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henniggroup / MPInterfaces

Python package that enables high throughput analysis of interfaces(two dimensional materials, hetero-structures, nanoparticles with and without ligands/solvents).
http://henniggroup.github.io/MPInterfaces/
MIT License
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Missing atom on interface #17

Open petavazohi opened 6 years ago

petavazohi commented 6 years ago

Hi, Thank you for the very useful script. I am using your script to match surfaces of periodic systems. I follow the steps like the example in MPInterfaces/examples/hetero_interface.py. For some systems I am missing atoms of the top 2d structure in the interface. Do you know how I can fix this?

joshgabriel commented 6 years ago

Thanks for your interest in this. Is it be possible for you to describe which system you are using? What is the vacuum spacing you are using in the input for the substrate and the 2d structure? This info would help.

petavazohi commented 6 years ago

This is a random example : Substrate : AgO, space group 2 , direction 010. 2d-slab : FeS , space group 129 , direction 001 min_thick=10,min_vac=25 max_area= 400 ,max_mismatch = 0.03,max_angle_diff = 1, r1r2_tol = 0.01 I wrote a script that fills up the missing atoms but I'm not sure If this is correct scientifically. sorry for the long file but here is the matched poscar : Fe26 Ag72 S26 O72 1.0 -0.000000 5.096687 0.000000 32.195031 2.548344 0.000000 -0.000000 -0.000000 -33.534154 Ag O Ag O Ag O Fe S 24 24 24 24 24 24 26 26 Selective dynamics direct 0.507954 0.709924 0.372754 F F F Ag 0.007954 0.709924 0.372754 F F F Ag 0.591287 0.543258 0.372754 F F F Ag 0.091287 0.543258 0.372754 F F F Ag 0.674621 0.376591 0.372754 F F F Ag 0.174621 0.376591 0.372754 F F F Ag 0.757954 0.209924 0.372754 F F F Ag 0.257954 0.209924 0.372754 F F F Ag 0.841287 0.043258 0.372754 F F F Ag 0.341287 0.043258 0.372754 F F F Ag 0.424621 0.876591 0.372754 F F F Ag 0.924621 0.876591 0.372754 F F F Ag 0.605281 0.789434 0.383764 F F F Ag 0.105281 0.789434 0.383764 F F F Ag 0.688614 0.622767 0.383764 F F F Ag 0.188614 0.622767 0.383764 F F F Ag 0.771947 0.456100 0.383764 F F F Ag 0.271947 0.456100 0.383764 F F F Ag 0.855281 0.289434 0.383764 F F F Ag 0.355281 0.289434 0.383764 F F F Ag 0.938614 0.122767 0.383764 F F F Ag 0.438614 0.122767 0.383764 F F F Ag 0.521947 0.956100 0.383764 F F F Ag 0.021947 0.956100 0.383764 F F F Ag 0.511356 0.671872 0.394210 F F F O 0.011356 0.671872 0.394210 F F F O 0.594689 0.505205 0.394210 F F F O 0.094689 0.505205 0.394210 F F F O 0.678022 0.338539 0.394210 F F F O 0.178022 0.338539 0.394210 F F F O 0.761356 0.171872 0.394210 F F F O 0.261356 0.171872 0.394210 F F F O 0.844689 0.005205 0.394210 F F F O 0.344689 0.005205 0.394210 F F F O 0.428022 0.838539 0.394210 F F F O 0.928022 0.838539 