#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 1000 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_N_atom id 4657
1 atoms in group deposition_atoms_N_atom
delete_atoms group deposition_atoms_N_atom
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 1 atoms, new total = 4656
molecule depositing_species_N_atom deposition_N_atom.dat
Read molecule template depositing_species_N_atom:
1 molecules
0 fragments
1 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_N_atom block EDGE EDGE EDGE EDGE 50 60 units box
region evaporation_region block EDGE EDGE EDGE EDGE 90 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 N Si terse yes
fix 3 all evaporate 1000 1000 evaporation_region 27657 molecule yes
fix dlan subset_thermostat langevin 300 300 20.0 59 tally yes
fix 4 movable ave/time 1 500000 500000 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 50000000 1 50000000 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_N_atom_1 deposition_atoms_N_atom deposit 500 0 10000 27657 region deposition_region_N_atom mol depositing_species_N_atom vz -0.10564503102330547 -0.12912170458404001 vx 0.020697854830212851 -0.020697854830212851 vy 0.020697854830212851 -0.020697854830212851 near 1.50 id next units box
fix deposition_N_atom_2 deposition_atoms_N_atom nve
dump trj all custom 500000 2.3.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 500000 1 500000 v_etotal v_pe v_ke file 2.3.energies.txt
dump trj_N_atom deposition_atoms_N_atom custom 500000 2.3.trajectory_1.xyz id mol type q xs ys zs
timestep 0.2
run 5000000
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 = 8 3 8
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) = 52.27 | 52.27 | 52.27 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 -17821.944 253683.8 0.85517953 300.04333 0 0 0 0 -614732.23 -2.9797843e-12 0 0 -614732.23 3476.4246
5000000 1000000 -4943.6245 253683.8 0.90099949 297.32885 0 0 0 0 -710916.04 -2189.8477 0 0 -713105.89 3444.9736
Loop time of 245842 on 1 procs for 5000000 steps with 5156 atoms
Performance: 0.351 ns/day, 68.289 hours/ns, 20.338 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 45217 | 45217 | 45217 | 0.0 | 18.39
Bond | 0.55587 | 0.55587 | 0.55587 | 0.0 | 0.00
Neigh | 138.62 | 138.62 | 138.62 | 0.0 | 0.06
Comm | 109.81 | 109.81 | 109.81 | 0.0 | 0.04
Output | 0.024975 | 0.024975 | 0.024975 | 0.0 | 0.00
Modify | 1.9949e+05 | 1.9949e+05 | 1.9949e+05 | 0.0 | 81.15
Other | | 883.7 | | | 0.36
Nlocal: 5156 ave 5156 max 5156 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9655 ave 9655 max 9655 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.0541e+06 ave 1.0541e+06 max 1.0541e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.73902e+06 ave 1.73902e+06 max 1.73902e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1739022
Ave neighs/atom = 337.28123
Ave special neighs/atom = 0
Neighbor list builds = 33202
Dangerous builds = 0
write_dump all xyz final_2.3.xyz modify element N Si
undump trj
unfix trjE
undump trj_N_atom
write_dump deposition_atoms_N_atom custom 2.3.deposited_1.xyz id mol type q xs ys zs
restart 0
dump sci all custom 5000000 2.3.xyz id mol type q xs ys zs
run 0
Per MPI rank memory allocation (min/avg/max) = 118.5 | 118.5 | 118.5 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
5000000 1000000 -4943.6241 253683.8 0.90099949 297.32885 0 0 0 0 -710916.04 -2189.8477 0 0 -713105.89 3444.9736
Loop time of 0.000372319 on 1 procs for 0 steps with 5156 atoms
100.2% 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 | | 0.0003723 | | |100.00
Nlocal: 5156 ave 5156 max 5156 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9655 ave 9655 max 9655 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.0541e+06 ave 1.0541e+06 max 1.0541e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.73902e+06 ave 1.73902e+06 max 1.73902e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1739022
Ave neighs/atom = 337.28123
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_N_atom_1
unfix deposition_N_atom_2
unfix dlan
Total wall time: 68:17:23