[Pw_forum] Pw_forum Digest, Vol 27, Issue 47
Stefano Baroni
baroni at sissa.it
Fri Sep 11 21:10:36 CEST 2009
please, stop hitting "reply" to digest dispatches of forum posts.
this practice results in the forum members' mailboxes to be cluttered
with garbage, and also decreases YOUR chance to get meaningul and
prompt responses to your posts (people tend to throw into the
wastebasket messages with generic subjects such as " Pw_forum Digest,
Vol 27, Issue 47")
SB
causes nuisances to the mempers of the forum who have their
mailboxes cluttered with gar
On Sep 11, 2009, at 3:23 PM, Shaptrishi Sharma wrote:
> Hi Stefano,
>
> My nband value is 122 as my total number of atoms are 66 .of which
> 21 Hydrogen.And if I remove the option nelup and neldw, I got it as
> "too many bands are not converged" thus I increased my vaccum,
> however it still remains the same.
>
> Thanks
> S
>
> On 9/11/09, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org>
> wrote:
> Send Pw_forum mailing list submissions to
> pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'help' to
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
> 1. Re: problem with charge density with xcrysden
> (Stefano de Gironcoli)
> 2. [Fwd: Re: problem with charge density with xcrysden]
> (Gabriele Sclauzero)
> 3. Re: input file for isolated atom (Paolo Giannozzi)
> 4. K Points and Band structures (Shaptrishi Sharma)
> 5. Re: K Points and Band structures (Lorenzo Paulatto)
> 6. Re: K Points and Band structures (Stefano de Gironcoli)
> 7. Problem in spin polarisation (Shaptrishi Sharma)
> 8. Re: Problem in spin polarisation (Stefano de Gironcoli)
> 9. Re: Problem in spin polarisation (Duy Le)
> 10. Re: Problem in spin polarisation (Stefano de Gironcoli)
> 11. Re: Problem in spin polarisation (Paolo Giannozzi)
> 12. The low usage of CUPs (wangqj1)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 11 Sep 2009 11:57:37 +0200
> From: Stefano de Gironcoli <degironc at sissa.it>
> Subject: Re: [Pw_forum] problem with charge density with xcrysden
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4AAA1F11.3000805 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> dear Dev Sharma
> the xsf file with the DATAGRID field IS NOT the output of pp.x!
> Rather its name needs to be specified in variable fileout in the &plot
> namelist of your density.in input
> Please read the documentation of pp.x code for the meaning of the
> other variables.
> HTH
>
> Stefano de Gironcoli - SISSA and DEMOCRITOS
>
> dev sharma wrote:
> > hi 2 all,
> > I am trying to plot the charge density with the XCrysden, but
> when i
> > am opening's XSF(file--> open structure--> open XSF(xcryden
> structure
> > file)) file , generated by my calculations, it is showing the
> > structure of my system. And i am not getting the option tools-->
> > DATA GRID as ready. Please help or advice ?? Thankful to all of you.
> > What i did is listed below.
> > I run my input file with command
> > /home/physics/espresso-4.0.2/bin/pp.x <density.inp> density.xsf
> > and inputs of density.in <http://density.in> are
> > &inputpp
> > prefix = 'yvo'
> > outdir = '/home/physics/work/yvo/temp/',
> > filplot = 'yvocharge'
> > plot_num= 0
> > /
> > &plot
> > nfile = 1
> > filepp(1) = 'yvocharge'
> > weight(1) = 1.0
> > iflag = 3
> > output_format = 5,
> > /
> >
> > with regards,
> > Dev Sharma,
> > University of Delhi,
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 11 Sep 2009 13:42:19 +0200
> From: Gabriele Sclauzero <sclauzer at sissa.it>
> Subject: [Pw_forum] [Fwd: Re: problem with charge density with
> xcrysden]
> To: PWscf Mailing List <pw_forum at pwscf.org>
> Message-ID: <4AAA379B.4070804 at sissa.it>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed
>
> Forwarding e-mail from Emine. So I guess it may be a compatibility
> issue.
>
> GS
>
> -------- Original Message --------
> Subject: Re: [Pw_forum] problem with charge density with
> xcrysden
> Date: Fri, 11 Sep 2009 03:50:17 -0700 (PDT)
> From: e kb <eminekb at yahoo.com>
> To: sclauzer at sissa.it
>
>
>
>
> The old version of xcrysden that i had didnt work with this line :
> > DATAGRID_3D_UNKNOWN
> but with this one:
> > BEGIN_DATAGRID_3D_UNKNOWN
>
> I am not up to date on this but you can check it.
