The ABINIT Users Mailing List ( CLOSED )

["D. R. Hamann" <drh@bell-labs.com>]

Dear Chun,

Please send your Abinit questions to the forum rather than my personal
email.

I think your anaddb issue relates to your first run being cut off.  Abinit
only writes the DDB file after in completes all the perturbations in
a given dataset, so I believe that is why part was missing.  You can
divide perturbations among different datasets, or even among different
runs and use the mrgddb utility.

There is a more serious issue.  If I am interpreting your data correctly,
it looks as if you have set up a slab surface model of ZnO with a vacuum
region.  The elastic tensor and piezoelectric tensor are bulk properties,
and are meaningless for such a model.

D. R. Hamann

Chun Li wrote:

Dear Hamann,

When I calculate the dielectric and piezoelectric tensor of wurtzite
structures using abinit, I encountered some problems.

1) When I perform such calculations on my supercell model, the
calculation cannot complete in the limited time of the machine. So I
restart the calculation by reading from the output WF files. That is,
read *_WFK and *_1WF13~15 obtained from the first two datasets. And for
the third dataset, I only calculate the perturbations that have not been
completed in the previous calculation. Is it right?

2) After the restart calculation completed, I used anaddb to analyze the
DDB file, but the result can not be obtained with some COMMENT like:
gtblk9 : COMMENT -
  The blok     1 does not match the requirement
  because it lacks the element with
  idir1,ipert1,idir2,ipert2,index=    1    1    1    1    1

and the following bug in the end of the log file:
matrginv : BUG -
  The matrix that has been passed in argument of this subroutine
  is probably either singular or nearly singular.
  Action : contact ABINIT group.

 Delivered    0 WARNINGs and  21 COMMENTs to log file.

I think this is relative to the restart calculation. But if the method I
used to restart the calculation is incorrect, then how to do it? Can you
give me some ideas? Thanks a lot.

The input file:
  ndtset  3

   iscf1  3
 kptopt1  1
 tolvrs1  1.0d-18 

   iscf2 -3
 rfelfd2  2
 getwfk2  -1
   nqpt2  1
    qpt2  0.0 0.0 0.0
 kptopt2  2
#getden2  1
  rfdir2  1 1 1
 tolwfr2  1.0d-20

 rfphon3  1
rfatpol3  1 4
   iscf3  3     
 rfelfd3  3 
   nqpt3  1
    qpt3  0.0 0.0 0.0   
 getwfk3  -2     
 getddk3  -1
  rfdir3  1 1 1
 rfstrs3  3
 kptopt3  2
 tolvrs3  1.0d-10

# Common data
  acell  6.15956186 18.47868558 12.16199678
  diemac  9.0
  diemix  0.1
    ecut  56.0
    iscf  3
   natom  4 
   nband  24
   ngkpt  6 2 2
  nloalg  4
 nshiftk  1
   nstep  500
  ntypat  2
  prtvol  10
  angdeg  90 90 120
  shiftk  0.0 0.0 0.5
    xred
0.0 0.0 0.0000000000
2/3 1/9 0.0954692557
2/3 1/9 0.4045307443
0.0 0.0 0.5000000000
# tolwfr  1.d-12
   typat  1 2 1 2 
   znucl  8 30

After the first calculation, the dataset2 is completed, and then I
restart the calculation with only the dataset3. After second
calculation, the dataset3 have not completed (only the phonon
perturbation is completed), so I restart again with only rfreld and
rfstrs. Then the DDB file (attached) is obtained after the third
calculation is completed.

Then I use the following anaddb input file to analyze it:

!the flags
dieflag 3  !the frequency dependent dielectric tensor is calculated
elaflag  3  !the flag for the elastic constant
piezoflag 3
instrflag 1  !the flag for the internal strain tensor

!the effective charge part
asr 1
chneut  1

! Wavevector list number 1

nph1l 1 !number of phonons in list 1
qph1l  0.0 0.0 0.0 1.0 !the Gamma point

! Wave vector list no. 2

nph2l 1  !number of phonons in list 2
qph2l 0.0 0.0 1.0 0.0  ! why here the normalization factor is 0

Sorry for wasting your time. Any advice from you is appreciated. Thank
you again.

Best regards.

