On Fri, Feb 16, 2018 at 2:54 PM, Krishnendu Mukherjee < [email protected]> wrote:
> > 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). > > However, in output I notice, > > Found symmetry operation: I + ( -0.5000 0.5000 0.0000) > This is a supercell, fractional translations are disabled > > 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. > 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. Paolo > > > I will be grateful for your kind explanation. I am attaching the input > below and some part of the output. > ------------------------------------------- > cat > thermo_control << EOF > &INPUT_THERMO > what='mur_lc_elastic_constants', > frozen_ions=.FALSE. > / > EOF > > cat > zr.elastic.in << EOF > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='zr', > tstress = .true., > tprnfor = .true., > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav= 4, > celldm(1) =12.241645, > celldm(3) = 1.59185, > nat= 16, > ntyp= 1, > ecutwfc=50.0, > ecutrho = 430, > occupations='smearing', > smearing='marzari-vanderbilt', > degauss=0.02 > starting_magnetization(1) = 0.7, > use_all_frac = .true. > / > &electrons > conv_thr = 1.0d-10 > / > ATOMIC_SPECIES > Zr 91.22 Zr.pz-spn-kjpaw_psl.1.0.0.UPF > ATOMIC_POSITIONS (angstrom) > Zr 0.000000 1.870038 1.289000 > Zr 3.239000 3.740075 9.023001 > Zr 1.619500 4.675094 1.289000 > Zr 1.619500 0.935019 9.023001 > Zr -1.619500 4.675094 1.289000 > Zr 4.858500 0.935019 9.023001 > Zr 3.239000 3.740075 3.867000 > Zr 1.619500 0.935019 3.867000 > Zr 4.858500 0.935019 3.867000 > Zr 0.000000 1.870038 6.445000 > Zr 1.619500 4.675094 6.445000 > Zr -1.619500 4.675094 6.445000 > Zr 3.239000 1.870038 1.289000 > Zr 0.000000 3.740075 9.023001 > Zr 0.000000 3.740075 3.867000 > Zr 3.239000 1.870038 6.445000 > K_POINTS AUTOMATIC > 5 5 3 0 0 0 > > > EOF > > --------------------------------------------------------------------- > > Info: using nr1, nr2, nr3 values from input > Found symmetry operation: I + ( -0.5000 0.5000 0.0000) > This is a supercell, fractional translations are disabled > Found symmetry operation: I + ( -0.5000 0.5000 0.0000) > This is a supercell, fractional translations are disabled > > > Computing the elastic constants at the minimum volume > > FFT mesh: ( 81, 81, 135 ) > > Bravais lattice: > > ibrav= 4: hexagonal > Cell parameters: > > alat= 12.241645 a.u., c/a= 1.591850 > > > Starting primitive lattice vectors: > crystal axes: (cart. coord. in units of alat) > > a(1) = ( 1.000000 0.000000 0.000000 ) > a(2) = ( -0.500000 0.866025 0.000000 ) > a(3) = ( 0.000000 0.000000 1.591850 ) > > Starting reciprocal lattice vectors: > reciprocal axes: (cart. coord. in units 2 pi/alat) > > b(1) = ( 1.000000 0.577350 -0.000000 ) > b(2) = ( 0.000000 1.154701 0.000000 ) > b(3) = ( 0.000000 -0.000000 0.628200 ) > > Starting atomic positions in Cartesian axes: > > site n. atom positions (alat units) > 1 Zr tau( 1) = ( 0.0000000 0.2886752 > 0.1989812 ) > 2 Zr tau( 2) = ( 0.5000000 0.5773503 > 1.3928684 ) > 3 Zr tau( 3) = ( 0.2500000 0.7216879 > 0.1989812 ) > 4 Zr tau( 4) = ( 0.2500000 0.1443376 > 1.3928684 ) > 5 Zr tau( 5) = ( -0.2500000 0.7216879 > 0.1989812 ) > 6 Zr tau( 6) = ( 0.7500001 0.1443376 > 1.3928684 ) > 7 Zr tau( 7) = ( 0.5000000 0.5773503 > 0.5969435 ) > 8 Zr tau( 8) = ( 0.2500000 0.1443376 > 0.5969435 ) > 9 Zr tau( 9) = ( 0.7500001 0.1443376 > 0.5969435 ) > 10 Zr tau( 10) = ( 0.0000000 0.2886752 > 0.9949059 ) > 11 Zr tau( 11) = ( 0.2500000 0.7216879 > 0.9949059 ) > 12 Zr tau( 12) = ( -0.2500000 0.7216879 > 0.9949059 ) > 13 Zr tau( 13) = ( 0.5000000 0.2886752 > 0.1989812 ) > 14 Zr tau( 14) = ( 0.0000000 0.5773503 > 1.3928684 ) > 15 Zr tau( 15) = ( 0.0000000 0.5773503 > 0.5969435 ) > 16 Zr tau( 16) = ( 0.5000000 0.2886752 > 0.9949059 ) > > Starting atomic positions in crystallographic axes: > > site n. atom positions (cryst. coord.) > 1 Zr tau( 1) = ( 0.1666667 0.3333334 0.1250000 ) > 2 Zr tau( 2) = ( 0.8333334 0.6666667 0.8749998 ) > 3 Zr tau( 3) = ( 0.6666667 0.8333334 0.1250000 ) > 4 Zr tau( 4) = ( 0.3333334 0.1666667 0.8749998 ) > 5 Zr tau( 5) = ( 0.1666667 0.8333334 0.1250000 ) > 6 Zr tau( 6) = ( 0.8333334 0.1666667 0.8749998 ) > 7 Zr tau( 7) = ( 0.8333334 0.6666667 0.3749999 ) > 8 Zr tau( 8) = ( 0.3333334 0.1666667 0.3749999 ) > 9 Zr tau( 9) = ( 0.8333334 0.1666667 0.3749999 ) > 10 Zr tau( 10) = ( 0.1666667 0.3333334 0.6249998 ) > 11 Zr tau( 11) = ( 0.6666667 0.8333334 0.6249998 ) > 12 Zr tau( 12) = ( 0.1666667 0.8333334 0.6249998 ) > 13 Zr tau( 13) = ( 0.6666668 0.3333334 0.1250000 ) > 14 Zr tau( 14) = ( 0.3333334 0.6666667 0.8749998 ) > 15 Zr tau( 15) = ( 0.3333334 0.6666667 0.3749999 ) > 16 Zr tau( 16) = ( 0.6666668 0.3333334 0.6249998 ) > > The energy minimization will require 9 scf calculations > > The point group 118 D_3d (-3m) is compatible with the Bravais lattice. > > The rotation matrices with the order used inside thermo_pw are: > > 12 Sym. Ops., with inversion, found > > > s frac. trans. > > isym = 1 identity > > cryst. s( 1) = ( 1 0 0 ) > ( 0 1 0 ) > ( 0 0 1 ) > > cart. s( 1) = ( 1.000 0.000 0.000 ) > ( 0.000 1.000 0.000 ) > ( 0.000 0.000 1.000 ) > > > isym = 2 180 deg rotation - cart. axis [1,0,0] > > cryst. s( 2) = ( 1 0 0 ) > ( -1 -1 0 ) > ( 0 0 -1 ) > > cart. s( 2) = ( 1.000 0.000 0.000 ) > ( 0.000 -1.000 0.000 ) > ( 0.000 0.000 -1.000 ) > > > isym = 3 120 deg rotation - cryst. axis [0,0,1] > > cryst. s( 3) = ( 0 1 0 ) > ( -1 -1 0 ) > ( 0 0 1 ) > > cart. s( 3) = ( -0.500 -0.866 0.000 ) > ( 0.866 -0.500 0.000 ) > ( 0.000 0.000 1.000 ) > > > isym = 4 120 deg rotation - cryst. axis [0,0,-1] > > cryst. s( 4) = ( -1 -1 0 ) > ( 1 0 0 ) > ( 0 0 1 ) > > cart. s( 4) = ( -0.500 0.866 0.000 ) > ( -0.866 -0.500 0.000 ) > ( 0.000 0.000 1.000 ) > > > isym = 5 180 deg rotation - cryst. axis [0,1,0] > > cryst. s( 5) = ( -1 -1 0 ) > ( 0 1 0 ) > ( 0 0 -1 ) > > cart. s( 5) = ( -0.500 -0.866 0.000 ) > ( -0.866 0.500 0.000 ) > ( 0.000 0.000 -1.000 ) > > > isym = 6 180 deg rotation - cryst. axis [1,1,0] > > cryst. s( 6) = ( 0 1 0 ) > ( 1 0 0 ) > ( 0 0 -1 ) > > cart. s( 6) = ( -0.500 0.866 0.000 ) > ( 0.866 0.500 0.000 ) > ( 0.000 0.000 -1.000 ) > > > isym = 7 inversion > > cryst. s( 7) = ( -1 0 0 ) > ( 0 -1 0 ) > ( 0 0 -1 ) > > cart. s( 7) = ( -1.000 0.000 0.000 ) > ( 0.000 -1.000 0.000 ) > ( 0.000 0.000 -1.000 ) > > > isym = 8 inv. 180 deg rotation - cart. axis [1,0,0] > > cryst. s( 8) = ( -1 0 0 ) > ( 1 1 0 ) > ( 0 0 1 ) > > cart. s( 8) = ( -1.000 0.000 0.000 ) > ( 0.000 1.000 0.000 ) > ( 0.000 0.000 1.000 ) > > > isym = 9 inv. 120 deg rotation - cryst. axis [0,0,1] > > cryst. s( 9) = ( 0 -1 0 ) > ( 1 1 0 ) > ( 0 0 -1 ) > > cart. s( 9) = ( 0.500 0.866 0.000 ) > ( -0.866 0.500 0.000 ) > ( 0.000 0.000 -1.000 ) > > > isym = 10 inv. 120 deg rotation - cryst. axis [0,0,-1] > > cryst. s(10) = ( 1 1 0 ) > ( -1 0 0 ) > ( 0 0 -1 ) > > cart. s(10) = ( 0.500 -0.866 0.000 ) > ( 0.866 0.500 0.000 ) > ( 0.000 0.000 -1.000 ) > > > isym = 11 inv. 180 deg rotation - cryst. axis [0,1,0] > > cryst. s(11) = ( 1 1 0 ) > ( 0 -1 0 ) > ( 0 0 1 ) > > cart. s(11) = ( 0.500 0.866 0.000 ) > ( 0.866 -0.500 0.000 ) > ( 0.000 0.000 1.000 ) > > > isym = 12 inv. 180 deg rotation - cryst. axis [1,1,0] > > cryst. s(12) = ( 0 -1 0 ) > ( -1 0 0 ) > ( 0 0 1 ) > > cart. s(12) = ( 0.500 -0.866 0.000 ) > ( -0.866 -0.500 0.000 ) > ( 0.000 0.000 1.000 ) > > > point group D_3d (-3m) > there are 6 classes > the character table: > > E 2C3 3C2' i 2S6 3s_d > A_1g 1.00 1.00 1.00 1.00 1.00 1.00 > A_2g 1.00 1.00 -1.00 1.00 1.00 -1.00 > E_g 2.00 -1.00 0.00 2.00 -1.00 0.00 > A_1u 1.00 1.00 1.00 -1.00 -1.00 -1.00 > A_2u 1.00 1.00 -1.00 -1.00 -1.00 1.00 > E_u 2.00 -1.00 0.00 -2.00 1.00 0.00 > > the symmetry operations in each class and the name of the first > element: > > E 1 > identity > 2C3 3 4 > 120 deg rotation - cryst. axis [0,0,1] > 3C2' 2 5 6 > 180 deg rotation - cart. axis [1,0,0] > i 7 > inversion > 2S6 9 10 > inv. 120 deg rotation - cryst. axis [0,0,1] > 3s_d 8 11 12 > inv. 180 deg rotation - cart. axis [1,0,0] > > Space group identification, 12 symmetries: > > Bravais lattice 4 hexagonal > Point group number 25 / 118 D_3d (-3m) > > Nonsymmorphic operations not found: All fractional translations vanish > Symmetries of the point group in standard order > > 1 E 1 > 2 3z 27 > 3 3-z 28 > 4 2x 4 > 5 2110 32 > 6 2010 31 > 7 i 33 > 8 i3z 59 > 9 i3-z 60 > 10 i2x 36 > 11 i2110 64 > 12 i2010 63 > > > Space group nymber 164 > > Space group P-3m1 (group number 164). > The origin coincides with the ITA tables. > > The Laue class is D_3d (-3m) > > In this class the elastic tensor is > > ( c11 c12 c13 c14 . . ) > ( c12 c11 c13 -c14 . . ) > ( c13 c13 c33 . . . ) > ( c14 -c14 . c44 . . ) > ( . . . . c44 c14 ) > ( . . . . c14 X ) > X=(c11-c12)/2 > > It requires three strains: e1, e3, and e4 > for a total of 12 scf calculations > > ------------------------------------------------------------ > ---------- > Ions are relaxed in each calculation > ------------------------------------------------------------ > ---------- > > -------------------------------------------------------- > > Thanks, > Best regards, > Krishnendu > > > -- > Dr. Krishnendu Mukherjee, > > Principal Scientist, > CSIR-NML, > Jamshedpur. > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
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