<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I would introduce a penalty function such as A(N-C)**2, where C is the constraining coordination, and N the effective number of neighbors, calculated using your favorite definition. Not sure this has ever been implemented in QE, but it should not be a difficult task ... SB<div><br><div><div>On Jun 12, 2011, at 4:41 AM, <a href="mailto:m.g.p.krishna@chem.leidenuniv.nl">m.g.p.krishna@chem.leidenuniv.nl</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear List,<br><br>In many situations, one need to constraint the .coordination. number <br>of atoms, so that, say, a chemically adsorbed molecule wont move away <br>from the reactant<br>surface (ie. to keep coordination number as a constant, bonds never <br>break w.r.t. a cutoff radius).<br><br>In order to test that constraint optimization in Quantum Espresso <br>[4.3], I use an ethane molecule as test case.<br><br>My doubt:<br>How can one constraint the .coordination number. of an atom (so that <br>the bonds of that particular atom, will remain the same before and <br>after the optimizatio<br>n, regardless of the ions displacements).<br><br>Please note that in my test.in I used a shorter C-C bond length <br>(1.3Ang.) which is supposed to increase and it didn.t. I used <br>'atom_coord' and 'type_coord'<br> and in all time it tried to keep the bond fixed!<br><br>Can any one give an idea on how to fix the coordination number in a <br>geometry optimization? Hope some one can also explain why it always <br>fixes the bondlength<br>and not following the <0 0 0> and <0 0 1> flags?<br><br>Please also see below for my test run,<br><br>Thanks in advance,<br><br>Krishna Mohan GP<br>Center for Superfunctional Materials<br>POSTECH<br>Sotuh Korea.<br><br><br>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br><br>&CONTROL<br> calculation = 'relax' ,<br> restart_mode = 'from_scratch' ,<br> outdir = './' ,<br> pseudo_dir = '/home01/a202kks/krishna/myPSP' ,<br> prefix = 'Final_' ,<br> verbosity = 'high' ,<br> nstep = 50 ,<br> tprnfor = .true.,<br> /<br> &SYSTEM<br> ibrav = 0,<br> celldm(1)= 1.,<br> nat = 8,<br> ntyp = 2,<br> ecutwfc = 20 ,<br> nosym = .true. ,<br>occupations = 'smearing',<br>smearing = 'gauss',<br>degauss = 0.002,<br>/<br> &ELECTRONS<br>/<br> &IONS<br>ion_dynamics='damp',<br>/<br><br> CONSTRAINTS<br> 1 0.5<br> 'atom_coord' 5 1 3.5 0.5<br><br> CELL_PARAMETERS Cubic<br>12 0 0<br>0 12 0<br>0 0 12<br> ATOMIC_SPECIES<br> C 12.0107 C.pbe-paw_kj.UPF<br> H 1.00674 H.pbe-paw_kj.UPF<br> K_POINTS automatic<br> 3 3 3 0 0 0<br> ATOMIC_POSITIONS angstrom<br> C -0.00000000 -0.00000000 0.6500000 0 0 1<br> H 0.00000000 1.00880567 1.0066666 0 0 0<br> H 0.87365134 -0.50440284 1.0066666 0 0 0<br> H -0.87365134 -0.50440284 1.0066666 0 0 0<br> C -0.00000000 -0.00000000 -0.6500000 0 0 1<br> H 0.87365134 0.50440284 -1.0066666 0 0 0<br> H -0.87365134 0.50440284 -1.0066666 0 0 0<br> H -0.00000000 -1.00880567 -1.0066666 0 0 0<br><br>-----------------------------------------------------------------------------<br>After geometry optimization, I Got:<br> Damped Dynamics: convergence achieved in 11 steps<br>. . . . . .<br>Begin final coordinates<br> new unit-cell volume = 1728.00000 a.u.^3 ( 256.06318 Ang^3 )<br><br>CELL_PARAMETERS (alat= 1.00000000)<br> 12.000000000 0.000000000 0.000000000<br> 0.000000000 12.000000000 0.000000000<br> 0.000000000 0.000000000 12.000000000<br><br>ATOMIC_POSITIONS (angstrom)<br>C 0.000000000 -0.001564190 0.649998147<br>H 0.000000000 1.058348951 1.147005976<br>H 0.919069360 -0.531092625 1.145321656<br>H -0.919069360 -0.531092625 1.145321656<br>C 0.000000000 0.001564190 -0.649998147<br>H 0.919069360 0.531092625 -1.145321656<br>H -0.919069360 0.531092625 -1.145321656<br>H 0.000000000 -1.058348951 -1.147005976<br>End final coordinates<br><br><br>_______________________________________________<br>Pw_forum mailing list<br><a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>http://www.democritos.it/mailman/listinfo/pw_forum<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 14px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">---</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 14px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Stefano Baroni - SISSA</span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "> </span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">&</span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "> </span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">DEMOCRITOS National Simulation Center - Trieste</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 14px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "><a href="http://stefano.baroni.me/">http://stefano.baroni.me</a> [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; font-size: 12px; "><br style="font-size: 12px; "></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; font-size: 12px; "><span class="Apple-style-span" style="font-size: 14px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">La morale est une logique de l'action comme la logique est une morale de la pensée - Jean Piaget</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br></span></font></div></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 14px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Please, if possible, don't</span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "> </span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">send me MS Word or PowerPoint attachments</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 14px; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; ">Why? See:</span></font><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "> </span></font><font class="Apple-style-span" color="#0023E9" size="3"><span class="Apple-style-span" style="font-size: 12px; "><a href="http://www.gnu.org/philosophy/no-word-attachments.html">http://www.gnu.org/philosophy/no-word-attachments.html</a></span></font></div></div><div><font class="Apple-style-span" color="#0023E9" size="3"><br></font></div></span><br class="Apple-interchange-newline">
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