> emine kucukbenli, SISSA, Italy
>
>
>
> --
>
>
> o ------------------------------------------------ o
> | Gabriele Sclauzero, PhD Student |
> | c/o: SISSA & CNR-INFM Democritos, |
> | via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it |
> | phone: +39 040 3787 511 |
> | skype: gurlonotturno |
> o ------------------------------------------------ o
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 11 Sep 2009 13:44:13 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] input file for isolated atom
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <8F9E43BE-144C-4B5B-B984-327C99F59649 at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>
> On Sep 11, 2009, at 10:36 , Prasenjit Ghosh wrote:
>
> > (a) while doing calculations for any zero dimensions
> > you should always set nosym =.true.
>
> for Gamma-point calculations it shouldn't make any
> difference
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 11 Sep 2009 12:45:43 +0100
> From: Shaptrishi Sharma <sh.shapt at gmail.com>
> Subject: [Pw_forum] K Points and Band structures
> To: pw_forum at pwscf.org
> Message-ID:
> <a8a0c4080909110445j1699c8d7hccc7aeb11d00be5b at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi QEs users,
>
> Can anybody please help me in understanding what are the k points ??
> I have
> read books a lot but its difficult to understand.
>
> And also how do we choose k points while performing a band structure
> calculation in quantum espresso when we are having 330 atoms.
>
> Thanks
>
> S
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> ------------------------------
>
> Message: 5
> Date: Fri, 11 Sep 2009 13:58:19 +0200
> From: "Lorenzo Paulatto" <paulatto at sissa.it>
> Subject: Re: [Pw_forum] K Points and Band structures
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <op.uz3cvhgda8x26q at paulax>
> Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>
> In data 11 settembre 2009 alle ore 13:45:43, Shaptrishi Sharma
> <sh.shapt at gmail.com> ha scritto:
>
> > Can anybody please help me in understanding what are the k
> points ?? I
> > have read books a lot but its difficult to understand.
>
> They are eigenvalues of the translation operator, T(R) where
> R=n1*a1+n2*a2+n3*a3; a1,a2,a3 are the cell basis vectors and n1,n2,n3
> integer numbers. The eigenvectors are, of course, the Bloch
> wavefunctions.
>
> Because the hamiltonian is periodic it commutes with the translation
> operator, you can diagonalize both the hamiltonian and the translation
> operator at the same time. As a consequence each Bloch wavefunction
> has a
> well-defined energy (hamiltonian's eigenvalue) and k-point
> (translation
> eigenvalue). Using both eigenvalues you can classify the states
> without
> ambiguity, except where the bands cross.
>
> > And also how do we choose k points while performing a band
> structure
> > calculation in quantum espresso when we are having 330 atoms.
>
> It does not depend on the number of atoms.
>
> You have to test the convergence at fixed smearing. E.g. you choose a
> smearing that's small enough for you, than you increase the number of
> k-points until total energy converges. You may then try again for a
> smaller/larger smearing and see if the results are consistent.
>
> I would advise starting with a smaller system, it would take ages to
> do it
> on 330 atoms. Keep in mind that the number of k-points needed for an
> accurate sampling is directly proportional to the size of the
> Brillouin
> zone, hence inversely proportional to the size of the cell.
>
> E.g. if you estimate that 6x6x6 k-points converge a certain
> calculation
> than 3x3x3 k-points will be converge a 2x2x2 supercell to exactly
> the same
> level.
>
> Best regards
>
>
> --
> Lorenzo Paulatto
> SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www: http://people.sissa.it/~paulatto/
>
> *** save italian brains ***
> http://saveitalianbrains.wordpress.com/
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 11 Sep 2009 13:59:05 +0200
> From: Stefano de Gironcoli <degironc at sissa.it>
> Subject: Re: [Pw_forum] K Points and Band structures
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4AAA3B89.9020002 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Shaptrishi Sharma wrote:
> > Hi QEs users,
> >
> > Can anybody please help me in understanding what are the k
> points ?? I
> > have read books a lot but its difficult to understand.
> Please ask to any solid state physicist nearby.
