Hi,
I am building a cylinder from within a box but am getting an error message with lost atoms that I assume is due to overlapping atoms. When I add the delete atoms it runs but the structure does not look like a perfect cylinder anymore. However, what is very odd to me is that certain geometries do not appear to have this overlap. For example, if I change my block to 0 50 0 50 0 80 and my cylinder to x 25 25 20 INF INF it will run fine? Also, if I change from box units back to lattice it works. Why are certain geometries causing overlap?
Thanks!
------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p s s
atom_style atomic
variable latparam equal 2.856
----------------------- ATOM DEFINITION ----------------------------
lattice bcc {latparam}
region whole block 0 100 0 100 0 120 units box
create_box 1 whole
region wire cylinder x 50 50 30 INF INF units box
lattice bcc {latparam} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
create_atoms 1 region wire
mass 1 55.85
------------------------ FORCE FIELDS ------------------------------
pair_style eam/fs
pair_coeff * * Fe_mm.eam.fs Fe
#delete_atoms overlap 0.5 all all
------------------------- pressure calculations ---------------------------------
compute csym all centro/atom bcc
#compute peratomp all pe/atom
####################################### EQUILIBRATION
#set timestep
reset_timestep 0
timestep 0.001
#set temperature
velocity all create 300 12345 mom yes rot no
#fix 2 all npt temp 300 300 0.1 iso 0 0 1 drag 1
fix 2 all nvt temp 300 300 0.1
Set thermo output
thermo 500
thermo_style custom step lx ly lz press pxx pyy pzz pe temp
Run for at least 10 picosecond (assuming 1 fs timestep)
run 20000
unfix 2