Re: [Pw_forum] about C2/c point group symmetry of a monoclinic lattice.
Dear All,
I tried to modify the source code of cif2qe.sh, also cleaning the code a
little bit...
At my first attempt apparently the code now is working better and print the
correct number of atoms.
I would greatly appreciate if anyone will test it with some cif files.
Merry Chrstmas and Happy New Year!
Carlo
#!/bin/bash
#
# CIF to Quantum Espresso format converter
# Version 1.1 Date: 23-Dec-2014 Bug Fix
# Version 1.0 Date: 15-Mar-2014 First Full conversion
# Version 0.5 Date: 02-Oct-2013
# Version 0.4 Date: 12 Jun 2013
# Version 0.3 Date: 15 Nov 2012
#
# Copyright (C) 2012 Carlo Nervi
# This file is distributed under the terms of the
# GNU General Public License. See the file `License'
# in the root directory of the present distribution,
# or http://www.gnu.org/copyleft/gpl.txt .
#
# Use dos2unix to strip carriage returns at the end of the .cif files
#
# symmetry x,-y+1/2,z+y without ''
#
version="1.0"
USAGE="cif2qe.sh Version ${version}\nUsage: cif2qe.sh [-i] File\n( -i
uses the ibrav of QE. Do not add .cif extension!) - Requires File.cif\n"
if [ $# == 0 -o $# -gt 2 ]; then
printf "$USAGE"
exit
fi
do_ibrav=0
if [ $# == 2 ]; then
if [ $1 == "-i" ]; then
do_ibrav=1
shift
else
printf "$USAGE"
exit
fi
fi
if [ ! -f $1.cif ]; then
echo "Error. Cannot find file $1.cif"
exit
fi
awk -v FILE="$1" -v VERSION="$version" -v do_IBRAV=$do_ibrav '
BEGIN {
bohr = 0.52917721092
nfield=split("H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V
Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr " \
"Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La
Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb " \
"Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th
Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr Rf " \
"Db Sg Bh Hs Mt", AtomSymb, " ")
split("1.0079 4.0026 6.941 9.0122 10.811 12.0107 14.0067 15.9994 18.9984
20.1797 22.9897 24.305 26.9815 28.0855 30.9738 32.065 35.453 " \
"39.948 39.0983 40.078 44.9559 47.867 50.9415 51.9961 54.938 55.845
58.9332 58.6934 63.546 65.39 69.723 72.64 74.9216 78.96 79.904 " \
"83.8 85.4678 87.62 88.9059 91.224 92.9064 95.94 98 101.07 102.906
106.42 107.868 112.411 114.818 118.71 121.76 127.6 126.904 131.293 " \
"132.905 137.327 138.905 140.116 140.908 144.24 145 150.36 151.964
157.25 158.925 162.5 164.93 167.259 168.934 173.04 174.967 178.49 " \
"180.948 183.84 186.207 190.23 192.217 195.078 196.966 200.59
204.383 207.2 208.98 209 210 222 223 226 227 232.038 231.036 238.029 " \
"237 244 243 247 247 251 252 257 258 259 262 261 262 266 264 277
268", AtomMass, " ")
for (i=1; i<=nfield; i++) Atoms[AtomSymb[i]] = AtomMass[i]
#
# nKey = number of recognized Keywords
# KeyW[0][1..nKey] = recognized Keywords
# KeyW[1][1..nKey] = first synonym
# ...
#
nsynon=2
nKey=13
KeyW[0][1] ="_cell_length_a"; KeyW[1][1]=""
KeyW[0][2] ="_cell_length_b"; KeyW[1][2]=""
KeyW[0][3] ="_cell_length_c"; KeyW[1][3]=""
KeyW[0][4] ="_cell_angle_alpha";KeyW[1][4]=""
KeyW[0][5] ="_cell_angle_beta"; KeyW[1][5]=""
KeyW[0][6] ="_cell_angle_gamma";KeyW[1][6]=""
KeyW[0][7] ="_atom_site_type_symbol"; KeyW[1][7]=""
KeyW[0][8] ="_atom_site_fract_x"; KeyW[1][8]=""
KeyW[0][9] ="_atom_site_fract_y"; KeyW[1][9]=""
KeyW[0][10]="_atom_site_fract_z"; KeyW[1][10]=""
KeyW[0][11]="_symmetry_equiv_pos_as_xyz";
KeyW[1][11]="_space_group_symop_operation_xyz"
KeyW[0][12]="_symmetry_cell_setting";
KeyW[1][12]="_space_group_crystal_system"
KeyW[0][13]="_symmetry_Int_Tables_number";
KeyW[1][13]="_space_group_IT_number"
