[Pw_forum] Pw_forum Digest, Vol 53, Issue 23
Sanjay D. Gupta
guptasanjay.56 at gmail.com
Mon Nov 14 08:10:03 CET 2011
~Best Regards
...........................................................
Sanjay D. Gupta
Research Fellow
Department of Physics,
Bhavnagar University, Bhavnagar-364 022
Gujarat, Mobile-9879666643
email:guptasanjay_56 at yahoo.co.in
...........................................................
On Mon, Nov 14, 2011 at 10:07 AM, <pw_forum-request at pwscf.org> wrote:
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> Today's Topics:
>
> 1. Re: QHA frequency is higher than *.freq (KangYun Song)
> 2. Re: Query on Xcrysden (Huiqun Zhou)
> 3. Problem with DFT + U calculations (Lai Jiang)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 13 Nov 2011 11:18:45 +0000
> From: KangYun Song <songsong19840614 at hotmail.com>
> Subject: Re: [Pw_forum] QHA frequency is higher than *.freq
> To: pwscf <pw_forum at pwscf.org>
> Message-ID: <COL113-W29A4F4173D14BAEB988022C8C30 at phx.gbl>
> Content-Type: text/plain; charset="gb2312"
>
>
>
>
> Yun Song,Kang
> Department Physical Science and Technology of Inner Mongolia University.
>
>
>
>
> From: songsong19840614 at hotmail.com
> To: pw_forum at pwscf.org
> Date: Fri, 11 Nov 2011 12:55:14 +0000
> Subject: Re: [Pw_forum] QHA frequency is higher than *.freq
>
>
>
>
>
> Hi,
> The pdos is not similar to phonon dispersion and the frequency is not
> negative from ph.x.
>
> Yun Song,Kang
> Department Physical Science and Technology of Inner Mongolia University.
>
>
>
>
> From: songsong19840614 at hotmail.com
> To: pw_forum at pwscf.org
> Date: Thu, 10 Nov 2011 12:15:50 +0000
> Subject: [Pw_forum] QHA frequency is higher than *.freq
>
>
>
>
> Hi,
> Recently,I calculated the phonon dispersion.And I use the *.fc
> from matdyn q2r.x to calculate frequecy and pdos.But this is a problem the
> freqency from matdyn.x of QHA is higher than *.freq from matdyn.x of phonon
> dispersion calculation.Why?Could anyone help me?The other material I use
> this method did not meet this problem.
> The matdyn.in of QHA is:
>
> &input
> amass(1)=*,
> amass(2)=*,
> asr='crystal',
> flfrc=*.fc,
> flfrq='frequency'
> &end
> 1183
> -0.33333 0.57735 0.81850 1.00000
> -0.30555 0.52924 0.75029 1.00000
> -0.30555 0.57735 0.75029 1.00000
> ??????
>
> The matdyn.in of phonon dispersion calculating is :
>
> &input
> asr='simple', amass(1)=*, amass(2)=*,
> flfrc='*.fc', flfrq='*.freq' ,la2F=.false. ,
> /
> 85
> 0.0000000 0.0000000 0.3092146, wk = 0.0235294
> 0.0555560 0.0000000 0.3092146, wk = 0.0235294
> 0.1111110 -0.0000006 0.3092146, wk = 0.0235294
> 0.1666670 0.0000006 0.3092146, wk = 0.0235294
> 0.2222220 0.0000000 0.3092146, wk = 0.0235294
> 0.2777780 0.0000000 0.3092146, wk = 0.0235294
> ????
>
>
Dear
Yun Song,Kang,
you should have to correct your Edit.me file
as for example u have 4 atoms per unir cell then write like this
"ibrav=1
atoms="Cd1 Cd2 N1 N2"
mass="112.411 112.411 14.0067 14.0067"
Cheers...!!!!
> Yun Song,Kang
> Department Physical Science and Technology of Inner Mongolia University.
