[Pw_forum] about C2/c point group symmetry of a monoclinic lattice.

Paolo Giannozzi paolo.giannozzi at uniud.it
Wed Dec 17 16:11:38 CET 2014


On Wed, 2014-12-17 at 15:07 +0100, Carlo Nervi wrote:
> Hi,
> the cif2qe.sh -i command gave to me:

there is something I don't understand here. The cif file contains
a line "_cell_formula_units_Z 16" which means I think that there 
are 16*(GaSe2Tl) = 64 atoms in the unit cell. This is consistent
with the listing of atoms and multiplicities:

> Tl1 Tl1+ 8 f 0.4647(6) 0.3109(5) 0.1140(9) 1. 0
> Tl2 Tl1+ 8 f 0.2844(4) 0.0623(5) 0.3864(8) 1. 0
> Ga1 Ga3+ 8 f 0.100(1) 0.191(2) 0.162(2) 1. 0
> Ga2 Ga3+ 8 f 0.145(1) 0.438(1) 0.339(2) 1. 0
> Se1 Se2- 4 e 0. 0.054(2) 0.250 1. 0
> Se2 Se2- 4 e 0. 0.574(1) 0.250 1. 0
> Se3 Se2- 8 f 0.207(1) 0.062(1) 0.071(2) 1. 0
> Se4 Se2- 8 f 0.262(1) 0.310(1) 0.252(2) 1. 0
> Se5 Se2- 8 f 0.048(2) 0.312(1) 0.438(3) 1. 0

The converted data contains instead 72 atoms, that is,
18 formula units

Paolo

> 
> ! Generated by using cif2qe Version 1.0 - Date: Wed Dec 17 16:05:24
> CET 2014
> !   _symmetry_space_group_name_H-M = 
> !   _symmetry_Int_Tables_number = 15
> !   _symmetry_cell_setting = 
> ! a=10.779  b=10.776  c=15.663  alpha=90  beta=99.993  gamma=90
> ! Found by cif2qe: lattice = monoclinic    Space group = C2/c   ibrav
> = 13
> !
> ! Symmetry found:
> !   1                   x, -y, z+1/2    [x]  [ -y]  [ z+1/2]
> !   2                     -x, -y, -z    [-x]  [ -y]  [ -z]
> !   3                  -x, y, -z+1/2    [-x]  [ y]  [ -z+1/2]
> !   4                        x, y, z    [x]  [ y]  [ z]
> !   5           x+1/2, -y+1/2, z+1/2    [x+1/2]  [ -y+1/2]  [ z+1/2]
> !   6             -x+1/2, -y+1/2, -z    [-x+1/2]  [ -y+1/2]  [ -z]
> !   7          -x+1/2, y+1/2, -z+1/2    [-x+1/2]  [ y+1/2]  [ -z+1/2]
> !   8                x+1/2, y+1/2, z    [x+1/2]  [ y+1/2]  [ z]
> &CONTROL
>                        title = 'xx'
>                  calculation = 'relax'
>                 restart_mode = 'from_scratch'
>                       outdir = './1'
>                   pseudo_dir = '../PP/atompaw'
>                       prefix = 'xx'
>                      disk_io = 'none'
>                    verbosity = 'default'
>                etot_conv_thr = 0.0001
>                forc_conv_thr = 0.001
>                        nstep = 400
>                      tstress = .true.
>                      tprnfor = .true.
>  /
>  &SYSTEM
>                        ibrav = 13
>                    celldm(1) =  20.369357896686800
>                    celldm(2) =   0.999721681046479, celldm(3) =
> 1.453103256331756
>                    celldm(4) =   0.000000000000000
>                          nat = 72
>                         ntyp = 3
>                      ecutwfc = 50
>                      ecutrho = 400
>                       london = .true.
