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[ilukacevic@fizika.unios.hr]

Hullo everyone,

after many attempts, I decided to post my problem. I am trying to calculate 
the GS total energy of a ZnTe in its cinnabar phase, where it forms a 
trigonal unit cell.

Before the echo of input file, abinit recognizes the space group (spgroup= 
152  P3_1 2 1   (=D3^4)), which I entered in the input file. But when the 
calculation starts, I get a error message in the .log file that either the 
space group entered is wrong or the xred coordinates of atoms.

I am pasting here now my input file, whereas the .log file is attached bellow


ecut       40
toldfe 1.0d-6
diemac 12.0

#nbdbuf 0
ixc 11
kptopt 3
nshiftk  1
shiftk  0.0  0.0  0.0 
ngkpt 12 12 12

#   ZnTe  cinn structure (semiconducting phase)
#   hexagonal (trigonal) unit cell (angdeg, xred)
#   acell: Nelmes&McMahon 1995
acell          7.7573257  7.7573257  17.757756
angdeg     90 90 120
occopt  1
#tsmear 0.01
ntime 30
nstep 40
nband  12
spgroup   152
brvltt       -1
natom  2
ntypat   2
typat  1 2
xred     0.248888888   -0.042222222   0.291111111
         0.058222222   -0.387555555   0.445777777   
znucl     30.      52.

mkmem       500
mkqmem      500
mk1mem      500


The reference about cinnabar phase was Nelmes&McMahon (1995), from where I 
found out that this is a trigonal unit cell and the acell value. From the 
International Crystallographic Tables I found out the space group number and 
the Wyckoff sites, which were (u,0,1/3) and (v,0,5/6), where u=0.540 and 
v=0.504. 
I had to use the angdeg for hexagonal unit cell, because trigonal axes could 
not be recognized (alpha=beta=gamma=63.008932).
Above mentioned xreds also didn't work (the are the xreds for the trigonal 
system), so I thought that maybe I should transform them to hexagonal system 
(because my axes are for the hexagonal system), using the trasformations 
matrix found in Burns&Glazer page 50. But that also doesn't work.

Could anyone help me with this problem and provide me a continuation of my 
calculations.
Thank You all in advance.

Igor Lukacevic


This is a (little shortened) .log file

  ABINIT 
  
  Give name for formatted input file: 
../tNCO.in
  Give name for formatted output file:
tNCO.out
  Give root name for generic input files:
tNCOi
  Give root name for generic output files:
tNCOo
  Give root name for generic temporary files:
tNCO

 Version 4.6.5  of ABINIT 
 (sequential version, prepared for a P6/Linux computer) 

...

 ingeo : use angdeg to generate rprim.
 ingeo : takes atomic coordinates from input array xred
 symspgr : the symmetry operation no.   1 is the identity
 symaxes : the symmetry operation no.   2 is a 3_1 or 3_2-axis 
 symaxes : the symmetry operation no.   3 is a secondary 2-axis 
 symaxes : the symmetry operation no.   4 is a 3_1 or 3_2-axis 
 symaxes : the symmetry operation no.   5 is a secondary 2-axis 
 symaxes : the symmetry operation no.   6 is a secondary 2-axis 
 symspgr : spgroup= 152  P3_1 2 1   (=D3^4)
 getkgrid : length of smallest supercell vector (bohr)=    9.308791E+01
       Simple Lattice Grid
 invars1: With nkpt_me= 1728 and mkmem  =   500 ground state wf require disk 
i/o.
 Resetting mkmem  to zero to save memory space.
 invars1: With nkpt_me= 1728 and mkqmem =   500 ground state wf require disk 
i/o.
 Resetting mkqmem to zero to save memory space.
 invars1: With nkpt_me= 1728 and mk1mem =   500 ground state wf require disk 
i/o.
 Resetting mk1mem to zero to save memory space.