>
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> ------------------------------
>
> Message: 2
> Date: Mon, 14 Nov 2011 11:41:41 +0800
> From: "Huiqun Zhou" <hqzhou at nju.edu.cn>
> Subject: Re: [Pw_forum] Query on Xcrysden
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <9049400A0E124656AC9501EECC6E6451 at solarflare>
> Content-Type: text/plain; format=flowed; charset="iso-8859-1";
> reply-type=original
>
> When you try to use XCrysden from PWgui, you still need to have a copy of
> XCrysden to be installed in advance.
>
>
> dr. zhou huiqun
> @earth sciences, nanjing university, china
>
> ----- Original Message -----
> From: "Ren PJ" <renpj at dicp.ac.cn>
> To: <pw_forum at pwscf.org>
> Sent: Monday, November 07, 2011 10:50 PM
> Subject: Re: [Pw_forum] Query on Xcrysden
>
>
> >
> > There is a executable file which need not to install. The latest version
> > is 4.3. The url is: http://www-k3.ijs.si/kokalj/pwgui/
> >
> >
> >
> >
> > Pengju Ren
> > renpj at dicp.ac.cn
> > State Key Laboratory of Catalysis,
> > Dalian Institute of Chemical Physics,
> > Chinese Academy of Sciences
> > 457 zhongshan Road, Dalian, 116023, P.R. China
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 13 Nov 2011 23:31:49 -0500
> From: Lai Jiang <jianglai at sas.upenn.edu>
> Subject: [Pw_forum] Problem with DFT + U calculations
> To: pw_forum at pwscf.org
> Message-ID: <BLU0-SMTP246E9EC22BDF1927DE0943C80C00 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Greetings all,
>
> I'm having some problem getting convergence in my DFT +U calculations. My
> system is anti-ferromagnetic double perovskite Sr2FeWO6. It is
> experimentally an insulator but there are reports that state one needs
> Hubbard U on Fe 3d orbital to account for the on site repulsion. However
> after adding an U value it doesn't converge after 500 iterations and
> sometimes the job got killed by the batch system (not walltime, something
> like buffer overflow), typical pbs output looks like this (varies
> on different platform):
>
>
> Rank 16 [Wed Nov 9 23:21:11 2011] [c0-0c0s4n1] Fatal error in PMPI_Bcast:
> Message truncated, error stack:
> PMPI_Bcast(1308)......................: MPI_Bcast(buf=0x3e0def0,
> count=26208, MPI_DOUBLE_PRECISION, root=1, comm=0xc4000000) failed
> MPIR_Bcast(998).......................:
> MPIR_Bcast_scatter_ring_allgather(842):
> MPIR_Bcast_binomial(157)..............:
> MPID_nem_gni_lmt_start_recv(920)......: Message from rank 0 and tag 2
> truncated; 213408 bytes received but buffer size is 209664
> [0] ERROR - nem_gni_error_handler(): a transaction error was detected,error
> category 0x4 error code 0xb2e
> Rank 0 [Wed Nov 9 23:21:11 2011] [c0-0c0s4n0] GNI transaction error
> detected
> [NID 00009] 2011-11-09 23:21:11 Apid 1944384: initiated application
> termination
>
>
> And the pw.x output ends like this:
>
>
> atom 24 Tr[ns(na)]= 6.1782057
> atom 24 spin 1
> eigenvalues: 0.9740685 0.9841342 0.9842280 0.9899863 0.9914280
> eigenvectors
> 1 0.0332876 0.0801355 -0.2854709 0.9362259 -0.1856276