Chun Li
  

 **** DERIVATIVE DATABASE ****    
+DDB, Version number     10929

  Note : temporary (transfer) database                                                                                               

     natom         4
      nkpt        12
    nsppol         1
      nsym         2
    ntypat         2
    occopt         1
     nband        24
     acell  0.61595618600000D+01  0.18478685580000D+02  0.12161996780000D+02
       amu  0.15999400000000D+02  0.65390000000000D+02
   dilatmx  0.10000000000000D+01
      ecut  0.56000000000000D+02
    ecutsm  0.00000000000000D+00
     intxc         0
      iscf         3
       ixc         2
       kpt  0.00000000000000D+00  0.00000000000000D+00  0.25000000000000D+00
            0.16666666666667D+00  0.00000000000000D+00  0.25000000000000D+00
            0.33333333333333D+00  0.00000000000000D+00  0.25000000000000D+00
            0.50000000000000D+00  0.00000000000000D+00  0.25000000000000D+00
           -0.33333333333333D+00  0.00000000000000D+00  0.25000000000000D+00
           -0.16666666666667D+00  0.00000000000000D+00  0.25000000000000D+00
            0.00000000000000D+00  0.50000000000000D+00  0.25000000000000D+00
            0.16666666666667D+00  0.50000000000000D+00  0.25000000000000D+00
            0.33333333333333D+00  0.50000000000000D+00  0.25000000000000D+00
            0.50000000000000D+00  0.50000000000000D+00  0.25000000000000D+00
           -0.33333333333333D+00  0.50000000000000D+00  0.25000000000000D+00
           -0.16666666666667D+00  0.50000000000000D+00  0.25000000000000D+00
    kptnrm  0.10000000000000D+01
     ngfft        45  135   90
    nspden         1
   nspinor         1
       occ  0.20000000000000D+01  0.20000000000000D+01  0.20000000000000D+01
            0.20000000000000D+01  0.20000000000000D+01  0.20000000000000D+01
            0.20000000000000D+01  0.20000000000000D+01  0.20000000000000D+01
            0.20000000000000D+01  0.20000000000000D+01  0.20000000000000D+01
            0.20000000000000D+01  0.20000000000000D+01  0.20000000000000D+01
            0.20000000000000D+01  0.20000000000000D+01  0.20000000000000D+01
            0.00000000000000D+00  0.00000000000000D+00  0.00000000000000D+00
            0.00000000000000D+00  0.00000000000000D+00  0.00000000000000D+00
     rprim  0.10000000000000D+01  0.00000000000000D+00  0.00000000000000D+00
           -0.50000000000000D+00  0.86602540378444D+00  0.00000000000000D+00
            0.61232339957368D-16  0.10605752387249D-15  0.10000000000000D+01
     sciss  0.00000000000000D+00
    spinat  0.00000000000000D+00  0.00000000000000D+00  0.00000000000000D+00
            0.00000000000000D+00  0.00000000000000D+00  0.00000000000000D+00
            0.00000000000000D+00  0.00000000000000D+00  0.00000000000000D+00
            0.00000000000000D+00  0.00000000000000D+00  0.00000000000000D+00
    symafm         1    1
    symrel         1    0    0    0    1    0    0    0    1
                  -1    0    0    3    1    0    0    0    1
     tnons  0.00000000000000D+00  0.00000000000000D+00  0.00000000000000D+00
            0.00000000000000D+00  0.00000000000000D+00  0.00000000000000D+00
    tolwfr  0.10000000000000D+01
   tphysel  0.00000000000000D+00
    tsmear  0.40000000000000D-01
     typat         1    2    1    2
       wtk  0.83333333333333D-01  0.83333333333333D-01  0.83333333333333D-01
            0.83333333333333D-01  0.83333333333333D-01  0.83333333333333D-01
            0.83333333333333D-01  0.83333333333333D-01  0.83333333333333D-01
            0.83333333333333D-01  0.83333333333333D-01  0.83333333333333D-01
      xred  0.00000000000000D+00  0.00000000000000D+00  0.00000000000000D+00
            0.66666666666667D+00  0.11111111111111D+00  0.95469255700000D-01
            0.66666666666667D+00  0.11111111111111D+00  0.40453074430000D+00
            0.25431029499041D-32  0.16954019666027D-32  0.50000000000000D+00
     znucl  0.80000000000000D+01  0.30000000000000D+02
      zion  0.60000000000000D+01  0.12000000000000D+02
 
  Description of the potentials (KB energies)
  vrsio8 (for pseudopotentials)= 10929
  dimekb =  3       lmnmax=  3       usepaw=  0
  Atom type=    1   pspso=  1   nekb=   1
  iln lpsang iproj  ekb(:)
     1     1     1    -4.6233336E+00
  Atom type=    2   pspso=  1   nekb=   2
  iln lpsang iproj  ekb(:)
     1     1     1     3.4796927E+01  0.0000000E+00
     2     2     1     0.0000000E+00 -1.3650335E+01
 
