i new the format but confusion is from where to see what id lammps has assigned to my selected atom? does it depends upon the order in which atoms are created? for example i have added one or two adatoms on the surface i want to write coordinates of these adatoms in this file. i can easily find the coordinates of the created atoms but i didnot find exact method to find id of these coordinates as assigned by lammps. i have created these atoms using
lattice fcc 3.63 orient x 1 -1 0 orient y 1 1 -2 orient z 1 1 1 origin 0 0 0
region domain block 2.1 52.1 2.1 52.1 -5.1 22.1 units box
region rod block 0.1 50.1 0.1 50.1 0.1 15.1 units box side in
region adatoms block 23 27 23 27 16.1 17.1 units box
create_box 3 domain
create_atoms 1 region rod
create_atoms 1 region adatoms
the first command creates 2869 atoms
whereas second creat_atoms command creats 2 atoms , now what should be the id of these two atoms which i can write in the file include in the neb command.
previously i used label option in vmd to find id but not sure this is correct in neb calculations as well.
thanks.
imran
i new the format but confusion is from where to see what id lammps has
assigned to my selected atom? does it depends upon the order in which atoms
are created? for example i have added one or two adatoms on the surface i
want to write coordinates of these adatoms in this file. i can easily find
the coordinates of the created atoms but i didnot find exact method to find
id of these coordinates as assigned by lammps. i have created these atoms
using
lattice fcc 3.63 orient x 1 -1 0 orient y 1 1 -2 orient z 1 1 1 origin
0 0 0
region domain block 2.1 52.1 2.1 52.1 -5.1 22.1 units box
region rod block 0.1 50.1 0.1 50.1 0.1 15.1 units box side in
region adatoms block 23 27 23 27 16.1 17.1 units box
create_box 3 domain
create_atoms 1 region rod
create_atoms 1 region adatoms
the first command creates 2869 atoms
whereas second creat_atoms command creats 2 atoms , now what should be the
id of these two atoms which i can write in the file include in the neb
command.
previously i used label option in vmd to find id but not sure this is
correct in neb calculations as well.
the documentation of the create_atoms command clearly states what atom IDs
are assigned to newly created atoms:
Atom IDs are assigned to created atoms in the following way. The collection
of created atoms are assigned consecutive IDs that start immediately
following the largest atom ID existing before the create_atoms command was
invoked. When a simulation is performed on different numbers of processors,
there is no guarantee a particular created atom will be assigned the same
ID. If molecules are being created, molecule IDs are assigned to created
molecules in a similar fashion.
you may need to also set:
atom_modify id yes
to actually trigger the allocation of storage for atom ids, since by
default for systems created entirely from create_atoms that is not the
case.
axel.
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thanks.