Stage_2/2.3_Deposition.out output for 498: From job 492, 488,479, 400_5_1500 500ps 50000*C2H+50000*H, 10eV, +/-0 EVAC ON_10
Status:
finished
#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 500 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_C2H id 140251 140252 140253
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 = 140251
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 140254
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 = 140250
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 10
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 10 removed_fragments.out element C H Si terse yes
fix 3 all evaporate 10 1000 evaporation_region 1 molecule yes
fix dlan subset_thermoset langevin 300 300 20.0 229 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 1 region deposition_region_C2H mol depositing_species_C2H vz -0.079029221583197085 -0.096591270823907546 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 50000 0 50 40860637 region deposition_region_H mol depositing_species_H vz -0.39382226744058629 -0.48133832687182776 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. Gr