0.394210 F F F O 0.508372 0.740331 0.373318 F F F O 0.008372 0.740331 0.373318 F F F O 0.591705 0.573664 0.373318 F F F O 0.091705 0.573664 0.373318 F F F O 0.675038 0.406997 0.373318 F F F O 0.175038 0.406997 0.373318 F F F O 0.758372 0.240331 0.373318 F F F O 0.258372 0.240331 0.373318 F F F O 0.841705 0.073664 0.373318 F F F O 0.341705 0.073664 0.373318 F F F O 0.425038 0.906997 0.373318 F F F O 0.925038 0.906997 0.373318 F F F O 0.487773 0.750286 0.489272 F F F Ag 0.987773 0.750286 0.489272 F F F Ag 0.571107 0.583619 0.489272 F F F Ag 0.071107 0.583619 0.489272 F F F Ag 0.654440 0.416952 0.489272 F F F Ag 0.154440 0.416952 0.489272 F F F Ag 0.737773 0.250286 0.489272 F F F Ag 0.237773 0.250286 0.489272 F F F Ag 0.821107 0.083619 0.489272 F F F Ag 0.321107 0.083619 0.489272 F F F Ag 0.404440 0.916952 0.489272 F F F Ag 0.904440 0.916952 0.489272 F F F Ag 0.585100 0.829795 0.500282 F F F Ag 0.085100 0.829795 0.500282 F F F Ag 0.668433 0.663129 0.500282 F F F Ag 0.168433 0.663129 0.500282 F F F Ag 0.751767 0.496462 0.500282 F F F Ag 0.251767 0.496462 0.500282 F F F Ag 0.835100 0.329795 0.500282 F F F Ag 0.335100 0.329795 0.500282 F F F Ag 0.918433 0.163129 0.500282 F F F Ag 0.418433 0.163129 0.500282 F F F Ag 0.501767 0.996462 0.500282 F F F Ag 0.001767 0.996462 0.500282 F F F Ag 0.491175 0.712234 0.510728 F F F O 0.991175 0.712234 0.510728 F F F O 0.574508 0.545567 0.510728 F F F O 0.074508 0.545567 0.510728 F F F O 0.657842 0.378900 0.510728 F F F O 0.157842 0.378900 0.510728 F F F O 0.741175 0.212234 0.510728 F F F O 0.241175 0.212234 0.510728 F F F O 0.824508 0.045567 0.510728 F F F O 0.324508 0.045567 0.510728 F F F O 0.407842 0.878900 0.510728 F F F O 0.907842 0.878900 0.510728 F F F O 0.488191 0.780692 0.489835 F F F O 0.988191 0.780692 0.489835 F F F O 0.571524 0.614025 0.489835 F F F O 0.071524 0.614025 0.489835 F F F O 0.654858 0.447359 0.489835 F F F O 0.154858 0.447359 0.489835 F F F O 0.738191 0.280692 0.489835 F F F O 0.238191 0.280692 0.489835 F F F O 0.821524 0.114025 0.489835 F F F O 0.321524 0.114025 0.489835 F F F O 0.404858 0.947359 0.489835 F F F O 0.904858 0.947359 0.489835 F F F O 0.467593 0.790647 0.605790 F F F Ag 0.967593 0.790647 0.605790 F F F Ag 0.550926 0.623980 0.605790 F F F Ag 0.050926 0.623980 0.605790 F F F Ag 0.634259 0.457314 0.605790 F F F Ag 0.134259 0.457314 0.605790 F F F Ag 0.717593 0.290647 0.605790 F F F Ag 0.217593 0.290647 0.605790 F F F Ag 0.800926 0.123980 0.605790 F F F Ag 0.300926 0.123980 0.605790 F F F Ag 0.384259 0.957314 0.605790 F F F Ag 0.884259 0.957314 0.605790 F F F Ag 0.648253 0.703490 0.616799 F F F Ag 0.148253 0.703490 0.616799 F F F Ag 0.731586 0.536823 0.616799 F F F Ag 0.231586 0.536823 0.616799 F F F Ag 0.814919 0.370157 0.616799 F F F Ag 0.314919 0.370157 0.616799 F F F Ag 0.898253 0.203490 0.616799 F F F Ag 0.398253 0.203490 0.616799 F F F Ag 