 Symmetries : space group P3_1 2 1 (#152); Bravais hP (primitive hexag.)
 getkgrid : length of smallest supercell vector (bohr)=    9.308791E+01
       Simple Lattice Grid

 inkpts : istwfk preprocessed, gives following first values (max. 6): 2 1 1 1 
1 1
 chkneu : initialized the occupation numbers for occopt=    1
    spin-unpolarized case :
  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  2.00  0.00  0.00  0.00
 For input ecut=  4.000000E+01 best grid ngfft=      48      48     108
       max ecut=  4.563322E+01
 getng: value of mgfft=     108 and nfft=      248832
 getng: values of ngfft(4),ngfft(5),ngfft(6)      49      49     108
 getmpw: optimal value of mpw=   11232

 iofn2 : deduce lmnmax  =   8, lnmax  =   2,
                lmnmaxso=   8, lnmaxso=   2.
 memory : analysis of memory needs
================================================================================
 Values of the parameters that define the memory need of the present run
   intxc =         0  ionmov =         0    iscf =         5     ixc =        
11
  lmnmax =         2   lnmax =         2   mband =        12  mffmem =        
 1
P  mgfft =       108   mkmem =         0 mpssoang=         3     mpw =     
11232
  mqgrid =      1201   natom =         2    nfft =    248832    nkpt =      
1728
  nloalg =         4  nspden =         1 nspinor =         1  nsppol =        
 1
    nsym =         6  n1xccc =      2501  ntypat =         2  occopt =        
 1
================================================================================
P This job should need less than                      69.584 Mbytes of memory.
  Rough estimation (10% accuracy) of disk space for files :
  WF disk file :   -542.123 Mbytes ; DEN or POT disk file :      1.900 Mbytes.
  mkmem==0 => use of 2 WF temporary disk files
================================================================================

