Hi folks!
This question is primarily for Steve, but any responses would be appreciated. I'm planning to use fix_coord_original and have some questions regarding the variable xoriginal:
1. Are there entries in xoriginal for ghost atoms as well as local atoms?
2. If so, are periodic boundary conditions taken into account for the values of xoriginal for ghost atoms? I.e. When xoriginal is set, does the entry for xoriginal for a ghost atom differ from the entry for its local 'parent'?
3. How do we access xoriginal from a different fix?
Thank you,
Jon Zimmerman
Hi Jon.
1. Are there entries in xoriginal for ghost atoms as well as local atoms?
Ghost atoms are local atoms on some processor, so there are xoriginal
coordinates stored for ghost atoms, but only on the processor that
owns them. So the information is available, but it might need to be
communicated.
2. If so, are periodic boundary conditions taken into account for the values of xoriginal for ghost atoms? I.e. When xoriginal is set, does the entry for xoriginal for a ghost atom differ from the entry for its local 'parent'?
"Unwrapped" coordinates are stored in xoriginal, so PBCs are taken
into account. Ghost atoms do not have their own independent xoriginal
coordinates stored. To get xoriginal coordinates for a ghost atom,
there would have to be a query to the "parent", which likely lives on
a different processor.
3. How do we access xoriginal from a different fix?
Here's an example input script that accesses xoriginal for output:
# 3d Lennard-Jones melt
variable x index 20
variable y index 20
variable z index 20
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
fix 2 all coord/original
dump 1 all custom 100 jons.dump tag type x y z f_2[1] f_2[2] f_2[3]
run 100
Also, see:
http://lammps.sandia.gov/doc/Section_howto.html#4_15
Paul