<div dir="ltr">On Fri, Feb 16, 2018 at 2:54 PM, Krishnendu Mukherjee <span dir="ltr"><<a href="mailto:krishnendu.mukherjee789@gmail.com" target="_blank">krishnendu.mukherjee789@gmail.com</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div><div><br></div>I have created a Zr supercell with 16 atoms (the positions of the atoms are given in the input file below). Zr has the spacegroup P 63/m m c (No. 194). <br><br></div> However, in output I notice, <br><br>Found symmetry operation: I + ( -0.5000 0.5000 0.0000)<br> This is a supercell, fractional translations are disabled<br><br></div>Now, although the space group has no fractional translational along a and b, I think the fractional translations are identified as it is a supercell. But why there is no fractional translation identified along c? There is a fractional transformation along c in this spacegroup.</div></div></div></div></div></blockquote><div><br></div><div>The symmetry-detecting algorithm does not allow symmetry operations with fractional translations in a supercell. It's a limitation of the algorithm and there is no easy workaround.<br><br></div><div>Paolo<br></div><div> <br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div> <br><br></div> I will be grateful for your kind explanation. I am attaching the input below and some part of the output.<br>------------------------------<wbr>-------------<br>cat > thermo_control << EOF<br> &INPUT_THERMO<br> what='mur_lc_elastic_<wbr>constants',<br> frozen_ions=.FALSE.<br> /<br>EOF<br><br>cat > <a href="http://zr.elastic.in" target="_blank">zr.elastic.in</a> << EOF<br> &control<br> calculation = 'scf'<br> restart_mode='from_scratch',<br> prefix='zr',<br> tstress = .true., <br> tprnfor = .true.,<br> pseudo_dir = '$PSEUDO_DIR/',<br> outdir='$TMP_DIR/'<br> /<br> &system<br> ibrav= 4, <br> celldm(1) =12.241645, <br> celldm(3) = 1.59185, <br> nat= 16, <br> ntyp= 1,<br> ecutwfc=50.0,<br> ecutrho = 430,<br> occupations='smearing', <br> smearing='marzari-vanderbilt', <br> degauss=0.02<br> starting_magnetization(1) = 0.7,<br> use_all_frac = .true. <br> /<br> &electrons<br> conv_thr = 1.0d-10<br> /<br>ATOMIC_SPECIES<br> Zr 91.22 Zr.pz-spn-kjpaw_psl.1.0.0.UPF<br>ATOMIC_POSITIONS (angstrom)<br>Zr 0.000000 1.870038 1.289000<br>Zr 3.239000 3.740075 9.023001<br>Zr 1.619500 4.675094 1.289000<br>Zr 1.619500 0.935019 9.023001<br>Zr -1.619500 4.675094 1.289000<br>Zr 4.858500 0.935019 9.023001<br>Zr 3.239000 3.740075 3.867000<br>Zr 1.619500 0.935019 3.867000<br>Zr 4.858500 0.935019 3.867000<br>Zr 0.000000 1.870038 6.445000<br>Zr 1.619500 4.675094 6.445000<br>Zr -1.619500 4.675094 6.445000<br>Zr 3.239000 1.870038 1.289000<br>Zr 0.000000 3.740075 9.023001<br>Zr 0.000000 3.740075 3.867000<br>Zr 3.239000 1.870038 6.445000<br>K_POINTS AUTOMATIC<br>5 5 3 0 0 0 <br><br><br>EOF<br><br>------------------------------<wbr>------------------------------<wbr>---------<br><br>Info: using nr1, nr2, nr3 values from input<br> Found symmetry operation: I + ( -0.5000 0.5000 0.0000)<br> This is a supercell, fractional translations are disabled<br> Found symmetry operation: I + ( -0.5000 0.5000 0.0000)<br> This is a supercell, fractional translations are disabled<br><br><br> Computing the elastic constants at the minimum volume <br><br> FFT mesh: ( 81, 81, 135 )<br><br> Bravais lattice:<br><br> ibrav= 4: hexagonal<br> Cell parameters:<br><br> alat= 12.241645 a.u., c/a= 1.591850<br><br><br> Starting primitive lattice vectors:<br> crystal axes: (cart. coord. in units of alat)<br><br> a(1) = ( 1.000000 0.000000 0.000000 ) <br> a(2) = ( -0.500000 0.866025 0.000000 ) <br> a(3) = ( 0.000000 0.000000 1.591850 ) <br><br> Starting reciprocal lattice vectors:<br> reciprocal axes: (cart. coord. in units 2 pi/alat)<br><br> b(1) = ( 1.000000 0.577350 -0.000000 ) <br> b(2) = ( 0.000000 1.154701 0.000000 ) <br> b(3) = ( 0.000000 -0.000000 0.628200 ) <br><br> Starting atomic positions in Cartesian axes:<br><br> site n. atom positions (alat units)<br> 1 Zr tau( 1) = ( 0.0000000 0.2886752 0.1989812 )<br> 2 Zr tau( 2) = ( 0.5000000 0.5773503 1.3928684 )<br> 3 Zr tau( 3) = ( 0.2500000 0.7216879 0.1989812 )<br> 4 Zr tau( 4) = ( 0.2500000 0.1443376 1.3928684 )<br> 5 Zr tau( 5) = ( -0.2500000 0.7216879 0.1989812 )<br> 6 Zr tau( 6) = ( 0.7500001 0.1443376 1.3928684 )<br> 7 Zr tau( 7) = ( 0.5000000 0.5773503 0.5969435 )<br> 8 Zr tau( 8) = ( 0.2500000 0.1443376 0.5969435 )<br> 9 Zr tau( 9) = ( 0.7500001 0.1443376 0.5969435 )<br> 10 Zr tau( 10) = ( 0.0000000 0.2886752 0.9949059 )<br> 11 Zr tau( 11) = ( 0.2500000 0.7216879 0.9949059 )<br> 12 Zr tau( 12) = ( -0.2500000 0.7216879 0.9949059 )<br> 13 Zr tau( 13) = ( 0.5000000 0.2886752 0.1989812 )<br> 14 Zr tau( 14) = ( 0.0000000 0.5773503 1.3928684 )<br> 15 Zr tau( 15) = ( 0.0000000 0.5773503 0.5969435 )<br> 16 Zr tau( 16) = ( 0.5000000 0.2886752 0.9949059 )<br><br> Starting atomic positions in crystallographic axes:<br><br> site n. atom positions (cryst. coord.)<br> 1 Zr tau( 1) = ( 0.1666667 0.3333334 0.1250000 )<br> 2 Zr tau( 2) = ( 0.8333334 0.6666667 0.8749998 )<br> 3 Zr tau( 3) = ( 0.6666667 0.8333334 0.1250000 )<br> 4 Zr tau( 4) = ( 0.3333334 0.1666667 0.8749998 )<br> 5 Zr tau( 5) = ( 0.1666667 0.8333334 0.1250000 )<br> 6 Zr tau( 6) = ( 0.8333334 0.1666667 0.8749998 )<br> 7 Zr tau( 7) = ( 0.8333334 0.6666667 0.3749999 )<br> 8 Zr tau( 8) = ( 0.3333334 0.1666667 0.3749999 )<br> 9 Zr tau( 9) = ( 0.8333334 0.1666667 0.3749999 )<br> 10 Zr tau( 10) = ( 0.1666667 0.3333334 0.6249998 )<br> 11 Zr tau( 11) = ( 0.6666667 0.8333334 0.6249998 )<br> 12 Zr tau( 12) = ( 0.1666667 0.8333334 0.6249998 )<br> 13 Zr tau( 13) = ( 0.6666668 0.3333334 0.1250000 )<br> 14 Zr tau( 14) = ( 0.3333334 0.6666667 0.8749998 )<br> 15 Zr tau( 15) = ( 0.3333334 0.6666667 0.3749999 )<br> 16 Zr tau( 16) = ( 0.6666668 0.3333334 0.6249998 )<br><br> The energy minimization will require 9 scf calculations<br><br> The point group 118 D_3d (-3m) is compatible with the Bravais lattice.