 **** Database of total energy derivatives ****
 Number of data blocks=    1

 2rd derivatives (non-stat.)  - # elements :     239
 qpt  0.00000000E+00  0.00000000E+00  0.00000000E+00   1.0
   1   1   3   1  0.00000000000000D+00  0.00000000000000D+00
   1   1   3   2  0.00000000000000D+00  0.00000000000000D+00
   1   1   3   3  0.00000000000000D+00  0.00000000000000D+00
   1   1   3   4  0.00000000000000D+00  0.00000000000000D+00
   1   1   1   6 -0.50859795675800D+02  0.00000000000000D+00
   1   1   2   6 -0.10080031888440D-12  0.00000000000000D+00
   1   1   3   6 -0.69302569371436D-13  0.00000000000000D+00
   1   1   1   7 -0.45702385318229D-13  0.00000000000000D+00
   1   1   2   7  0.56025935368386D-14  0.00000000000000D+00
   1   1   3   7 -0.24107819435486D-14  0.00000000000000D+00
   1   1   1   8 -0.69151598822178D-14  0.00000000000000D+00
   1   1   2   8 -0.68421752719346D+00  0.00000000000000D+00
   1   1   3   8 -0.91302803396521D+00  0.00000000000000D+00
   2   1   1   6  0.14895597965130D+02  0.00000000000000D+00
   2   1   2   6 -0.40929396867052D+02  0.00000000000000D+00
   2   1   3   6 -0.52461977224748D+01  0.00000000000000D+00
   2   1   1   7 -0.16922857561349D+01  0.00000000000000D+00
   2   1   2   7 -0.16882700819234D+01  0.00000000000000D+00
   2   1   3   7 -0.13940933022715D+01  0.00000000000000D+00
   2   1   1   8 -0.45143867200671D+00  0.00000000000000D+00
   2   1   2   8  0.10263262907912D+01  0.00000000000000D+00
   2   1   3   8  0.13695420509378D+01  0.00000000000000D+00
   3   1   1   1  0.00000000000000D+00  0.00000000000000D+00
   3   1   1   2  0.00000000000000D+00  0.00000000000000D+00
   3   1   1   3  0.00000000000000D+00  0.00000000000000D+00
   3   1   1   4  0.00000000000000D+00  0.00000000000000D+00
   3   1   1   6 -0.78199504690861D-01  0.00000000000000D+00
   3   1   2   6 -0.52133042297922D-01  0.00000000000000D+00
   3   1   3   6 -0.51786245378947D+02  0.00000000000000D+00
   3   1   1   7 -0.11693853962317D+01  0.00000000000000D+00
   3   1   2   7 -0.20054940898677D+00  0.00000000000000D+00
   3   1   3   7 -0.19306856014354D+01  0.00000000000000D+00
   3   1   1   8 -0.11375497295453D+01  0.00000000000000D+00
   3   1   2   8 -0.61496985013532D-11  0.00000000000000D+00
   3   1   3   8  0.67129878585857D-12  0.00000000000000D+00
   1   2   3   1  0.00000000000000D+00  0.00000000000000D+00
   1   2   3   2  0.00000000000000D+00  0.00000000000000D+00
   1   2   3   3  0.00000000000000D+00  0.00000000000000D+00
   1   2   3   4  0.00000000000000D+00  0.00000000000000D+00
   1   2   1   6 -0.62052331618840D+02  0.00000000000000D+00
   1   2   2   6  0.12533701400216D-12  0.00000000000000D+00
   1   2   3   6  0.36053343788600D-11  0.00000000000000D+00
   1   2   1   7 -0.10973866845631D-11  0.00000000000000D+00
   1   2   2   7  0.51405121722782D-12  0.00000000000000D+00
   1   2   3   7  0.70615463192859D-12  0.00000000000000D+00
   1   2   1   8  0.10507418862223D-13  0.00000000000000D+00
   1   2   2   8  0.43187459889689D+00  0.00000000000000D+00
   1   2   3   8  0.84423665973659D+00  0.00000000000000D+00
   2   2   1   6 -0.16004165155429D+02  0.00000000000000D+00
   2   2   2   6 -0.72721774848180D+02  0.00000000000000D+00
   2   2   3   6  0.43741316162215D+01  0.00000000000000D+00
   2   2   1   7  0.17320704981305D+01  0.00000000000000D+00
   2   2   2   7  0.20369220003952D+01  0.00000000000000D+00
   2   2   3   7  0.10929395509824D+01  0.00000000000000D+00
   2   2   1   8  0.39154278050495D+00  0.00000000000000D+00
