Homec4science
Diffusion lammps (master) Browse

lammps/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/run.in
6e7504f15328master

Last Change
Raw File

run.in
View Options

# -- Init Section --
include system.in.init
boundary p p f
# -- Atom Definition Section --
read_data system.data
# -- Settings Section --
include system.in.settings
# -- Run Section --
timestep 0.0025
dump 1 all custom 200 traj.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal
thermo 100 # time interval for printing out "thermo" data
# ---- Set up the physical environment ----
# Add gravity:
fix fxGrav gMobile gravity 0.05 vector 0 0 -1
# Create a "ground" surface.
# This is a repulsive "wall" which particles can bounce off of:
fix fxWall gMobile wall/lj126 zlo EDGE 1.0 0.8908987181403393 1.0
# ---- Evolve the system: ----
# Evolve the (mobile) atoms using ordinary Newton's laws (NVE)
fix fxNVE gMobile nve
# IF YOU WANT TO ADD DAMPING, THEN UNCOMMENT THE NEXT LINE:
#fix fxLan gMobile langevin 0.001 0.001 10000.0 48279
# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve"
# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)
# This was not tested.
# OPTIONAL:
# For efficient simulation in parallel, try using "fix balance":
# (This will adjust the spatial decomposition as the distribution of
# particles changes over time.)
# http://lammps.sandia.gov/doc/fix_balance.html
# fix fxBalance gMobile balance 1000 1.1 shift 1000 xy 20 1.1
# Alternatiely, try this:
#fix fxBalance gMobile balance 1000 1.2 rcb
# OPTIONAL: Improve efficiency by omitting the calcuation of interactions
# between immobile atoms:
neigh_modify exclude group gImmobile gImmobile
restart 50000 restart_nvt
run 200000
write_data system_after_nvt.data
c4science · Help