Missing atom on interface

[petavazohi]

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]

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]

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