>                    london_s6 = 0.75
>  /
>  &ELECTRONS
>             electron_maxstep = 200
>                     conv_thr = 1.0D-7
>               diago_thr_init = 1e-4
>                  startingpot = 'atomic'
>                  startingwfc = 'atomic'
>                  mixing_mode = 'plain'
>                  mixing_beta = 0.5
>                  mixing_ndim = 8
>              diagonalization = 'david'
>  /
> &IONS
>                 ion_dynamics = 'bfgs'
>  /
> 
> 
> ATOMIC_SPECIES
>   Tl1+    0.0000000000  Tl1+.pbe-n-rrkjus_psl.0.1.UPF
>   Ga3+    0.0000000000  Ga3+.pbe-n-rrkjus_psl.0.1.UPF
>   Se2-    0.0000000000  Se2-.pbe-n-rrkjus_psl.0.1.UPF
> 
> 
> ATOMIC_POSITIONS crystal
> Tl1+     0.464700000000000     0.689100000000000     0.614000000000000
> Tl1+     0.284400000000000     0.937700000000000     0.886400000000000
> Ga3+     0.100000000000000     0.809000000000000     0.662000000000000
> Ga3+     0.145000000000000     0.562000000000000     0.839000000000000
> Se2-     0.000000000000000     0.946000000000000     0.750000000000000
> Se2-     0.000000000000000     0.426000000000000     0.750000000000000
> Se2-     0.207000000000000     0.938000000000000     0.571000000000000
> Se2-     0.262000000000000     0.690000000000000     0.752000000000000
> Se2-     0.048000000000000     0.688000000000000     0.938000000000000
> Tl1+     0.535300000000000     0.689100000000000     0.886000000000000
> Tl1+     0.715600000000000     0.937700000000000     0.613600000000000
> Ga3+     0.900000000000000     0.809000000000000     0.838000000000000
> Ga3+     0.855000000000000     0.562000000000000     0.661000000000000
> Se2-    -0.000000000000000     0.946000000000000     0.750000000000000
> Se2-    -0.000000000000000     0.426000000000000     0.750000000000000
> Se2-     0.793000000000000     0.938000000000000     0.929000000000000
> Se2-     0.738000000000000     0.690000000000000     0.748000000000000
> Se2-     0.952000000000000     0.688000000000000     0.562000000000000
> Tl1+     0.535300000000000     0.310900000000000     0.386000000000000
> Tl1+     0.715600000000000     0.062300000000000     0.113600000000000
> Ga3+     0.900000000000000     0.191000000000000     0.338000000000000
> Ga3+     0.855000000000000     0.438000000000000     0.161000000000000
> Se2-    -0.000000000000000     0.054000000000000     0.250000000000000
> Se2-    -0.000000000000000     0.574000000000000     0.250000000000000
> Se2-     0.793000000000000     0.062000000000000     0.429000000000000
> Se2-     0.738000000000000     0.310000000000000     0.248000000000000
> Se2-     0.952000000000000     0.312000000000000     0.062000000000000
> Tl1+     0.464700000000000     0.310900000000000     0.114000000000000
> Tl1+     0.284400000000000     0.062300000000000     0.386400000000000
> Ga3+     0.100000000000000     0.191000000000000     0.162000000000000
> Ga3+     0.145000000000000     0.438000000000000     0.339000000000000
> Se2-     0.000000000000000     0.054000000000000     0.250000000000000
> Se2-     0.000000000000000     0.574000000000000     0.250000000000000
> Se2-     0.207000000000000     0.062000000000000     0.071000000000000
> Se2-     0.262000000000000     0.310000000000000     0.252000000000000
> Se2-     0.048000000000000     0.312000000000000     0.438000000000000
> Tl1+     0.964700000000000     0.189100000000000     0.614000000000000
> Tl1+     0.784400000000000     0.437700000000000     0.886400000000000
> Ga3+     0.600000000000000     0.309000000000000     0.662000000000000
> Ga3+     0.645000000000000     0.062000000000000     0.839000000000000
> Se2-     0.500000000000000     0.446000000000000     0.750000000000000
> Se2-     0.500000000000000     0.926000000000000     0.750000000000000
> Se2-     0.707000000000000     0.438000000000000     0.571000000000000
> Se2-     0.762000000000000     0.190000000000000     0.752000000000000
> Se2-     0.548000000000000     0.188000000000000     0.938000000000000
> Tl1+     0.035300000000000     0.189100000000000     0.886000000000000
> Tl1+     0.215600000000000     0.437700000000000     0.613600000000000
> Ga3+     0.400000000000000     0.309000000000000     0.838000000000000