0.981586 0.036823 0.616799 F F F Ag 0.481586 0.036823 0.616799 F F F Ag 0.564919 0.870157 0.616799 F F F Ag 0.064919 0.870157 0.616799 F F F Ag 0.470994 0.752595 0.627246 F F F O 0.970994 0.752595 0.627246 F F F O 0.554327 0.585928 0.627246 F F F O 0.054327 0.585928 0.627246 F F F O 0.637661 0.419262 0.627246 F F F O 0.137661 0.419262 0.627246 F F F O 0.720994 0.252595 0.627246 F F F O 0.220994 0.252595 0.627246 F F F O 0.804327 0.085928 0.627246 F F F O 0.304327 0.085928 0.627246 F F F O 0.387661 0.919262 0.627246 F F F O 0.887661 0.919262 0.627246 F F F O 0.468010 0.821054 0.606353 F F F O 0.968010 0.821054 0.606353 F F F O 0.551344 0.654387 0.606353 F F F O 0.051344 0.654387 0.606353 F F F O 0.634677 0.487720 0.606353 F F F O 0.134677 0.487720 0.606353 F F F O 0.718010 0.321054 0.606353 F F F O 0.218010 0.321054 0.606353 F F F O 0.801344 0.154387 0.606353 F F F O 0.301344 0.154387 0.606353 F F F O 0.384677 0.987720 0.606353 F F F O 0.884677 0.987720 0.606353 F F F O -0.571330 1.142664 0.716707 F F F Fe -0.494406 0.988818 0.879360 T T T Fe -0.032868 1.065741 0.716707 F F F Fe -0.417483 0.834972 0.716707 F F F Fe 0.044055 0.911895 0.716707 F F F Fe -0.340560 0.681125 0.879360 T T T Fe 0.120978 0.758048 0.879360 T T T Fe -0.263637 0.527279 0.879360 T T T Fe 0.197901 0.604202 0.879360 T T T Fe -0.186714 0.373433 0.879360 T T T Fe 0.274824 0.450356 0.879360 T T T Fe 0.351747 0.296510 0.879360 T T T Fe -0.109791 0.219587 0.716707 F F F Fe -0.071330 1.142664 0.879360 T T T Fe 0.005594 0.988818 0.879360 T T T Fe -0.532868 1.065741 0.716707 F F F Fe 0.082517 0.834972 0.879360 T T T Fe -0.455945 0.911895 0.879360 T T T Fe 0.159440 0.681125 0.716707 F F F Fe -0.379022 0.758048 0.879360 T T T Fe 0.236363 0.527279 0.879360 T T T Fe -0.302099 0.604202 0.879360 T T T Fe 0.313286 0.373433 0.716707 F F F Fe -0.225176 0.450356 0.716707 F F F Fe -0.148253 0.296510 0.716707 F F F Fe -0.609791 0.219587 0.716707 F F F Fe -0.302099 1.104202 0.752829 F F F S -0.225176 0.950356 0.752829 F F F S 0.236363 1.027279 0.752829 F F F S -0.148253 0.796510 0.752829 F F F S 0.313286 0.873433 0.752829 F F F S -0.071330 0.642664 0.752829 F F F S -0.609791 0.719587 0.752829 F F F S 0.005594 0.488818 0.752829 F F F S -0.532868 0.565741 0.752829 F F F S 0.082517 0.334972 0.752829 F F F S -0.455945 0.411895 0.752829 F F F S -0.379022 0.258048 0.752829 F F F S 0.159440 1.181125 0.752829 F F F S -0.340560 1.181125 0.843238 T T T S -0.263637 1.027279 0.843238 T T T S 0.197901 1.104202 0.843238 T T T S -0.186714 0.873433 0.843238 T T T S 0.274824 0.950356 0.843238 T T T S -0.109791 0.719587 0.843238 T T T S 0.351747 0.796510 0.843238 T T T S -0.032868 0.565741 0.843238 T T T S -0.571330 0.642664 0.843238 T T T S 0.044055 0.411895 0.843238 T T T S -0.494406 0.488818 0.843238 T T T S -0.417483 0.334972 0.843238 T T T S 0.120978 0.258048 0.843238 T T T S