# for (i=1; i<=nKey; i++) {
# for (j=0; j= 1.) val-=1.
return val
}
function abs(numero) {
if (numero < 0) numero=-numero;
return numero
}
function Find_Lattice(a,b,c,alpha,beta,gamma) {
#
# find the bravais lattice name from lattice parameters
#
thr = 1.e-4
reticolo=""
if ( (abs(alpha-90.0) 0) Var[ivar++]=KeyW[0][tmp]; else Var[ivar++]=$1
Num_Var=ivar
} else {
ivar=0
loop_switch=0
if (tmp > 0) Var2[KeyW[0][tmp]]=$2
}
}
$1 ~ /^[^_]/ {
ivar=0
if (loop_switch==1 || loop_switch==2) {
loop_switch=2
for (i=0; i 0 ) tmpspacegroup=Int_Tables[tmptablenumber]
ibrav=Find_ibrav(tmpspacegroup, reticolo)
KP_x = int(1./(a*separation)+0.5)
KP_y = int(1./(b*separation)+0.5)
KP_z = int(1./(c*separation)+0.5)
ntyp=0
for (i=0; i___
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Re: [Pw_forum] about C2/c point group symmetry of a monoclinic lattice.
Dear Andrea, Thanks alot for your great explanation. With my best wishes, Mutlu. --Dr. Mutlu ÇOLAKOĞULLARITrakya Universitesi Fen FakultesiFizik Bolumu22030 Merkez-EDİRNE > Dear Carlo, Andrea and Paolo; > The taking responds and advices from people who has experienced makes me > happy. > As Paolo and Carlo also said, cif2qe.sh is not working properly, (at > least for this case). Therefore, I used the other codes for double cross > check: pymatgen and cif2cell. The conventional cell has 64 atoms whereas its > primitive has 32 atoms. > Pymatgen is very proper for POSCAR output because it takes symmetry > analysis depend on Curtarolo-Setyawan's paper > [http://arxiv.org/abs/1004.2974v1 (http://arxiv.org/abs/1004.2974v1)] (MCLC5 > - it gives also gamma angle, for this case)...so, it is not matching with > QE's ibrav settings depend on cell vectors. Cif2Cell code gives the exactly > same CELL_PARAMETERS card with Quantum-ESPRESSO's ibrav=-13...that is the > reason why I chose Cif2Cell code. > Andrea, it was my fault. I had been complicated among space groups(2/m > for sg:12 and 2/C for sg:15) and Herman-Mauguin notations(2/m for space > groups 12-15). You said that ?Using ibrav=-13 it is not necessary to add > these atoms in the list of atoms inside the unit cell." Andrea, you mean that > could I decrease the number of atoms in primitive cell if they have > symmetrized by last 4 symmetry operations in this case? By this way, the cell > lost half of atoms inside which is good news for computational resources. > I think so. As far as I understand there are two possibilities: 1) You apply all the 8 symmetry operations and use ibrav=-12 (simple monoclinic) obtaining 64 atoms. 2) You apply only the first four symmetry operations and use ibrav=-13 (one base centered monoclinic). Note however that in this case you have to refer the positions to the base centered monoclinic axes, while the positions that you obtain applying the symmetry are still referred to the simple monoclinic cell. The base centered monoclinic cell has one half the number of atoms of the simple monoclinic cell. In no cases however QE will find 8 symmetry operations. In the first case because fractional translations will be disabled (the cell is actually a supercell). In the second case because there are only 4. It is not a question of notations, the point group for the space group C2/c is C_2h (that has 4 operations), there is no way to obtain a larger point group. HTH, Andrea ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] about C2/c point group symmetry of a monoclinic lattice.
