#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 500 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_OMCTS id 79921 79922 79923 79924 79925 79926 79927 79928
8 atoms in group deposition_atoms_OMCTS
group deposition_atoms_OMCTS id 79929 79930 79931 79932 79933 79934 79935 79936
16 atoms in group deposition_atoms_OMCTS
group deposition_atoms_OMCTS id 79937 79938 79939 79940 79941 79942 79943 79944
24 atoms in group deposition_atoms_OMCTS
group deposition_atoms_OMCTS id 79945 79946 79947 79948 79949 79950 79951 79952
32 atoms in group deposition_atoms_OMCTS
group deposition_atoms_OMCTS id 79953 79954 79955 79956 79957 79958 79959 79960
40 atoms in group deposition_atoms_OMCTS
delete_atoms group deposition_atoms_OMCTS
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 40 atoms, new total = 79920
molecule depositing_species_OMCTS deposition_OMCTS.dat
Read molecule template depositing_species_OMCTS:
1 molecules
0 fragments
40 atoms with max type 4
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_OMCTS block EDGE EDGE EDGE EDGE 560 780 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 (src/output.cpp:903)
thermo ${Nthermo}
thermo 0
fix 1 movable nve
fix dlan subset_thermoset langevin 300 300 20.0 60 tally yes
fix 2 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 3 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 4 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix deposition_OMCTS_1 deposition_atoms_OMCTS deposit 500 0 5000 42 region deposition_region_OMCTS mol depositing_species_OMCTS vz -0.030300013054885184 -0.037033349289304116 vx 0.0 0.0 vy -0.058312402312290436 0.058312402312290436 near 1.50 id next units box
fix deposition_OMCTS_2 deposition_atoms_OMCTS 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_OMCTS deposition_atoms_OMCTS custom 50000 2.3.trajectory_1.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 3 67
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
b