> Ga3+     0.355000000000000     0.062000000000000     0.661000000000000
> Se2-     0.500000000000000     0.446000000000000     0.750000000000000
> Se2-     0.500000000000000     0.926000000000000     0.750000000000000
> Se2-     0.293000000000000     0.438000000000000     0.929000000000000
> Se2-     0.238000000000000     0.190000000000000     0.748000000000000
> Se2-     0.452000000000000     0.188000000000000     0.562000000000000
> Tl1+     0.035300000000000     0.810900000000000     0.386000000000000
> Tl1+     0.215600000000000     0.562300000000000     0.113600000000000
> Ga3+     0.400000000000000     0.691000000000000     0.338000000000000
> Ga3+     0.355000000000000     0.938000000000000     0.161000000000000
> Se2-     0.500000000000000     0.554000000000000     0.250000000000000
> Se2-     0.500000000000000     0.074000000000000     0.250000000000000
> Se2-     0.293000000000000     0.562000000000000     0.429000000000000
> Se2-     0.238000000000000     0.810000000000000     0.248000000000000
> Se2-     0.452000000000000     0.812000000000000     0.062000000000000
> Tl1+     0.964700000000000     0.810900000000000     0.114000000000000
> Tl1+     0.784400000000000     0.562300000000000     0.386400000000000
> Ga3+     0.600000000000000     0.691000000000000     0.162000000000000
> Ga3+     0.645000000000000     0.938000000000000     0.339000000000000
> Se2-     0.500000000000000     0.554000000000000     0.250000000000000
> Se2-     0.500000000000000     0.074000000000000     0.250000000000000
> Se2-     0.707000000000000     0.562000000000000     0.071000000000000
> Se2-     0.762000000000000     0.810000000000000     0.252000000000000
> Se2-     0.548000000000000     0.812000000000000     0.438000000000000
> 
> 
> K_POINTS automatic
> 1  1  1   0 0 0
> 
> 
> 
> 
> I'm wondering if with this input pwscf give to you the same
> symmetry...
> 
> 
> HTH,
> Carlo
> 
> 
> 
> 2014-12-17 14:08 GMT+01:00 Mutlu COLAKOGULLARI
> <mutlucolakogullari at trakya.edu.tr>:
>         Dear All,
>         
>         
>         I am working on a monoclinic material which has space group
>         15. It has C2/c point group.
>         
>         
>         When I run the pwscf, it gives me the C2/m point group that
>         corresponds to the space group 12.
>         
>         
>              point group C_2h (2/m) 
>              there are  4 classes
>              the character table:
>         
>         
>                       E     C2      i     s_h  
>         A_g    1.00  1.00  1.00  1.00
>         B_g    1.00 -1.00  1.00 -1.00
>         A_u    1.00  1.00 -1.00 -1.00
>         B_u    1.00 -1.00 -1.00  1.00
>         
>         
>         
>         
>         The symmetry operations of these two monoclinic space groups
>         have 8 symmetry operations.  pwscf symmetry calculations found
>         just 4...what about the other 4? 
>         
>         
>         I have checked the space groups  from
>         "http://www.cryst.ehu.es/cryst/get_gen.html":
>         General Positions of the Group 12 (C2/m) [unique axis b]
>         
>         1. x,y,z
>         2. -x,y,-z
>         3. -x,-y,-z
>         4. x,-y,z
>         5. x+1/2,y+1/2,z
>         6. -x+1/2,y+1/2,-z
>         7. -x+1/2,-y+1/2,-z
>         8. x+1/2,-y+1/2,z  
>         
>         
>         General Positions of the Group 15 (C2/c) [unique axis b]
>         1. x,y,z
>         2. -x,y,-z+1/2
>         3. -x,-y,-z
>         4. x,-y,z+1/2
>         5. x+1/2,y+1/2,z
>         6. -x+1/2,y+1/2,-z+1/2
>         7. -x+1/2,-y+1/2,-z
>         8. x+1/2,-y+1/2,z+1/2
>         
>          
>         
>         
>         
>         Here is the lite-input:
>         &control
>                 calculation  = 'scf',
>                 restart_mode = 'from_scratch',
>                 pseudo_dir   = '/home//tlg2/pseudos',
>                 outdir       = './outdir',
>                 prefix       = 'TlGaSe2',
>                 verbosity    = 'high'
>         
>         /
>         
>         &system
>         ibrav = -13
>         
>         celldm(1)=20.166973593
>         celldm(2)=0.999721681046