On Thu, 2014-12-18 at 19:29 +, Mutlu COLAKOGULLARI wrote: > Dear Carlo, Andrea and Paolo; > The taking responds and advices from people who has experienced makes > me happy. > As Paolo and Carlo also said, cif2qe.sh is not working properly, (at > least for this case). Therefore, I used the other codes for double cross > check: pymatgen and cif2cell. The conventional cell has 64 atoms whereas its > primitive has 32 atoms. > Pymatgen is very proper for POSCAR output because it takes symmetry > analysis depend on Curtarolo-Setyawan's paper > [http://arxiv.org/abs/1004.2974v1] (MCLC5 - it gives also gamma angle, for > this case)...so, it is not matching with QE's ibrav settings depend on cell > vectors. Cif2Cell code gives the exactly same CELL_PARAMETERS card with > Quantum-ESPRESSO's ibrav=-13...that is the reason why I chose Cif2Cell code. > Andrea, it was my fault. I had been complicated among space groups(2/m > for sg:12 and 2/C for sg:15) and Herman-Mauguin notations(2/m for space > groups 12-15). You said that ”Using ibrav=-13 it is not necessary to add > these atoms in the list of atoms inside the unit cell." Andrea, you mean that > could I decrease the number of atoms in primitive cell if they have > symmetrized by last 4 symmetry operations in this case? By this way, the cell > lost half of atoms inside which is good news for computational resources. > I think so. As far as I understand there are two possibilities: 1) You apply all the 8 symmetry operations and use ibrav=-12 (simple monoclinic) obtaining 64 atoms. 2) You apply only the first four symmetry operations and use ibrav=-13 (one base centered monoclinic). Note however that in this case you have to refer the positions to the base centered monoclinic axes, while the positions that you obtain applying the symmetry are still referred to the simple monoclinic cell. The base centered monoclinic cell has one half the number of atoms of the simple monoclinic cell. In no cases however QE will find 8 symmetry operations. In the first case because fractional translations will be disabled (the cell is actually a supercell). In the second case because there are only 4. It is not a question of notations, the point group for the space group C2/c is C_2h (that has 4 operations), there is no way to obtain a larger point group. HTH, Andrea > With my best wishes, >Mutlu. > > --Dr. Mutlu COLAKOGULLARITrakya > Universitesi Fen FakultesiFizik Bolumu22030 Merkez-EDİRNE > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Andrea Dal CorsoTel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalco...@sissa.it ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] about C2/c point group symmetry of a monoclinic lattice.
Dear Carlo, Andrea and Paolo; The taking responds and advices from people who has experienced makes me happy. As Paolo and Carlo also said, cif2qe.sh is not working properly, (at least for this case). Therefore, I used the other codes for double cross check: pymatgen and cif2cell. The conventional cell has 64 atoms whereas its primitive has 32 atoms. Pymatgen is very proper for POSCAR output because it takes symmetry analysis depend on Curtarolo-Setyawan's paper [http://arxiv.org/abs/1004.2974v1] (MCLC5 - it gives also gamma angle, for this case)...so, it is not matching with QE's ibrav settings depend on cell vectors. Cif2Cell code gives the exactly same CELL_PARAMETERS card with Quantum-ESPRESSO's ibrav=-13...that is the reason why I chose Cif2Cell code. Andrea, it was my fault. I had been complicated among space groups(2/m for sg:12 and 2/C for sg:15) and Herman-Mauguin notations(2/m for space groups 12-15). You said that ”Using ibrav=-13 it is not necessary to add these atoms in the list of atoms inside the unit cell." Andrea, you mean that could I decrease the number of atoms in primitive cell if they have symmetrized by last 4 symmetry operations in this case? By this way, the cell lost half of atoms inside which is good news for computational resources. With my best wishes, Mutlu. --Dr. Mutlu COLAKOGULLARITrakya Universitesi Fen FakultesiFizik Bolumu22030 Merkez-EDİRNE ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] about C2/c point group symmetry of a monoclinic lattice.
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 : > > 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 = monoclinicSpace 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] > > ! 4x, 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] > > ! 8x+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) = 0.000 > > 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+0.00 Tl1+.pbe-n-rrkjus_psl.0.1.UPF > > Ga3+0.00 Ga3+.pbe-n-rrkjus_psl.0.1.UPF > > Se2-0.00 Se2-.pbe-n-rrkjus_psl.0.1.UPF > > > > > > ATOMIC_POSITIONS crystal > > Tl1+ 0.4647000 0.6891000 0.614 > > Tl1+ 0.2844000 0.9377000 0.8864000 > > Ga3+ 0.100 0.809 0.662 > > Ga3+ 0.145 0.562 0.839 > > Se2- 0.000 0.946 0.750 > > Se2- 0.000 0.426 0.750 > > Se2- 0.207 0.938 0.571 > > Se2- 0.262 0.690 0.752 > > Se2- 0.048 0.688 0.938 > > Tl1+ 0.5353000 0.6891000 0.886 > > Tl1+ 0.7156000 0.9377000 0.6136000 > > Ga3+ 0.900 0.809 0.838 > > Ga3+ 0.855 0.562 0.661 > > Se2--0.000 0.946 0.750 > > Se2--0.000 0.426 0.750 > > Se2- 0.79300
Re: [Pw_forum] about C2/c point group symmetry of a monoclinic lattice.
