Good time of day,
dear lammps users.
I found an interesting work of David Farrel.
Is it necessary to use fixed volume in z direction?
Thank you for your attention.
boundary p p p # periodic BCs on x,y plane faces, z dimension fixed volume
http://lammps.sandia.gov/threads/msg05267.html
units metal # sets units to 'metal' units - Atomic units w/ ps timescale
dimension 3
boundary p p p # periodic BCs on x,y plane faces, z dimension fixed volume
atom_style atomic # default attribute style
neighbor 1.0 bin # sets maximum neighbor search radius to cutoff+value, using bin-sort algorithm
neigh_modify delay 5 check yes # checks if neighbor list should be rebuilt every 5 steps
# Create geometry using internal stuff
lattice diamond 4.3765
region box block 0 50 0 50 0 50
create_box 2 box # initialize box
create_atoms 2 box basis 1 2 basis 2 2 basis 3 2 basis 4 2 basis 5 1 basis 6 1 basis 7 1 basis 8 1 # create atoms
region rPKA sphere 25 24.5 49.5 .1
mass 1 12.0 # type 1 = C
mass 2 28.1 # type 2 = Si
# Define potential
pair_style zbl/tersoff .529 .00552635 1.0
pair_coeff * * SiC_Devanathan_JNM_1998_zbl.tersoff C Si
# Groups
region rallatoms block INF INF INF INF INF INF
region rinterior block 2 48 2 48 2 INF
region rexterior block 2 48 2 48 2 INF side out
group interior region rinterior
group exterior region rexterior
group PKA region rPKA
# Initialization
compute 1 all temp
compute 2 interior coord/atom 2.2
compute 3 interior ke/atom
#velocity all create 1200.0 34986 # initialize atom velocities to temperature, seed random num generator
fix 1 all nve
fix 2 exterior temp/rescale 1 1200.0 1200.0 0.5 1.0 region rexterior
fix 3 interior temp/rescale 1 1200.0 1200.0 0.5 1.0 region rinterior
timestep 0.001
thermo 100
thermo_style custom step temp pe etotal press
run 1000 # run the equilibriation phase
unfix 3 # remove the rescaling fix from the interior
run 1000 # continue to equilibriate
# set PKA velocity to correspond to ~ 10 keV - 2620.549 Ang/ps
set group PKA vx 109.5108
set group PKA vy 301.1547
set group PKA vz -2600.8815
# set timestep to smaller value for initial phase of collisions (.01 fs for .2 ps)
timestep 0.00001
thermo 100
dump 1 interior custom 100 test_init_col.dump x y z c_3 tag type c_2
dump 2 PKA custom 100 PKA_traj_init_col.dump x y z c_3 tag type c_2
run 20000 # run the collisional phase for .2 ps
# run intermediate phase with intermediate timestep (.1 fs for 1 ps)
timestep 0.0001
undump 1
undump 2
dump 3 interior custom 100 test_inter_evolve.dump x y z c_3 tag type c_2
dump 4 PKA custom 100 PKA_traj_inter_evolve.dump x y z c_3 tag type c_2
run 10000
# after initial phase, let evolve for remainder of time using .001 ps timestep (1 fs for 10 ps)
undump 3 # close the previous dumps
undump 4
timestep .001
dump 5 interior custom 100 test_final_evolve.dump x y z c_3 tag type c_2
dump 6 PKA custom 100 PKA_traj_final_evolve.dump x y z c_3 tag type c_2
run 10000