[Pw_forum] the dynmaical matrix are like "***********" when the phonons calculation at gama

Eyvaz Isaev eyvaz_isaev at yahoo.com
Sun Mar 1 20:38:18 CET 2009


Hi,

As the dynamical matrix is written in the fixed format (like 3(2F12,8, 2x)), and you have large components (say, larger than 999.99999999, or -99.99999999 ), then it can not be printed properly. In my opinion, such kind components will be quite unusual. 
I have no experience in calculation of H2O properties, but I would recommend the use of thr2_ph=1.d-18, at least, use different thr2_ph and see what happens.

If you are really interested in these values then change the format in line 32, write_dyn_on_file.f90 (in /PH, of course), say, to f16.8, then recompile ph.x, and enjoy seeing these values.

Bests,
Eyvaz.

-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


--- On Sun, 3/1/09, xu yuehua <njuxuyuehua at gmail.com> wrote:

> From: xu yuehua <njuxuyuehua at gmail.com>
> Subject: [Pw_forum] the dynmaical matrix are like "***********" when the phonons calculation at gama
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Sunday, March 1, 2009, 9:45 AM
> hello all :
> 
> 
> i am facing unkonwn problem when i calculated the phonons
> at gama:
> 
> the  dynamical matrix  file  wrote:
> ................
>  Dynamical  Matrix in cartesian axes
> 
>      q = (    0.000000000   0.000000000   0.000000000 )
> 
>   1  1
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
>   1  2
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
>   1  3
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
>   1  4
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
>   1  5
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
>   1  6
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
>   1  7
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
>   1  8
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
>   1  9
> ************  0.00000000  ************  0.00000000 
> ************  0.00000000
> .......
> 
> my phone input file :
> phonons at Gamma
>  &inputph
>   tr2_ph=1.0d-15,
>   prefix='scf_two_b_type',
>   epsil=.true.,
>   amass(1)=1.0,
>   amass(2)=15.999,
>   outdir='/disk2/xxx/xxx/espresso-3.2.3/tmp',
>   fildyn='fourringwater.dynG',
>  /
> 0.0 0.0 0.0
> 
> 
> and my scf input file is :&CONTROL
> calculation  = "scf",
>   prefix       = "scf_two_b_type"
>   pseudo_dir   =
> "/disk2/xxx/xxx/espresso-3.2.3/pseudo",
>   outdir       =
> "/disk2/jdong/xyh/espresso-3.2.3/tmp",
> /
> &SYSTEM
>   ibrav     = 4,
>   a=20,b=20,c=5.60,cosab=-0.5,cosac=0,cosbc=0,
>   nat       = 24,
>   ntyp      = 2,
>   ecutwfc   =35 ,
>   ecutrho   =420
> /
> &ELECTRONS
>   conv_thr    = 1.D-9,
>   mixing_beta = 0.2D0,
> /
>  ATOMIC_SPECIES
> H  1.0  H.pbe-rrkjus.UPF
> O 15.999 O.pbe-rrkjus.UPF
> ATOMIC_POSITIONS { crystal }
> H        0.040592899  -0.047115761   0.485459003
> H        0.114704004  -0.001940711   0.646569902
> H        0.077728017   0.073838408   0.485209132
> H        0.068286628   0.133313508   0.646050213
> H       -0.040592899   0.047115761   0.485459003
> H       -0.114704004   0.001940711   0.646569902
> H       -0.077728017  -0.073838408   0.485209132
> H       -0.068286628  -0.133313508   0.646050213
> H        0.087725644   0.047173264   0.985851842
> H        0.116757198   0.001980553   1.146554001
> H       -0.003964894   0.073814692   0.985604262
> H        0.065042531   0.133450775   1.145919070
> H       -0.087725644  -0.047173264   0.985851842
> H       -0.116757198  -0.001980553   1.146554001
> H        0.003964894  -0.073814692   0.985604262
