The ABINIT Users Mailing List ( CLOSED )

[matthieu verstraete <matthieu.jean.verstraete@gmail.com>]

This looks like a numerical fluke, rather than a bug, and once your
ground state wf are corrupted, the rest follows. You might try iscf 7
for DS1, or perhaps increase nline further. Try just doing the GS
alone until it works correctly, perhaps reading the DS1_WFK with cut3d
to check it is correct.

And the simplest, you should try a more recent version of abinit too.

Matthieu

On Wed, Mar 25, 2009 at 9:19 AM,  <ilukacevic@fizika.unios.hr> wrote:
> Dear all!
>
> I'm trying to calculate the elastic constants at various pressures for SiO2
> crystal. The calculations are run on a cluster with intel's mpich and 
> abinit's
> 5.4.4p version. With 5.4.4 version (until 31.12.2008.) I had no problems
> running these calculations (I'm not saying that there is a problem with 
> patched
> abinit).
>
> The problem is that I get an .out file full of NaN values instead of 
> numbers:
>
>
>
> the end of DS1 ->
>  ETOT 29  -72.138266970276    -2.132E-13 6.893E-11 1.611E-20 2.717E-13
> 4.352E-06
>  ETOT 30 NaN                   NaN       3.834E-11 NaN       NaN       NaN
>
>  At SCF step   30       vres2   = NaN       < tolvrs=  1.00E-20 =>converged.
>
>  Components of total free energy (in Hartree) :
>
>    Kinetic energy  =  NaN
>    Hartree energy  =  NaN
>    XC energy       =  NaN
>    Ewald energy    = -6.58401175816303E+01
>    PspCore energy  =  1.57491814011899E+00
>    Loc. psp. energy=  NaN
>    NL   psp  energy=  NaN
>    >>>>>>>>> Etotal=  NaN
>
>  Other information on the energy :
>    Total energy(eV)=  NaN                  ; Band energy (Ha)=  NaN
> --------------------------------------------------------------------------------
>
>  Cartesian components of stress tensor (hartree/bohr^3)
>  sigma(1 1)= NaN              sigma(3 2)= NaN
>  sigma(2 2)= NaN              sigma(3 1)= NaN
>  sigma(3 3)= NaN              sigma(2 1)= NaN
>
> -Cartesian components of stress tensor (GPa)         [Pressure= NaN
> GPa]
> - sigma(1 1)= NaN              sigma(3 2)= NaN
> - sigma(2 2)= NaN              sigma(3 1)= NaN
> - sigma(3 3)= NaN              sigma(2 1)= NaN
>
>
>
> DS2 ->
>     iter   2DEtotal(Ha)        deltaE(Ha) residm    vres2
> -ETOT  1 NaN                    NaN       0.000E+00 NaN
>
>  At SCF step    1   max residual=  0.00E+00 < tolwfr=  1.00E-20 =>converged.
> ================================================================================
>
>  ----iterations are completed or convergence reached----
>
>  Mean square residual over all n,k,spin=  -1.0000E+00; max=  0.0000E+00
>   0.0625  0.0625  0.0417    1 -1.00000E+00 kpt; spin; max resid(k); each 
> band:
> -1.00E+00-1.00E+00-1.00E+00-1.00E+00-1.00E+00-1.00E+00-1.00E+00-1.00E+00
> -1.00E+00-1.00E+00-1.00E+00-1.00E+00-1.00E+00-1.00E+00-1.00E+00-1.00E+00
> -1.00E+00-1.00E+00
>
>  Eight components of 2nd-order total energy (hartree) are
>  1,2,3: 0th-order hamiltonian combined with 1st-order wavefunctions
>     kin0=   0.00000000E+00 eigvalue= NaN               local= NaN
>  4,5,6: 1st-order hamiltonian combined with 1st and 0th-order wfs
>     kin1= NaN               Hartree=   0.00000000E+00     xc= NaN
>  7,8,9: eventually, occupation + non-local contributions
>    edocc= NaN                  enl0=   0.00000000E+00   enl1=   
> 0.00000000E+00
>  1-9 gives the relaxation energy (to be shifted if some occ is /=2.0)
>   erelax= NaN
>  No Ewald or frozen-wf contrib.: the relaxation energy is the total one
>  2DEtotal= NaN                 Ha. Also 2DEtotal= NaN                   eV
>    (  non-var. 2DEtotal : NaN                 Ha)
>
>
>
> DS3 ->
>     iter   2DEtotal(Ha)        deltaE(Ha) residm    vres2
> -ETOT  1 NaN                    NaN       0.000E+00 NaN
>
>  At SCF step    1       vres2   = NaN       < tolvrs=  1.00E-14 =>converged.
> -open ddk wf file :t11o_DS2_1WF19
> -open ddk wf file :t11o_DS2_1WF20
