Non detection of the whole primitive cell

[Zino10]

Dear Pr. Tadano,
I begin to use ALAMODE code ; I have a problem and I need your help.
I created a 2x2x2 supercell with 96 (8*12) atoms from a tetragonal 12 atoms primitive cell. When using alm, it detects perfecly the space group of my structure, but it says that there is only 6 atoms in the premitive cell !!? That consideration continues with anphon and finally not all phonon branches are calculated.
Please, help me on that issue.
Thankx in advance!

[ttadano]

Can you show your complete input parameters?

[Zino10]

My alm0.in is as follows:

&general
PREFIX = super222_0.01
MODE = suggest
NAT = 96
NKD = 2; KD = Ag Li
TOLERANCE = 1.0e-3
/

&interaction
NORDER = 1 # 1: harmonic, 2: cubic, ..
/

&cutoff
- None
/

&cell
15.1767926200000005 # factor in Bohr unit # factor in Bohr unit
1.0000000000000 0.0000000000000 0.0000000000000
0.0000000000000 1.0000000000000 0.0000000000000
0.0000000000000 0.0000000000000 1.9650507000207003
/

&position
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1 0.5000000000000000 0.5000000000000000 0.4995735960400411
1 0.2500000000000000 0.2500000000000000 0.0004264762227254
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/

---

[ttadano]

Indeed, the primitive cell contains only 6 atoms. The tetragonal cell (12 atoms) you mentioned is not a primitive cell; it is a conventional cell.

[Zino10]

Thank you for the time spent here!
From anphon output (Below), in the volume taken as "Primitive cell " and defined as half the axis of supercell, we must have 1/8 the content of supercell : 96/8=12 , not only 6 atoms as given by anphon.

---

...

Lattice Vectors:

• Supercell (from super222_0.01.xml )

  1.517679e+01 0.000000e+00 0.000000e+00 : a1
  0.000000e+00 1.517679e+01 0.000000e+00 : a2
  0.000000e+00 0.000000e+00 2.982317e+01 : a3

  4.139995e-01 0.000000e+00 0.000000e+00 : b1
  0.000000e+00 4.139995e-01 0.000000e+00 : b2
  0.000000e+00 0.000000e+00 2.106814e-01 : b3

• Primitive cell

  7.588396e+00 0.000000e+00 0.000000e+00 : a1
  0.000000e+00 7.588396e+00 0.000000e+00 : a2
  0.000000e+00 0.000000e+00 1.491158e+01 : a3

  8.279991e-01 0.000000e+00 0.000000e+00 : b1
  0.000000e+00 8.279991e-01 0.000000e+00 : b2
  0.000000e+00 0.000000e+00 4.213627e-01 : b3

Volume of the primitive cell : 8.586650e+02 (a.u.)^3

Number of atoms in the supercell : 96
Number of atoms in the primitive cell: 6

Atomic positions in the primitive cell (fractional):
1: 0.000000e+00 0.000000e+00 1.999147e+00 Ag
2: 5.000000e-01 5.000000e-01 8.529524e-04 Ag
3: 5.000000e-01 0.000000e+00 2.508528e-01 Ag
4: 0.000000e+00 5.000000e-01 2.491472e-01 Ag
5: 0.000000e+00 5.000000e-01 8.905623e-08 Li
6: 5.000000e-01 5.000000e-01 2.500001e-01 Li

Mass of atomic species (u):
...
...

---

[ttadano]

The anphon code assumes the lattice vector given in the &cell field is a primitive lattice vector even if it is not so. That why something unexpected happened. Please make sure to give a primitive lattice vector in the &cell field.

In the 2.0dev version, the anphon code can compute phonons using non-primitive lattice vectors. However, it is still recommended to use a primitive cell to avoid extra computational costs (unless a non-primitive cell is desired).

[Zino10]

I don't find where reside the problem, but again I don't know how a tetragonal structure, as described below, can be generated by a cell with only 6 atoms ?! .. Please check this case !
Best Regards !

---

Tetragonal structure
a= 8 Bohr
c/a= 2

Atomic positions
X 0.00 0.00 0.0
X 0.50 0.50 0.0
X 0.50 0.00 0.5
X 0.00 0.50 0.5
X 0.00 0.00 1.0
X 0.50 0.50 1.0
X 0.50 0.00 1.5
X 0.00 0.50 1.5

Y 0.00 0.50 0.0
Y 0.50 0.50 0.5
Y 0.50 0.00 1.0
Y 0.00 0.00 1.5

---

[ttadano]

A standardized primitive cell is

 -3.794198e+00   3.794198e+00   7.455792e+00 : a1
  3.794198e+00  -3.794198e+00   7.455792e+00 : a2
  3.794198e+00   3.794198e+00  -7.455792e+00 : a3

and the corresponding atomic positions are

   Atomic positions in fractional basis and atomic species
     1   9.991472e-01   9.991472e-01   0.000000e+00   Pd
     2   5.008530e-01   5.008530e-01   0.000000e+00   Pd
     3   2.508528e-01   7.508528e-01   5.000000e-01   Pd
     4   7.491472e-01   2.491472e-01   5.000000e-01   Pd
     5   5.000001e-01   8.905623e-08   5.000000e-01    H
     6   7.500001e-01   7.500001e-01   0.000000e+00    H

You can find the above primitive cell vectors using spglib.