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 = monoclinicSpace 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] > ! 4x, 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] > ! 8x+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) = 0.000 > 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+0.00 Tl1+.pbe-n-rrkjus_psl.0.1.UPF > Ga3+0.00 Ga3+.pbe-n-rrkjus_psl.0.1.UPF > Se2-0.00 Se2-.pbe-n-rrkjus_psl.0.1.UPF > > > ATOMIC_POSITIONS crystal > Tl1+ 0.4647000 0.6891000 0.614 > Tl1+ 0.2844000 0.9377000 0.8864000 > Ga3+ 0.100 0.809 0.662 > Ga3+ 0.145 0.562 0.839 > Se2- 0.000 0.946 0.750 > Se2- 0.000 0.426 0.750 > Se2- 0.207 0.938 0.571 > Se2- 0.262 0.690 0.752 > Se2- 0.048 0.688 0.938 > Tl1+ 0.5353000 0.6891000 0.886 > Tl1+ 0.7156000 0.9377000 0.6136000 > Ga3+ 0.900 0.809 0.838 > Ga3+ 0.855 0.562 0.661 > Se2--0.000 0.946 0.750 > Se2--0.000 0.426 0.750 > Se2- 0.793 0.938 0.929 > Se2- 0.738 0.690 0.748 > Se2- 0.952 0.688 0.562 > Tl1+ 0.5353000 0.3109000 0.386 > Tl1+ 0.7156000 0.0623000 0.1136000 > Ga3+ 0.900 0.191 0.338 > Ga3+ 0.855 0.438 0.161 > Se2-
Re: [Pw_forum] about C2/c point group symmetry of a monoclinic lattice.
You cannot obtain 8 symmetry operations for a monoclinic system. C_2h is the correct point group for a system with space group C2/c. Actually the last four symmetry equivalent positions are due to the translations of the base centered monoclinic Bravais lattice. Using ibrav=-13 it is not necessary to add these atoms in the list of atoms inside the unit cell. HTH, Andrea On Wed, 2014-12-17 at 13:08 +, Mutlu COLAKOGULLARI wrote: > 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_g1.00 1.00 1.00 1.00 > B_g1.00 -1.00 1.00 -1.00 > A_u1.00 1.00 -1.00 -1.00 > B_u1.00 -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 > Ga69.7230 Ga.pbesol-dn-rrkjus_psl.1.0.0.UPF > Se78.9600 Se.pbesol-dn-rrkjus_psl.1.0.0.UPF > ATOMIC_POSITIONS crystal > Tl 0.1538000 0.7756000 0.114 > Tl 0.2244000 0.8462000 0.386 > Tl 0.8462000 0.2244000 0.886 > Tl 0.7756000 0.1538000 0.614 > Tl 0.2221000 0.3467000 0.3864000 > Tl 0.6533000 0.7779000 0.1136000 > Tl 0.7779000 0.6533000 0.6136000 > Tl 0.3467000 0.2221000 0.8864000 > Se 0.946 0.054 0.250 > Se 0.054 0.946 0.750 > Se 0.426 0.574 0.250 > Se 0.574 0.426 0.750 > Se 0.145 0.269 0.071 > Se 0.731 0.855 0.429 > Se 0.855 0.731 0.929 > Se 0.269 0.145 0.571 > Se 0.952 0.572 0.252 > Se 0.428 0.048 0.248 > Se 0.048 0.428 0.748 > Se 0.572 0.952 0.752 > Se 0.736 0.360 0.438 > Se 0.640 0.264 0.062 > Se 0.264 0.640 0.562 > Se 0.360 0.736 0.938 > Ga 0.909 0.291 0.162 > Ga 0.709 0.091 0.338 > Ga 0.091 0.709 0.838 > Ga 0.291 0.909 0.662 > Ga 0.707 0.583 0.339 > Ga 0.417 0.293 0.161 > Ga 0.293 0.417 0.661 > Ga 0.583 0.707 0.839 > 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_year2011 > _chemical_formula_structural 'Tl Ga Se2' >
Re: [Pw_forum] about C2/c point group symmetry of a monoclinic lattice.