 Biggest array : f_fftgr(disk), with     18.9864 MBytes.
 memana : allocated an array of     18.986 Mbytes, for testing purposes.
 memana : allocated      69.584 Mbytes, for testing purposes.
 The job will continue.
 -outvars: echo values of preprocessed input variables --------
     acell    7.7573257000E+00  7.7573257000E+00  1.7757756000E+01 Bohr
       amu    6.53900000E+01  1.27600000E+02
    diemac    1.20000000E+01
      ecut    4.00000000E+01 Hartree
    istwfk      2    0    0    0    0    0    3    0    0    0
                0    0    0    0    0    0    0    0    0    0
                0    0    0    0    0    0    0    0    0    0
                0    0    0    0    0    0    0    0    0    0
                0    0    0    0    0    0    0    0    0    0
                outvar1 : prtvol=0, do not print more k-points.
       ixc        11
       kpt    0.00000000E+00  0.00000000E+00  0.00000000E+00
              8.33333333E-02  0.00000000E+00  0.00000000E+00
              1.66666667E-01  0.00000000E+00  0.00000000E+00
              2.50000000E-01  0.00000000E+00  0.00000000E+00
              3.33333333E-01  0.00000000E+00  0.00000000E+00
              4.16666667E-01  0.00000000E+00  0.00000000E+00
              5.00000000E-01  0.00000000E+00  0.00000000E+00
             -4.16666667E-01  0.00000000E+00  0.00000000E+00
             -3.33333333E-01  0.00000000E+00  0.00000000E+00
             -2.50000000E-01  0.00000000E+00  0.00000000E+00
             -1.66666667E-01  0.00000000E+00  0.00000000E+00
             -8.33333333E-02  0.00000000E+00  0.00000000E+00
              0.00000000E+00  8.33333333E-02  0.00000000E+00
              8.33333333E-02  8.33333333E-02  0.00000000E+00
              1.66666667E-01  8.33333333E-02  0.00000000E+00
              2.50000000E-01  8.33333333E-02  0.00000000E+00
              3.33333333E-01  8.33333333E-02  0.00000000E+00
              4.16666667E-01  8.33333333E-02  0.00000000E+00
              5.00000000E-01  8.33333333E-02  0.00000000E+00
             -4.16666667E-01  8.33333333E-02  0.00000000E+00
             -3.33333333E-01  8.33333333E-02  0.00000000E+00
             -2.50000000E-01  8.33333333E-02  0.00000000E+00
             -1.66666667E-01  8.33333333E-02  0.00000000E+00
             -8.33333333E-02  8.33333333E-02  0.00000000E+00
              0.00000000E+00  1.66666667E-01  0.00000000E+00
              8.33333333E-02  1.66666667E-01  0.00000000E+00
              1.66666667E-01  1.66666667E-01  0.00000000E+00
              2.50000000E-01  1.66666667E-01  0.00000000E+00
              3.33333333E-01  1.66666667E-01  0.00000000E+00
              4.16666667E-01  1.66666667E-01  0.00000000E+00
              5.00000000E-01  1.66666667E-01  0.00000000E+00
             -4.16666667E-01  1.66666667E-01  0.00000000E+00
             -3.33333333E-01  1.66666667E-01  0.00000000E+00
             -2.50000000E-01  1.66666667E-01  0.00000000E+00
             -1.66666667E-01  1.66666667E-01  0.00000000E+00
             -8.33333333E-02  1.66666667E-01  0.00000000E+00
              0.00000000E+00  2.50000000E-01  0.00000000E+00
              8.33333333E-02  2.50000000E-01  0.00000000E+00
              1.66666667E-01  2.50000000E-01  0.00000000E+00
              2.50000000E-01  2.50000000E-01  0.00000000E+00
              3.33333333E-01  2.50000000E-01  0.00000000E+00
              4.16666667E-01  2.50000000E-01  0.00000000E+00
              5.00000000E-01  2.50000000E-01  0.00000000E+00
             -4.16666667E-01  2.50000000E-01  0.00000000E+00
             -3.33333333E-01  2.50000000E-01  0.00000000E+00
             -2.50000000E-01  2.50000000E-01  0.00000000E+00
             -1.66666667E-01  2.50000000E-01  0.00000000E+00
             -8.33333333E-02  2.50000000E-01  0.00000000E+00
              0.00000000E+00  3.33333333E-01  0.00000000E+00
              8.33333333E-02  3.33333333E-01  0.00000000E+00
                       outvar1 : prtvol=0, do not print more k-points.
   kptrlen    9.30879084E+01
    kptopt         3
  kptrlatt   12  0  0   0 12  0   0  0 12
P    mkmem         0
     natom         2
     nband        12
     ngfft        48      48     108
      nkpt      1728
     nstep        40
      nsym         6
     ntime        30
    ntypat         2
       occ    2.000000  2.000000  2.000000  2.000000  2.000000  2.000000
              2.000000  2.000000  2.000000  0.000000  0.000000  0.000000
     rprim    1.0000000000E+00  0.0000000000E+00  0.0000000000E+00
             -5.0000000000E-01  8.6602540378E-01  0.0000000000E+00
              0.0000000000E+00  0.0000000000E+00  1.0000000000E+00
   spgroup       152
    symrel    1  0  0   0  1  0   0  0  1      -1 -1  0   1  0  0   0  0  1
              0  1  0   1  0  0   0  0 -1       0  1  0  -1 -1  0   0  0  1
              1  0  0  -1 -1  0   0  0 -1      -1 -1  0   0  1  0   0  0 -1
     tnons    0.0000000  0.0000000  0.0000000     0.0000000  0.0000000 
-0.3333333
              0.0000000  0.0000000  0.0000000     0.0000000  0.0000000  
0.3333333
              0.0000000  0.0000000 -0.3333333     0.0000000  0.0000000  
0.3333333
    toldfe    1.00000000E-06 Hartree
     typat    1  2
       wtk      0.00058    0.00058    0.00058    0.00058    0.00058    0.00058
                0.00058    0.00058    0.00058    0.00058    0.00058    0.00058
                0.00058    0.00058    0.00058    0.00058    0.00058    0.00058
                0.00058    0.00058    0.00058    0.00058    0.00058    0.00058
                0.00058    0.00058    0.00058    0.00058    0.00058    0.00058
                0.00058    0.00058    0.00058    0.00058    0.00058    0.00058
                0.00058    0.00058    0.00058    0.00058    0.00058    0.00058
                0.00058    0.00058    0.00058    0.00058    0.00058    0.00058
                0.00058    0.00058
                outvar1 : prtvol=0, do not print more k-points.
    xangst    1.1083499897E+00 -1.5010144586E-01  2.7355710490E+00
              1.0344599922E+00 -1.3777732768E+00  4.1889736769E+00
     xcart    2.0944779312E+00 -2.8365062364E-01  5.1694800780E+00
              1.9548460725E+00 -2.6036141554E+00  7.9160129942E+00
      xred    2.4888888800E-01 -4.2222222000E-02  2.9111111100E-01
              5.8222222000E-02 -3.8755555500E-01  4.4577777700E-01
     znucl     30.00000   52.00000

================================================================================

 chkinp: machine precision is   2.2204460492503131E-16

 chkinp: Checking input parameters for consistency.

