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Identifying atoms on the grain boundaries


I am trying to figure out how to identify and modify only the atoms along the grain boundaries in my model. What parameters does OVITO consider to identify the grain boundary atoms? Is there any other way (like the nearest-neighbour analysis) to separately identify the atoms on the grain boundaries from the rest of the atoms in the model? Thank you.


Hi Rajesh,

Can you please be more specific about which function in OVITO your question refers to? If you speak about identification of grain boundary atoms in OVITO, do you mean the Grain Segmentation modifier or one of the atomistic structure identification modifiers like PTM or CNA? The latter tools each use different nearest-neighbour based classification schemes to discriminate crystalline atoms from "defective" atoms, including GB atoms. The Grain Segmentation modifier, on the other hand, is a higher level function, which uses local lattice orientation information to partition the atoms into crystallite grains. It doesn't select grain boundary atoms specifically, but rather identifies entire grains.


Hello Dr. Stukowski,

Thank you for the reply. I was referring to PTM actually. I am trying to identify and isolate the grain boundary atoms, and then modify them (substitute the existing GB metal atoms with another metal atom) using a code. I was trying to understand how the nearest-neighbour analysis is done to differentiate the GB atoms from the rest of the atoms. Is it done by calculating the number of nearest neighbours of the atoms in a single-crystal model, and then comparing that with the number of nearest neighbours of the atoms in the polycrystalline model? I tried the nearest-neighbour distance analysis in a code by calculating the distance of one atom with all the other atoms and giving a cutoff distance based on the distance of atoms in the crystalline part of the model. But I was not able to successfully isolate the GB atoms. Thanks in advance!


The PTM algorithm is designed to identify bulk atoms in the interior of the grains, e.g. fully-coordinated FCC or BCC atoms. Grain boundary atoms are then typically those atoms which were not identified as perfect crystal atoms by the PTM, i.e. unidentified atoms which get assigned the special structure class "Other". For details of the PTM algorithm, please have a look in the original publication. It's more complex than just simply counting nearest neighbor atoms.

Whether you can treat any non-crystalline atom identified by PTM as a grain boundary atom depends on whether your system contains other types of crystal defects too, e.g. dislocations, point-defects, etc. PTM itself only determines that an atom has a defective local environment. It cannot discriminate between different kinds of crystal defects.

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