[xcrysden] create supercell from Mishchenko, BSUIR

[Tone Kokalj]

Dear Valery,

These additional atoms are the periodic images. To avoid seeing them,
use the menu:

Display-->Unit of Repetition...-->Translational asymmetric unit

This can also be achieved with the button on the bottom toolbar (the
second image-button from the left).

Note that in your structure, a vacuum region along the y-axis appear in
the diamond slab. Is this what you intend? 

Best regards,
Tone
-- 
Jožef Stefan Institute, Ljubljana, Slovenia


On Mon, 2025-12-15 at 14:01 +0300, Мищенко В.Н. wrote:
> 
> Good afternoon,
> Thank you for your reply. I corrected my error related to atom 8; it
> should have the coordinate (1.00 0.00 1.00). After that, I tried
> running the simulation in the Quantum Espresso program (version
> 7.4.1) with the input file scf.in. However, when running the program,
> I encountered the following error:
> Error in routine check_atoms (1): atoms # 1 and # 6 differ by lattice
> vector (-1, 0, 0) in crystal axis.
> This error was resolved when I deleted atom number 6 in the
> ATOMIC_POSITIONS alat section.
> Subsequent program runs produced similar errors, which I list below.
> These errors were resolved in a similar way, by deleting atoms
> numbered 7, 4, 5, 10.
> Error in routine check_atoms (1): atoms # 2 and # 7 differ by lattice
> vector (-1, 0, 0) in crystal axis.
> Error in routine check_atoms (1): atoms # 3 and # 4 differ by lattice
> vector (-1, 0, 0) in crystal axis.
> Error in routine check_atoms (1): atoms # 4 and # 5 differ by lattice
> vector (1, 0, 0) in crystal axis.
> And atom 10 too.
> As a result, I arrived at a combination of 19 atoms, the information
> about which is presented below in the input file scf.in. However,
> when viewing the resulting structure, which is presented in the
> appendix as an image from the XCrySden program (version xcrysden-
> 1.5.60-bin-semishared), I noticed a number of discrepancies between
> the declared number of carbon atoms in the file – 19 and the actual
> total number of atoms, which turned out to be 38 (their coordinates:
> some atoms have z=2.2 alat, while other some atoms have x=1.0 alat),
> and they are highlighted in green on the right and in the foreground
> of the structure photo.
> Could you advise me on how to exclude (do not show) these 19 atoms
> from the structure image?
> Sincerely,
> Valery Mishchenko
> PhD, BSUIR
> Gavin Abo пишет 15.12.2025 01:47:
> > 
> > 
> > Should you have 24 unique positions in your .in file?  It looks
> > like Atom 4 and 8 under ATOMIC_POSITIONS are not unique and have
> > the same atomic position of 1,1,1.  Also, is the position of atom
> > 20 correct, because that atom looks to be overlapping with Atom 3?
> > When opening the the .in file, did you try selecting the "reduce
> > dimension to 0D"?  With that, it look like it displays just the 23
> > atoms (not the 24 because Atom 4 and 8 have identical positions).
> > ATOMIC_POSITIONS alat
> >   C   0.00  0.00  0.00
> >   C   0.00  0.00  1.00
> >   C   0.00  1.00  1.00 <- Atom 3
> >   C   1.00  1.00  1.00 <- Atom 4
> >   C   1.00  1.00  0.00
> >   C   1.00  0.00  0.00
> >   C   0.00  1.00  0.00
> >   C   1.00  1.00  1.00 <- Atom 8
> >   C   0.00  0.50  0.50
> >   C   0.50  0.50  0.00
> >   C   0.50  0.50  1.00
> >   C   0.50  0.00  0.50
> >   C   0.50  1.00  0.50
> >   C   1.00  0.50  0.50
> >   C   0.75  0.75  0.25
> >   C   0.25  0.25  0.25
> >   C   0.75  0.25  0.75
> >   C   0.25  0.75  0.75
> >   C   0.00  0.70  1.15
> >   C   0.00  1.10  1.15 <- Atom 20
> >   C   0.00  1.25  1.50
> >   C   0.00  1.10  1.85
> >   C   0.00  0.70  1.85
> >   C   0.00  0.55  1.50
> > Hope that helps,
> > Gavin
> > XCrySDen user
> >  
> > On 12/14/2025 1:19 PM, Мищенко В.Н. wrote:
> > > 
> > > 
> > > Good afternoon,
> > > For modeling purposes in the Quantum Espresso program (version
> > > 7.4.1), I want to create an input file scf.in that would include
> > > a supercell combining two materials with different crystal
> > > lattices – diamond (lattice parameter ibrav=2) and vertical
> > > graphene (lattice parameter ibrav=12), whose plane is
> > > perpendicular to the surface of the diamond. For the input file,
> > > I chose ibrav = 0 and a number of other parameters, which are
> > > presented below in the scf.in file. However, when viewing the
> > > resulting structure, which is shown  as an image from the
> > > XCrySden program (version xcrysden-1.5.60-bin-semishared), I
> > > found a number of discrepancies between the stated number of
> > > carbon atoms (their total number in the ATOMIC_POSITIONS alat
> > > section is 24) and the number of atoms, which is greater than 30
> > > and shown in the structure image. There are also other
> > > discrepancies.
> > > Could you advise me on a possible solution to this problem?
> > > Sincerely,
> > > Valery Mishchenko
> > > PhD, BSUIR
> > > &control
> > >   calculation='scf',
> > >   prefix='gra',
> > >   verbosity= 'low',
> > >   pseudo_dir = './',
> > >   outdir='./',
> > > /
> > > &system
> > >   ibrav=0,
> > >   celldm(1)=6.64245
> > >   nbnd=48,
> > >   nat=24,
> > >   ntyp=1,
> > >   ecutwfc=40,
> > > /
> > > &electrons
> > >    conv_thr = 1d-06,
> > > /
> > > ATOMIC_SPECIES
> > > C  12.011 C_ONCV_PBE-1.2.upf
> > > CELL_PARAMETERS (alat)
> > >    1.00  0.00   0.00
> > >    0.00  2.00   0.00
> > >    0.00  0.00   2.00
> > > ATOMIC_POSITIONS alat
> > >   C   0.00  0.00  0.00
> > >   C   0.00  0.00  1.00
> > >   C   0.00  1.00  1.00
> > >   C   1.00  1.00  1.00
> > >   C   1.00  1.00  0.00
> > >   C   1.00  0.00  0.00
> > >   C   0.00  1.00  0.00
> > >   C   1.00  1.00  1.00
> > >   C   0.00  0.50  0.50
> > >   C   0.50  0.50  0.00
> > >   C   0.50  0.50  1.00
> > >   C   0.50  0.00  0.50
> > >   C   0.50  1.00  0.50
> > >   C   1.00  0.50  0.50
> > >   C   0.75  0.75  0.25
> > >   C   0.25  0.25  0.25
> > >   C   0.75  0.25  0.75
> > >   C   0.25  0.75  0.75
> > >   C   0.00  0.70  1.15
> > >   C   0.00  1.10  1.15
> > >   C   0.00  1.25  1.50
> > >   C   0.00  1.10  1.85
> > >   C   0.00  0.70  1.85
> > >   C   0.00  0.55  1.50
> > > K_POINTS   automatic
> > > 1 1 1 0 0 0
> > 
> >