tetragonal lattice with two atoms in primitive cell

Total energy, geometry optimization, DFT+U, spin....

Moderator: bguster

Locked
roginovicci
Posts: 75
Joined: Thu Dec 02, 2010 10:36 pm

tetragonal lattice with two atoms in primitive cell

Post by roginovicci » Thu Dec 02, 2010 10:41 pm

Hello. Sorry for my very newbie question. I want to optimize structure of Hg2Cl2 compound (linear molecule Cl-Hg-Hg-Cl in tetragonal bodycentered lattice). My input file is as follows:

Code: Select all

   angdeg 90.000  90.000 90.000                                                                             
   spgroup 139                                                                                             
                                                                                                           
                                                                                                           
# Definition of the atom                                                                                   
   ntypat 2                 # Two types of atoms                                                           
   znucl 17 80               # Cl and Hg atomic numbers of the structure                                   
   natom 2                  # There are 2 atoms in a cell                                                   
   typat 2 1             # Type 1 is Cl, type 2 is Hg                                                       
   xred                     # Fractional coordinates                                                       
      0.0        0.0        0.1147                                                                         
      0.0        0.0        0.3440                                                                         
   rprim  1   0.0     0.0                                                                                   
          0.0    1    0.0                                                                                   
          0.5   0.5    0.5                                                                                 
   scalecart  4.48  4.48  10.9                                                                             
   acell 3*1

but I always get the same error while running abinit:
chkprimit : ERROR -
According to the symmetry finder, the unit cell is
NOT primitive. The multiplicity is 2 .
The use of non-primitive unit cells is allowed
only when the input variable chkprim is 0.
Action : either change your unit cell (rprim or angdeg),

Please tell me what am I doing wrong? Many thanks in advance!
or set chkprim to 0.

blackburn
Posts: 42
Joined: Fri Aug 14, 2009 8:03 pm

Re: tetragonal lattice with two atoms in primitive cell

Post by blackburn » Fri Dec 03, 2010 7:20 pm

You're specifying rprim and angdeg in an incoherent way. Indeed, the vectors (100), (010) and (1/2 1/2 1/2) do not make a 90 degrees angle with each other. I would remove angdeg and spgroup. Abinit should find the correct space group by itself.

Simon

roginovicci
Posts: 75
Joined: Thu Dec 02, 2010 10:36 pm

Re: tetragonal lattice with two atoms in primitive cell

Post by roginovicci » Sat Dec 04, 2010 11:28 am

edit by december 5-th.

After removing space group in the input I got wrong symmetry. Here comes the output:

symlatt : the Bravais lattice is tI (body-centered tetragonal)
xred is defined in input file
ingeo : takes atomic coordinates from input array xred

symlatt : the Bravais lattice is tI (body-centered tetragonal)

symlatt : the Bravais lattice is tI (body-centered tetragonal)

symbrav : COMMENT -
The Bravais lattice determined only from the primitive
vectors, bravais(1)= 4, is more symmetric
than the real one, iholohedry= 2, obtained by taking into
account the atomic positions. Start deforming the primitive vector set.

symlatt : the Bravais lattice is mC (one-face-centered monoclinic)
symspgr : the symmetry operation no. 1 is the identity
symspgr : the symmetry operation no. 2 is an inversion
symplanes : the symmetry operation no. 3 is a mirror plane
symaxes : the symmetry operation no. 4 is a 2-axis
symspgr : the symmetry operation no. 5 is a pure translation
symspgr : the symmetry operation no. 6 is an inversion
symplanes : the symmetry operation no. 7 is an a,b, or c plane
symaxes : the symmetry operation no. 8 is a 2_1-axis
symspgr : spgroup= 12 C2/m (=C2h^3)


Abinit assumes it spgroup 12? Is it normal?

BENGHIA
Posts: 1
Joined: Tue Feb 14, 2017 9:47 am

Re: tetragonal lattice with two atoms in primitive cell

Post by BENGHIA » Tue Feb 14, 2017 9:48 am

data_1010948
_audit_creation_date 2017-02-14
_audit_creation_method 'Materials Studio'
_symmetry_space_group_name_H-M ' '
_symmetry_Int_Tables_number 0
_symmetry_cell_setting tetragonal
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
y-z,x-z,-z
y,y-z,-x+y
x-z,x,x-y
-y+z,-y,x-y
-x,-x+z,-x+y
-x+z,-y+z,z
-y,-x,-z
-x,-y,-z
-y+z,-x+z,z
-y,-y+z,x-y
-x+z,-x,-x+y
y-z,y,-x+y
x,x-z,x-y
x-z,y-z,-z
y,x,z
_cell_length_a 6.2981 Angstrom
_cell_length_b 6.2981 Angstrom
_cell_length_c 6.2981 Angstrom
_cell_angle_alpha 138.4876
_cell_angle_beta 138.4876
_cell_angle_gamma 60.1570
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
Hg1 Hg 0.11700 0.11700 0.00000 0.00000 Uiso 1.00
Cl1 Cl 0.34700 0.34700 -0.00000 0.00000 Uiso 1.00

Locked