[Pw_forum] Pw_forum Digest, Vol 116, Issue 24

Yusuf Zuntu yzunt at yahoo.com
Tue Mar 28 01:13:02 CEST 2017


Dear all,
I would appreciate if any one can help bail me out of this unknown error I encounter while running phonon calculation.
Input files:
SCF RUN
&control calculation = 'scf' , title      = 'striz' prefix='scftriazs', restart_mode = 'from_scratch' , pseudo_dir ='./', outdir='./', tstress = .true. , tprnfor = .true. , verbosity = 'high',  / &system        ibrav=4, celldm(1)= 13.480341442, celldm(3)= 2.4     nat= 12, ntyp= 2,    ecutwfc =70.0, tot_charge = 0.00,    occupations = 'smearing' ,    degauss = 0.0001 ,    smearing = 'gauss' ,    ecutrho=700.0,  / &ELECTRONS          /ATOMIC_SPECIES C  12.0107 C.pbe-high.UPF N  14.0067  N.pbe-hgh.UPFATOMIC_POSITIONS (angstrom)*********K_POINTS {automatic}8 8 1 0 0 0
PHONON
phonons of striazine &inputph  tr2_ph=1.0d-14,  prefix='scftriazs',  ldisp=.true.,  nq1=3, nq2=3, nq3=1  amass(1)=12.011,  amass(2)=14.0067,  start_irr=0,  last_irr=0,  outdir='./'  fildyn='st.dyn',  fildrho='drho',  drho_star%open = .true.  drho_star%ext  = 'drho_rot' /
OUTPUT Phonon:
Error message:
Number of q in the star =    1     List of q in the star:          1   0.000000000   0.000000000   0.000000000
     Diagonalizing the dynamical matrix
     q = (    0.000000000   0.000000000   0.000000000 ) 
 **************************************************************************     freq (    1) =      -2.685422 [THz] =     -89.576022 [cm-1]     freq (    2) =       2.166375 [THz] =      72.262491 [cm-1]     freq (    3) =       2.262167 [THz] =      75.457765 [cm-1]     freq (    4) =       2.795952 [THz] =      93.262925 [cm-1]     freq (    5) =       2.800915 [THz] =      93.428454 [cm-1]     freq (    6) =       5.367825 [THz] =     179.051357 [cm-1]     freq (    7) =       5.376191 [THz] =     179.330415 [cm-1]     freq (    8) =       7.114105 [THz] =     237.300992 [cm-1]     freq (    9) =       8.749782 [THz] =     291.861295 [cm-1]     freq (   10) =      13.822947 [THz] =     461.083895 [cm-1]     freq (   11) =      13.841348 [THz] =     461.697679 [cm-1]     freq (   12) =      14.514078 [THz] =     484.137536 [cm-1]     freq (   13) =      14.521303 [THz] =     484.378514 [cm-1]     freq (   14) =      20.777060 [THz] =     693.048115 [cm-1]     freq (   15) =      20.813114 [THz] =     694.250756 [cm-1]     freq (   16) =      20.833890 [THz] =     694.943750 [cm-1]     freq (   17) =      24.038110 [THz] =     801.825027 [cm-1]     freq (   18) =      24.044236 [THz] =     802.029396 [cm-1]     freq (   19) =      24.709545 [THz] =     824.221696 [cm-1]     freq (   20) =      25.155077 [THz] =     839.083047 [cm-1]     freq (   21) =      28.512415 [THz] =     951.071795 [cm-1]     freq (   22) =      28.732938 [THz] =     958.427641 [cm-1]     freq (   23) =      28.773861 [THz] =     959.792687 [cm-1]     freq (   24) =      28.847960 [THz] =     962.264381 [cm-1]     freq (   25) =      34.004390 [THz] =    1134.264368 [cm-1]     freq (   26) =      34.267687 [THz] =    1143.047015 [cm-1]     freq (   27) =      35.717724 [THz] =    1191.415021 [cm-1]     freq (   28) =      36.592384 [THz] =    1220.590558 [cm-1]     freq (   29) =      36.627331 [THz] =    1221.756249 [cm-1]     freq (   30) =      40.930843 [THz] =    1365.305974 [cm-1]     freq (   31) =      40.947318 [THz] =    1365.855501 [cm-1]     freq (   32) =      42.933525 [THz] =    1432.108239 [cm-1]     freq (   33) =      43.516286 [THz] =    1451.547057 [cm-1]     freq (   34) =      43.549882 [THz] =    1452.667701 [cm-1]     freq (   35) =      44.805500 [THz] =    1494.550613 [cm-1]     freq (   36) =      44.820738 [THz] =    1495.058881 [cm-1] **************************************************************************
     Mode symmetry, C_1 (1)     point group:
     freq (  1 -  1) =        -89.6  [cm-1]   --> A               I+R     freq (  2 -  2) =         72.3  [cm-1]   --> A               I+R     freq (  3 -  3) =         75.5  [cm-1]   --> A               I+R     freq (  4 -  4) =         93.3  [cm-1]   --> A               I+R     freq (  5 -  5) =         93.4  [cm-1]   --> A               I+R     freq (  6 -  6) =        179.1  [cm-1]   --> A               I+R     freq (  7 -  7) =        179.3  [cm-1]   --> A               I+R     freq (  8 -  8) =        237.3  [cm-1]   --> A               I+R     freq (  9 -  9) =        291.9  [cm-1]   --> A               I+R     freq ( 10 - 10) =        461.1  [cm-1]   --> A               I+R     freq ( 11 - 11) =        461.7  [cm-1]   --> A               I+R     freq ( 12 - 12) =        484.1  [cm-1]   --> A               I+R     freq ( 13 - 13) =        484.4  [cm-1]   --> A               I+R     freq ( 14 - 14) =        693.0  [cm-1]   --> A               I+R     freq ( 15 - 15) =        694.3  [cm-1]   --> A               I+R     freq ( 16 - 16) =        694.9  [cm-1]   --> A               I+R     freq ( 17 - 17) =        801.8  [cm-1]   --> A               I+R     freq ( 18 - 18) =        802.0  [cm-1]   --> A               I+R     freq ( 19 - 19) =        824.2  [cm-1]   --> A               I+R     freq ( 20 - 20) =        839.1  [cm-1]   --> A               I+R     freq ( 21 - 21) =        951.1  [cm-1]   --> A               I+R     freq ( 22 - 22) =        958.4  [cm-1]   --> A               I+R     freq ( 23 - 23) =        959.8  [cm-1]   --> A               I+R     freq ( 24 - 24) =        962.3  [cm-1]   --> A               I+R     freq ( 25 - 25) =       1134.3  [cm-1]   --> A               I+R     freq ( 26 - 26) =       1143.0  [cm-1]   --> A               I+R     freq ( 27 - 27) =       1191.4  [cm-1]   --> A               I+R     freq ( 28 - 28) =       1220.6  [cm-1]   --> A               I+R     freq ( 29 - 29) =       1221.8  [cm-1]   --> A               I+R     freq ( 30 - 30) =       1365.3  [cm-1]   --> A               I+R     freq ( 31 - 31) =       1365.9  [cm-1]   --> A               I+R     freq ( 32 - 32) =       1432.1  [cm-1]   --> A               I+R     freq ( 33 - 33) =       1451.5  [cm-1]   --> A               I+R     freq ( 34 - 34) =       1452.7  [cm-1]   --> A               I+R     freq ( 35 - 35) =       1494.6  [cm-1]   --> A               I+R     freq ( 36 - 36) =       1495.1  [cm-1]   --> A               I+R
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%     Error in routine write_dfile_star (1):     this subroutine produces random garbage without symmetry! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...

