[Pw_forum] How to use tools dipole.x, voronoy.x and epsilon.x?

[Weiguang Chen]

Thanks, I'll try it

On Sat, Mar 28, 2009 at 10:14 PM, Paolo Giannozzi
 wrote:
>
> On Mar 28, 2009, at 14:42 , Weiguang Chen wrote:
>
>> Thanks very much.The epsilon.x has a detail guide, could ?you told to
>> me the input files of the other two programs. I just try to read the
>> source code of these two tools, but too many calls that i can not
>> understand it.
>
> dipole.x one reads the data file from pw.x, voronoy.x reads the
> intermediate
> file produced by pp.x .
>
> P.
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
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>



-- 
Best Wishes
ChenWeiguang


#   Chen, Weiguang
#
#Postgraduate,  Ph. D
#  75 University Road, Physics Buliding  #  218
#  School of Physics & Engineering
#  Zhengzhou University
#  Zhengzhou, Henan 450052  CHINA
#
#  Tel: 86-13203730117;
#  E-mail:chenweiguang82 at gmail.com;
#chenweiguang82 at qq.com
#**

[Pw_forum] How to use tools dipole.x, voronoy.x and epsilon.x?

[Weiguang Chen]

Thanks very much.The epsilon.x has a detail guide, could  you told to
me the input files of the other two programs. I just try to read the
source code of these two tools, but too many calls that i can not
understand it.

Thanks again.

On Sat, Mar 28, 2009 at 9:30 PM, Paolo Giannozzi  
wrote:
>
> On Mar 28, 2009, at 14:21 , Weiguang Chen wrote:
>
>> ?I am a newbie about pwscf. There is a little information about the
>> above three tools, what's the usages for these programs although they
>> are not used frequently? I just what to know how to use for preparing
>> the future possible application.
>
> epsilon.x => Doc/eps_man.tex
> voronoy.x : Voronoy polyhedra around atoms, see the header of PP/
> voronoy.f90
> dipole.x: see the header of PP/dipole.f90
>
> P.
> ---
> 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
>



-- 
Best Wishes
ChenWeiguang


#   Chen, Weiguang
#
#Postgraduate,  Ph. D
#  75 University Road, Physics Buliding  #  218
#  School of Physics & Engineering
#  Zhengzhou University
#  Zhengzhou, Henan 450052  CHINA
#
#  Tel: 86-13203730117;
#  E-mail:chenweiguang82 at gmail.com;
#chenweiguang82 at qq.com
#**

[Pw_forum] Pw_forum Digest, Vol 21, Issue 81

[ding yi]

Subject: Re: Line 325 in bands_FS.f90
I think that there is a mistake in the bands_FS.f90. In the bands_FS.f90,
line 310," backspace(5) "
should be replace by "
! back nlines+1 positions (number of eigenvalues lines plus one blank line) !
do k=1,nlines+1
backspace(5)
enddo !
"
The bands_FS counts the lines of the spin-polarized calculations, while for
the non-spin-polarised case it forgets to counts.


Yi Ding, Ph.D Candidate Department of Physics, Tsinghua University Beijing
100084, P.R.China