   2   2   2   8 -0.64781189836802D+00  0.00000000000000D+00
   2   2   3   8 -0.12663549896201D+01  0.00000000000000D+00
   3   2   1   1  0.00000000000000D+00  0.00000000000000D+00
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   3   2   1   3  0.00000000000000D+00  0.00000000000000D+00
   3   2   1   4  0.00000000000000D+00  0.00000000000000D+00
   3   2   1   6  0.42835199866719D+00  0.00000000000000D+00
   3   2   2   6  0.28556787507609D+00  0.00000000000000D+00
   3   2   3   6 -0.61801846409615D+02  0.00000000000000D+00
   3   2   1   7  0.27482838451352D+00  0.00000000000000D+00
   3   2   2   7 -0.15380119652261D+00  0.00000000000000D+00
   3   2   3   7 -0.21154122534844D+01  0.00000000000000D+00
   3   2   1   8  0.10302402131459D+01  0.00000000000000D+00
   3   2   2   8  0.69831589956568D-11  0.00000000000000D+00
   3   2   3   8  0.47606426194100D-10  0.00000000000000D+00
   1   3   3   1  0.00000000000000D+00  0.00000000000000D+00
   1   3   3   2  0.00000000000000D+00  0.00000000000000D+00
   1   3   3   3  0.00000000000000D+00  0.00000000000000D+00
   1   3   3   4  0.00000000000000D+00  0.00000000000000D+00
   1   3   1   6 -0.51708187341598D+02  0.00000000000000D+00
   1   3   2   6  0.38492968756661D-15  0.00000000000000D+00
   1   3   3   6  0.29828549267296D-13  0.00000000000000D+00
   1   3   1   7  0.24741040169765D-13  0.00000000000000D+00
   1   3   2   7  0.16984419387218D-13  0.00000000000000D+00
   1   3   3   7  0.13178229573699D-13  0.00000000000000D+00
   1   3   1   8  0.34838117642946D-14  0.00000000000000D+00
   1   3   2   8 -0.30725552266952D+00  0.00000000000000D+00
   1   3   3   8  0.95267664258889D+00  0.00000000000000D+00
   2   3   1   6  0.17629047988987D+02  0.00000000000000D+00
   2   3   2   6 -0.39955488533335D+02  0.00000000000000D+00
   2   3   3   6  0.50385793265965D+01  0.00000000000000D+00
   2   3   1   7  0.17549928529881D+01  0.00000000000000D+00
   2   3   2   7  0.14760462086182D+01  0.00000000000000D+00
   2   3   3   7  0.12371308457422D+01  0.00000000000000D+00
   2   3   1   8 -0.61100143762109D+00  0.00000000000000D+00
   2   3   2   8  0.46088328400868D+00  0.00000000000000D+00
   2   3   3   8 -0.14290149638779D+01  0.00000000000000D+00
   3   3   1   1  0.00000000000000D+00  0.00000000000000D+00
   3   3   1   2  0.00000000000000D+00  0.00000000000000D+00
   3   3   1   3  0.00000000000000D+00  0.00000000000000D+00
   3   3   1   4  0.00000000000000D+00  0.00000000000000D+00
   3   3   1   6 -0.34973776937240D+00  0.00000000000000D+00
   3   3   2   6 -0.23315841322323D+00  0.00000000000000D+00
   3   3   3   6 -0.52387371069926D+02  0.00000000000000D+00
   3   3   1   7 -0.37138722904545D+00  0.00000000000000D+00
   3   3   2   7  0.76189691988436D-01  0.00000000000000D+00
   3   3   3   7  0.21827031297789D+01  0.00000000000000D+00
   3   3   1   8  0.92849742672564D+00  0.00000000000000D+00
   3   3   2   8 -0.23526924580874D-11  0.00000000000000D+00
   3   3   3   8 -0.13358209285124D-10  0.00000000000000D+00
   1   4   3   1  0.00000000000000D+00  0.00000000000000D+00
   1   4   3   2  0.00000000000000D+00  0.00000000000000D+00
   1   4   3   3  0.00000000000000D+00  0.00000000000000D+00
   1   4   3   4  0.00000000000000D+00  0.00000000000000D+00
   1   4   1   6 -0.61866874731708D+02  0.00000000000000D+00
   1   4   2   6 -0.43355545681381D-13  0.00000000000000D+00
   1   4   3   6 -0.73806776116383D-13  0.00000000000000D+00
   1   4   1   7  0.16603841722506D-12  0.00000000000000D+00
   1   4   2   7  0.52011342713219D-13  0.00000000000000D+00
