[Pw_forum] Pw_forum Digest, Vol 27, Issue 47
Shaptrishi Sharma
sh.shapt at gmail.com
Fri Sep 11 15:23:39 CEST 2009
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:
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> 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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> _______________________________________________
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> Pw_forum at pwscf.org
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>
>
> End of Pw_forum Digest, Vol 27, Issue 47
> ****************************************
>
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