#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 100000 with a timestep of 0.2
#-------------------------------------------------------------------------------
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 (../delete_atoms.cpp:126)
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 (../output.cpp:888)
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 3869 molecule yes
fix dlan subset_thermostat langevin 300 300 20.0 27230 tally yes
fix 4 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 5 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 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 100000 3869 region deposition_region_N_atom mol depositing_species_N_atom vz -0.10564503102330547 -0.12912170458404001 vx -0.010269713969315307 0.010269713969315307 vy 0.0 0.0 near 1.50 id next units box
fix deposition_N_atom_2 deposition_atoms_N_atom nve
dump trj all custom 50 2.3.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 50 1 50 v_etotal v_pe v_ke file 2.3.energies.txt
dump trj_N_atom deposition_atoms_N_atom custom 50 2.3.trajectory_1.xyz id mol type q xs ys zs
timestep 0.2
run 500000
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
WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:171)
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, half/full from (2)
attributes: half, newton off, ghost, kokkos_device
pair build: halffull/newtoff/ghost/kk/device
stencil: none
bin: none
(2) fix qeq/reax/kk, perpetual
attributes: full, newton off, ghost, kokkos_device
pair build: full/bin/ghost/kk/device
stencil: full/ghost/bin/3d
bin: kk/device
WARNING: Fixes cannot yet send exchange data in Kokkos communication, switching to classic exchange/border communication (../comm_kokkos.cpp:581)
Per MPI rank memory allocation (min/avg/max) = 52.4 | 52.4 | 52.4 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 -18095.077 253683.8 0.85517953 298.03271 0 0 0 0 -614732.23 5.514091e-13 0 0 -614732.23 1960.6522
WARNING: Atom with cluster ID = maxmol included in fix reaxff/species group (../fix_reaxff_species.cpp:501)
ERROR on proc 0: Failed to allocate -37244 bytes for array reaxff/species:molmap (../memory.cpp:66)
Last command: run 500000