>
> > And also how do we choose k points while performing a band
> structure
> > calculation in quantum espresso when we are having 330 atoms.
> If you still have QE specific doubts after you have understood Bloch
> theorem, Real and Reciprocal Space lattices, Brilloun Zone and the
> like
> please formulate them again, trying to be specific.
> > Thanks
> > S
> Please provide your affilaition.
>
> Best regards,
>
> Stefano de Gironcoli - SISSA and DEMOCRITOS
>
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 11 Sep 2009 13:04:08 +0100
> From: Shaptrishi Sharma <sh.shapt at gmail.com>
> Subject: [Pw_forum] Problem in spin polarisation
> To: pw_forum at pwscf.org
> Message-ID:
> <a8a0c4080909110504l4e812201wc964e7f71fc4a2e9 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi QE users,
>
> In one of my previous mail, I have asked about the spin polarisation
> in a
> sytem having odd number of electrons , (I have 21 hydrogen atoms in my
> system ).
>
> As suggested I used nelup =11 and neldw = 10, however, it is showing
> me the
> same error, as
>
> nelp out of range.
> so what shall I do now??
>
> Thanks
>
> SS
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> ------------------------------
>
> Message: 8
> Date: Fri, 11 Sep 2009 14:05:20 +0200
> From: Stefano de Gironcoli <degironc at sissa.it>
> Subject: Re: [Pw_forum] Problem in spin polarisation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4AAA3D00.6020106 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> what is your value for nbnd ?
> stefano
>
> Shaptrishi Sharma wrote:
> > Hi QE users,
> >
> > In one of my previous mail, I have asked about the spin polarisation
> > in a sytem having odd number of electrons , (I have 21 hydrogen
> atoms
> > in my system ).
> >
> > As suggested I used nelup =11 and neldw = 10, however, it is showing
> > me the same error, as
> >
> > nelp out of range.
> > so what shall I do now??
> >
> > Thanks
> >
> > SS
> >
> >
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> ------------------------------
>
> Message: 9
> Date: Fri, 11 Sep 2009 08:16:52 -0400
> From: Duy Le <ttduyle at gmail.com>
> Subject: Re: [Pw_forum] Problem in spin polarisation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <8974d3b20909110516p4f2a7201y58e38d3a36a9d4a7 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Add nelec to input
> Please just reply instead of creating a new email starting with "In
> one of
> my previous mail" so that all your emails and communications are
> ordered in
> the same thread.
>
> :-)
>
> On Fri, Sep 11, 2009 at 8:05 AM, Stefano de Gironcoli <degironc at sissa.it
> >wrote:
>
> > what is your value for nbnd ?
> > stefano
> >
> > Shaptrishi Sharma wrote:
> > > Hi QE users,
> > >
> > > In one of my previous mail, I have asked about the spin
> polarisation
> > > in a sytem having odd number of electrons , (I have 21 hydrogen
> atoms
> > > in my system ).
> > >
> > > As suggested I used nelup =11 and neldw = 10, however, it is
> showing
> > > me the same error, as
> > >
> > > nelp out of range.
> > > so what shall I do now??
> > >
> > > Thanks
> > >
> > > SS
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
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> ------------------------------
>
> Message: 10
> Date: Fri, 11 Sep 2009 14:24:18 +0200
> From: Stefano de Gironcoli <degironc at sissa.it>
> Subject: Re: [Pw_forum] Problem in spin polarisation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4AAA4172.7020306 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> I think that in this case you need to explicitly specify also the
> value
> for nelec because a test that 0<=nelup< =nelec
> is performed before the default for nelec is calculated.
> It should be fixed but it is not so straightforward as the default
> value
> is presently defined much later.
> stefano
>
> Shaptrishi Sharma wrote:
> > Hi QE users,
> >
> > In one of my previous mail, I have asked about the spin polarisation
> > in a sytem having odd number of electrons , (I have 21 hydrogen
> atoms
> > in my system ).
> >
> > As suggested I used nelup =11 and neldw = 10, however, it is showing
> > me the same error, as
> >
> > nelp out of range.
> > so what shall I do now??