> -open ddk wf file :t11o_DS2_1WF21
>
>
> The calculation stopped with the message in the log file:
>
>  ----iterations are completed or convergence reached----
>
>  outwf  : write wavefunction to file t11o_DS3_1WF30
> -P-0000  leave_test : synchronization done...
>
>  Seventeen components of 2nd-order total energy (hartree) are
>  1,2,3: 0th-order hamiltonian combined with 1st-order wavefunctions
>     kin0=   0.00000000E+00 eigvalue= NaN               local= NaN
>  4,5,6,7: 1st-order hamiltonian combined with 1st and 0th-order wfs
>  loc psp = NaN               Hartree= NaN                  xc= NaN
>     kin1= NaN
>  8,9,10: eventually, occupation + non-local contributions
>    edocc= NaN                  enl0=   0.00000000E+00   enl1= NaN
>  1-10 gives the relaxation energy (to be shifted if some occ is /=2.0)
>   erelax= NaN
>  11,12,13 Non-relaxation  contributions : frozen-wavefunctions and Ewald
>  fr.hart= NaN                fr.kin= NaN              fr.loc= NaN
>  14,15,16 Non-relaxation  contributions : frozen-wavefunctions and Ewald
>  fr.nonl= NaN                 fr.xc= NaN               Ewald=   
> 2.25162750E+01
>  17 Non-relaxation  contributions : pseudopotential core energy
>  pspcore=   0.00000000E+00
>  prtene3 : non-relax= NaN
>  Resulting in :
>  2DEtotal= NaN                 Ha. Also 2DEtotal= NaN                   eV
>    (2DErelax= NaN                 Ha. 2DEnonrelax= NaN                 Ha)
>    (  non-var. 2DEtotal : NaN                 Ha)
>
>
>  loper3 : exiting
> ================================================================================
>
>  ---- first-order wavefunction calculations are completed ----
>
>
>  ==> Compute Derivative Database <==
>  gath3 : enter
>  dyout3 : exit
>
>
>
>
> Has anybody encountered before situation like this? It would be a great 
> help if
> someone could clarify this for me.
>
> Thank You in advance!
>
> Yours
> Igor Lukacevic
>
>
> PS. Input file
>
> #SiO2 stishovit phase - rutile (tetragonal) structure
> #Response function calculation for:
> #    * rigid-atom elastic tensor
> #    * rigid-atom piezoelectric tensor
> #    * interatomic force constants at gamma
>
>
> ndtset   3
>
> # Set 1
>  iscf1   5
> kptopt1   1
> tolvrs1   1.0d-20
>
>
> # Set 2 :
>
> getwfk2  -1
>  iscf2  -3
> kptopt2   2
>  nqpt2   1
>   qpt2   0 0 0
> rfelfd2   2
>  rfdir2   1 1 1
> tolwfr2   1.0d-20
>
> # Set 3 :
>
>  getddk3  -1
>  getwfk3  -2
>   iscf3   7
>  kptopt3   2
>   nqpt3   1
>    qpt3   0 0 0
>  rfphon3   1
> rfatpol3   1 2
>  rfstrs3   3
>  rfdir3   1 1 1
>  tolvrs3   1.0d-14
>
> # Common input data
> # pressure 40 GPa
> # acell...taken from the struct. relax. calc.
>
>  acell    2*7.6450548625E+00  4.9502082748E+00
>
> # xred...taken from the struct. relax. calc.
>   xred    0.00              0.00             0.00
>           3.0313187045E-01  3.0313187045E-01 0.00
>          -3.0313187045E-01 -3.0313187045E-01 0.00
>
> # Space group info
>  angdeg   90 90 90
> spgroup   136
>  brvltt  -1
>
> # Definition of the atom types and atoms
>  ntypat   2
>  znucl   14 8 8
>  natom   6
>  natrd   3
>  typat   1 2 2
>
> #Gives the number of bands, explicitely (do not take the default)
>  nband   18
>
>  occopt   1
>
> #Definition of the plane wave basis set
>   ecut   60
>  ecutsm   0.1
>
> #Definition of the k-point grid
>  kptopt   1
>  ngkpt   8 8 12
>
> #Definition of the self-consistency procedure
>  diemac  9.0
>    iscf  7
>  iprcel  45
> npulayit  7
>  nnsclo  2
>   nline  6
>   nstep  100
>
> #Definiton of the xc approximation
>     ixc  11
>



-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Matthieu Verstraete

European Theoretical Spectroscopy Facility (ETSF)
Dpto. Fisica de Materiales,
U. del Pais Vasco,
Centro Joxe Mari Korta, Av. de Tolosa, 72,   Phone: +34-943018393
E-20018 Donostia-San Sebastian, Spain        Fax  : +34-943018390

Mail : matthieu.jean.verstraete@gmail.com
http://www-users.york.ac.uk/~mjv500