<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>
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</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>
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