> H       -0.065042531  -0.133450775   1.145919070
> O        0.095295444  -0.003121003   0.483499312
> O        0.058352838   0.111476844   0.483127474
> O       -0.095295444   0.003121003   0.483499312
> O       -0.058352838  -0.111476844   0.483127474
> O        0.098444160   0.003183717   0.983638903
> O        0.053053024   0.111436979   0.983231173
> O       -0.098444160  -0.003183717   0.983638903
> O       -0.053053024  -0.111436979   0.983231173
> 
> 
> 
> 
> 
> 
> 
> K_POINTS {automatic}
> 1 1 12 0 0 0
> 
> 
> and my relax out file  wrote:
> 
> 
>      convergence has been achieved
> 
>      Forces acting on atoms (Ry/au):
> 
>      atom   1 type  1   force =    -0.00000712  
> -0.00004363    0.00001631
>      atom   2 type  1   force =     0.00004994   
> 0.00001718   -0.00006583
>      atom   3 type  1   force =     0.00001729  
> -0.00001573    0.00002699
>      atom   4 type  1   force =    -0.00000656   
> 0.00003062    0.00005285
>      atom   5 type  1   force =     0.00000712   
> 0.00004363    0.00001631
>      atom   6 type  1   force =    -0.00004994  
> -0.00001718   -0.00006583
>      atom   7 type  1   force =    -0.00001729   
> 0.00001573    0.00002699
>      atom   8 type  1   force =     0.00000656  
> -0.00003062    0.00005285
>      atom   9 type  1   force =    -0.00000156  
> -0.00006167   -0.00005767
>      atom  10 type  1   force =     0.00001092   
> 0.00004788   -0.00001249
>      atom  11 type  1   force =     0.00005214  
> -0.00008085   -0.00005460
>      atom  12 type  1   force =    -0.00002474  
> -0.00007499    0.00003358
>      atom  13 type  1   force =     0.00000156   
> 0.00006167   -0.00005767
>      atom  14 type  1   force =    -0.00001092  
> -0.00004788   -0.00001249
>      atom  15 type  1   force =    -0.00005214   
> 0.00008085   -0.00005460
>      atom  16 type  1   force =     0.00002474   
> 0.00007499    0.00003358
>      atom  17 type  2   force =     0.00001005   
> 0.00004653    0.00008656
>      atom  18 type  2   force =     0.00001760  
> -0.00007784    0.00003639
>      atom  19 type  2   force =    -0.00001005  
> -0.00004653    0.00008656
>      atom  20 type  2   force =    -0.00001760   
> 0.00007784    0.00003639
>      atom  21 type  2   force =     0.00002956  
> -0.00007076   -0.00004942
>      atom  22 type  2   force =    -0.00000699   
> 0.00005606   -0.00001264
>      atom  23 type  2   force =    -0.00002956   
> 0.00007076   -0.00004942
>      atom  24 type  2   force =     0.00000699  
> -0.00005606   -0.00001264
> 
>      Total force =     0.000382     Total SCF correction = 
>    0.000010
> 
> 
>      entering subroutine stress ...
> 
>           total   stress  (Ry/bohr**3)                  
> (kbar)     P=   -0.40
>   -0.00000194   0.00000001   0.00000000         -0.29     
> 0.00      0.00
>    0.00000001  -0.00000179   0.00000000          0.00    
> -0.26      0.00
>    0.00000000   0.00000000  -0.00000434          0.00     
> 0.00     -0.64
> 
> 
>      bfgs converged in  47 scf cycles and  45 bfgs steps
> 
>      End of BFGS Geometry Optimization
> 
>      Final energy =    -274.4689566789 Ry
> 
> 
> so i think the problem is not caused by the structure
> relaxation.
> but where is the problem? i can find it . i need your help.
> thank you if you could give me some hints about the
> problem!
> 
> 
> cheers
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ~
> 
> 
> 
> 
> 
> the
> -- 
> Xu Yuehua
> physics Department of Nanjing university
> China
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