Dear Meili<div><br></div><div>I am not sure that I understand what you mean and what the problem is.</div><div>Just two comments:</div><div>- PBC are taken into account working with distances</div><div>- CP2K works with atomic units</div><div><br></div><div>Regards</div><div>Marcella<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, July 13, 2022 at 2:45:28 PM UTC+2 meilil...@gmail.com wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Dear Marcella,<div><br></div><div>I will try XYZ_DIAG or XYZ_OUTERDIAG. And Please allow me to ask question.</div><div><br></div><div>I tried the &DISTANCE (ATOMS 1 97) to set up the CVs. Below is part of my input file for your reference: </div><div>#1 is a fixed Fe atom in the metal during MTD. Its coordinates are (0, 0, -9.7). </div><div>#97 is the Oxygen atom and is flexible. </div><div>Picture 2 is the output file including CV1 and CV2 and size of cell box(ABC information). </div><div>Picture 1 is sketch showing the box size and position of O atom and Fe atom in 2D plot.<br><br> I found a different description for CV1. I try to use picture 1 and picture 2 to describe it. </div><div>I add the WALL of position at Lx/2 and Ly/2. The input file(MD_meta.inp) is attached. </div><div>However, the trajectory looks strange. I guess the problems are between PBC and distance </div><div>instead of Position to result in the WALL setup maybe wrong. I am not sure other description for distance</div><div>will have this issue or not. However, I didn't find the description for position of one atom. </div><div><br>Thanks so much for any advice and ideas.<br><br>%%%%%%COLVAR%%%%%%%%<br> &COLVAR<br><br> &DISTANCE<br><br> ATOMS 1 97<br><br> AXIS X<br><br> &END<br><br> &END COLVAR<br><br> &COLVAR<br><br> &DISTANCE<br><br> ATOMS 1 97<br><br> AXIS Y<br><br> &END<br><br> &END COLVAR<br><br>%%%%%%WALL setup%%%%%%%%<br><br> &METAVAR<br><br> SCALE 0.1<br><br> COLVAR 1<br><br> &WALL<br><br> POSITION 4.8<br><br> TYPE QUARTIC<br><br> &QUARTIC<br><br> DIRECTION WALL_PLUS<br><br> K 100.0<br><br> &END<br><br> &END<br><br> &METAVAR<br><br> SCALE 0.1<br><br> COLVAR 2<br><br> &WALL<br><br> POSITION 4.2<br><br> TYPE QUARTIC<br><br> &QUARTIC<br><br> DIRECTION WALL_PLUS<br><br> K 100.0<br><br> &END<br><br> &END<br><br>%%%%%%%%%%%%%%</div><div><br></div><div><br></div><div>Best,</div><div>Meili</div><div>University of Miami<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">在2022年7月13日星期三 UTC-4 07:51:54<Marcella Iannuzzi> 写道：<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Meili<div><br></div><div>You can try</div><div><ul><li><a href="https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/XYZ_DIAG.html" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/XYZ_DIAG.html&source=gmail&ust=1657802860795000&usg=AOvVaw017nxbxWx4n6fktzYj90Pq">XYZ_DIAG</a></li></ul>or</div><div><ul><li><a href="https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/XYZ_OUTERDIAG.html" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/XYZ_OUTERDIAG.html&source=gmail&ust=1657802860795000&usg=AOvVaw1ogxImjMs868htpscM6Xgi">XYZ_OUTERDIAG</a></li></ul></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">or the distance from a point.</div><div dir="auto" class="gmail_attr">The wall is applied via</div><div dir="auto" class="gmail_attr"><ul><li><a href="https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/MOTION/FREE_ENERGY/METADYN/METAVAR/WALL.html" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://manual.cp2k.org/cp2k-9_1-branch/CP2K_INPUT/MOTION/FREE_ENERGY/METADYN/METAVAR/WALL.html&source=gmail&ust=1657802860795000&usg=AOvVaw3bgYRXM5hMlyXhDMA9o-cc">WALL</a></li></ul></div><div dir="auto" class="gmail_attr">It can be used multiple times to define a confinement region</div><div dir="auto" class="gmail_attr"><br></div><div dir="auto" class="gmail_attr">Regards</div><div dir="auto" class="gmail_attr">Marcella</div></div><div class="gmail_quote"><div dir="auto" class="gmail_attr"><br></div><div dir="auto" class="gmail_attr"><br></div><div dir="auto" class="gmail_attr">On Tuesday, July 12, 2022 at 6:11:25 PM UTC+2 <a rel="nofollow">meilil...@gmail.com</a> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Dear CP2K users</div><div><br></div>I am using Metadynamics to research the adsorption of one O atom on the surface of metal. I plan to use x-axis of O atom as CV1 and y-axis of same O atom as CV2. <div><div><br></div><div>I am wondering how to set up the position (instead of distance) of &COLVAR. and how to set up the WALL to constrain the O atom within a certain small region on the metal surface. </div><div><br></div><div>Please let us know if any advices, and many thanks in advance!</div><div><br></div><div><div><div><div>Best,</div><div>Meili</div><div>University of Miami</div><div><br></div><div><br></div><div><br></div></div></div></div></div></blockquote></div></blockquote></div></blockquote></div>
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