#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 2000 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_NH_SiH3_2 id 162001 162002 162003 162004 162005 162006 162007 162008
8 atoms in group deposition_atoms_NH_SiH3_2
group deposition_atoms_NH_SiH3_2 id 162009 162010 162011 162012 162013 162014 162015 162016
16 atoms in group deposition_atoms_NH_SiH3_2
group deposition_atoms_NH_SiH3_2 id 162017 162018 162019 162020
20 atoms in group deposition_atoms_NH_SiH3_2
delete_atoms group deposition_atoms_NH_SiH3_2
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 20 atoms, new total = 162020
molecule depositing_species_NH_SiH3_2 deposition_NH_SiH3_2.dat
Read molecule template depositing_species_NH_SiH3_2:
1 molecules
0 fragments
20 atoms with max type 3
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_NH_SiH3_2 block EDGE EDGE EDGE EDGE 1100 1200 units box
group deposition_atoms_NH_SiH3_2_1 id 162011 162012 162013 162014 162015 162016 162017 162018
0 atoms in group deposition_atoms_NH_SiH3_2_1
group deposition_atoms_NH_SiH3_2_1 id 162019 162020
0 atoms in group deposition_atoms_NH_SiH3_2_1
delete_atoms group deposition_atoms_NH_SiH3_2_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 0 atoms, new total = 162020
molecule depositing_species_NH_SiH3_2_1 deposition_NH_SiH3_2_1.dat
Read molecule template depositing_species_NH_SiH3_2_1:
1 molecules
0 fragments
10 atoms with max type 3
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_NH_SiH3_2_1 block EDGE EDGE EDGE EDGE 1100 1200 units box
group deposition_atoms_NH_SiH3_2_1_1 id 162021 162022 162023 162024 162025 162026 162027 162028
8 atoms in group deposition_atoms_NH_SiH3_2_1_1
group deposition_atoms_NH_SiH3_2_1_1 id 162029 162030
10 atoms in group deposition_atoms_NH_SiH3_2_1_1
delete_atoms group deposition_atoms_NH_SiH3_2_1_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 10 atoms, new total = 162010
molecule depositing_species_NH_SiH3_2_1_1 deposition_NH_SiH3_2_1_1.dat
Read molecule template depositing_species_NH_SiH3_2_1_1:
1 molecules
0 fragments
10 atoms with max type 3
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_NH_SiH3_2_1_1 block EDGE EDGE EDGE EDGE 1100 1200 units box
group deposition_atoms_NH_SiH3_2_1_2 id 162031 162032 162033 162034 162035 162036 162037 162038
8 atoms in group deposition_atoms_NH_SiH3_2_1_2
group deposition_atoms_NH_SiH3_2_1_2 id 162039 162040
10 atoms in group deposition_atoms_NH_SiH3_2_1_2
delete_atoms group deposition_atoms_NH_SiH3_2_1_2
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 10 atoms, new total = 162000
molecule depositing_species_NH_SiH3_2_1_2 deposition_NH_SiH3_2_1_2.dat
Read molecule template depositing_species_NH_SiH3_2_1_2:
1 molecules
0 fragments
10 atoms with max type 3
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_NH_SiH3_2_1_2 block EDGE EDGE EDGE EDGE 1100 1200 units box
region evaporation_region block EDGE EDGE EDGE EDGE 1250 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 H N Si terse yes
fix 3 all evaporate 1000 1000 evaporation_region 558 molecule yes
fix dlan subset_thermoset langevin 300 300 20.0 3537 tally yes
fix 4 movable ave/time 1 1000000 1000000 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 1000 1 1000 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_NH_SiH3_2_1 deposition_atoms_NH_SiH3_2 deposit 10000 0 1000 558 region deposition_region_NH_SiH3_2 mol depositing_species_NH_SiH3_2 vz -0.010060052766598833 -0.012295620048065241 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_NH_SiH3_2_2 deposition_atoms_NH_SiH3_2 nve
fix deposition_NH_SiH3_2_1_1 deposition_atoms_NH_SiH3_2_1 deposit 10000 0 1000 8038803 region deposition_region_NH_SiH3_2_1 mol depositing_species_NH_SiH3_2_1 vz -0.014227063060713042 -0.017388632629760387 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_NH_SiH3_2_1_2 deposition_atoms_NH_SiH3_2_1 nve
fix deposition_NH_SiH3_2_1_1_1 deposition_atoms_NH_SiH3_2_1_1 deposit 10000 0 1000 15450655 region deposition_region_NH_SiH3_2_1_1 mol depositing_species_NH_SiH3_2_1_1 vz -0.014227063060713042 -0.017388632629760387 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_NH_SiH3_2_1_1_2 deposition_atoms_NH_SiH3_2_1_1 nve
fix deposition_NH_SiH3_2_1_2_1 deposition_atoms_NH_SiH3_2_1_2 deposit 10000 0 1000 9887856 region deposition_region_NH_SiH3_2_1_2 mol depositing_species_NH_SiH3_2_1_2 vz -0.014227063060713042 -0.017388632629760387 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_NH_SiH3_2_1_2_2 deposition_atoms_NH_SiH3_2_1_2 nve
dump trj all custom 5000 2.3.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 5000 1 5000 v_etotal v_pe v_ke file 2.3.energies.txt
dump trj_NH_SiH3_2 deposition_atoms_NH_SiH3_2 custom 5000 2.3.trajectory_1.xyz id mol type q xs ys zs
dump trj_NH_SiH3_2_1 deposition_atoms_NH_SiH3_2_1 custom 5000 2.3.trajectory_2.xyz id mol type q xs ys zs
dump trj_NH_SiH3_2_1_1 deposition_atoms_NH_SiH3_2_1_1 custom 5000 2.3.trajectory_3.xyz id mol type q xs ys zs
dump trj_NH_SiH3_2_1_2 deposition_atoms_NH_SiH3_2_1_2 custom 5000 2.3.trajectory_4.xyz id mol type q xs ys zs
timestep 0.2
run 10000000
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 3 109
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