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If the coordinates of the atoms are correct for the bilayer, you just need to add vacuum by adding 15 to 20 Ang to the c value.
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<div>Cheers,</div>
<div>Vahid</div>
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<div>Vahid Askarpour</div>
<div>Department of Physics</div>
<div>Dalhousie University</div>
<div>Halifax, NS</div>
<div>CANADA<br>
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<div>On Aug 4, 2023, at 7:08 AM, Giuseppe Scala <g.scala2@campus.unimib.it> wrote:</div>
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<span style="font-weight:bold;font-size:12px;">CAUTION:</span> The Sender of this email is not from within Dalhousie.</div>
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<div dir="auto">The c parameter is set in that way in order to have 10 angstrom vacuum between two sets of Bilayer in my structure. If I reduce the c parameter i think that my system won't be a Bilayer anymore. Is that line of reasoning wrong?</div>
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<div dir="ltr" class="gmail_attr">Il ven 4 ago 2023, 05:15 ANAND JHA <<a href="mailto:anandkj21@iitk.ac.in">anandkj21@iitk.ac.in</a>> ha scritto:<br>
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<div dir="auto">C parameter and a parameter are wrong they are too high and low</div>
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<div dir="ltr" class="gmail_attr">On Thu, 3 Aug 2023 at 20:01, Giuseppe Scala <<a href="mailto:g.scala2@campus.unimib.it" target="_blank" rel="noreferrer">g.scala2@campus.unimib.it</a>> wrote:<br>
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Hi ANAND,
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<div dir="auto">Would you mind if I ask you to tell me where's the problem in the structure? Maybe that c parameter is too high or low?<br>
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<div dir="ltr">Il gio 3 ago 2023, 12:58 ANAND JHA <<a href="mailto:anandkj21@iitk.ac.in" target="_blank" rel="noreferrer">anandkj21@iitk.ac.in</a>> ha scritto:<br>
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<div dir="auto">There is some issue in your bilayer </div>
<div dir="auto">Try to make a new bilayer with CRYSTAL SOFTWARE </div>
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<div dir="ltr">On Thu, 3 Aug 2023 at 03:55, Giuseppe Scala <<a href="mailto:g.scala2@campus.unimib.it" target="_blank" rel="noreferrer">g.scala2@campus.unimib.it</a>> wrote:<br>
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<div dir="auto">I get negative frequencies at gamma points for Bilayer MoS2. I relaxed my structure and checked convergence with respect to energy cutoff. That's my input file for the scf calculation:
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<div dir="auto">##############</div>
<div dir="auto"><br>
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<div dir="auto">&CONTROL</div>
<div dir="auto">calculation ='scf'</div>
<div dir="auto">prefix = 'MoS2_BI'</div>
<div dir="auto">pseudo_dir = '/home/Giuseppe'</div>
<div dir="auto">outdir = './'</div>
<div dir="auto">tstress = .true.</div>
<div dir="auto">tprnfor = .true.</div>
<div dir="auto">forc_conv_thr = 1.0d-3</div>
<div dir="auto">nstep = 200</div>
<div dir="auto">/</div>
<div dir="auto"><br>
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<div dir="auto"> &SYSTEM</div>
<div dir="auto">ibrav = 4</div>
<div dir="auto">a = 3.1429635960300000000</div>
<div dir="auto">c = 20.006663000000000000</div>
<div dir="auto">nat = 6</div>
<div dir="auto">ntyp = 2</div>
<div dir="auto">ecutwfc = 60</div>
<div dir="auto">ecutrho = 240</div>
<div dir="auto">occupations = 'smearing'</div>
<div dir="auto">degauss = 0.01</div>
<div dir="auto">/</div>
<div dir="auto"><br>
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<div dir="auto"> &ELECTRONS</div>
<div dir="auto">mixing_beta = 0.7</div>
<div dir="auto">conv_thr = 1.0d-8</div>
<div dir="auto">diagonalization = 'david'</div>
<div dir="auto">electron_maxstep=200</div>
<div dir="auto">/</div>
<div dir="auto"><br>
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<div dir="auto"> &IONS</div>
<div dir="auto">trust_radius_max = 0.2</div>
<div dir="auto">/</div>
<div dir="auto"> &CELL</div>
<div dir="auto">cell_dynamics = "bfgs"</div>
<div dir="auto">cell_dofree = '2Dxy'</div>
<div dir="auto">/</div>
<div dir="auto"><br>
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<div dir="auto">ATOMIC_SPECIES</div>
<div dir="auto">Mo 95.9400 Mo.pbesol-spn-kjpaw_psl.1.0.0.UPF</div>
<div dir="auto">S 32.0660 S.pbesol-n-kjpaw_psl.1.0.0.UPF</div>
<div dir="auto">ATOMIC_POSITIONS {angstrom}</div>
<div dir="auto">Mo 1.5714815237 0.9072955423 6.6890512735</div>
<div dir="auto">Mo 0.0000000000 1.8145901001 13.377562735</div>
<div dir="auto"> S 1.5714815237 0.9072955423 11.825385701</div>
<div dir="auto"> S 1.5714815237 0.9072955423 14.928508325</div>
<div dir="auto"> S 0.0000000000 1.8145901001 8.2412092563</div>
<div dir="auto"> S 0.0000000000 1.8145901001 5.1381015776</div>
<div dir="auto"><br>
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<div dir="auto">K_POINTS {automatic}</div>
<div dir="auto">4 4 4 0 0 0</div>
<div dir="auto"><br>
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<div dir="auto">######### </div>
<div dir="auto"><br>
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<div dir="auto"><br>
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<div dir="auto">And here my input file for ph.x</div>
<div dir="auto"><br>
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<div dir="auto"><br>
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<div dir="auto">#######</div>
<div dir="auto"><br>
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<div dir="auto">&inputph</div>
<div dir="auto">prefix = 'MoS2_BI'</div>
<div dir="auto">fildvscf = 'dvscf'</div>
<div dir="auto">ldisp = .true.</div>
<div dir="auto">fildyn = 'MoS2_BI.dyn'</div>
<div dir="auto">alpha_mix(1) = 0.3</div>
<div dir="auto">nq1 = 2,</div>
<div dir="auto">nq2 = 2,</div>
<div dir="auto">nq3 = 2,</div>
<div dir="auto">tr2_ph = 1.0d-12</div>
<div dir="auto">/</div>
<div dir="auto">########</div>
<div dir="auto"><br>
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<div dir="auto">Is my bilayer wrong? I've come the exact same calculations for Bulk and Monolayer MoS2 and everything went smoothly</div>
<div dir="auto"><br>
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