
> >
> > --
> > Thanks and Regards
> > Bramha Prasad Pandey
> > Ph.D Student Indian School of Mines(ISM)
> > Dhanbad, INDIA.
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
Thanks and Regards
Bramha Prasad Pandey
Ph.D Student Indian School of Mines(ISM)
Dhanbad, INDIA.
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Message: 7
Date: Fri, 12 Oct 2012 17:16:35 +0530
From: koushik pal <koushik.pal.physics at gmail.com>
Subject: [Pw_forum] assignment of spin label to electronic band
To: pw_forum at pwscf.org
Message-ID:
<CAMhFyZpMQ0iyEncTEW_DUd6bvHwBxm3ybVfAtybpQesjHVTgMg at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear PW users,
Is it possible to assign spin label to the electronic bands? That means,
can we tell which band is associated with up spin and which one due to down
spin? If possible, can somebody please tell me how to do that?
P.S.- I'm doing fully relativistic calculation with spin-orbit coupling.
Thanks in advance,
Koushik Pal
MS student
JNCASR, Bangalore, India
--
*
Koushik Pal
Materials Theory
Group<http://www.jncasr.ac.in/waghmare/index.php?menu_id=9&user_id=27&page_id=164>
Int PhD student
JNCASR <http://www/>
CPMU
*
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