>         celldm(3)=1.453103256
>         celldm(5)=-0.173527859407
>                 nat              = 32
>                 ntyp             = 3
>                 ecutwfc          = 65
>                 ecutrho          = 650
>         /
>         &electrons
>                 diagonalization = 'david'
>                 diago_david_ndim  = 8
>                 mixing_mode      = 'plain'
>                 mixing_beta      = 0.7
>                 mixing_ndim      = 8
>                 conv_thr         = 1.0d-8,
>         /
>         ATOMIC_SPECIES
>          Tl   204.3833  Tl.pbesol-dn-rrkjus_psl.1.0.0.UPF
>          Ga    69.7230  Ga.pbesol-dn-rrkjus_psl.1.0.0.UPF
>          Se    78.9600  Se.pbesol-dn-rrkjus_psl.1.0.0.UPF
>         
>         
>         ATOMIC_POSITIONS crystal
>         Tl   0.153800000000000   0.775600000000000   0.114000000000000
>         Tl   0.224400000000000   0.846200000000000   0.386000000000000
>         Tl   0.846200000000000   0.224400000000000   0.886000000000000
>         Tl   0.775600000000000   0.153800000000000   0.614000000000000
>         Tl   0.222100000000000   0.346700000000000   0.386400000000000
>         Tl   0.653300000000000   0.777900000000000   0.113600000000000
>         Tl   0.777900000000000   0.653300000000000   0.613600000000000
>         Tl   0.346700000000000   0.222100000000000   0.886400000000000
>         Se   0.946000000000000   0.054000000000000   0.250000000000000
>         Se   0.054000000000000   0.946000000000000   0.750000000000000
>         Se   0.426000000000000   0.574000000000000   0.250000000000000
>         Se   0.574000000000000   0.426000000000000   0.750000000000000
>         Se   0.145000000000000   0.269000000000000   0.071000000000000
>         Se   0.731000000000000   0.855000000000000   0.429000000000000
>         Se   0.855000000000000   0.731000000000000   0.929000000000000
>         Se   0.269000000000000   0.145000000000000   0.571000000000000
>         Se   0.952000000000000   0.572000000000000   0.252000000000000
>         Se   0.428000000000000   0.048000000000000   0.248000000000000
>         Se   0.048000000000000   0.428000000000000   0.748000000000000
>         Se   0.572000000000000   0.952000000000000   0.752000000000000
>         Se   0.736000000000000   0.360000000000000   0.438000000000000
>         Se   0.640000000000000   0.264000000000000   0.062000000000000
>         Se   0.264000000000000   0.640000000000000   0.562000000000000
>         Se   0.360000000000000   0.736000000000000   0.938000000000000
>         Ga   0.909000000000000   0.291000000000000   0.162000000000000
>         Ga   0.709000000000000   0.091000000000000   0.338000000000000
>         Ga   0.091000000000000   0.709000000000000   0.838000000000000
>         Ga   0.291000000000000   0.909000000000000   0.662000000000000
>         Ga   0.707000000000000   0.583000000000000   0.339000000000000
>         Ga   0.417000000000000   0.293000000000000   0.161000000000000
>         Ga   0.293000000000000   0.417000000000000   0.661000000000000
>         Ga   0.583000000000000   0.707000000000000   0.839000000000000
>         K_POINTS automatic
>         2 2 1 1 1 1
>         
>         
>         The primitive cell has been created by cif2cell code using the
>         cif file as following:
>         
>         
>         _journal_issue                   12
>         _journal_name_full               'Chemistry of Materials'
>         _journal_page_first              3120
>         _journal_volume                  23
>         _journal_year                    2011
>         _chemical_formula_structural     'Tl Ga Se2'
>         _chemical_formula_sum            'Ga Se2 Tl'
>         _chemical_name_systematic        'Thallium Gallium Selenide'
>         _space_group_IT_number           15
>         _symmetry_Int_Tables_number      15
>         _symmetry_space_group_name_Hall  '-C 2yc'
>         _symmetry_space_group_name_H-M   'C 1 2/c 1'
>         _audit_creation_date             2008/02/01
>         _cell_angle_alpha                90.
>         _cell_angle_beta                 99.993(6)
>         _cell_angle_gamma                90.