================================================================================
== DATASET  1 
==================================================================


 iofn2 : deduce lmnmax  =   8, lnmax  =   2,
                lmnmaxso=   8, lnmaxso=   2.
 Unit cell volume ucvol=  9.2542828E+02 bohr^3
 Angles (23,13,12)=  9.00000000E+01  9.00000000E+01  1.20000000E+02 degrees

 getcut: wavevector=  0.0000  0.0000  0.0000  ngfft=  48  48 108
         ecut(hartree)=     40.000   => boxcut(ratio)=   2.13619
...
 wfconv:    12 bands initialized randomly with npw=  5594, for ikpt=     1
 ...
 wfconv:    12 bands initialized randomly with npw= 11211, for ikpt=    50
 inwffil: copy wf on disk file tNCO_WF1
 
 gstate about to open unit  12 for file=tNCO_WF2
 setup2: Arith. and geom. avg. npw (full set) are   11182.337   11182.323

 symatm : WARNING -
  Trouble finding symmetrically equivalent atoms
  Applying inv of symm number  2 to atom number   1  of typat  1
  gives tratom=  4.2222E-02  2.9111E-01  6.2444E-01.
  This is further away from every atom in crystal than the allowed tolerance.
  The inverse symmetry matrix is  0  1  0
                                 -1 -1  0
                                  0  0  1
  and the nonsymmorphic transl. tnons =    0.0000000    0.0000000   -0.3333333
  The nearest coordinate differs by -2.067E-01  3.333E-01  3.333E-01
  for indsym(nearest atom)=    1

  This indicates that when symatm attempts to find atoms symmetrically
  related to a given atom, the nearest candidate is further away than some
  tolerance.  Should check atomic coordinates and symmetry group input data.

 symatm : WARNING -
  Trouble finding symmetrically equivalent atoms
  Applying inv of symm number  2 to atom number   2  of typat  2
  gives tratom=  3.8756E-01  4.4578E-01  7.7911E-01.
  This is further away from every atom in crystal than the allowed tolerance.
  The inverse symmetry matrix is  0  1  0
                                 -1 -1  0
                                  0  0  1
  and the nonsymmorphic transl. tnons =    0.0000000    0.0000000   -0.3333333
  The nearest coordinate differs by  3.293E-01 -1.667E-01  3.333E-01
  for indsym(nearest atom)=    2

 symatm : WARNING -
  Trouble finding symmetrically equivalent atoms
  Applying inv of symm number  3 to atom number   1  of typat  1
  gives tratom= -4.2222E-02  2.4889E-01 -2.9111E-01.
  This is further away from every atom in crystal than the allowed tolerance.
  The inverse symmetry matrix is  0  1  0
                                  1  0  0
                                  0  0 -1
  and the nonsymmorphic transl. tnons =    0.0000000    0.0000000    0.0000000
  The nearest coordinate differs by -2.911E-01  2.911E-01  4.178E-01
  for indsym(nearest atom)=    1

 symatm : WARNING -
  Trouble finding symmetrically equivalent atoms
  Applying inv of symm number  3 to atom number   2  of typat  2
  gives tratom= -3.8756E-01  5.8222E-02 -4.4578E-01.
  This is further away from every atom in crystal than the allowed tolerance.
  The inverse symmetry matrix is  0  1  0
                                  1  0  0
                                  0  0 -1
  and the nonsymmorphic transl. tnons =    0.0000000    0.0000000    0.0000000
  The nearest coordinate differs by -4.458E-01  4.458E-01  1.084E-01
  for indsym(nearest atom)=    2

