Stage_2/2.3_Deposition.out output for 501: From job 496,489, 400_5_1500 500ps 50000*C2H+500*H, 1eV, +/-0 EVAC ON_1000
Status:
finished
#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 500 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_C2H id 116944 116945 116946
3 atoms in group deposition_atoms_C2H
delete_atoms group deposition_atoms_C2H
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 3 atoms, new total = 116944
molecule depositing_species_C2H deposition_C2H.dat
Read molecule template depositing_species_C2H:
1 molecules
0 fragments
3 atoms with max type 2
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_C2H block EDGE EDGE EDGE EDGE 1300 1400 units box
group deposition_atoms_H id 116947
1 atoms in group deposition_atoms_H
delete_atoms group deposition_atoms_H
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 1 atoms, new total = 116943
molecule depositing_species_H deposition_H.dat
Read molecule template depositing_species_H:
1 molecules
0 fragments
1 atoms with max type 2
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_H block EDGE EDGE EDGE EDGE 1300 1400 units box
region evaporation_region block EDGE EDGE EDGE EDGE 1450 EDGE units box
group evaporation_group dynamic all region evaporation_region every 1000
dynamic group evaporation_group defined
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 (src/output.cpp:903)
thermo ${Nthermo}
thermo 0
fix 1 movable nve
fix 2 evaporation_group reax/c/species 1 1 1000 removed_fragments.out element C H Si terse yes
fix 3 all evaporate 1000 1000 evaporation_region 823965 molecule yes
fix dlan subset_thermoset langevin 300 300 20.0 564023 tally yes
fix 4 movable ave/time 1 250000 250000 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 5 movable ave/time 250 1 250 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 6 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix deposition_C2H_1 deposition_atoms_C2H deposit 50000 0 50 823965 region deposition_region_C2H mol depositing_species_C2H vz -0.024991234191304085 -0.030544841789371658 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_C2H_2 deposition_atoms_C2H nve
fix deposition_H_1 deposition_atoms_H deposit 500 0 5000 851 region deposition_region_H mol depositing_species_H vz -0.12453753584042228 -0.15221254380496058 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_H_2 deposition_atoms_H nve
dump trj all custom 50000 2.3.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 50000 1 50000 v_etotal v_pe v_ke file 2.3.energies.txt
dump trj_C2H deposition_atoms_C2H custom 50000 2.3.trajectory_1.xyz id mol type q xs ys zs
dump trj_H deposition_atoms_H custom 50000 2.3.trajectory_2.xyz id mol type q xs ys zs
timestep 0.2
run 2500000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 12, bins = 34 1 125
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c/kk, perpetual
attributes: half, newton off, ghost, kokkos_device
pair build: half/bin/ghost/kk/device
stencil: full/ghost/bin/3d
bin: kk/device
(2) fix qeq/reax/kk, perpetual
attributes: full, newton off, kokkos_device
pair build: full/bin/kk/device
stencil: full/bin/3d
bin: kk/device
WARNING: Fixes cannot yet send exchange data in Kokkos communication, switching to classic exchange/border communication (src/KOKKOS/comm_kokkos.cpp:581)
Per MPI rank memory allocation (min/avg/max) = 5174 | 5174 | 5174 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 -6748.716 3259132.2 1.0666859 300.00346 0 0 0 0 -14799838 -13789.387 0 0 -14813628 104575.77
2500000 500000 -3314.4069 3259132.2 1.0992717 889.55868 0 0 0 0 -15786050 -14739.101 0 0 -15800790 310084.04
Loop time of 410270 on 1 procs for 2500000 steps with 123283 atoms
Performance: 0.105 ns/day, 227.928 hours/ns, 6.094 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7527e+05 | 2.7527e+05 | 2.7527e+05 | 0.0 | 67.10
Bond | 0.71416 | 0.71416 | 0.71416 | 0.0 | 0.00
Neigh | 16674 | 16674 | 16674 | 0.0 | 4.06
Comm | 3406.5 | 3406.5 | 3406.5 | 0.0 | 0.83
Output | 3.0022 | 3.0022 | 3.0022 | 0.0 | 0.00
Modify | 1.1403e+05 | 1.1403e+05 | 1.1403e+05 | 0.0 | 27.79
Other | | 887.2 | | | 0.22
Nlocal: 123283 ave 123283 max 123283 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 583315 ave 583315 max 583315 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5.27221e+07 ave 5.27221e+07 max 5.27221e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 6.28993e+07 ave 6.28993e+07 max 6.28993e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 62899270
Ave neighs/atom = 510.2023
Ave special neighs/atom = 0
Neighbor list builds = 246481
Dangerous builds = 54390
write_dump all xyz final_2.3.xyz modify element C H Si
undump trj
unfix trjE
undump trj_C2H
undump trj_H
write_dump deposition_atoms_C2H custom 2.3.deposited_1.xyz id mol type q xs ys zs
write_dump deposition_atoms_H custom 2.3.deposited_2.xyz id mol type q xs ys zs
restart 0
dump sci all custom 2500000 2.3.xyz id mol type q xs ys zs
run 0
Per MPI rank memory allocation (min/avg/max) = 8054 | 8054 | 8054 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
2500000 500000 -3314.4069 3259132.2 1.0992717 915.39824 0 0 0 0 -15786050 -14739.101 0 0 -15800790 310084.04
Loop time of 0.00744418 on 1 procs for 0 steps with 123283 atoms
99.9% CPU use with 1 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 | | 0.007444 | | |100.00
Nlocal: 123283 ave 123283 max 123283 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 583315 ave 583315 max 583315 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5.27221e+07 ave 5.27221e+07 max 5.27221e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 6.28993e+07 ave 6.28993e+07 max 6.28993e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 62899270
Ave neighs/atom = 510.2023
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
undump sci
unfix 1
unfix 2
unfix 3
unfix 4
unfix 5
unfix 6
unfix deposition_C2H_1
unfix deposition_C2H_2
unfix deposition_H_1
unfix deposition_H_2
unfix dlan
Total wall time: 113:57:59