Hi everyone
I have attached two image. one is before simulation and another is during simulation. Can anyone tell me why my oxygen particle is not contributing on the simulation?
# -------------- Initialize Simulation ------------
echo both
units metal # set 'metal' units (Angstrom,ps timescale)
dimension 3
boundary p p p # periodic BCs
atom_style charge
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes # neighbor command modifies potential's natural cutoff_needed?
# ----------------------- ATOM DEFINITION ----------------------------
read_data Fe_Fe3O4_center.lmp
write_dump all atom sinusoid_4.lammpstrj
# --------------- Creat Atoms / Geometry -----------------------
mass 1 55.847
mass 2 15.999
region rPKA sphere 52.127 52.127 104.255 .1 # Create spherical region 'rpka' at x, y, x with radius
# ------------------Define Interatomic Potential -----------------
pair_style eam/fs # Finnis-Sinclair EAM Potential from NIST
pair_coeff * * Fe_2.eam.fs Fe Fe # Applies Fe coefficients to all atom pairs # Fe-Fe
pair_style morse 2.5
pair_coeff 1 2 0.3 2.0 2.5 # Fe-O
pair_style buck 2.5
pair_coeff 2 2 22764.3 0.1490 20.4 7.4 # O-O
pair_style coul/dsf 0.15 15
pair_coeff * *
# Groups
region rallatoms block INF INF INF INF INF INF # define region of entire domain
region rinterior block 2 102.255 2 102.255 2 INF # define inner box region used for simulation domain
region rexterior block 2 102.255 2 102.255 2 INF side out # define thermostat region outside of simulation domain
group interior region rinterior # define group called 'interior' comprised of region 'rinterior'
group exterior region rexterior
group PKA region rPKA
# --------------Initialization----------------
compute 1 all temp
compute 2 interior coord/atom cutoff 2.2
compute 3 interior ke/atom
velocity all create 1200.0 34986 # initialize atom velocites to temperature, seed random num generator
fix 1 all nve # specifiy constant NVE interation to update position andn velocity for atoms in ther group each timestep
fix 2 exterior temp/rescale 1 100.0 100.0 0.5 1.0 region rexterior # set atoms in exterior group temperature to 100k by rescalling velocities.
fix 3 interior temp/rescale 1 100.0 100.0 0.5 1.0 region rinterior # set atoms in interior group temperature to 100k by rescalling velocities.
timestep 0.001
thermo 100 # compute & Print thermodynamics info every 100 steps
thermo_style custom step temp pe etotal press # 'custom' specifies what thermo info is printed
run 1000 # run the equilibration phase
unfix 3 # remove the rescaling fix from the interior
run 1000 # continue to equilibrate
# set PKA velocities to correspond to ~ 10keV - 2620.549 Ang/ps
velocity PKA set 109.5108 301.1547 -2600.8815 units box
# set timestep to smaller value for initial phase of collision (.01 fs for .2 ps)
timestep 0.00001
thermo 100
dump 1 interior custom 100 test_init_col.dump type x y z c_3 c_2
dump 2 PKA custom 100 PKA_traj_init_col.dump type x y z c_3 c_2
run 2000 # 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 type x y z c_3 c_2
dump 4 PKA custom 100 PKA_traj_inter_evolve.dump type x y z c_3 c_2
run 1000 # run the collisional phase for .1 ps
# run intermediate phase with intermediate timestep (.1 fs for 1 ps)
timestep 0.0001
undump 3 # close the previous dumps
undump 4
timestep 0.001
dump 5 interior custom 100 test_final_evolve.dump type x y z c_3 c_2
dump 6 PKA custom 100 PKA_traj_final_evolve.dump type x y z c_3 c_2
run 1000 # run the collisional phase for .1 ps
Hi Zahidul,
As far I know, pair_coeff command can override a previous setting for the same I,J pair. You may try pair style hybrid or hybrid/overlay for assigning multiple pair styles.
http://lammps.sandia.gov/doc/pair_hybrid.html
Thanks
Gourav
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