<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><br></div><div>Hello,</div><div><br></div><div>My brute force suggestion:</div><div>1. Select a chemically consistent axis so that the bond length is around 1.5 angstrom.</div><div>2. Optimize the cell parameters and atomic positions using vc-relax</div><div><br></div><div>Pascal</div><div><br></div><br><div><div>Le 14 janv. 2015 à 09:16, Naseem Hassan <<a href="mailto:raheskoon@gmail.com">raheskoon@gmail.com</a>> a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div><div>Dear All<br><br></div>I have made a structure similar to propylene using chemcraft. Then I picked the Cartesian coordinates and made an input file for relaxation. But I am not sure How long a Cell vector I should select along z-axis (along the Carbon chain). I want this structure to be periodic along the chain only. I selected 9 and 10 Angstrom of lattice vector along Z-axis and obtained C-C distance 5 and 6 Angstrom (Approx) respectively. It seems with 10 Angstrom a little vacuum is added and C-C bonds are elongated more. if I give small lattice vector (say 7 Ang) then C-C bond shrinks. <b>How to obtain an optimized C-C bond length ? What is proper method of avoiding vacuum and obtaining a perfect periodic relaxed structure. <br></b><br></div><div>Kindly have a look at the input file.<br><br> &control<br> calculation='relax'<br> restart_mode='from_scratch'<br> pseudo_dir = '/share/QE_pseudo'<br> outdir='./'<br> prefix='Graphane'<br> forc_conv_thr=1.0D-4<br> nstep=3000<br>/<br> &system<br> ibrav= 0<br> nat= 24, ntyp= 2<br> ecutwfc =60.0<br> occupations='smearing'<br> degauss=0.002<br> /<br> &electrons<br> scf_must_converge = .false.<br> mixing_mode='plain'<br> /<br> &ions<br> ion_dynamics = 'damp'<br>! ion_temperature='not_controlled'<br> /<br>CELL_PARAMETERS {angstrom}<br> 10.00000000000 0.0000000000000000 0.000<br> 0.0000000000 10.000000 0.000<br> 0.0000000000000000 0.0000000000000000 10.0<br>ATOMIC_SPECIES<br>H 1.0079 H.pw-mt_fhi.UPF<br>C 12.0111 C.pw-mt_fhi.UPF<br>ATOMIC_POSITIONS {angstrom}<br>C 5.367107970 4.716603635 1.053018481<br>C 6.255850131 5.148617707 2.197431688<br>C 5.604070962 5.956723221 3.300642187<br>C 5.221138074 5.110436404 4.489234599<br>C 4.929412403 5.933432549 5.718863005<br>C 4.751718300 5.084706368 6.956077606<br>C 5.325054303 5.689729332 8.206876709<br>C 4.097184203 4.164227727 4.168731293<br>H 6.706474032 4.257638763 2.659887322<br>H 4.344006686 3.515258124 3.319860376<br>H 3.854647824 3.519241858 5.021187742<br>H 3.190910142 4.727029043 3.904250319<br>H 3.696251345 4.818294626 7.110426161<br>H 4.348967601 4.517546557 1.417990955<br>H 5.731392495 3.757052353 0.655098847<br>H 7.101013257 5.709772742 1.774202810<br>H 6.288921269 6.743142271 3.648137411<br>H 4.714167633 6.481058689 2.916034182<br>H 6.110659580 4.502596625 4.738962908<br>H 4.050783951 6.573507244 5.541152210<br>H 5.775952152 6.619568616 5.878615758<br>H 4.786163229 6.607591885 8.486624196<br>H 6.356503452 6.007847752 7.983988564<br>H 5.270145007 4.125317908 6.789870671<br>K_POINTS {automatic}<br> 3 3 1 0 0 0<br></div><div>Many thanks<br></div><div>Naseem </div></div>
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<div>Pascal Boulet</div><div><br></div><div>--</div><div><a href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a></div><div>Aix-Marseille University</div><div>MADIREL Laboratory</div><div>Avenue Normandie-Niemen</div><div>F-13397 Marseille Cedex 20</div><div>Tel.: +33 413.55.18.10</div><div>Fax: +33 413.55.18.50</div><div><a href="http://allos.up.univ-mrs.fr/pascal/">http://allos.up.univ-mrs.fr/pascal/</a></div><div><br></div><br class="Apple-interchange-newline">
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