<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi, </div><div class="">this is the reply to the message you sent me, it is better for me to continue di discussion on PW_forum, being a way</div><div class="">to share doubts, mistakes, problems with many other people that might help!</div><div class=""><br class=""></div><div class="">You can build your Si(111) surface with any tool (by hand, using VNL, any other builder), but this tool will do just what</div><div class="">you ask it to do, so before using the tool you ALWAYS need basic understanding. In this respect, I also suggest to look</div><div class="">to the extensive documentation of Quantum-ESPRESSO and to the tutorials that are freely available in the web.</div><div class=""><br class=""></div><div class="">Coming to your problem, Quantum-ESPRESSO, as you know, is based on plane waves, as such can only handle</div><div class="">systems that are periodic in all three directions. If you need to simulate something that is periodic in only two, one or no</div><div class="">direction in space (a surface, a 1D wire, a cluster/molecule/quantum dot respectively) you use the supercell approach.</div><div class=""><br class=""></div><div class="">Let’s consider the case of a surface and let’s choose x and y as directions parallel to the surface, such that the z direction is orthogonal</div><div class="">to it (you can make a different choice, of course).</div><div class=""><br class=""></div><div class="">1) In the x-y plane you have to identify the surface unit cell, spanned by two vectors a1 and a2 that describe the surface periodicity.</div><div class="">Beware the choice of a1 and a2: they might be deduced from the bulk crystals or be more complicated if the surface</div><div class="">is along special directions or if it undergoes some reconstruction.</div><div class=""><br class=""></div><div class="">In the case of Si(111) you should first decide if you want to choose the minimal cell, or if you want to consider complex reconstruction</div><div class="">(that is structures where one or more surface unit cells are gathered to build more complex structures) The minimal cell is obtained</div><div class="">by considering the 111 plane of Si and trying to understand the periodicity vectors within that plane. The complex reconstruction are instead</div><div class="">obtained once you know how many cells are gathered along the a1 and a2 directions. For example, in the case of Si(111), whose structure</div><div class="">had been long debated many years ago, it can undergo a 7x7 reconstruction (with a very large surface unit cell). You can find details wherever,</div><div class="">for example this is one of the Google search results:</div><div class=""><a href="http://nanowiz.tripod.com/sisteps/si111.htm" class="">http://nanowiz.tripod.com/sisteps/si111.htm</a></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">2) once the surface unit cell is identified, you must decide how many planes you want to consider in the direction (z-axis) orthogonal to the surface.</div><div class="">In this case beware the fact that as you move in along z, you might meet one or more planes that are not equivalent to the 1st one. In other words,</div><div class="">the second plane might not be obtained simply through a rigid shift along z of the 1st one, but there might be 2 or more planes before one equivalent</div><div class="">to the first one is found</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">3) at this point you have the minimal number of atomic coordinates that, replicated along a1 and a2 reproduce a slab, that is, a Si(111) surface composed</div><div class="">by a certain number of planes. How to choose a3 (this is one of the issues in your input file)? You measure the distance d along the z axis between the two furthermost planes</div><div class="">AND and set the length of a3 to d+V, where V=vacuum space. The latter is needed because, in the supercell approach, you system is replicated</div><div class="">also along a3, but you don’t want that periodic replicas interact with each other. The amount of V, let’s say 10 A (but a larger value might be needed), is chosen</div><div class="">just to avoid interaction and convergence with respect to it must always be checked</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">4) because the z direction is not a true periodicity direction, if V is large enough you expect that the band dispersion is zero along the z direction, that is,</div><div class="">you should obtain flat bands along that direction. As such, Brillouin zone sampling along that direction is useless, and the k-point grid you use for scf/relax</div><div class="">calculations is in the form N x M x 1</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Whether you performs steps 1-4 by hand or using some tool such as VNL is up to you. I suggest to start with simple surfaces and simple crystals, to start with.</div><div class=""><br class=""></div><div class="">Giovanni</div><div class=""><br class=""></div><div class="">PS after writing this message, I have tried the Google search</div><div class="">build surface supercell Quantum-ESPRESSO</div><div class="">The 1st result is this link (I’m sure that many many others of interest for you show up!)