#-------------------------------------------------------------------------------
# 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 89374397 molecule yes
fix dlan subset_thermostat langevin 300 300 20.0 8 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 89374397 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 1718.9132 93956.963 1.0420072 370.33227 0 0 0 0 -225146.87 0 0 0 -225146.87 2118.3652
Loop time of 195.619 on 40 procs for 500000 steps with 2138 atoms
Performance: 44.167 ns/day, 0.543 hours/ns, 2555.989 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 | 0.039474 | 58.434 | 150.01 | 811.2 | 29.87
Bond | 0.018634 | 0.027844 | 0.040945 | 4.5 | 0.01
Neigh | 0.0023059 | 0.18231 | 0.45267 | 44.6 | 0.09
Comm | 0.21312 | 30.645 | 89.531 | 593.6 | 15.67
Output | 0.042072 | 0.044483 | 0.04749 | 0.8 | 0.02
Modify | 24.741 | 104.67 | 193.66 | 740.8 | 53.51
Other | | 1.618 | | | 0.83
Nlocal: 53.45 ave 130 max 0 min
Histogram: 20 0 0 0 4 0 0 0 11 5
Nghost: 229.375 ave 532 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: 1422.35 ave 3636 max 0 min
Histogram: 20 0 0 0 4 0 0 2 10 4
Total # of neighbors = 56894
Ave neighs/atom = 26.610851
Ave special neighs/atom = 0
Neighbor list builds = 2285
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 | 7.625 | 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 1718.9132 93956.963 1.0420072 370.33227 0 0 0 0 -225146.87 0 0 0 -225146.87 2118.3652
Loop time of 2.49978e-06 on 40 procs for 0 steps with 2138 atoms
119.0% 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 | 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 | | 2.5e-06 | | |100.00
Nlocal: 53.45 ave 130 max 0 min
Histogram: 20 0 0 0 4 0 0 0 11 5
Nghost: 229.375 ave 532 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: 1422.35 ave 3636 max 0 min
Histogram: 20 0 0 0 4 0 0 2 10 4
Total # of neighbors = 56894
Ave neighs/atom = 26.610851
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: 0:03:15