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 > <[email protected]>: > 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 > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > ------------------------------------------------------------ > Prof. Carlo Nervi [email protected] Tel:+39 0116707507/8 > Fax: +39 0116707855 - Dipartimento di Chimica, via > P. Giuria 7, 10125 Torino, Italy. http://lem.ch.unito.it/ > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ Pw_forum mailing list [email protected] http://pwscf.org/mailman/listinfo/pw_forum