</div><div class=""><a href="http://www.democritos.it/events/pw-tutorial/lectures/pw-tutorial.pdf" class="">http://www.democritos.it/events/pw-tutorial/lectures/pw-tutorial.pdf</a> </div><div class="">If I were you, I would start with the exercises described therein.</div><div class=""><br class=""></div><blockquote type="cite" class="">Actually sir I am trying to create a silicon 111 surface adsorbed by an Indium atom.To do this what should I be do first? The input file which I am using is create by the VNL GUI. Is there any other way to create a quantum espresso input file.<div class="">Thanx</div><div class=""><br class=""></div><div class=""><br class=""></div><div><blockquote type="cite" class=""><div class="">On 23 Feb 2017, at 10:18, Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it" class="">giovanni.cantele@spin.cnr.it</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">1) the atomic positions are likely wrong, I cannot understand what is the system you want to calculate. For example, the Si-In distance is 1.1 A, that looks<div class="">very small. Try to look at your structure, opening the input file with XCrysDen. It is worth, before performing any further calculation, to check whether it is EXACTLY what you want.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">2) in the case you would like to simulate the Si(111) SURFACE in the presence of In, your input does not correspond to a surface calculation. There is not vacuum space</div><div class="">introduced between periodic replicas of the same slab, and there is k-point sampling in the direction orthogonal to the surface. If instead you are studying something like</div><div class="">a Si heterostructure (e.g. a superlattice), please disregard this point</div><div class=""><br class=""></div><div class="">3) you are using ultra soft pseudo potential, the ecutwfc is likely too high (this however does not give convergence issues, but can make your calculation much slower</div><div class="">than needed!). On the other hand, you are not setting the ecutrho variable, that by default is 4*ecutwfc. For ultrasoft pseudo potentials, as you might learn reading</div><div class="">the relevant literature on the subject, a higher charge density cut-off is required, usually from 6 to 12 times ecutwfc</div><div class=""><br class=""></div><div class="">4) to improve convergence, increasing degauss might help, for systems very difficult to converge (but even in this case you should be aware of what degauss is and how to use it)</div><div class="">and also decrease mixing_beta to 0.3, or 0.1 or maybe even less</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Giovanni</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div class="">On 23 Feb 2017, at 06:59, Ubaid Mohd <<a href="mailto:onlymubaid@gmail.com" class="">onlymubaid@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><span class="" style="font-size: 12.8px;">Hi,</span><div class="" style="font-size: 12.8px;"><br class=""></div><div class="" style="font-size: 12.8px;">I am trying to scf calculation of silicon(111)_Indium and the total force on the atom is not converging. Initially, the scf cycle itself was not converging.</div><div class="" style="font-size: 12.8px;">What is wron with my input file.</div><div class="" style="font-size: 12.8px;">Thanx,</div><div class="" style="font-size: 12.8px;">Ubaid</div><div class="" style="font-size: 12.8px;"><br class=""></div><div class="" style="font-size: 12.8px;"><br class=""></div><div class="" style="font-size: 12.8px;"><br class=""></div><div class="" style="font-size: 12.8px;"><br class=""></div><div class="" style="font-size: 12.8px;">Input File</div><div class="" style="font-size: 12.8px;"><br class=""></div><div class=""><div class=""><span class="" style="font-size: 12.8px;"><br class=""></span></div><div class=""><span class="" style="font-size: 12.8px;">&CONTROL</span></div><div class=""><span class="" style="font-size: 12.8px;"> calculation='scf',</span></div><div class=""><span class="" style="font-size: 12.8px;"> outdir='Pwscf',</span></div><div class=""><span class="" style="font-size: 12.8px;"> prefix='Si_In',</span></div><div class=""><span class="" style="font-size: 12.8px;"> pseudo_dir='.',</span></div><div class=""><span class="" style="font-size: 12.8px;"> verbosity='low',</span></div><div class=""><span class="" style="font-size: 12.8px;">/</span></div><div class=""><span class="" style="font-size: 12.8px;"><br class=""></span></div><div class=""><span class="" style="font-size: 12.8px;">&SYSTEM</span></div><div class=""><span class="" style="font-size: 12.8px;"> ibrav=0,</span></div><div class=""><span class="" style="font-size: 12.8px;"> celldm(1)=7.2565749368d0,</span></div><div class=""><span class="" style="font-size: 12.8px;"> nat=7,</span></div><div class=""><span class="" style="font-size: 12.8px;"> ntyp=2,</span></div><div class=""><span class="" style="font-size: 12.8px;"> ecutwfc=90,</span></div><div class=""><span class="" style="font-size: 