Thank you



Yusuf ZuntuStudentUniversiti Sains Malaysiyzunt at yahoo.com 

    On Monday, March 27, 2017 6:01 PM, "pw_forum-request at pwscf.org" <pw_forum-request at pwscf.org> wrote:
 

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Today's Topics:

  1. vc-md calculation (ade wale)
  2. Phonon axsf does not move in XCrysden (Huang, Xu)
  3. Re: vc-md calculation (Paolo Giannozzi)
  4. Re: Phonon axsf does not move in XCrysden (Louis Fry-Bouriaux)
  5. Re: Phonon axsf does not move in XCrysden (Lorenzo Paulatto)


----------------------------------------------------------------------

Message: 1
Date: Mon, 27 Mar 2017 09:17:18 +0800
From: ade wale <adewaleakeem12 at gmail.com>
Subject: [Pw_forum] vc-md calculation
To: pw_forum at pwscf.org
Message-ID:
    <CAHyXNtsEf1g5f530tth0UCZ85cwu6Ooy5Sf5CEfdvHRANZPGJw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Q.E family,

  Can the program continue from where its stop when their is power failure?
  (any of the calculation; scf, vc-relax, vc-md...)

Thanks
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Message: 2
Date: Mon, 27 Mar 2017 04:40:51 +0000
From: "Huang, Xu" <xu-huang at uiowa.edu>
Subject: [Pw_forum] Phonon axsf does not move in XCrysden
To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
Message-ID:
    <CY4PR04MB07426412F4086A82831BC20C90330 at CY4PR04MB0742.namprd04.prod.outlook.com>
    
Content-Type: text/plain; charset="iso-8859-1"

Dear all,


I'm using QE-5.2.0 to do the phonon calculation to test some small gas molecules, such as O2, CH4 etc.

I got a "dynmat.axsf" for O2 with 6 modes shown below.

However, when I type "xcrysden --axsf dynmat.axsf" to visualize the vibrational mode,

I can't see any movement when I click the <- and -> arrows back and forth.

(I do see the arrows of forces when display them.)

Is there anything wrong with this axsf file?

Or is there any parameter for the dynmat.x to produce specific axsf to animate a certain mode?


Thank you,

Xu Huang


-----------------------------------------------------

ANIMSTEPS  6
CRYSTAL
PRIMVEC
  21.167088344    0.000000000    0.000000000
    0.000000000  21.167088344    0.000000000
    0.000000000    0.000000000  21.167088344
PRIMCOORD  1
      2  1
  O      1.23655  0.00000  0.00000  0.00000  -0.00000  -0.07722
  O      0.00000  0.00000  0.00000  0.00000  0.00000  0.06354
PRIMCOORD  2
      2  1
  O      1.23655  0.00000  0.00000  0.00000  -0.07071  -0.00000
  O      0.00000  0.00000  0.00000  0.00000  0.07071  -0.00000
PRIMCOORD  3
      2  1
  O      1.23655  0.00000  0.00000  0.00000  -0.00000  0.06354
  O      0.00000  0.00000  0.00000  0.00000  0.00000  0.07722
PRIMCOORD  4
      2  1
  O      1.23655  0.00000  0.00000  -0.07071  -0.00000  0.00000
  O      0.00000  0.00000  0.00000  -0.07071  0.00000  0.00000
PRIMCOORD  5
      2  1
  O      1.23655  0.00000  0.00000  0.00000  -0.07071  -0.00000
  O      0.00000  0.00000  0.00000  0.00000  -0.07071  -0.00000
PRIMCOORD  6
      2  1
  O      1.23655  0.00000  0.00000  -0.07071  0.00000  0.00000
  O      0.00000  0.00000  0.00000  0.07071  0.00000  0.00000


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Message: 3
Date: Mon, 27 Mar 2017 08:03:32 +0200
From: Paolo Giannozzi <p.giannozzi at gmail.com>
Subject: Re: [Pw_forum] vc-md calculation
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
    <CAPMgbCvDMXwSWcpmqSf00ZbuyLRUYBenytq0-cANdVcHqAFFqg at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

It might work for CP, if a good restart file is left on disk.
Otherwise, no, it is no longer possible (restart from hard crashes was
implemented in the past but it never worked in a satisfactory way)

Paolo

On Mon, Mar 27, 2017 at 3:17 AM, ade wale <adewaleakeem12 at gmail.com> wrote:
> Dear Q.E family,
>
>  Can the program continue from where its stop when their is power failure?
>  (any of the calculation; scf, vc-relax, vc-md...)
>
> Thanks
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222


------------------------------

Message: 4
Date: Mon, 27 Mar 2017 08:18:08 +0000
From: Louis Fry-Bouriaux <ellf at leeds.ac.uk>
Subject: Re: [Pw_forum] Phonon axsf does not move in XCrysden
To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
Message-ID:
    <HE1PR03MB311360F8A1D51D1C59A994869E330 at HE1PR03MB3113.eurprd03.prod.outlook.com>
    
Content-Type: text/plain; charset="iso-8859-1"

Hi Xu Huang,


  All I know is there is a similar question to this on the forum asked recently: Lorenzo Paulatto answered the following:


Hello, in density function perturbation theory, contrary to finite-differenes
method, there is no atom displacement: quantum-mechanics perturbation theory
is used.

