<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">There are three issues that might be among the causes of the strange behaviour you observe:<div class=""><br class=""><div class="">1) you should add dipfield = .true. , the dipole correction is needed due to the periodic boundary corrections</div><div class=""><br class=""></div><div class="">2) you set edir=3, emaxpos=0.9 and eopreg=0.1: the saw-like potential decreases from emaxpos within an eopreg interval,</div><div class="">that is, from 0.9 to 0.9 + 0.1 in units of the unit cell parameter along edir. Since along the z direction you have atoms at z=0</div><div class="">that, due to the periodic boundary conditions are replicated at z=1, the (unphysical but needed) decrease of the saw-like potential</div><div class="">occurs in a region of not zero charge density, thus adding spurious interaction to the calculation.</div><div class="">Usually you set emaxpos in the middle of the vacuum space separating two periodic replicas along z. For example, if I’m not wrong,</div><div class="">you have atoms ranging from z=0 to z=0.5, so I would set emaxpos=0.75. Moreover, I would choose a small eopreg.</div><div class=""><br class=""></div><div class="">3) You should also check whether the 28 Ry cutoff is enough to get converged properties with all the pseudo potentials included in your</div><div class="">calculation.</div><div class=""><br class=""></div><div class="">Giovanni<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 30 Jul 2019, at 13:31, Helen Eisenberg <<a href="mailto:helen@fh.huji.ac.il" class="">helen@fh.huji.ac.il</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear Users,<br class=""><br class="">I am trying to implement a bias potential on a Si slab with a Li ion in the vacuum, and I am getting unphysical things happening to the Si slab (it gets squashed or stretched depending on which bias I use). This makes me think I'm doing something wrong...Do I need to use a dipole correction (dipfield=TRUE)? Am I doing something else wrong? Does it not work with molecular dynamics only ionic relaxation?<br class=""><br class="">Thank you for your help (I have copied my input file below, note the various parameters, such as kpoints and ecutwfc are not yet converged, as these are initial calculations )<br class=""><br class="">Dr. Helen Eisenberg,<br class=""><br class="">Fritz Haber Center for Molecular Dynamics,<br class=""><br class="">Hebrew University<br class=""><br class=""><br class="">&CONTROL<br class=""> calculation = "md",<br class=""> restart_mode='from_scratch',<br class=""> pseudo_dir = "$PSEUDO_DIR",<br class=""> prefix = "Energy_Si_2x2",<br class=""> tstress = .true.<br class=""> tprnfor = .true.<br class=""> outdir = "$TMP_DIR"<br class="">dt=40,<br class="">nstep=800<br class="">tefield=TRUE<br class="">/<br class="">&SYSTEM<br class=""> ibrav = 0,<br class=""> nat = 33,<br class=""> ntyp = 3,<br class=""> ecutwfc = 28.D0,<br class=""> occupations = 'smearing',<br class=""> smearing = 'mv',<br class=""> degauss = 0.0001,<br class=""> tot_charge = 0.0,<br class=""> nspin = 2,<br class=""> starting_magnetization(1)=0.0<br class="">edir=3<br class="">emaxpos=0.9<br class="">eopreg=0.1<br class="">eamp=0.01<br class="">/<br class="">&ELECTRONS<br class="">electron_maxstep=500<br class=""> mixing_mode = 'plain'<br class=""> mixing_beta = 0.7<br class=""> conv_thr = 1.0d-6<br class="">/<br class=""> &ions<br class=""> pot_extrapolation='second-order'<br class=""> wfc_extrapolation='second-order'<br class=""> /<br class=""><br class="">ATOMIC_SPECIES<br class="">Si 28.086 Si.pbe-mt_gipaw.UPF<br class="">H 1.00794 H.pbe-vbc.UPF<br class="">Li 6.941 Li.pbe-s-mt.UPF<br class="">ATOMIC_POSITIONS (crystal)<br class="">H 0.25 -0.00517 0 0 0 0<br class="">H 0.75 -0.00517 0 0 0 0<br class="">Si 0.51097 0.49804 0.16473<br class="">Si 0.35376 0.49734 0.35774<br class="">Si 0.25 0.24742 0.05541 0 0 0<br class="">Si 0.24944 0.24765 0.27061<br class="">Si 0.75 0.24742 0.05541 0 0 0<br class="">Si 0.75919 0.24761 0.28048<br class="">Si 6.33534E-4 0.49808 0.16495<br class="">Si 0.07141 0.49748 0.38744<br class="">Si -5.17962E-4 0.2482 0.10971<br class="">Si 0.01902 0.24763 0.33382<br class="">Si 0.75553 0.49764 0.22403<br class="">Si 0.50177 0.24816 0.10965<br class="">Si 0.4958 0.24746 0.33137<br class="">Si 0.25633 0.49758 0.21703<br class="">H 0.25 0.49483 0 0 0 0<br class="">H 0.75 0.49483 0 0 0 0<br class="">Si 0.51097 0.99804 0.16473<br class="">Si 0.35376 0.99734 0.35774<br class="">Si 0.25 0.74742 0.05541 0 0 0<br class="">Si 0.24944 0.74765 0.27061<br class="">Si 0.75 0.74742 0.05541 0 0 0<br class="">Si 0.75919 0.74761 0.28048<br class="">Si 6.33534E-4 0.99808 0.16495<br class="">Si 0.07141 0.99748 0.38744<br class="">Si -5.17962E-4 0.7482 0.10971<br class="">Si 0.01902 0.74763 0.33382<br class="">Si 0.75553 0.99764 0.22403<br class="">Si 0.50177 0.74816 0.10965<br class="">Si 0.4958 0.74746 0.33137<br class="">Si 0.25633 0.99758 0.21703<br class="">Li 0.625 0.5 0.5<br class="">K_POINTS automatic<br class="">2 2 1 0 0 0<br class="">CELL_PARAMETERS {angstrom}<br class=""> 7.6801695932 0.0000000000 0.0000000000<br class=""> 0.0000000000 7.76034 0.0000000000<br class=""> 0.0000000000 0.0000000000 24.5037250000<br class="">EOF<br class=""><br class="">_______________________________________________<br class="">Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" class="">www.max-centre.eu/quantum-espresso</a>)<br class="">users mailing list <a href="mailto:users@lists.quantum-espresso.org" class="">users@lists.quantum-espresso.org</a><br class=""><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" class="">https://lists.quantum-espresso.org/mailman/listinfo/users</a></div></div></blockquote></div><br class=""><div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">-- <br class=""><br class="">Giovanni Cantele, PhD</span></div><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><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</span></div><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""><a href="mailto:giovanni.cantele@spin.cnr.it" class="">e-mail: giovanni.cantele@spin.cnr.it</a></span></div><div style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <a href="mailto:gcantele@gmail.com" class="">gcantele@gmail.com</a><br class="">Phone: +39 081 676910<br class="">Skype contact: giocan74<br class="">Web page:<span class="Apple-converted-space"> </span></span><a href="https://sites.google.com/view/giovanni-cantele" class="">https://sites.google.com/view/giovanni-cantele</a></div></div></div></div>
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