[xcrysden] create supercell from Mishchenko, BSUIR
Мищенко В.Н.
mishchenko at bsuir.by
Mon Dec 15 12:01:01 CET 2025
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
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&control
calculation = 'scf'
prefix = 'diam'
verbosity = 'low'
pseudo_dir = './'
outdir = './'
! tprnfor = .true.
! tstress = .true.
/
&system
ibrav = 0
celldm(1) = 6.64245
nat = 19
ntyp = 1
ecutwfc = 50
occupations = 'smearing'
smearing = 'mp'
degauss = 0.02
nbnd = 48
/
&electrons
diagonalization = 'david'
mixing_beta = 0.7
conv_thr = 1.0d-10
/
ATOMIC_SPECIES
C 12.011 C_ONCV_PBE-1.2.upf
CELL_PARAMETERS (alat)
1.00 0.00 0.00
0.00 2.20 0.00
0.00 0.00 2.20
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 0.00
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 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 1.25
C 0.00 1.10 1.25
C 0.00 1.25 1.60
C 0.00 1.10 1.95
C 0.00 0.70 1.95
C 0.00 0.55 1.60
K_POINTS automatic
6 6 6 1 1 1
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