#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 100000 with a timestep of 0.2
#-------------------------------------------------------------------------------
group deposition_atoms_O2 id 2049 2050
2 atoms in group deposition_atoms_O2
delete_atoms group deposition_atoms_O2
WARNING: Ignoring 'compress yes' for molecular system (../delete_atoms.cpp:126)
Deleted 2 atoms, new total = 2048
molecule depositing_species_O2 deposition_O2.dat
Read molecule template depositing_species_O2:
1 molecules
0 fragments
2 atoms with max type 1
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region deposition_region_O2 block EDGE EDGE EDGE EDGE 50 60 units box
region evaporation_region block EDGE EDGE EDGE EDGE 90 EDGE units box
uncompute thermo_temp
compute thermo_temp movable temp
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:888)
thermo ${Nthermo}
thermo 0
fix 1 movable nve
fix 2 all evaporate 1000 1000 evaporation_region 9828 molecule yes
fix dlan subset_thermostat langevin 300 300 20.0 352 tally yes
fix 3 movable ave/time 1 50000 50000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy f_dlan file 2.3_averages.txt off 1
fix 4 movable ave/time 50 1 50 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy f_dlan file 2.3_instantaneous.txt
fix deposition_O2_1 deposition_atoms_O2 deposit 50 0 10000 9828 region deposition_region_O2 mol depositing_species_O2 vz -0.06989574890928181 -0.085428137555788888 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_O2_2 deposition_atoms_O2 nve
dump trj all custom 5000 2.3.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 5000 1 5000 v_etotal v_pe v_ke file 2.3.energies.txt
dump trj_O2 deposition_atoms_O2 custom 5000 2.3.trajectory_1.xyz id mol type q xs ys zs
compute chunk_1 deposition_atoms_O2 chunk/atom bin/1d z lower 1.0 units box
fix chunk_1 deposition_atoms_O2 ave/chunk 1 50000 50000 chunk_1 density/number norm sample file 2.3_distribution_O2_1.out
timestep 0.2
run 500000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4, bins = 13 13 42
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.02 | 7.592 | 8.167 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
0 1e-06 3321.0139 93956.963 1.0165589 299.37531 0 0 0 0 -212361.64 0 0 0 -212361.64 1712.479
500000 100000 2395.05 93956.963 1.0431382 381.18831 0 0 0 0 -226058.66 0 0 0 -226058.66 2180.4636
Loop time of 190.832 on 40 procs for 500000 steps with 2142 atoms
Performance: 45.275 ns/day, 0.530 hours/ns, 2620.108 timesteps/s
98.0% CPU use with 40 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.035414 | 58.63 | 147.9 | 812.1 | 30.72
Bond | 0.01855 | 0.027219 | 0.042277 | 4.9 | 0.01
Neigh | 0.002072 | 0.17358 | 0.42995 | 43.5 | 0.09
Comm | 0.18763 | 28.96 | 94.63 | 617.0 | 15.18
Output | 0.043449 | 0.045847 | 0.048889 | 0.8 | 0.02
Modify | 25.582 | 101.36 | 188.89 | 733.9 | 53.11
Other | | 1.637 | | | 0.86
Nlocal: 53.55 ave 134 max 0 min
Histogram: 20 0 0 0 4 0 0 0 11 5
Nghost: 226.35 ave 525 max 0 min
Histogram: 16 0 0 4 4 0 3 1 4 8
Neighs: 0 ave 0 max 0 min
Histogram: 40 0 0 0 0 0 0 0 0 0
FullNghs: 1428.7 ave 3741 max 0 min
Histogram: 20 0 0 2 2 0 0 3 9 4
Total # of neighbors = 57148
Ave neighs/atom = 26.679739
Ave special neighs/atom = 0
Neighbor list builds = 2159
Dangerous builds = 0
write_dump all xyz final_2.3.xyz modify element O Si
undump trj
unfix trjE
undump trj_O2
write_dump deposition_atoms_O2 custom 2.3.deposited_1.xyz id mol type q xs ys zs
restart 0
dump sci all custom 500000 2.3.xyz id mol type q xs ys zs
run 0
Per MPI rank memory allocation (min/avg/max) = 6.9 | 7.622 | 8.047 Mbytes
Step v_time Press Volume v_sysdensity Temp E_bond E_angle E_dihed E_impro E_vdwl E_coul E_tail E_long PotEng KinEng
500000 100000 2395.05 93956.963 1.0431382 381.18831 0 0 0 0 -226058.66 0 0 0 -226058.66 2180.4636
Loop time of 2.10392e-06 on 40 procs for 0 steps with 2142 atoms
95.1% CPU use with 40 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.104e-06 | | |100.00
Nlocal: 53.55 ave 134 max 0 min
Histogram: 20 0 0 0 4 0 0 0 11 5
Nghost: 226.35 ave 525 max 0 min
Histogram: 16 0 0 4 4 0 3 1 4 8
Neighs: 0 ave 0 max 0 min
Histogram: 40 0 0 0 0 0 0 0 0 0
FullNghs: 1428.7 ave 3741 max 0 min
Histogram: 20 0 0 2 2 0 0 3 9 4
Total # of neighbors = 57148
Ave neighs/atom = 26.679739
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
undump sci
uncompute chunk_1
unfix chunk_1
unfix 1
unfix 2
unfix 3
unfix 4
unfix deposition_O2_1
unfix deposition_O2_2
unfix dlan
Total wall time: 0:03:10