12.8px;"> input_dft='PBE',</span></div><div class=""><span class="" style="font-size: 12.8px;"> occupations='smearing',</span></div><div class=""><span class="" style="font-size: 12.8px;"> smearing='mv',</span></div><div class=""><span class="" style="font-size: 12.8px;"> degauss=0.005d0,</span></div><div class=""><span class="" style="font-size: 12.8px;">/</span></div><div class=""><span class="" style="font-size: 12.8px;"><br class=""></span></div><div class=""><span class="" style="font-size: 12.8px;">&ELECTRONS</span></div><div class=""><span class="" style="font-size: 12.8px;"> conv_thr=1d-06,</span></div><div class=""><span class="" style="font-size: 12.8px;"> mixing_beta=0.7d0,</span></div><div class=""><span class="" style="font-size: 12.8px;">/</span></div><div class=""><span class="" style="font-size: 12.8px;"><br class=""></span></div><div class=""><span class="" style="font-size: 12.8px;">ATOMIC_SPECIES</span></div><div class=""><span class="" style="font-size: 12.8px;"> In 114.818000d0 In.pbe-d-rrkjus.UPF</span></div><div class=""><span class="" style="font-size: 12.8px;"> Si 28.085500d0 Si.pbe-n-rrkjus_psl.0.1.UPF</span></div><div class=""><span class="" style="font-size: 12.8px;"><br class=""></span></div><div class=""><span class="" style="font-size: 12.8px;">ATOMIC_POSITIONS {crystal}</span></div><div class=""><span class="" style="font-size: 12.8px;"> Si 0.1708493746d0 0.3787081237d0 0.2302895286d0</span></div><div class=""><span class="" style="font-size: 12.8px;"> Si 0.8375160412d0 0.7120414570d0 0.3136228619d0</span></div><div class=""><span class="" style="font-size: 12.8px;"> Si 0.8375160412d0 0.7120414570d0 0.5636228619d0</span></div><div class=""><span class="" style="font-size: 12.8px;"> Si 0.5041827079d0 1.0453747903d0 0.6469561953d0</span></div><div class=""><span class="" style="font-size: 12.8px;"> Si 0.5041827079d0 1.0453747903d0 0.8969561953d0</span></div><div class=""><span class="" style="font-size: 12.8px;"> Si 0.1708493746d0 0.3787081237d0 0.9802895286d0</span></div><div class=""><span class="" style="font-size: 12.8px;"> In 0.2708493746d0 0.4787081237d0 0.3397104714d0</span></div><div class=""><span class="" style="font-size: 12.8px;"><br class=""></span></div><div class=""><span class="" style="font-size: 12.8px;">K_POINTS {automatic}</span></div><div class=""><span class="" style="font-size: 12.8px;"> 5 5 5 0 0 0</span></div><div class=""><span class="" style="font-size: 12.8px;"><br class=""></span></div><div class=""><span class="" style="font-size: 12.8px;">CELL_PARAMETERS {alat}</span></div><div class=""><span class="" style="font-size: 12.8px;"> 1.000000000000d0 0.000000000000d0 0.000000000000d0</span></div><div class=""><span class="" style="font-size: 12.8px;"> -0.500000000000d0 0.866025403784d0 0.000000000000d0</span></div><div class=""><span class="" style="font-size: 12.8px;"> 0.000000000000d0 0.000000000000d0 2.449489742783d0</span></div><div class="" style="font-size: 12.8px;"><br class=""></div></div><div class=""><br class=""></div></div>_______________________________________________<br class="">Pw_forum mailing list<br class=""><a href="mailto:Pw_forum@pwscf.org" class="">Pw_forum@pwscf.org</a><br class=""><a href="http://pwscf.org/mailman/listinfo/pw_forum" class="">http://pwscf.org/mailman/listinfo/pw_forum</a></div></blockquote></div><br class=""><div class="">-- <br class=""><br class="">Giovanni Cantele, PhD<br class="">CNR-SPIN<br class="">c/o Dipartimento di Fisica<br class="">Universita' di Napoli "Federico II"<br class="">Complesso Universitario M. S. Angelo - Ed. 6<br class="">Via Cintia, I-80126, Napoli, Italy<br class="">e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it" class="">giovanni.cantele@spin.cnr.it</a><br class="">Phone: +39 081 676910<br class="">Skype contact: giocan74<br class=""><br class="">ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" class="">http://www.researcherid.com/rid/A-1951-2009</a><br class="">Web page: <a href="http://people.na.infn.it/~cantele" class="">http://people.na.infn.it/~cantele</a><br class=""></div><br class=""></div>_______________________________________________<br class="">Pw_forum mailing list<br class=""><a href="mailto:Pw_forum@pwscf.org" class="">Pw_forum@pwscf.org</a><br class="">http://pwscf.org/mailman/listinfo/pw_forum</div></blockquote></div></blockquote><br class=""><div class="">
-- <br class=""><br class="">Giovanni Cantele, PhD<br class="">CNR-SPIN<br class="">c/o Dipartimento di Fisica<br class="">Universita' di Napoli "Federico II"<br class="">Complesso Universitario M. S. Angelo - Ed. 6<br class="">Via Cintia, I-80126, Napoli, Italy<br class="">e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it" class="">giovanni.cantele@spin.cnr.it</a><br class="">Phone: +39 081 676910<br class="">Skype contact: giocan74<br class=""><br class="">ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" class="">http://www.researcherid.com/rid/A-1951-2009</a><br class="">Web page: <a href="http://people.na.infn.it/~cantele" class="">http://people.na.infn.it/~cantele</a><br class="">
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