> >
> > Thanks
> >
> > SS
> >
> >
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> ------------------------------
>
> Message: 11
> Date: Fri, 11 Sep 2009 14:35:30 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Problem in spin polarisation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <6132C5CA-B5C3-413F-ACFD-E31C9269D719 at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>
> On Sep 11, 2009, at 14:24 , Stefano de Gironcoli wrote:
>
> > It should be fixed
>
> or even better, removed, since there are alternative
> and simpler methods to specify occupancies
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
> ------------------------------
>
> Message: 12
> Date: Fri, 11 Sep 2009 20:29:34 +0800 (CST)
> From: wangqj1 <wangqj1 at 126.com>
> Subject: [Pw_forum] The low usage of CUPs
> To: pw_forum <pw_forum at pwscf.org>
> Message-ID:
> <29861561.516411252672174463.JavaMail.coremail at bj126app106.126.com
> >
> Content-Type: text/plain; charset="gbk"
>
> Dear pwscf users
> I use 16 CPUs to run a job,but the usage of CPUs is very
> slow ,it as like:
>
> Tasks: 179 total, 1 running, 178 sleeping, 0 stopped, 0 zombie
> Cpu0 : 0.0%us, 4.8%sy, 0.0%ni, 90.3%id, 0.3%wa, 0.0%hi,
> 4.5%si, 0.0%st
> Cpu1 : 0.0%us, 1.0%sy, 0.0%ni, 95.8%id, 3.3%wa, 0.0%hi,
> 0.0%si, 0.0%st
> Cpu2 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi,
> 0.0%si, 0.0%st
> Cpu3 : 0.7%us, 0.0%sy, 0.0%ni, 99.0%id, 0.3%wa, 0.0%hi,
> 0.0%si, 0.0%st
> Cpu4 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi,
> 0.0%si, 0.0%st
> Cpu5 : 0.0%us, 0.3%sy, 0.0%ni, 99.7%id, 0.0%wa, 0.0%hi,
> 0.0%si, 0.0%st
> Cpu6 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi,
> 0.0%si, 0.0%st
> Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi,
> 0.0%si, 0.0%st
> Mem: 8048812k total, 7995856k used, 52956k free, 283692k
> buffers
> Swap: 4192956k total, 124k used, 4192832k free, 7492420k
> cached
> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
> 4522 root 15 -5 0 0 0 S 5 0.0 17:59.16 nfsd
> 2012 root 15 -5 0 0 0 S 1 0.0 6:29.01
> kjournald
> 4404 root 20 0 104m 17m 5044 S 0 0.2 55:07.93 X
> 4519 root 15 -5 0 0 0 S 0 0.0 18:05.58 nfsd
> 4521 root 15 -5 0 0 0 S 0 0.0 16:55.33 nfsd
> 5023 gdm 20 0 235m 31m 11m S 0 0.4 13:39.99 gdm-
> simple-gree
> 1 root 20 0 1064 408 348 S 0 0.0 0:02.90 init
> 2 root 15 -5 0 0 0 S 0 0.0 0:00.02 kthreadd
> 3 root RT -5 0 0 0 S 0 0.0 0:00.00
> migration/0
> 4 root 15 -5 0 0 0 S 0 0.0 0:00.22
> ksoftirqd/0
>
> The ifort ,MKL,and mpi I used is :
> INTFC=/opt/intel/Compiler/11.0/081
> INTMKL=/opt/intel/mkl/10.1.1.019
> /opt/mpich2/bin/mpd
> My machine model is as following :
> processor : 0
> vendor_id : GenuineIntel
> cpu family : 6
> model : 23
> model name : Intel(R) Xeon(R) CPU E5410 @ 2.33GHz
> stepping : 10
> cpu MHz : 2327.489
> cache size : 6144 KB
> physical id : 0
> siblings : 4
> core id : 0
> cpu cores : 4
> apicid : 0
> initial apicid : 0
> fpu : yes
> fpu_exception : yes
> cpuid level : 13
> wp : yes
> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr
> pge mca cmov
> pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx
> lm constant
> _tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx est
> tm2 ssse3 cx
> 16 xtpr dca sse4_1 lahf_lm
> bogomips : 4654.97
> ...............
> The pwscf version is espresso-4.0.3 .
>
> So , I want to know why the usage is so slow ?
> How can I solve this problem ? Anybody who meet the same problem ?
> Your kind help will be appreciated !
> Best regards
> Q.J.Wang
> XiangTan University
>
>
>
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>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 27, Issue 47
> ****************************************
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center -
Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) /
stefanobaroni (skype)
La morale est une logique de l'action comme la logique est une morale
de la pensée - Jean Piaget
Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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