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lammps/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt
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run.in.nvt
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# PREREQUISITES:
#
# You must use moltemplate.sh to create 3 files:
# system.data system.in.init system.in.settings
# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
# (You do not need to run LAMMPS to equilibrate the system before
# using this file.)
# ----------------------------- Initialization Section --------------------
include system.in.init
# ----------------------------- Atom Definition Section -------------------
read_data system.data
# ----------------------------- Settings Section --------------------------
include system.in.settings
# ----------------------------- Run Section -------------------------------
# Optional: Improve efficiency by omitting the calcuation of interactions
# between immobile atoms. (Note: This is not optional under NPT conditions.)
neigh_modify exclude group Cgraphene Cgraphene
# Only the Cgraphene atoms are immobile.
group mobile subtract all Cgraphene
# -- minimization protocol --
# Unfortunately you can not use the LAMMPS "minimize" command on this system
# because there is no way to immobilize the carbon graphene & nanotube atoms
# during minimization. Instead, we can use langevin dynamics with a large
# damping parameter and a small timestep.
print "--------- beginning minimization (using fix langevin) ---------"
timestep 0.1
fix fxlan mobile langevin 1.0 1.0 100.0 48279
fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation)
thermo 100
run 2500
unfix fxlan
unfix fxnve
# -- simulation protocol --
print "--------- beginning simulation (using fix nvt) ---------"
timestep 1.0
dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal press vol epair #ebond eangle edihed
thermo 500 # time interval for printing out "thermo" data
# Integrate the equations of motion:
fix fxMoveStuff mobile nvt temp 300.0 300.0 100.0
# The next two lines recalculate the temperature
# using only the mobile degrees of freedom:
compute tempMobile mobile temp
fix_modify fxMoveStuff temp tempMobile
restart 5000000 restart_nvt
run 10000000
write_data system_after_nvt.data
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