<br><br> The rotation matrices with the order used inside thermo_pw are:<br><br> 12 Sym. Ops., with inversion, found<br><br><br> s frac. trans.<br><br> isym = 1 identity <wbr> <br><br> cryst. s( 1) = ( 1 0 0 )<br> ( 0 1 0 )<br> ( 0 0 1 )<br><br> cart. s( 1) = ( 1.000 0.000 0.000 )<br> ( 0.000 1.000 0.000 )<br> ( 0.000 0.000 1.000 )<br><br><br> isym = 2 180 deg rotation - cart. axis [1,0,0] <br><br> cryst. s( 2) = ( 1 0 0 )<br> ( -1 -1 0 )<br> ( 0 0 -1 )<br><br> cart. s( 2) = ( 1.000 0.000 0.000 )<br> ( 0.000 -1.000 0.000 )<br> ( 0.000 0.000 -1.000 )<br><br><br> isym = 3 120 deg rotation - cryst. axis [0,0,1] <br><br> cryst. s( 3) = ( 0 1 0 )<br> ( -1 -1 0 )<br> ( 0 0 1 )<br><br> cart. s( 3) = ( -0.500 -0.866 0.000 )<br> ( 0.866 -0.500 0.000 )<br> ( 0.000 0.000 1.000 )<br><br><br> isym = 4 120 deg rotation - cryst. axis [0,0,-1] <br><br> cryst. s( 4) = ( -1 -1 0 )<br> ( 1 0 0 )<br> ( 0 0 1 )<br><br> cart. s( 4) = ( -0.500 0.866 0.000 )<br> ( -0.866 -0.500 0.000 )<br> ( 0.000 0.000 1.000 )<br><br><br> isym = 5 180 deg rotation - cryst. axis [0,1,0] <br><br> cryst. s( 5) = ( -1 -1 0 )<br> ( 0 1 0 )<br> ( 0 0 -1 )<br><br> cart. s( 5) = ( -0.500 -0.866 0.000 )<br> ( -0.866 0.500 0.000 )<br> ( 0.000 0.000 -1.000 )<br><br><br> isym = 6 180 deg rotation - cryst. axis [1,1,0] <br><br> cryst. s( 6) = ( 0 1 0 )<br> ( 1 0 0 )<br> ( 0 0 -1 )<br><br> cart. s( 6) = ( -0.500 0.866 0.000 )<br> ( 0.866 0.500 0.000 )<br> ( 0.000 0.000 -1.000 )<br><br><br> isym = 7 inversion <wbr> <br><br> cryst. s( 7) = ( -1 0 0 )<br> ( 0 -1 0 )<br> ( 0 0 -1 )<br><br> cart. s( 7) = ( -1.000 0.000 0.000 )<br> ( 0.000 -1.000 0.000 )<br> ( 0.000 0.000 -1.000 )<br><br><br> isym = 8 inv. 180 deg rotation - cart. axis [1,0,0] <br><br> cryst. s( 8) = ( -1 0 0 )<br> ( 1 1 0 )<br> ( 0 0 1 )<br><br> cart. s( 8) = ( -1.000 0.000 0.000 )<br> ( 0.000 1.000 0.000 )<br> ( 0.000 0.000 1.000 )<br><br><br> isym = 9 inv. 120 deg rotation - cryst. axis [0,0,1] <br><br> cryst. s( 9) = ( 0 -1 0 )<br> ( 1 1 0 )<br> ( 0 0 -1 )<br><br> cart. s( 9) = ( 0.500 0.866 0.000 )<br> ( -0.866 0.500 0.000 )<br> ( 0.000 0.000 -1.000 )<br><br><br> isym = 10 inv. 120 deg rotation - cryst. axis [0,0,-1] <br><br> cryst. s(10) = ( 1 1 0 )<br> ( -1 0 0 )<br> ( 0 0 -1 )<br><br> cart. s(10) = ( 0.500 -0.866 0.000 )<br> ( 0.866 0.500 0.000 )<br> ( 0.000 0.000 -1.000 )<br><br><br> isym = 11 inv. 180 deg rotation - cryst. axis [0,1,0] <br><br> cryst. s(11) = ( 1 1 0 )<br> ( 0 -1 0 )<br> ( 0 0 1 )<br><br> cart. s(11) = ( 0.500 0.866 0.000 )<br> ( 0.866 -0.500 0.000 )<br> ( 0.000 