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 [email protected]
On Monday, March 27, 2017 6:01 PM, "[email protected]"
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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 <[email protected]>
Subject: [Pw_forum] vc-md calculation
To: [email protected]
Message-ID:
<cahyxntsef1g5f530tth0ucz85cwu6ooy5sf5cefdvhranzp...@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" <[email protected]>
Subject: [Pw_forum] Phonon axsf does not move in XCrysden
To: "[email protected]" <[email protected]>
Message-ID:
<cy4pr04mb07426412f4086a82831bc20c90...@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 <[email protected]>
Subject: Re: [Pw_forum] vc-md calculation
To: PWSCF Forum <[email protected]>
Message-ID:
<capmgbcvdmxwswcpmqsf00zbuylruybenytq0-candvchqaf...@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 <[email protected]> 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
> [email protected]
> 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 <[email protected]>
Subject: Re: [Pw_forum] Phonon axsf does not move in XCrysden
To: "[email protected]" <[email protected]>
Message-ID:
<he1pr03mb311360f8a1d51d1c59a994869e...@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: [email protected] <[email protected]> on behalf of
Huang, Xu <[email protected]>
Sent: 27 March 2017 05:40:51
To: [email protected]
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 <[email protected]>
Subject: Re: [Pw_forum] Phonon axsf does not move in XCrysden
To: [email protected]
Message-ID: <2819941.Ia5yuB6n9L@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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