ABINIT Discussion Forums

Dear abinit users,

I am trying to build a monoclinic cell of naphthalene, C10H8. From the international tables, this belongs to space group #4, with two melecules per cell results in 36 atoms. What is strange is the abinit-made cif file. The number of atoms in this file has been printed 36 instead of 18 and chemical formula C20H16 instead of C10H8. Here is my input, original and abinit cif files:

acell 8.0846 5.9375 8.6335 angstroms
angdeg 90 124.673 90
spgroup 4
ntypat 2
znucl 6 1
ecut 15
natom 36
natrd 18
typat 5*1 4*2 5*1 4*2
xred
0.0860 0.0174 0.3268
0.1150 0.1593 0.2194
0.04860 0.1030 0.0362
0.0757 0.2471 -0.0777
-0.0106 -0.1877 0.2544
0.1372 0.0632 0.4651
0.1891 0.3174 0.2726
0.1486 0.4031 -0.0232
-0.0339 -0.2986 0.3387
-0.0860 -0.0174 -0.3268
-0.1150 -0.1593 -0.2194
-0.04860 -0.1030 -0.0362
-0.0757 -0.2471 0.0777
0.0106 0.1877 -0.2544
-0.1372 -0.0632 -0.4651
-0.1891 -0.3174 -0.2726
-0.1486 -0.4031 0.0232
0.0339 0.2986 -0.3387
brvltt 0
kptopt 1
prtcif 1
....

The original cif file:

...
_refine_ls_R_factor_gt 0.0281
_refine_ls_wR_factor_gt 0.0281
_symmetry_cell_setting monoclinic
_symmetry_space_group_name_H-M 'P 21/a'
_symmetry_Int_Tables_number 14
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/2-x,1/2+y,-z
3 -x,-y,-z
4 -1/2+x,-1/2-y,z
_cell_length_a 8.256(2)
_cell_length_b 5.983(2)
_cell_length_c 8.677(3)
_cell_angle_alpha 90
_cell_angle_beta 122.729(7)
_cell_angle_gamma 90
_cell_formula_units_Z 2
loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
H 0.23
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
C1 C 0.0860(3) 0.0174(4) 0.3268(3)
C2 C 0.1150(2) 0.1593(4) 0.2194(2)
C3 C 0.04860(19) 0.1030(3) 0.0362(2)
C4 C 0.0757(2) 0.2471(4) -0.0777(3)
C5 C -0.0106(2) -0.1877(4) 0.2544(3)
H1 H 0.1372(7) 0.0632(10) 0.4651(6)
H2 H 0.1891(6) 0.3174(9) 0.2726(6)
H3 H 0.1486(6) 0.4031(8) -0.0232(6)
H4 H -0.0339(7) -0.2986(9) 0.3387(7)
C1B C -0.0860(3) -0.0174(4) -0.3268(3)
C2B C -0.1150(2) -0.1593(4) -0.2194(2)
C3B C -0.04860(19) -0.1030(3) -0.0362(2)
C4B C -0.0757(2) -0.2471(4) 0.0777(3)
C5B C 0.0106(2) 0.1877(4) -0.2544(3)
H1B H -0.1372(7) -0.0632(10) -0.4651(6)
H2B H -0.1891(6) -0.3174(9) -0.2726(6)
H3B H -0.1486(6) -0.4031(8) 0.0232(6)
H4B H 0.0339(7) 0.2986(9) -0.3387(7)



And at last abinit-made cif file:
data_set
_cell_length_a 0.8084600000E+01
_cell_length_b 0.5937500000E+01
_cell_length_c 0.8633500000E+01
_cell_angle_alpha 0.9000000000E+02
_cell_angle_beta 0.1246730000E+03
_cell_angle_gamma 0.9000000000E+02
_cell_volume 0.3408306212E+03
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
C 0.8600000000E-01 0.1740000000E-01 0.3268000000E+00
C 0.1150000000E+00 0.1593000000E+00 0.2194000000E+00
C 0.4860000000E-01 0.1030000000E+00 0.3620000000E-01
C 0.7570000000E-01 0.2471000000E+00 0.9223000000E+00
C 0.9894000000E+00 0.8123000000E+00 0.2544000000E+00
H 0.1372000000E+00 0.6320000000E-01 0.4651000000E+00
H 0.1891000000E+00 0.3174000000E+00 0.2726000000E+00
H 0.1486000000E+00 0.4031000000E+00 0.9768000000E+00
H 0.9661000000E+00 0.7014000000E+00 0.3387000000E+00
C 0.9140000000E+00 0.9826000000E+00 0.6732000000E+00
C 0.8850000000E+00 0.8407000000E+00 0.7806000000E+00
C 0.9514000000E+00 0.8970000000E+00 0.9638000000E+00
C 0.9243000000E+00 0.7529000000E+00 0.7770000000E-01
C 0.1060000000E-01 0.1877000000E+00 0.7456000000E+00
H 0.8628000000E+00 0.9368000000E+00 0.5349000000E+00
H 0.8109000000E+00 0.6826000000E+00 0.7274000000E+00
H 0.8514000000E+00 0.5969000000E+00 0.2320000000E-01
H 0.3390000000E-01 0.2986000000E+00 0.6613000000E+00
C 0.9140000000E+00 0.5174000000E+00 0.6732000000E+00
C 0.8850000000E+00 0.6593000000E+00 0.7806000000E+00
C 0.9514000000E+00 0.6030000000E+00 0.9638000000E+00
C 0.9243000000E+00 0.7471000000E+00 0.7770000000E-01
C 0.1060000000E-01 0.3123000000E+00 0.7456000000E+00
H 0.8628000000E+00 0.5632000000E+00 0.5349000000E+00
H 0.8109000000E+00 0.8174000000E+00 0.7274000000E+00
H 0.8514000000E+00 0.9031000000E+00 0.2320000000E-01
H 0.3390000000E-01 0.2014000000E+00 0.6613000000E+00
C 0.8600000000E-01 0.4826000000E+00 0.3268000000E+00
C 0.1150000000E+00 0.3407000000E+00 0.2194000000E+00
C 0.4860000000E-01 0.3970000000E+00 0.3620000000E-01
C 0.7570000000E-01 0.2529000000E+00 0.9223000000E+00
C 0.9894000000E+00 0.6877000000E+00 0.2544000000E+00
H 0.1372000000E+00 0.4368000000E+00 0.4651000000E+00
H 0.1891000000E+00 0.1826000000E+00 0.2726000000E+00
H 0.1486000000E+00 0.9690000000E-01 0.9768000000E+00
H 0.9661000000E+00 0.7986000000E+00 0.3387000000E+00
_chemical_formula_analytical ' C20 H16'
_symmetry_Int_Tables_number 4
_symmetry_space_group_name_H-M 'P 2_1'

Is there any mistake in my input file?
Many thanks,
Marsusi.

Hi

There's probably no mistake in the abinit made cif files. In your original cif files, there are only 18 atoms listed but there are additional information on the space group and the associated symmetries, so that only 18 positions are needed and the other 18 are determined by symmetry considerations.

In the abinit-made cif files, there is no information on the space group, so all 36 atomic positions are printed.

Dear Boris,

Thanks a lot.

Marsusi,
Amirkabir university, Tehran.