Great catch! In VMD and using the same exact cell dimensions: ``` pbc set {18.3675 18.3675 20.1312} -all pbc box ``` <img alt="Screen Shot 2024-01-26 at 1.11.49 PM.png" width="220px" height="188px" src="cid:b488d658-e8bb-48ad-bd92-bb894c4afa07" /><div>it is off in XY plane. It seems that in ASE-PyCP2K, ``` structure = read('thickness-1-A_1.cif') structure.center(axis=2) ``` is not centering anything. Should I try using `&CENTER_COORDINATES` to center it? </div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Friday, January 26, 2024 at 12:59:00 PM UTC-6 Станислав Бачурин wrote: </div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><span style="color:rgb(55,65,81);font-family:Söhne,ui-sans-serif,system-ui,-apple-system,"Segoe UI",Roboto,Ubuntu,Cantarell,"Noto Sans",sans-serif,"Helvetica Neue",Arial,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";font-size:16px">Could you check if your system is aligned in the xy plane? Maybe, before applying xy periodicity, it needs to be properly oriented. <span style="color:rgb(55,65,81);font-family:Söhne,ui-sans-serif,system-ui,-apple-system,"Segoe UI",Roboto,Ubuntu,Cantarell,"Noto Sans",sans-serif,"Helvetica Neue",Arial,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";font-size:16px">Also, it is necessary to set the dimensions along the Z-axis with a slight margin in the cell settings until this warning disappears. I struggled a lot with calculations under gas-phase conditions. <span style="color:rgb(55,65,81);font-family:Söhne,ui-sans-serif,system-ui,-apple-system,"Segoe UI",Roboto,Ubuntu,Cantarell,"Noto Sans",sans-serif,"Helvetica Neue",Arial,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";font-size:16px">I had exactly the same strange behavior - the nuclei almost merged in the organic molecule. When I figured out the cell settings and Poisson, everything was optimized correctly.<div class="gmail_quote"><div dir="auto" class="gmail_attr">пятница, 26 января 2024 г. в 21:49:57 UTC+3, Ardalan Hayatifar: </div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Thanks for your comment. I have been trying `PERIODIC XYZ` or `PERIODIC XY` and that doesn't fix it either. Having more layers also shows the same behavior. <div class="gmail_quote"><div dir="auto" class="gmail_attr">On Friday, January 26, 2024 at 12:46:41 PM UTC-6 Станислав Бачурин wrote: </div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">*** WARNING in pw_env_methods.F:738 :: The selected periodicities in the *** *** sections &CELL and &POISSON do not match *** You set periodicity to None, but use the periodic Poisson solver. Try wavelet or switch to Periodic in your Cell's settings. <div class="gmail_quote"><div dir="auto" class="gmail_attr">пятница, 26 января 2024 г. в 21:38:47 UTC+3, Ardalan Hayatifar: </div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> I am using CP2K version 2023.2. I want to perform `GEO_OPT`on FeS layers that I have made using Pymatgen. I am using .cif file from published data. Input File:Note: `MAX_SCF` set to 100 results in the same behavior.(attached)Problem:This is a convergence problem. Upon visualization I can see that things get closer than they should and the system acts crazy.Pictures:Initial:<img alt="Screen Shot 2024-01-26 at 10.46.20 AM.png" width="213px" height="182px" src="https://groups.google.com/group/cp2k/attach/33366aeb3f013/Screen%20Shot%202024-01-26%20at%2010.46.20%20AM.png?part=0.5&view=1"> After some SCF cycels:<img alt="Screen Shot 2024-01-26 at 10.46.45 AM.png" width="213px" height="169px" src="https://groups.google.com/group/cp2k/attach/33366aeb3f013/Screen%20Shot%202024-01-26%20at%2010.46.45%20AM.png?part=0.1&view=1"> Another representation:<img alt="Screen Shot 2024-01-26 at 10.10.58 AM.png" width="213px" height="102px" src="https://groups.google.com/group/cp2k/attach/33366aeb3f013/Screen%20Shot%202024-01-26%20at%2010.10.58%20AM.png?part=0.2&view=1"> (shown atoms distance ~1A!)What I’ve tried: - I have changed the slab size in X and Y directions to remove size effects. Tried dimensions that are at least 1X1 A and 1.8 X1.8 A dimensions - all while having 15 A vacuum in Z- I have monitored the input file for close contacts using `CHECK_INTERATOMIC_DISTANCES 1`. There are no pair-wise distances below 2.5 A.- PBC effects: I have tried adding 1 A to cell dimensions `ABC` to again eliminate possible overlaps, but the behavior persists.- I have tried higher cutoff values (e.g. 1200).- I have tried writing the input so that it uses a `.xyz` file instead of PyCP2K-ASE format and that doesn’t change anything.- Centering the solid layer using `&CENTER_COORDINATES` also did not help. At this point I’d like to ask for any help or suggestions. It it possible that my parameters are wrong? Thanks in advance for your time. </blockquote></div></blockquote></div></blockquote></div></blockquote></div> -- You received this message because you are subscribed to the Google Groups "cp2k" group. 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