2009/3/27  :
> Send Pw_forum mailing list submissions to
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> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'help' to
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>
> You can reach the person managing the list at
> ? ? ? ?pw_forum-owner 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. Line 325 in bands_FS.f90 (Paul M. Grant)
> ? 2. Re: Line 325 in bands_FS.f90 (Axel Kohlmeyer)
> ? 3. Re: Line 325 in bands_FS.f90 (Eyvaz Isaev)
> ? 4. Re: Line 325 in bands_FS.f90 (Eyvaz Isaev)
> ? 5. Re: Line 325 in bands_FS.f90 (Paul M. Grant)
> ? 6. Re: Line 325 in bands_FS.f90 (Eyvaz Isaev)
>
>
> --
>
> Message: 1
> Date: Thu, 26 Mar 2009 12:34:19 -0700
> From: "Paul M. Grant" 
> Subject: [Pw_forum] Line 325 in bands_FS.f90
> To: "'PWSCF Forum'" 
> Message-ID: <016001c9ae49$dcaada80$96008f80$@net>
> Content-Type: text/plain; charset="us-ascii"
>
> While running bands_FS.x (espresso-4.0 distro) on the output of an PW nscf
> non-spin-polarized job, I get the following error:
>
> At line 325 of file bands_FS.f90
> Fortran runtime error: Bad real number in item 5 of list input
>
> This only happens for my LSDA=F runs, spin-polarized are OK. ?(BTW, the
> LSDA=F run for Ni in example 08 does work. ?The only difference is that
> ex08 deals with only 8 bands and 1 formated line, whilst my task computes 20
> taking up 3 formated lines.) ?Line 325 is in the LSDA=F portion of the code
> follows a commented-out read command line with explicit formatting. ?I can't
> see any problem with the output of my nscf run. ?Before I start messing
> around with the bands_FS.f90 source, has anyone else run into this issue
> (Eyvaz?)? ?Is it possible there is a "line counting" error in the LSDA=F
> portion when the band energy listing exceeds one line? ?Sorry if I've made
> some stupid blunder.
>
> Paul M. Grant, PhD
> Physicist and Science Writer
> Principal, W2AGZ Technologies
> Visiting Scholar, Applied Physics, Stanford (2005-2008)
> EPRI Science Fellow (Retired)
> IBM Research Staff Member Emeritus
> w2agz at pacbell.net
> http://www.w2agz.com 
>
>
>
>
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> --
>
> Message: 2
> Date: Thu, 26 Mar 2009 16:00:07 -0400
> From: Axel Kohlmeyer 
> Subject: Re: [Pw_forum] Line 325 in bands_FS.f90
> To: PWSCF Forum 
> Message-ID: <1238097607.3704.119.camel at zero>
> Content-Type: text/plain; charset="us-ascii"
>
> On Thu, 2009-03-26 at 12:34 -0700, Paul M. Grant wrote:
>> While running bands_FS.x (espresso-4.0 distro) on the output of an PW
>> nscf non-spin-polarized job, I get the following error:
>>
>> At line 325 of file bands_FS.f90
>>
>> Fortran runtime error: Bad real number in item 5 of list input
>
> paul,
>
> please check your input carefully with hexdump to make
> sure you have no non-ascii characters in there. with some
> fonts it is hard to tell. i'm attaching a wrapper script that
> i use myself, which is little bit easier to read (at least for
> me, as it emulates the hexdumper display that i was
> using back in the days when i was hacking 6502 processors
> which almost broke the 1MHz barrier...). i miss begin able
> to fix bugs in running programs by replacing goto opcodes
> with NOPs... ;-)
>
> cheers,
> ? axel.
>
>
>>
>> This only happens for my LSDA=F runs, spin-polarized are OK. ?(BTW,
>> the LSDA=F run for Ni in example 08 does work. ?The only difference is
>> that
>>
>> ex08 deals with only 8 bands and 1 formated line, whilst my task
>> computes 20 taking up 3 formated lines.) ?Line 325 is in the LSDA=F
>> portion of the code follows a commented-out read command line with
>> explicit formatting. ?I can't see any problem with the output of my
>> nscf run. ?Before I start messing around with the bands_FS.f90 source,
>> has anyone else run into this issue (Eyvaz?)? ?Is it possible there is
>> a "line counting" error in the LSDA=F portion when the band energy
>> listing exceeds one line? ?Sorry if I've made some stupid blunder.
>>
>> Paul M. Grant, PhD
>>
>> Physicist and Science Writer
>>
>> 

[Pw_forum] stress and mimimun of total energy

[hanghui chen]

 1
0.5 0.5 0.583 1
0.5 0.5 0.667 1
0.5 0.5 0.75 1
0.5 0.5 0.833 1
0.5 0.5 0.917 1
0.5 0.75 0 1
0.5 0.75 0.0833 1
0.5 0.75 0.167 1
0.5 0.75 0.25 1
0.5 0.75 0.333 1
0.5 0.75 0.417 1
0.5 0.75 0.5 1
0.5 0.75 0.583 1
0.5 0.75 0.667 1
0.5 0.75 0.75 1
0.5 0.75 0.833 1
0.5 0.75 0.917 1
0.75 0 0 1
0.75 0 0.0833 1
0.75 0 0.167 1
0.75 0 0.25 1
0.75 0 0.333 1
0.75 0 0.417 1
0.75 0 0.5 1
0.75 0 0.583 1
0.75 0 0.667 1
0.75 0 0.75 1
0.75 0 0.833 1
0.75 0 0.917 1
0.75 0.25 0 1
0.75 0.25 0.0833 1
0.75 0.25 0.167 1
0.75 0.25 0.25 1
0.75 0.25 0.333 1
0.75 0.25 0.417 1
0.75 0.25 0.5 1
0.75 0.25 0.583 1
0.75 0.25 0.667 1
0.75 0.25 0.75 1
0.75 0.25 0.833 1
0.75 0.25 0.917 1
0.75 0.5 0 1
0.75 0.5 0.0833 1
0.75 0.5 0.167 1
0.75 0.5 0.25 1
0.75 0.5 0.333 1
0.75 0.5 0.417 1
0.75 0.5 0.5 1
0.75 0.5 0.583 1
0.75 0.5 0.667 1
0.75 0.5 0.75 1
0.75 0.5 0.833 1
0.75 0.5 0.917 1
0.75 0.75 0 1
0.75 0.75 0.0833 1
0.75 0.75 0.167 1
0.75 0.75 0.25 1
0.75 0.75 0.333 1
0.75 0.75 0.417 1
0.75 0.75 0.5 1
0.75 0.75 0.583 1
0.75 0.75 0.667 1
0.75 0.75 0.75 1
0.75 0.75 0.833 1
0.75 0.75 0.917 1
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[Pw_forum] HUMO and LUMO