>         _cell_formula_units_Z            16
>         _cell_length_a                   10.779(2)
>         _cell_length_b                   10.776(1)
>         _cell_length_c                   15.663(5)
>         _cell_volume                     1791.7(7)
>         _refine_ls_R_factor_all          0.0652
>         _[local]_cod_data_source_file    cm200946y_si_002.cif
>         _[local]_cod_data_source_block   157752-ICSD
>         _[local]_cod_chemical_formula_sum_orig 'Ga1 Se2 Tl1'
>         _cod_original_cell_volume        1791.73
>         _cod_database_code               4000782
>         loop_
>         _symmetry_equiv_pos_site_id
>         _symmetry_equiv_pos_as_xyz
>         1 'x, -y, z+1/2'
>         2 '-x, -y, -z'
>         3 '-x, y, -z+1/2'
>         4 'x, y, z'
>         5 'x+1/2, -y+1/2, z+1/2'
>         6 '-x+1/2, -y+1/2, -z'
>         7 '-x+1/2, y+1/2, -z+1/2'
>         8 'x+1/2, y+1/2, z'
>         loop_
>         _atom_site_aniso_label
>         _atom_site_aniso_type_symbol
>         _atom_site_aniso_U_11
>         _atom_site_aniso_U_22
>         _atom_site_aniso_U_33
>         _atom_site_aniso_U_12
>         _atom_site_aniso_U_13
>         _atom_site_aniso_U_23
>         Tl1 Tl1+ 0.052(6) 0.063(5) 0.06(2) -0.022(3) 0.005(8) 0.000(5)
>         Tl2 Tl1+ 0.044(6) 0.044(6) 0.07(2) -0.022(3) 0.005(8) 0.002(5)
>         Ga1 Ga3+ 0.015(9) 0.001(6) 0.05(3) 0.009(6) 0.01(2) -0.019(9)
>         Ga2 Ga3+ 0.019(7) 0.037(9) 0.00(3) -0.008(9) -0.01(1) -0.01(1)
>         Se1 Se2- 0.03(1) 0.02(1) 0.06(5) 0. 0.02(2) 0.
>         Se2 Se2- 0.006(9) 0.001(7) 0.06(4) 0. -0.01(2) 0.
>         Se3 Se2- 0.04(1) 0.05(1) 0.01(4) 0.01(1) -0.01(2) -0.02(1)
>         Se4 Se2- 0.012(6) 0.021(7) 0.06(4) 0.01(1) -0.018(9) -0.018(5)
>         Se5 Se2- 0.05(1) 0.06(1) 0.00(4) -0.053(9) -0.01(2) -0.02(1)
>         loop_
>         _atom_site_label
>         _atom_site_type_symbol
>         _atom_site_symmetry_multiplicity
>         _atom_site_Wyckoff_symbol
>         _atom_site_fract_x
>         _atom_site_fract_y
>         _atom_site_fract_z
>         _atom_site_occupancy
>         _atom_site_attached_hydrogens
>         Tl1 Tl1+ 8 f 0.4647(6) 0.3109(5) 0.1140(9) 1. 0
>         Tl2 Tl1+ 8 f 0.2844(4) 0.0623(5) 0.3864(8) 1. 0
>         Ga1 Ga3+ 8 f 0.100(1) 0.191(2) 0.162(2) 1. 0
>         Ga2 Ga3+ 8 f 0.145(1) 0.438(1) 0.339(2) 1. 0
>         Se1 Se2- 4 e 0. 0.054(2) 0.250 1. 0
>         Se2 Se2- 4 e 0. 0.574(1) 0.250 1. 0
>         Se3 Se2- 8 f 0.207(1) 0.062(1) 0.071(2) 1. 0
>         Se4 Se2- 8 f 0.262(1) 0.310(1) 0.252(2) 1. 0
>         Se5 Se2- 8 f 0.048(2) 0.312(1) 0.438(3) 1. 0
>         loop_
>         _atom_type_symbol
>         _atom_type_oxidation_number
>         Ga3+ 3
>         Se2- -2
>         Tl1+ 1
>         loop_
>         _citation_id
>         _citation_year
>         _citation_page_first
>         _citation_page_last
>         primary 2007 663 666
>         
>         
>         Are there something wrong in my input file or primitive cell?
>         
>         
>         With my best wishes,
>         
>         
>              Mutlu.
>         ------------------------------------------
>         Dr. Mutlu COLAKOGULLARI
>         Trakya Universitesi 
>         Fen Fakultesi
>         Fizik Bolumu
>         22030 Merkez-EDİRNE
>         
>         _______________________________________________
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>         http://pwscf.org/mailman/listinfo/pw_forum
> 
> 
> 
> -- 
> ------------------------------------------------------------
> Prof. Carlo Nervi carlo.nervi at unito.it  Tel:+39 0116707507/8
> Fax: +39 0116707855      -      Dipartimento di Chimica, via
> P. Giuria 7, 10125 Torino, Italy.    http://lem.ch.unito.it/
> _______________________________________________
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-- 
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 




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