[Pw_forum] the dynmaical matrix are like "***********" when thephonons calculation at gama
Huiqun Zhou
hqzhou at nju.edu.cn
Wed Mar 4 05:02:17 CET 2009
Hi, Yuehua,
This is not an answer to your question, but I think if you have no special
reason to use espresso 3.2.3, you'd better upgrade to 4.0.4 and try again.
Since we are on the same campus and I guess you're using our Altix 4700,
if this is true and you're willing to, you can run the command below to get
the latest compiled copy from my home:
scp -r hqzhou at 210.119.46.90:/disk3/hqzhou/espresso-4.0.4 /your/home
Call me at 83686750, I'll let you know my password.
Huiqun Zhou
@Nanjing University, China
----- Original Message -----
From: "xu yuehua" <njuxuyuehua at gmail.com>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Tuesday, March 03, 2009 10:11 PM
Subject: Re: [Pw_forum] the dynmaical matrix are like "***********" when
thephonons calculation at gama
> my problem is not the "nan" , it has aready sovled,
>
> my problem is the original problem :
> 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
>>>
>
>
> 2009/3/3, Paolo Giannozzi <giannozz at democritos.it>:
>> xu yuehua wrote:
>>
>>> kpoint 1 ibnd 33 solve_e: root not converged NaN
>>
>> "NaN" doesn't mean "Sodium Nitride" here but "Not a Number".
>> There is something seriously wrong going on here and it is
>> completely useless to go on
>>
>> Paolo
>> --
>> Paolo Giannozzi, Democritos and University of Udine, Italy
>> _______________________________________________
>> Pw_forum mailing list
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>>
>
>
> --
> Xu Yuehua
> physics Department of Nanjing university
> China
> _______________________________________________
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> Pw_forum at pwscf.org
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