> 2 0.0172615 0.0589306 0.8879786 0.1822775 -0.4177297
> 3 0.4670136 0.8765271 -0.0107306 -0.0778135 0.0861883
> 4 -0.0557289 -0.0272157 0.3597350 0.2894423 0.8848545
> 5 0.8816953 -0.4701756 0.0218145 0.0205958 0.0254629
> occupations
> 0.990 -0.003 0.000 0.000 0.000
> -0.003 0.986 0.000 -0.001 0.000
> 0.000 0.000 0.984 0.003 0.001
> 0.000 -0.001 0.003 0.976 0.003
> 0.000 0.000 0.001 0.003 0.988
> atom 24 spin 2
> eigenvalues: 0.0394193 0.0400804 0.1166033 0.1376013 0.9206564
> eigenvectors
> 1 -0.0457703 -0.2123040 -0.9448844 -0.2058039 0.1329300
> 2 0.1857246 0.9542619 -0.1868327 -0.1235578 0.0686851
> 3 -0.0675780 -0.0156072 0.1108752 0.1546050 0.9792822
> 4 -0.9788987 0.1940608 -0.0050595 -0.0004723 -0.0638113
> 5 -0.0245350 -0.0800506 0.2448840 -0.9583712 0.1206087
> occupations
> 0.134 -0.017 -0.005 0.020 -0.002
> -0.017 0.049 -0.018 0.067 -0.011
> -0.005 -0.018 0.093 -0.205 0.034
> 0.020 0.067 -0.205 0.851 -0.090
> -0.002 -0.011 0.034 -0.090 0.127
> nsum = 49.3436516
> exit write_ns
>
> total cpu time spent up to now is 4234.0 secs
>
> total energy = -5515.60273544 Ry
> Harris-Foulkes estimate = -5515.60272792 Ry
> estimated scf accuracy < 0.00001279 Ry
>
> total magnetization = 0.00 Bohr mag/cell
> absolute magnetization = 32.50 Bohr mag/cell
>
> iteration #102 ecut= 50.00 Ry beta=0.20
> Davidson diagonalization with overlap
> Application 1944384 exit codes: 1
> Application 1944384 exit signals: Killed
> Application 1944384 resources: utime ~4162s, stime ~88s
>
>
> My input file is:
>
>
> &control
> calculation = 'scf'
> title = 'Sr2FeWO6'
> verbosity = 'high'
> restart_mode = 'from_scratch'
> pseudo_dir = '/workdir/jianglai/psp/gga'
> etot_conv_thr = 1.D-6
> forc_conv_thr = 2.D-4
> disk_io = 'low'
> tstress = .true.
> tprnfor = .true.
> wf_collect = .true.
> nstep = 5000
> /
> &system
> ibrav = -12
> A = 11.301600
> B = 5.613600
> C = 15.885000
> cosAC = -0.000366588948
> nat = 80
> ntyp = 5
> nbnd = 351
> ecutwfc = 50
> occupations = 'smearing'
> degauss = 2.D-3
> nspin = 2
> starting_magnetization(2) =0.5
> starting_magnetization(3) =-0.5
> lda_plus_u = .true.
> hubbard_U(2) = 4
> hubbard_U(3) = 4
> /
> &electrons
> electron_maxstep = 500
> startingwfc = 'random'
> diagonalization = 'david'
> mixing_mode = 'plain'
> mixing_beta = 2.D-1
> mixing_ndim = 8
> conv_thr = 1.0D-8
> /
> &IONS
> bfgs_ndim = 4
> upscale = 25
> pot_extrapolation = 'second_order'
> wfc_extrapolation = 'second_order'
> /
> &CELL
> cell_dynamics = 'bfgs'
> press_conv_thr = 5.D-1
> /
> ATOMIC_SPECIES
> Sr 87.62 Sr.upf
> Fe1 55.847 Fe.semi.upf
> Fe2 55.847 Fe.semi.upf
> W 183.85 W.fhi.UPF
> O 15.999 O.upf
>
> ATOMIC_POSITIONS {crystal}
> Sr 0.499500 0.012900 0.124550
> Sr 0.500500 0.987100 0.875450
> Sr 0.750500 0.512900 0.125450
> Sr 0.749500 0.487100 0.374550
> Sr 0.499500 0.012900 0.624550
> Sr 0.500500 0.987100 0.375450
> Sr 0.750500 0.512900 0.625450
> Sr 0.749500 0.487100 0.874550
> Sr 0.999500 0.012900 0.124550
> Sr 0.000500 0.987100 0.875450
> Sr 0.250500 0.512900 0.125450
