3 Input data


A large percentage of the problems reported to the mailing list are caused by incorrect input data. Before reporting a problem with strange crashes or strange results, please have a look at your structure with XCrySDen (or another visualization software). XCrySDen can directly visualize the structure from both PWscf input data:

   xcrysden --pwi "input-data-file"

and from PWscf output as well:

   xcrysden --pwo "output-file".

Unlike most other visualizers, XCrySDen is periodicity-aware: you can easily visualize periodically repeated cells. You are advised to always use XCrySDen to check your input data!

 

3.1 Does QE use primitive or conventional unit cell? All atom or symmetry-inequivalent ones?

QE uses all atoms and the primitive unit cell. If you want to use the so-called “conventional” unit cell, you are free to do it, as long as you specify both the cell parameters and the atomic positions correctly.

3.2 Where can I find the crystal structure/atomic positions of XYZ?

Check the Library of Crystallographic Prototypes. The American Mineralogist Crystal Structure Database is another excellent place to find structures, though you will have to use it in conjunction with the Bilbao crystallography server, and have some understanding of space groups and Wyckoff positions. Another interesting site: http://cci.lbl.gov/cctbx/index.html. (most info here from Mike Mehl).

CIF files can be converted to using the PW/tools/pw2cif.sh script, courtesy of Carlo Nervi, or
using gdis v. 0.99 and later: Open CIF file with gdis and then save as ‘filename.pwi’. The code understands the extension ‘pwi’ and prepare a simple input file for Quantum ESPRESSO (info by Mutlu Colakogullari)

3.3 My crystal has a 4H2131c structure, how does this translate to QE input data?

There are several different ways to specify structures, described in detail in Doc/INPUT_PW.*. Please choose the one that better fits your needs. You can select your lattice from a list Bravais lattices; or you can specify crystallographic parameters a,b,c,cos(ab), cos(ac), cos(bc); or you can provide the three primitive lattice vectors. You can provide atomic positions in units of the primitive lattice vectors, or in cartesian axis and Bohr radii / A /units of the lattice parameter a.

3.4 How can I generate a supercell?

If you need to create a supercell and are too lazy to create a small program to translate atoms, or to do it manually, you can use one of the following codes:

  • XCrySDen (suggested by G. Mattioli)
  • gaussview, or Avogadro (suggested by A. Shearer)
  • use the VESTA program, it’s a beatiful and friendly program to see crystal structures and make supercell, this program save the atomic positions in XYZ format. Furthermore, runs on linux and win! (Arles V. Gil Rebaza)
  • Utility “genlat.f” of DL_POLY (suggested by G. Lapenna)
  • use the ‘spacegroup’ program in EXCITING package (http://exciting-code.org) to generate the supercell, use ‘fropho’ (http://fropho.sourceforge.net) to check the symmetry’ (Kun Yin, April 2009)
  • use the PHON code: http://www.homepages.ucl.ac.uk/~ucfbdxa/ (Eyvaz Isaev, April 2009).

3.5 Where can I find the Brillouin Zone/high-symmetry points/irreps for XYZ?

You might find this web site useful: http://www.cryst.ehu.es/cryst/get_kvec.html (info by Cyrille Barreteau, nov. 2007). Or else: in textbooks, such as e.g. The mathematical theory of symmetry in solids by Bradley and Cracknell.

3.6 Where can I find Monkhorst-Pack grids of k-points?

Auxiliary code kpoints.x, found in pwtools/ and produced by make tools, generates uniform grids of k-points that are equivalent to Monkhorst-Pack grids.

3.7 How do I force a given occupancy on a given atom?

Short answer: you cannot. See this tutorial if you want to convince two atoms of the same kind to have different oxidation states.

3.8 What are the atomic positions/k-points for graphene?

Here two examples out of the many ways to provide input data for a perfect graphene layer:
&system
ibrav= 4, celldm(1) =4.6542890, celldm(3)=something appropriate, nat= 2, ntyp= 1, [...]
/
ATOMIC_POSITIONS {alat}
C 0.000000 0.000000 0.000000
C 0.000000 0.5773503 0.000000
or
ATOMIC_POSITIONS {crystal}
C 0.0000000 0.0000000 0.000000
C 0.3333333 0.6666666 0.000000
HIgh-symmetry lines in k-space for band plotting:
K_POINTS {tpiba_b}
5
# A-Gamma-K-M-Gamma
0.0 0.0 0.16666667 10
0.0 0.0 0.0 20
0.33333333 0.57735027 0.0 20
0.33333333 0.0 0.0 20
0.0 0.0 0.0 0