[Axel Kohlmeyer]

On Sat, 2009-03-28 at 11:08 -0700, ?lvaro Alves wrote:
> Hello users. How to calculate the HUMO and LUMO in molecular systems
> in PWscf?
> A. S. Santos

can you please explain where _exactly_ your problem is?

apart from the fact that a LUMO in DFT is an entity
that needs to be treated with great care altogether,
you get them like with any other calculation that 
uses a diagonalization.

cheers,
   axel.


> 
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===
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   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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===
If you make something idiot-proof, the universe creates a better idiot.

[Pw_forum] How to use tools dipole.x, voronoy.x and epsilon.x?

[Paolo Giannozzi]

On Mar 28, 2009, at 14:42 , Weiguang Chen wrote:

> Thanks very much.The epsilon.x has a detail guide, could  you told to
> me the input files of the other two programs. I just try to read the
> source code of these two tools, but too many calls that i can not
> understand it.

dipole.x one reads the data file from pw.x, voronoy.x reads the  
intermediate
file produced by pp.x .

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

[Pw_forum] How to use tools dipole.x, voronoy.x and epsilon.x?

[Paolo Giannozzi]

On Mar 28, 2009, at 14:21 , Weiguang Chen wrote:

>  I am a newbie about pwscf. There is a little information about the
> above three tools, what's the usages for these programs although they
> are not used frequently? I just what to know how to use for preparing
> the future possible application.

epsilon.x => Doc/eps_man.tex
voronoy.x : Voronoy polyhedra around atoms, see the header of PP/ 
voronoy.f90
dipole.x: see the header of PP/dipole.f90

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

[Pw_forum] electrical polarization calculations for non-collinear magnetism

[Paolo Giannozzi]

On Mar 28, 2009, at 6:25 , Xun-Wang Yan wrote:

>  nspin=1 and nspin=2 cases is supported,   there is not   
> noncolin=.true.  case.
> how to modify the bp_c_phase.f90 to include the noncolin=.true.  
> case for electric
> polarization calculation?

I know nothing about polarization and noncolinear calculations, but  
basically
what you need in a polarization calculation is a sequence of scalar  
products
between electronic states at different k-points. In the case of  
noncolinear
calculations, electronic states are spinors and are expanded into plane
waves with both spin-up and spin-down components. Coefficients 1 to npw
are for spin-up plane waves, coefficients npwx+1 to npwx+npw are for
spin-down plane waves. Scalar products are summed over the two sets.

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

[Pw_forum] Can you help? (was "Fixed spin moment method & Phonon calculation")

[Nicola Marzari]

Dear Dr Ghosh,


I believe this is the current status - anyone please correct me:

1) you can only do phonons in magnetic systems (metallic or insulating)
using a "smearing" option in the SCF calculation - i.e. you cannot fix
the magnetization, but take whatever the system wants to be. You of 
course could try to do a standard SCF calculation imposing whatever 
magnetization you want, converge that, and restart it with no constraint 
and just smearing, and hope it remains where it is.

2) the NSCF calculation that follows can have or not have the smearing
(better test either). If your system is insulating, it should not matter
at all. If it is metallic/half-metallic, differences might arise (I 
would presume smearing in the NSCF would also be the right choice).

3) if the system is insulating, there is still something to do to fix
the effective charges, that at present are not correct. Hence, LO/TO
splitting at Gamma would be incorrect - everywhere else would be ok.

