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[yunhee.chang@kriss.re.kr]

Dear Abinit users,

I have one more question about generation of the derivative databases for 
phonon band structure.
I calculted the phonon frequencies to generate the derivative databases using 
tutorial trf2_1.in file.

My system is Si(001) surface.
Total number of atoms are 24, Si atoms are 21 and H atoms are 4.
After finishing the calculation, in outfile this message is occured
"The dynamical matrix was incomplete : phonon frequencies may be wrong ..."
I don't know what is the origin of this messages,
and what I have to check to fix these problems?

The output and input file shows below.

output file
-----------------------------------------------------------------------------

 Phonon wavevector (reduced coordinates) :  0.00000  0.00000  0.00000
 Phonon energies in Hartree :
  -1.105578E-03  0.000000E+00  0.000000E+00  0.000000E+00  0.000000E+00
   0.000000E+00  0.000000E+00  0.000000E+00  0.000000E+00  1.147428E-08
   1.147428E-08  1.147428E-08  1.147428E-08  1.243662E-04  1.536675E-04
   3.582086E-04  3.614045E-04  3.975110E-04  4.597652E-04  5.075614E-04
   5.269885E-04  5.520817E-04  5.531005E-04  5.845276E-04  5.947355E-04
   5.981996E-04  5.997179E-04  6.301051E-04  6.632132E-04  6.653182E-04
   7.463843E-04  7.674337E-04  8.380783E-04  9.460294E-04  1.062731E-03
   1.140595E-03  1.323622E-03  1.366902E-03  1.485605E-03  1.514528E-03
   1.600986E-03  1.710547E-03  1.783044E-03  1.831939E-03  1.871589E-03
   1.880937E-03  1.881882E-03  1.902800E-03  1.975642E-03  2.028960E-03
   2.054429E-03  2.055787E-03  2.085770E-03  2.097932E-03  2.131256E-03
   2.132040E-03  2.155761E-03  2.160453E-03  2.170549E-03  2.175160E-03
   2.177032E-03  2.199766E-03  2.233710E-03  2.237783E-03  2.241660E-03
   2.259993E-03  2.273112E-03  2.294444E-03  2.320347E-03  2.334104E-03
   2.358009E-03  2.368176E-03
 Phonon frequencies in cm-1    :
- -2.426464E+02  0.000000E+00  0.000000E+00  0.000000E+00  0.000000E+00
-  0.000000E+00  0.000000E+00  0.000000E+00  0.000000E+00  2.518314E-03
-  2.518314E-03  2.518314E-03  2.518314E-03  2.729522E+01  3.372611E+01
-  7.861771E+01  7.931911E+01  8.724358E+01  1.009068E+02  1.113968E+02
-  1.156606E+02  1.211679E+02  1.213915E+02  1.282890E+02  1.305294E+02
-  1.312896E+02  1.316229E+02  1.382921E+02  1.455585E+02  1.460205E+02
-  1.638124E+02  1.684322E+02  1.839369E+02  2.076294E+02  2.332425E+02
-  2.503317E+02  2.905015E+02  3.000004E+02  3.260527E+02  3.324004E+02
-  3.513757E+02  3.754216E+02  3.913330E+02  4.020641E+02  4.107664E+02
-  4.128179E+02  4.130253E+02  4.176164E+02  4.336033E+02  4.453053E+02
-  4.508950E+02  4.511930E+02  4.577736E+02  4.604429E+02  4.677567E+02
-  4.679287E+02  4.731348E+02  4.741647E+02  4.763805E+02  4.773924E+02
-  4.778033E+02  4.827929E+02  4.902427E+02  4.911365E+02  4.919875E+02
-  4.960112E+02  4.988905E+02  5.035723E+02  5.092573E+02  5.122767E+02
-  5.175231E+02  5.197546E+02
 chkph3 : WARNING -
  The dynamical matrix was incomplete : phonon frequencies may be wrong ...
------------------------------------------------------------------------------

And input file is like this.
------------------------------------------------------------------------------
# Si(001) surface p(2x1).R : Buckled Si dimer structure
 
   ndtset   6
#Set 1 : ground state self-consistency
 
  getwfk1   0            # Cancel default
  kptopt1   1            # Automatic generation of k points, taking
                         # into account the symmetry
    nqpt1   0            # Cancel default
  tolvrs1   1.0d-18      # SCF stopping criterion (modify default)
  rfphon1   0            # Cancel default
  irdwfk1   1          
   