   1   4   3   7 -0.31036494009550D-13  0.00000000000000D+00
   1   4   1   8  0.58807500462840D-14  0.00000000000000D+00
   1   4   2   8  0.55969419856811D+00  0.00000000000000D+00
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   2   4   3   7 -0.93611583440660D+00  0.00000000000000D+00
   2   4   1   8  0.67109152903021D+00  0.00000000000000D+00
   2   4   2   8 -0.83954129784597D+00  0.00000000000000D+00
   2   4   3   8  0.13257960006331D+01  0.00000000000000D+00
   3   4   1   1  0.00000000000000D+00  0.00000000000000D+00
   3   4   1   2  0.00000000000000D+00  0.00000000000000D+00
   3   4   1   3  0.00000000000000D+00  0.00000000000000D+00
   3   4   1   4  0.00000000000000D+00  0.00000000000000D+00
   3   4   1   6 -0.39793568440860D-03  0.00000000000000D+00
   3   4   2   6 -0.26521927467538D-03  0.00000000000000D+00
   3   4   3   6 -0.58684922915449D+02  0.00000000000000D+00
   3   4   1   7  0.12661849461343D+01  0.00000000000000D+00
   3   4   2   7  0.27831844248195D+00  0.00000000000000D+00
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   3   4   1   8 -0.82128313884904D+00  0.00000000000000D+00
   3   4   2   8  0.48890050511015D-11  0.00000000000000D+00
   3   4   3   8  0.69593708501367D-13  0.00000000000000D+00
   1   6   1   1 -0.50859795675800D+02  0.00000000000000D+00
   1   6   2   1  0.14895597965130D+02  0.00000000000000D+00
   1   6   3   1 -0.78199504690861D-01  0.00000000000000D+00
   1   6   1   2 -0.62052331618840D+02  0.00000000000000D+00
   1   6   2   2 -0.16004165155429D+02  0.00000000000000D+00
   1   6   3   2  0.42835199866719D+00  0.00000000000000D+00
   1   6   1   3 -0.51708187341598D+02  0.00000000000000D+00
   1   6   2   3  0.17629047988987D+02  0.00000000000000D+00
   1   6   3   3 -0.34973776937240D+00  0.00000000000000D+00
   1   6   1   4 -0.61866874731708D+02  0.00000000000000D+00
   1   6   2   4 -0.16080555574773D+02  0.00000000000000D+00
   1   6   3   4 -0.39793568440860D-03  0.00000000000000D+00
   1   6   1   6 -0.28091675849016D+03  0.00000000000000D+00
   1   6   2   6 -0.10493009096577D+02  0.00000000000000D+00
   1   6   3   6 -0.99973143960122D+00  0.00000000000000D+00
   1   6   1   7 -0.25829434196748D-01  0.00000000000000D+00
   1   6   2   7  0.66477782574004D-01  0.00000000000000D+00
   1   6   3   7 -0.11481232955613D+00  0.00000000000000D+00
   1   6   1   8  0.16931763525436D-01  0.00000000000000D+00
   1   6   2   8  0.17869048554522D+01  0.00000000000000D+00
   1   6   3   8 -0.15414486592434D+00  0.00000000000000D+00
   2   6   1   1 -0.10080031888440D-12  0.00000000000000D+00
   2   6   2   1 -0.40929396867052D+02  0.00000000000000D+00
   2   6   3   1 -0.52133042297922D-01  0.00000000000000D+00
   2   6   1   2  0.12533701400216D-12  0.00000000000000D+00
   2   6   2   2 -0.72721774848180D+02  0.00000000000000D+00
   2   6   3   2  0.28556787507609D+00  0.00000000000000D+00
   2   6   1   3  0.38492968756661D-15  0.00000000000000D+00
   2   6   2   3 -0.39955488533335D+02  0.00000000000000D+00
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   2   6   1   4 -0.43355545681381D-13  0.00000000000000D+00
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   3   8   2   8  0.42664140999881D-01  0.00000000000000D+00
   3   8   3   8  0.54694519809311D+00  0.00000000000000D+00

-- 
D. R. Hamann				Phone: 908-582-4454
Director, Theoretical Materials    	Fax:   908-582-4702
  Physics Research (retired)		email: drh@physics.bell-labs.com
Bell Laboratories 
Lucent Technologies
700 Mountain Ave, Room 1D-371
Murray Hill, NJ 07974-0636 USA