Subhradip Ghosh wrote:
> Dear Nicola,
> 
> A week back I had posted a question in the pw-forum. It is related to the
> feasibility of calculating phonons by fixing the magnetization. I had
> searched the archive for an answer but couldn't find one. Since I haven't
> gotten any reply from the forum, I am taking this liberty of disturbing
> you by forwarding the question. Can you please take some time from your
> schedule and send me a reply. The question is appended below.
> 
> Regards,
> 
> Subhradip
> 
>  Original Message 
> Subject: [Pw_forum] Fixed spin moment method & Phonon calculation
> From:"Subhradip Ghosh" 
> Date:Wed, March 18, 2009 2:54 pm
> To:  pw_forum at pwscf.org
> --
> 
> I am interested in calculating phonn dispersions in a metallic system by
> fixin
> g the magnetization. To do that, I had fixed the magnetization to a
> particular value and tried the phonon calculation. However, it failed
> apprently because "the constrained magnetization is not implemented in the
> phonon code". Therefore, my question is:
>   Is phonon calculation not possible by fixing total magnetization with
> the present QE code?
> 
> I had searched the archive to find answers but no definite solution was
> found apart from a comment from Paolo which suggests that
> 
> "If the magnetization you choose is the ground state one, the two Fermi
> energies would be the same. In that case, commenting out the check in
> phq_readin.f90 should work. If you constrain the magnetization to a value
> that is not the ground state, I have no idea what numbers will come out".
> 
> Does this mean that a phonon calculation(by commenting out the check in
> phq_readin) by fixing the magnetization at a value other than the ground
> state value is not reliable? The answer to this question is important to
> me because I am interested in doing phonons by fixing total magnetization
> at values other than the ground state value.
> 
> Help in this regard would be useful.
> 
> Subhradip
> 
> 
>   Dr. Subhradip Ghosh
>   Assistant Professor
>   Department of Physics
> Indian Institute of Technology
>Guwahati,Assam-781039
> India
>E-mail:subhra at iitg.ernet.in
>Phone: +91 361 2582717(O)
>   +91 361 2584717(R)
> Fax:  +91 361 2582749 (Physics)
>   +91 361 2690762 (General)
> 
> 
> 
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-- 
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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] antiferromagnetism in ZB input file with 2 atoms

[Paolo Giannozzi]

On Mar 28, 2009, at 13:37 , mazouz moulay wrote:

> starting_magnetization(1) = 0.5
> starting_magnetization(1) = 0.0

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

[Pw_forum] antiferromagnetism in ZB input file with 2 atoms

[mazouz moulay]

Sorry
It was a typing error
> starting_magnetization(1) = 0.5
> starting_magnetization(2) = 0.0
?
I added the second line when i wrote the message ! 
?
this is my original input file :
?

calculation = 'scf'
restart_mode='from_scratch',
prefix='1',
pseudo_dir = '/root/espresso-4.0/pseudo/',
outdir='/home/mazouz/coo/tmp/'
/
 
ibrav= 2, 
celldm(1)= 8.53
nat= 2, 
ntyp= 2,
ecutwfc =50, 
report=1,
nspin=2
occupations='smearing', smearing='gaussian', degauss=0.02
starting_magnetization(1) = 0.5

/

mixing_beta = 0.7 
conv_thr = 1.0d-8
/
ATOMIC_SPECIES
Co 58.933 Co.pbe-nd-rrkjus.UPF
O 15.999 O.pbe-van_ak.UPF
ATOMIC_POSITIONS
Co 0.00 0.00 0.00 
O 0.25 0.25 0.25 
K_POINTS AUTOMATIC
8 8 8 0 0 0 
?
thank you 

?
?


?


  
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[Pw_forum] electrical polarization calculations for non-collinear magnetism

[Xun-Wang Yan]

Dear Gabriele Sclauzero,
Thanks for your reply,
 the electric polarization calculation for noncolinear magnetism is not
available for espresso-4.0.4 version, which can be found from the code
'bp_c_phase.f90'.
  For this calculation , the nelec bands(in my calculation,87 bands) should
be  dealt with.
I found the 'nscf' calculation is finished, and next step to calculate
electric polarization with berry phase method is not implemented,
i.e.the running process stop at the code 'bp_c_phase.f90' .
In bp_c_phase.f90, the  nspin=1 and nspin=2 cases is supported,   there is
not  noncolin=.true.  case.
how to modify the bp_c_phase.f90 to include the noncolin=.true. case for
electric polarization calculation?
your suggestion and comment are expected.

