<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /></head><body style='font-size: 10pt; font-family: Verdana,Geneva,sans-serif'>
<p>Good afternoon,</p>
<p>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:</p>
<p>Error in routine check_atoms (1): atoms # 1 and # 6 differ by lattice vector (-1, 0, 0) in crystal axis.</p>
<p>This error was resolved when I deleted atom number 6 in the ATOMIC_POSITIONS alat section.</p>
<p>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.</p>
<p>Error in routine check_atoms (1): atoms # 2 and # 7 differ by lattice vector (-1, 0, 0) in crystal axis.</p>
<p>Error in routine check_atoms (1): atoms # 3 and # 4 differ by lattice vector (-1, 0, 0) in crystal axis.</p>
<p>Error in routine check_atoms (1): atoms # 4 and # 5 differ by lattice vector (1, 0, 0) in crystal axis.</p>
<p>And atom 10 too.</p>
<p>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.</p>
<p>Could you advise me on how to exclude (do not show) these 19 atoms from the structure image?</p>
<p>Sincerely,</p>
<p>Valery Mishchenko</p>
<p>PhD, BSUIR</p>
<p id="reply-intro">Gavin Abo пишет 15.12.2025 01:47:</p>
<blockquote type="cite" style="padding: 0 0.4em; border-left: #1010ff 2px solid; margin: 0">
<div id="replybody1">
<p>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?</p>
<p>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).</p>
<p>ATOMIC_POSITIONS alat<br /> C 0.00 0.00 0.00<br /> C 0.00 0.00 1.00<br /> C 0.00 1.00 1.00 <span style="color: #ff0000;"><- Atom 3</span><br /> C 1.00 1.00 1.00 <span style="color: #ff0000;"><- Atom 4</span><br /> C 1.00 1.00 0.00<br /> C 1.00 0.00 0.00<br /> C 0.00 1.00 0.00<br /> C 1.00 1.00 1.00<span style="color: #ff0000;"> <- Atom 8</span><br /> C 0.00 0.50 0.50<br /> C 0.50 0.50 0.00<br /> C 0.50 0.50 1.00<br /> C 0.50 0.00 0.50<br /> C 0.50 1.00 0.50<br /> C 1.00 0.50 0.50<br /> C 0.75 0.75 0.25<br /> C 0.25 0.25 0.25<br /> C 0.75 0.25 0.75<br /> C 0.25 0.75 0.75<br /> C 0.00 0.70 1.15<br /> C 0.00 1.10 1.15 <span style="color: #ff0000;"><- Atom 20</span><br /> C 0.00 1.25 1.50<br /> C 0.00 1.10 1.85<br /> C 0.00 0.70 1.85<br /> C 0.00 0.55 1.50</p>
<p>Hope that helps,</p>
Gavin<br />XCrySDen user
<div class="v1moz-cite-prefix"> </div>
<div class="v1moz-cite-prefix">On 12/14/2025 1:19 PM, Мищенко В.Н. wrote:</div>
<blockquote type="cite" style="padding: 0 0.4em; border-left: #1010ff 2px solid; margin: 0">
<div id="v1editbody1" style="font-size: 10pt; font-family: Verdana,Geneva,sans-serif;">
<p>Good afternoon,</p>
<p style="text-align: justify;">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.</p>
<p>Could you advise me on a possible solution to this problem?</p>
<p>Sincerely,</p>
<p>Valery Mishchenko</p>
<p>PhD, BSUIR</p>
<p>&control</p>
<p> calculation='scf',</p>
<p> prefix='gra',</p>
<p> verbosity= 'low',</p>
<p> pseudo_dir = './',</p>
<p> outdir='./',</p>
<p>/</p>
<p>&system</p>
<p> ibrav=0,</p>
<p> celldm(1)=6.64245</p>
<p> nbnd=48,</p>
<p> nat=24,</p>
<p> ntyp=1,</p>
<p> ecutwfc=40,</p>
<p>/</p>
<p>&electrons</p>
<p> conv_thr = 1d-06,</p>
<p>/</p>
<p>ATOMIC_SPECIES</p>
<p>C 12.011 C_ONCV_PBE-1.2.upf</p>
<p>CELL_PARAMETERS (alat)</p>
<p> 1.00 0.00 0.00</p>
<p> 0.00 2.00 0.00</p>
<p> 0.00 0.00 2.00</p>
<p>ATOMIC_POSITIONS alat</p>
<p> C 0.00 0.00 0.00</p>
<p> C 0.00 0.00 1.00</p>
<p> C 0.00 1.00 1.00</p>
<p> C 1.00 1.00 1.00</p>
<p> C 1.00 1.00 0.00</p>
<p> C 1.00 0.00 0.00</p>
<p> C 0.00 1.00 0.00</p>
<p> C 1.00 1.00 1.00</p>
<p> C 0.00 0.50 0.50</p>
<p> C 0.50 0.50 0.00</p>
<p> C 0.50 0.50 1.00</p>
<p> C 0.50 0.00 0.50</p>
<p> C 0.50 1.00 0.50</p>
<p> C 1.00 0.50 0.50</p>
<p> C 0.75 0.75 0.25</p>
<p> C 0.25 0.25 0.25</p>
<p> C 0.75 0.25 0.75</p>
<p> C 0.25 0.75 0.75</p>
<p> C 0.00 0.70 1.15</p>
<p> C 0.00 1.10 1.15</p>
<p> C 0.00 1.25 1.50</p>
<p> C 0.00 1.10 1.85</p>
<p> C 0.00 0.70 1.85</p>
<p> C 0.00 0.55 1.50</p>
<p>K_POINTS automatic</p>
<p>1 1 1 0 0 0</p>
</div>
</blockquote>
</div>
<br />
<div class="pre" style="margin: 0; padding: 0; font-family: monospace"> </div>
</blockquote>
<p><br /></p>
</body></html>