 symatm : WARNING -
  Trouble finding symmetrically equivalent atoms
  Applying inv of symm number  4 to atom number   1  of typat  1
  gives tratom= -2.9111E-01 -2.4889E-01 -4.2222E-02.
  This is further away from every atom in crystal than the allowed tolerance.
  The inverse symmetry matrix is -1 -1  0
                                  1  0  0
                                  0  0  1
  and the nonsymmorphic transl. tnons =    0.0000000    0.0000000    0.3333333
  The nearest coordinate differs by  4.600E-01 -2.067E-01 -3.333E-01
  for indsym(nearest atom)=    1

 symatm : WARNING -
  Trouble finding symmetrically equivalent atoms
  Applying inv of symm number  4 to atom number   2  of typat  2
  gives tratom= -4.4578E-01 -5.8222E-02  1.1244E-01.
  This is further away from every atom in crystal than the allowed tolerance.
  The inverse symmetry matrix is -1 -1  0
                                  1  0  0
                                  0  0  1
  and the nonsymmorphic transl. tnons =    0.0000000    0.0000000    0.3333333
  The nearest coordinate differs by  4.960E-01  3.293E-01 -3.333E-01
  for indsym(nearest atom)=    2

 symatm : WARNING -
  Trouble finding symmetrically equivalent atoms
  Applying inv of symm number  5 to atom number   1  of typat  1
  gives tratom=  2.9111E-01  4.2222E-02 -6.2444E-01.
  This is further away from every atom in crystal than the allowed tolerance.
  The inverse symmetry matrix is  1  0  0
                                 -1 -1  0
                                  0  0 -1
  and the nonsymmorphic transl. tnons =    0.0000000    0.0000000   -0.3333333
  The nearest coordinate differs by  4.222E-02  8.444E-02  8.444E-02
  for indsym(nearest atom)=    1

 symatm : WARNING -
  Trouble finding symmetrically equivalent atoms
  Applying inv of symm number  5 to atom number   2  of typat  2
  gives tratom=  4.4578E-01  3.8756E-01 -7.7911E-01.
  This is further away from every atom in crystal than the allowed tolerance.
  The inverse symmetry matrix is  1  0  0
                                 -1 -1  0
                                  0  0 -1
  and the nonsymmorphic transl. tnons =    0.0000000    0.0000000   -0.3333333
  The nearest coordinate differs by  3.876E-01 -2.249E-01 -2.249E-01
  for indsym(nearest atom)=    2

 symatm : WARNING -
  Trouble finding symmetrically equivalent atoms
  Applying inv of symm number  6 to atom number   1  of typat  1
  gives tratom= -2.4889E-01 -2.9111E-01  4.2222E-02.
  This is further away from every atom in crystal than the allowed tolerance.
  The inverse symmetry matrix is -1 -1  0
                                  0  1  0
                                  0  0 -1
  and the nonsymmorphic transl. tnons =    0.0000000    0.0000000    0.3333333
  The nearest coordinate differs by -4.978E-01 -2.489E-01 -2.489E-01
  for indsym(nearest atom)=    1

 symatm : WARNING -
  Trouble finding symmetrically equivalent atoms
  Applying inv of symm number  6 to atom number   2  of typat  2
  gives tratom= -5.8222E-02 -4.4578E-01 -1.1244E-01.
  This is further away from every atom in crystal than the allowed tolerance.
  The inverse symmetry matrix is -1 -1  0
                                  0  1  0
                                  0  0 -1
  and the nonsymmorphic transl. tnons =    0.0000000    0.0000000    0.3333333
  The nearest coordinate differs by -1.164E-01 -5.822E-02  4.418E-01
  for indsym(nearest atom)=    2
 symatm: atom number    1 is reached starting at atom
   1  1  1  1  1  1
 symatm: atom number    2 is reached starting at atom
   2  2  2  2  2  2
 symatm: maximum (delta t)=   4.97778E-01 is larger than tol=  1.0000E-08

 symatm : ERROR -
  Largest error (above) is so large that either input  atomic coordinates 
(xred)
  are wrong or space group symmetry data is wrong.
  Action : correct your input file.

 leave_new : decision taken to exit ...
1