See this reference: <<https://outlook.office.com/owa/?realm=leeds.ac.uk&path=/mail/search>http://journals.aps.org/rmp/abstract/10.1103/RevModPhys.
73.515> for details on the method how it is implemented in QE.

Tis lecture from Stefano Baroni to get a quick idea: < https://
www.dropbox.com/s/xi06fv6oz07j9du/EUSPec%202016%20%281%29.pdf?dl=0<http://www.dropbox.com/s/xi06fv6oz07j9du/EUSPec%202016%20%281%29.pdf?dl=0>>


So there is likely nothing wrong with the axsf file. For your second question however I am not sure how to animate, unless you do it manually using the force vector directions?


Regards,

Louis

________________________________
From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Huang, Xu <xu-huang at uiowa.edu>
Sent: 27 March 2017 05:40:51
To: pw_forum at pwscf.org
Subject: [Pw_forum] Phonon axsf does not move in XCrysden


Dear all,


I'm using QE-5.2.0 to do the phonon calculation to test some small gas molecules, such as O2, CH4 etc.

I got a "dynmat.axsf" for O2 with 6 modes shown below.

However, when I type "xcrysden --axsf dynmat.axsf" to visualize the vibrational mode,

I can't see any movement when I click the <- and -> arrows back and forth.

(I do see the arrows of forces when display them.)

Is there anything wrong with this axsf file?

Or is there any parameter for the dynmat.x to produce specific axsf to animate a certain mode?


Thank you,

Xu Huang


-----------------------------------------------------

ANIMSTEPS  6
CRYSTAL
PRIMVEC
  21.167088344    0.000000000    0.000000000
    0.000000000  21.167088344    0.000000000
    0.000000000    0.000000000  21.167088344
PRIMCOORD  1
      2  1
  O      1.23655  0.00000  0.00000  0.00000  -0.00000  -0.07722
  O      0.00000  0.00000  0.00000  0.00000  0.00000  0.06354
PRIMCOORD  2
      2  1
  O      1.23655  0.00000  0.00000  0.00000  -0.07071  -0.00000
  O      0.00000  0.00000  0.00000  0.00000  0.07071  -0.00000
PRIMCOORD  3
      2  1
  O      1.23655  0.00000  0.00000  0.00000  -0.00000  0.06354
  O      0.00000  0.00000  0.00000  0.00000  0.00000  0.07722
PRIMCOORD  4
      2  1
  O      1.23655  0.00000  0.00000  -0.07071  -0.00000  0.00000
  O      0.00000  0.00000  0.00000  -0.07071  0.00000  0.00000
PRIMCOORD  5
      2  1
  O      1.23655  0.00000  0.00000  0.00000  -0.07071  -0.00000
  O      0.00000  0.00000  0.00000  0.00000  -0.07071  -0.00000
PRIMCOORD  6
      2  1
  O      1.23655  0.00000  0.00000  -0.07071  0.00000  0.00000
  O      0.00000  0.00000  0.00000  0.07071  0.00000  0.00000


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Message: 5
Date: Mon, 27 Mar 2017 11:01:00 +0200
From: Lorenzo Paulatto <lorenzo.paulatto at impmc.upmc.fr>
Subject: Re: [Pw_forum] Phonon axsf does not move in XCrysden
To: pw_forum at pwscf.org
Message-ID: <2819941.Ia5yuB6n9L at naquite>
Content-Type: text/plain; charset="iso-8859-1"

On Monday, March 27, 2017 10:18:08 AM CEST Louis Fry-Bouriaux wrote:
> Hi Xu Huang,
> 
> 
>    All I know is there is a similar question to this on the forum asked
> recently: Lorenzo Paulatto answered the following:
> 

This is actually is a completely different issue, I met it myself some time 
ago. 

The problem is that the axsf file does contain the displaced positions? but 
xcrysden does not display them. It is an xcrysden bug and I recommed you ask 
to the xcrysden mailing list?, but there is a chance Tone will read this 
message here and he may have an answer.


[1] Even if in DFPT the atoms are not physically displaced, we can find the 
displacement patters along which they would move (with amplitude a function of 
the temperature), that's what is saved in the axsf file, the displacement 
length set to an arbitrary value.

[2] http://www.democritos.it/mailman/listinfo/xcrysden

-- 
Dr. Lorenzo Paulatto 
IdR @ IMPMC -- CNRS & Universit? Paris 6
phone: +33 (0)1 442 79822 / skype: paulatz
www:  http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/423 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05



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