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[lammps-users] How to delete molecules within a sphere
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[lammps-users] How to delete molecules within a sphere


From: wu5@llnl.gov
Date: Tue, 25 May 2010 14:26:14 -0700

Dear All,

I am trying to find a way to create a hole inside a molecular solid. The delete_atoms command deletes all atoms within a spherical region, but it doesn't protect molecular structures.

Is there a way in LAMMPS to delete molecules within a specified region? or specify the molecules within a group?

I have tried to use the compute property/molecule comment to find out all the molecules within a group, but I don't know why to access the computed molecular list to specify a group.

The following comments that I used resulted in 0 molecule in group group_holem.

----------------------------------------------
region hole sphere ${half_lx} ${half_ly} ${half_lz} 10.0 side in units box

group group_hole region hole

compute 3 group_hole property/molecule mol

group group_holem molecule c_3
----------------------------------------------------

Thank you very much,

Christine Wu