Bests

Xun-Wang

2009/3/27 Gabriele Sclauzero 

>
> Xun-Wang Yan wrote:
> > 
> >ibrav=14,
> >celldm(1)=9.73748132, celldm(2)=1.155067564,celldm(3)=1.00,
> >celldm(4)=-0.144291712,celldm(5)=-0.50,celldm(6)=0.288583423,
> >nat=12, ntyp=5,
> >ecutwfc=30, ecutrho=300,
> >report=10,
> >occupations='fixed',degauss=0.00,
> >noncolin=.true.
> >starting_magnetization(2)=0.5
> >angle1(2)=90.0
> >angle2(2)=0.0
> >starting_magnetization(3)=0.5
> >angle1(3)=90.0
> >angle2(3)=120.0
> >starting_magnetization(4)=0.5
> >angle1(4)=90.0
> >angle2(4)=-120.0
> >nbnd=87
>
>
>
> >
> %%
> >  task # 3
> >  from c_phase : error # 1
> >  Polarization only for insulators and no empty bands
> >
>  
> %%
> >
> > I look over 'bp_c_phase.f90' , and find that electrical polarization
> > calculation is applicable for nspin=1 and nspin=2.
>
> I don't know if this calculation is available for noncolinear calculation,
> but if you pay
> attention to the error message, what it says is different. You need to deal
> with an
> insulator (and you are) and you must compute only nelec bands, i.e. NOT
> adding extra bands
> through the nbnd keyword, as you're doing.
> Retry after removing the nbnd line.
>
> GS
>
>
> > I want to know to how to modify the bp_c_phase.f90 to implement the
> > electrical polarization calculation for non-collinear magnetism.
> > Any comments are welcome , many thanks in advance.
> >
> > regards,
> > Xun-wang Yan
> > 
> > Institute of Theoretical Physics, CAS
> > Address: No.55, Zhong-Guan-Cun East Road
> > Beijing, China
> > Email: xwyan at itp.ac.cn
> > <http://sun.itp.ac.cn/src/compose.php?send_to=fjma%40itp.ac.cn>
> >   yanxunwang2008 at gmail.com <mailto:yanxunwang2008 at gmail.com>
> > ===
> >
> >
> > 
> >
> > ___
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>
> --
>
>
> o  o
> | Gabriele Sclauzero, PhD Student  |
> | c/o:   SISSA & CNR-INFM Democritos,  |
> |via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it |
> | phone: +39 040 3787 511  |
> | skype: gurlonotturno |
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[Pw_forum] antiferromagnetism in ZB input file with 2 atoms

[mazouz moulay]

Dear PWscf users,
?
I performed a magnetic calculation for CoO in the zinc blende structure using 
the following input file.
?

calculation = 'scf'
restart_mode='from_scratch',
prefix='1',
pseudo_dir = '/root/espresso-4.0/pseudo/',
outdir='/home/mazouz/coo/tmp/'
/
 
ibrav= 2, 
celldm(1)= 8.53
nat= 2, 
ntyp= 2,
ecutwfc =50, 
report=1,
nspin=2
occupations='smearing', smearing='gaussian', degauss=0.02
starting_magnetization(1) = 0.5
starting_magnetization(1) = 0.0
/

mixing_beta = 0.7 
conv_thr = 1.0d-8
/
ATOMIC_SPECIES
Co 58.933 Co.pbe-nd-rrkjus.UPF
O 15.999 O.pbe-van_ak.UPF
ATOMIC_POSITIONS
Co 0.00 0.00 0.00 
O 0.25 0.25 0.25 
K_POINTS AUTOMATIC
8 8 8 0 0 0 
?
I would like to ask you if there is any way to specify the antiferromagnetic 
case for the same input file ? or must I use an input file of 8 atoms? or...
Thank you in advance
?
M. Mazouz
D?partement de Physique
Universit? des Sciences et de la Technologie d'Oran. USTO.
Mail: mazouz_moulay at yahoo.fr


  
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[Pw_forum] HUMO and LUMO

[Álvaro Alves]

Hello users. How to calculate the HUMO and LUMO in molecular systems in PWscf?

Regards,

A. S. Santos





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[Pw_forum] HUMO and LUMO

[Álvaro Alves]

Hello users. How to calculate the HUMO and LUMO in molecular systems in PWscf?

A. S. Santos


  Veja quais s?o os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
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