Importing Structures

Is there a way to import structures in file formats other than .emc? I’m trying to include a Pt(111) surface in my builds, but these are typically .xyz or .pdb files.

Thanks,
Nick

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Nick,

You can import InsightII and PDB formats in EMC by using the import keyword when defining your clusters:

surface import, name=“name.pdb”, ncells=3:auto:auto

which will import name.pdb with thickness 3*lcell_x when you are building in the x-direction. When using the “auto” keyword, EMC makes an estimate of the y- and z-direction number of cells based on the number of molecules and the box shape of what is supposed to be grown on top of the surface. Please note that you will have to provide a valid .psf in combination with your .pdb. In case of the InsightII format, you will have to provide both a .car and .mdf. EMC will not estimate existing bonds, since such algorithms can be ambiguous. Further information can be found in the EMC manual under

Simulation Setup → File Formats → Chemistry File → Clusters

Pieter