Hi, the cif2qe.sh -i command gave to me: ! 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 = monoclinicSpace 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] ! 4x, 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] ! 8x+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) = 0.000 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+0.00 Tl1+.pbe-n-rrkjus_psl.0.1.UPF Ga3+0.00 Ga3+.pbe-n-rrkjus_psl.0.1.UPF Se2-0.00 Se2-.pbe-n-rrkjus_psl.0.1.UPF ATOMIC_POSITIONS crystal Tl1+ 0.4647000 0.6891000 0.614 Tl1+ 0.2844000 0.9377000 0.8864000 Ga3+ 0.100 0.809 0.662 Ga3+ 0.145 0.562 0.839 Se2- 0.000 0.946 0.750 Se2- 0.000 0.426 0.750 Se2- 0.207 0.938 0.571 Se2- 0.262 0.690 0.752 Se2- 0.048 0.688 0.938 Tl1+ 0.5353000 0.6891000 0.886 Tl1+ 0.7156000 0.9377000 0.6136000 Ga3+ 0.900 0.809 0.838 Ga3+ 0.855 0.562 0.661 Se2--0.000 0.946 0.750 Se2--0.000 0.426 0.750 Se2- 0.793 0.938 0.929 Se2- 0.738 0.690 0.748 Se2- 0.952 0.688 0.562 Tl1+ 0.5353000 0.3109000 0.386 Tl1+ 0.7156000 0.0623000 0.1136000 Ga3+ 0.900 0.191 0.338 Ga3+ 0.855 0.438 0.161 Se2--0.000 0.054 0.250 Se2--0.000 0.574 0.250 Se2- 0.793 0.062 0.429 Se2- 0.738 0.310 0.248 Se2- 0.952 0.312 0.062 Tl1+ 0.4647000 0.3109000 0.114 Tl1+ 0.2844000 0.0623000 0.3864000 Ga3+ 0.100 0.191 0.162 Ga3+ 0.145 0.438 0.339 Se2- 0.000 0.054 0.250 Se2- 0.000 0.574 0.250 Se2- 0.207 0.062 0.071 Se2- 0.262 0.310 0.252 Se2- 0.048 0.312 0.438
[Pw_forum] about C2/c point group symmetry of a monoclinic lattice.
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_g1.00 1.00 1.00 1.00 B_g1.00 -1.00 1.00 -1.00 A_u1.00 1.00 -1.00 -1.00 B_u1.00 -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 Ga69.7230 Ga.pbesol-dn-rrkjus_psl.1.0.0.UPF Se78.9600 Se.pbesol-dn-rrkjus_psl.1.0.0.UPF ATOMIC_POSITIONS crystal Tl 0.1538000 0.7756000 0.114 Tl 0.2244000 0.8462000 0.386 Tl 0.8462000 0.2244000 0.886 Tl 0.7756000 0.1538000 0.614 Tl 0.2221000 0.3467000 0.3864000 Tl 0.6533000 0.7779000 0.1136000 Tl 0.7779000 0.6533000 0.6136000 Tl 0.3467000 0.2221000 0.8864000 Se 0.946 0.054 0.250 Se 0.054 0.946 0.750 Se 0.426 0.574 0.250 Se 0.574 0.426 0.750 Se 0.145 0.269 0.071 Se 0.731 0.855 0.429 Se 0.855 0.731 0.929 Se 0.269 0.145 0.571 Se 0.952 0.572 0.252 Se 0.428 0.048 0.248 Se 0.048 0.428 0.748 Se 0.572 0.952 0.752 Se 0.736 0.360 0.438 Se 0.640 0.264 0.062 Se 0.264 0.640 0.562 Se 0.360 0.736 0.938 Ga 0.909 0.291 0.162 Ga 0.709 0.091 0.338 Ga 0.091 0.709 0.838 Ga 0.291 0.909 0.662 Ga 0.707 0.583 0.339 Ga 0.417 0.293 0.161 Ga 0.293 0.417 0.661 Ga 0.583 0.707 0.839 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_year2011 _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_alpha90. _cell_angle_beta 99.993(6) _cell_angle_gamma90. _cell_formula_units_Z16 _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 _[lo