> Sr 0.249500 0.487100 0.374550
> Sr 0.250500 0.512900 0.625450
> Sr 0.249500 0.487100 0.874550
> Fe1 0.250000 -0.000000 0.250000
> Fe1 0.750000 -0.000000 0.750000
> Fe2 0.000000 0.500000 0.000000
> Fe2 0.500000 0.500000 0.500000
> Fe2 0.250000 -0.000000 0.750000
> Fe2 0.750000 -0.000000 0.250000
> Fe1 -0.000000 0.500000 0.500000
> Fe1 0.500000 0.500000 0.000000
> W 0.250000 0.000000 0.000000
> W 0.750000 0.000000 0.000000
> W -0.000000 0.500000 0.250000
> W 0.500000 0.500000 0.250000
> W 0.250000 -0.000000 0.500000
> W 0.750000 -0.000000 0.500000
> W 0.000000 0.500000 0.750000
> W 0.500000 0.500000 0.750000
> O 0.023650 0.496000 0.129500
> O 0.976350 0.504000 0.870500
> O 0.226350 0.996000 0.120500
> O 0.273650 0.004000 0.379500
> O 0.023650 0.496000 0.629500
> O 0.976350 0.504000 0.370500
> O 0.226350 0.996000 0.620500
> O 0.273650 0.004000 0.879500
> O 0.523650 0.496000 0.129500
> O 0.476350 0.504000 0.870500
> O 0.726350 0.996000 0.120500
> O 0.773650 0.004000 0.379500
> O 0.523650 0.496000 0.629500
> O 0.476350 0.504000 0.370500
> O 0.726350 0.996000 0.620500
> O 0.773650 0.004000 0.879500
> O 0.359500 0.261000 0.012500
> O 0.640500 0.739000 0.987500
> O 0.890500 0.761000 0.237500
> O 0.609500 0.239000 0.262500
> O 0.359500 0.261000 0.512500
> O 0.640500 0.739000 0.487500
> O 0.890500 0.761000 0.737500
> O 0.609500 0.239000 0.762500
> O 0.859500 0.261000 0.012500
> O 0.140500 0.739000 0.987500
> O 0.390500 0.761000 0.237500
> O 0.109500 0.239000 0.262500
> O 0.859500 0.261000 0.512500
> O 0.140500 0.739000 0.487500
> O 0.390500 0.761000 0.737500
> O 0.109500 0.239000 0.762500
> O 0.121000 0.224000 0.488000
> O 0.879000 0.776000 0.512000
> O 0.129000 0.724000 0.762000
> O 0.371000 0.276000 0.738000
> O 0.121000 0.224000 0.988000
> O 0.879000 0.776000 0.012000
> O 0.129000 0.724000 0.262000
> O 0.371000 0.276000 0.238000
> O 0.621000 0.224000 0.488000
> O 0.379000 0.776000 0.512000
> O 0.629000 0.724000 0.762000
> O 0.871000 0.276000 0.738000
> O 0.621000 0.224000 0.988000
> O 0.379000 0.776000 0.012000
> O 0.629000 0.724000 0.262000
> O 0.871000 0.276000 0.238000
>
> K_POINTS (automatic)
> 2 4 1 1 1 1
>
> I checked quantum espresso example files 25 and in README it says one needs
> to set starting_ns_eigenvalues sometimes. I'm not sure whether it's the
> case here but I'm gonna try. Still I don't quite understand the eigenvalues
> and eigenvectors in write_ns routine. Are eigenvalues the energy of each of
> the five d orbitals? The what are the eigenvectors?
>
> That all said, if someone has experienced problems like this or knows why
> convergence is so slow here, please let me know.
>
> Thanks!
>
> Lai Jiang
> *********************************
> Department of Chemistry
> School of Arts and Sciences
> University of Pennsylvania
> *********************************
> 231 South 34th Street, Box 46
> Philadelphia, PA 19104
> Tel: 215-573-4241
> Fax: 215-573-2112
> Email: jianglai at sas.upenn.edu
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