[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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>
>
>
> --
> ------------------------------------------------------------
> 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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