0.000 1.000 )<br><br><br> isym = 12 inv. 180 deg rotation - cryst. axis [1,1,0] <br><br> cryst. s(12) = ( 0 -1 0 )<br> ( -1 0 0 )<br> ( 0 0 1 )<br><br> cart. s(12) = ( 0.500 -0.866 0.000 )<br> ( -0.866 -0.500 0.000 )<br> ( 0.000 0.000 1.000 )<br><br><br> point group D_3d (-3m) <br> there are 6 classes<br> the character table:<br><br> E 2C3 3C2' i 2S6 3s_d <br>A_1g 1.00 1.00 1.00 1.00 1.00 1.00<br>A_2g 1.00 1.00 -1.00 1.00 1.00 -1.00<br>E_g 2.00 -1.00 0.00 2.00 -1.00 0.00<br>A_1u 1.00 1.00 1.00 -1.00 -1.00 -1.00<br>A_2u 1.00 1.00 -1.00 -1.00 -1.00 1.00<br>E_u 2.00 -1.00 0.00 -2.00 1.00 0.00<br><br> the symmetry operations in each class and the name of the first element:<br><br> E 1<br> identity <wbr> <br> 2C3 3 4<br> 120 deg rotation - cryst. axis [0,0,1] <br> 3C2' 2 5 6<br> 180 deg rotation - cart. axis [1,0,0] <br> i 7<br> inversion <wbr> <br> 2S6 9 10<br> inv. 120 deg rotation - cryst. axis [0,0,1] <br> 3s_d 8 11 12<br> inv. 180 deg rotation - cart. axis [1,0,0] <br><br> Space group identification, 12 symmetries:<br><br> Bravais lattice 4 hexagonal <wbr> <br> Point group number 25 / 118 D_3d (-3m)<br><br> Nonsymmorphic operations not found: All fractional translations vanish<br> Symmetries of the point group in standard order<br><br> 1 E 1<br> 2 3z 27<br> 3 3-z 28<br> 4 2x 4<br> 5 2110 32<br> 6 2010 31<br> 7 i 33<br> 8 i3z 59<br> 9 i3-z 60<br> 10 i2x 36<br> 11 i2110 64<br> 12 i2010 63<br><br><br> Space group nymber 164<br><br> Space group P-3m1 (group number 164).<br> The origin coincides with the ITA tables.<br><br> The Laue class is D_3d (-3m) <br><br> In this class the elastic tensor is<br><br> ( c11 c12 c13 c14 . . )<br> ( c12 c11 c13 -c14 . . )<br> ( c13 c13 c33 . . . )<br> ( c14 -c14 . c44 . . )<br> ( . . . . c44 c14 )<br> ( . . . . c14 X )<br> X=(c11-c12)/2<br><br> It requires three strains: e1, e3, and e4<br> for a total of 12 scf calculations<br><br> ------------------------------<wbr>------------------------------<wbr>----------<br> Ions are relaxed in each calculation<br> ------------------------------<wbr>------------------------------<wbr>----------<br><br>------------------------------<wbr>--------------------------<br><br></div>Thanks,<br></div>Best regards,<br></div>Krishnendu<span class="HOEnZb"><font color="#888888"><br clear="all"><div><div><div><div><div><div><div><div><br><br>-- <br><div class="m_7181591830205827386gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div>Dr. Krishnendu Mukherjee,</div></div><div><br></div><div>Principal Scientist,</div><div>CSIR-NML,</div><div>Jamshedpur.</div></div></div></div></div></div></div></div></div>
</div></div></div></div></div></div></div></div></font></span></div>
</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>Phone +39-0432-558216, fax +39-0432-558222<br><br></div></div></div></div></div>
</div></div>