Forum Navigation
You need to log in to create posts and topics.

fiind all bonds angels dihedral of a specific molecle

dear all

I have a lammps data file opened with ovito.

there is a lot of molecule. how can I see all the bonds, Angeles, dihedrals of a specific molecule? for example molecule number 10, how can I see the bonds number, angels number dihedrals number, or how can I find corresponding bonds, angles or dihedrals , either visualized or in text.

thanks

Hi,

In the data inspector panel of OVITO you can filter the list of bonds by entering a Boolean expression into the input field at the top of the panel. Similar to the Expression Selection modifier, you can include references to particle properties in the filter expression. They begin with the prefixes @1 or @2, referring to the two particles connected by a bond. This feature allows you to list only bonds between particles belonging to a specific molecule. For instance, to show only bonds that are part of the molecule with the ID 10:

  @1.MoleculeIdentifier == 10

Note that this is a rather new program feature, and you may have to update your OVITO version first.

This kind of filtering in the data inspector doesn't work for angles/dihedrals/impropers though. Unlike the bonds list, you cannot filter these lists based on some particle property. As you workaround you will thus have to (temporarily) delete the molecules from the system which you are not interested in. You can do this by inserting an Expression Selection modifier followed by the Delete Selected modifier. Use an expression such as MoleculeIdentifier != 10 to select all particles not part of the molecule you are interested in. The data inspector will then display only those angles/dihredrals/impropers of atoms that haven't been removed from the system. After you are done, you can disable or completely remove the two modifiers from the pipeline again to restore the full molecular system.

-Alex

thanks