[Pw_forum] about C2/c point group symmetry of a monoclinic lattice.
Carlo Nervi
carlo.nervi at unito.it
Wed Dec 17 18:22:45 CET 2014
Very probably cif2qe.sh is not working properly.
It generates all the atoms by applying the symmetry found and later try to
remove the equivalent atoms.
Probably some atoms are not properly removed.
The software is give "as it is".....
Carlo
2014-12-17 16:11 GMT+01:00 Paolo Giannozzi <paolo.giannozzi at uniud.it>:
>
> 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
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > 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/
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > 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
> Pw_forum at pwscf.org
> 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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