#Q vectors for all datasets
    
#Complete set of symmetry-inequivalent qpt chosen to be commensurate
# with kpt mesh so that only one set of GS wave functions is needed.
#Generated automatically by running GS calculation with kptopt=1,
# nshift=0, shiftk=0 0 0 (to include gamma) and taking output kpt set
# file as qpt set. Set nstep=1 so only one iteration runs.
 
     nqpt   1            # One qpt for each dataset (only 0 or 1 allowed)
                         # This is the default for all datasets and must 
                         #  be explicitly turned off for dataset 1.
            
     qpt2   0.00000000E+00  0.00000000E+00  0.00000000E+00   # Gamma point
     qpt3   0.00000000E+00  0.00000000E+00  0.00000000E+00   # Gamma point
     qpt4   5.00000000E-01  0.00000000E+00  0.00000000E+00   # J  point
     qpt5   5.00000000E-01  5.00000000E-01  0.00000000E+00   # K  point 
     qpt6   0.00000000E-01  5.00000000E-01  0.00000000E+00   # J' point
                      
#Set 2 : Response function calculation of d/dk wave function 
                      
    iscf2   -3         # Need this non-self-consistent option for d/dk
  kptopt2   2          # Modify default to use time-reversal symmetry
  rfphon2   0          # Cancel default
  rfelfd2   2          # Calculate d/dk wave function only
  tolvrs2   0.0        # Cancel default for d/dk
  tolwfr2   1.0d-22    # Use wave function residual criterion instead
            
                                                                              
                               40,0-1        Top
    xcart   5.9039889771E+00 -6.0729939581E-07  2.7204853253E+01
            1.0039419724E+01 -4.7860855073E-08  2.8568093438E+01
            3.8319078991E+00  3.6471293249E+00  2.5815824929E+01
            1.0714995504E+01  3.6471292512E+00  2.5945931209E+01
           -6.0517025514E-02  3.6471295365E+00  2.3501237786E+01
            7.4134326200E+00  3.6471306394E+00  2.2948528028E+01
           -4.0574759347E-03 -1.3695151790E-06  2.0844823466E+01
            7.2718944436E+00 -1.8887092077E-06  2.0429191107E+01
            3.5311323308E+00  1.5819469128E-06  1.8057940784E+01
            1.1026081704E+01 -3.5844043594E-06  1.8065100898E+01
            3.5699606282E+00  3.6471264817E+00  1.5482539097E+01
            1.1003352237E+01  3.6471323846E+00  1.5485711239E+01
           -8.8915116479E-03  3.6471243513E+00  1.2839272152E+01
            7.2875484129E+00  3.6471277774E+00  1.2974430170E+01
           -8.8817325561E-03  3.5407020319E-06  1.0280205027E+01
            7.2871615260E+00  4.9870247514E-07  1.0379176488E+01
            3.6641530994E+00 -3.2658218684E-06  7.7508602314E+00
            1.0908373951E+01 -2.7922012069E-06  7.7491057522E+00
            3.6610601969E+00  3.6471311504E+00  5.2171627558E+00
            1.0912345841E+01  3.6471298511E+00  5.2154365698E+00
            1.4473916786E+00  3.6471301284E+00  3.4697106985E+00
            5.8294009642E+00  3.6471293647E+00  3.4125663575E+00
            8.7451596235E+00  3.6471307904E+00  3.4093530778E+00
            1.3127195983E+01  3.6471314038E+00  3.4695504024E+00
            
#Gives the number of band, explicitely (do not take the default)
    nband   55        
   
#Exchange-correlation functional
                      
      ixc   11            # GGA Perdew-Burke-Ernzerhof GGA functional
                      
#Definition of the planewave basis set
 
     ecut   8.0           # Maximal kinetic energy cut-off, in Hartree
    
#Definition of the k-point grid
    ngkpt   4  8  1
  nshiftk   1              # Use one copy of grid only (default)
   shiftk   0.5 0.5 0.0    # This gives the usual fcc Monkhorst-Pack grid
                                                                              
                               77,5          89%
  nshiftk   1              # Use one copy of grid only (default)
   shiftk   0.5 0.5 0.0    # This gives the usual fcc Monkhorst-Pack grid
 
#Definition of the SCF procedure
     iscf   5          # Self-consistent calculation, using algorithm 5
    nstep   30         # Maximal number of SCF cycles
   diemac  12.0        # Although this is not mandatory, it is worth to
                       # precondition the SCF cycle. The model dielectric
                       # function used as the standard preconditioner
                       # is described in the "dielng" input variable section.
                       # The dielectric constant of AlAs is smaller that the 
one of Si (=12).
--------------------------------------------------------------------------------

Thank you very much for your helps~!

Best regards,
Yunhee Chang