#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 1000 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_TSA_1_1 id 79921 79922 79923 79924 79925 79926 79927 79928
8 atoms in group deposition_atoms_TSA_1_1
group deposition_atoms_TSA_1_1 id 79929 79930 79931 79932 79933 79934 79935
15 atoms in group deposition_atoms_TSA_1_1
delete_atoms group deposition_atoms_TSA_1_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 130374
molecule depositing_species_TSA_1_1 deposition_TSA_1_1.dat
Read molecule template depositing_species_TSA_1_1:
1 molecules
0 fragments
15 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_TSA_1_1 block EDGE EDGE EDGE EDGE 680 780 units box
group deposition_atoms_TSA_1_2 id 79936 79937 79938 79939 79940 79941 79942 79943
8 atoms in group deposition_atoms_TSA_1_2
group deposition_atoms_TSA_1_2 id 79944 79945 79946 79947 79948 79949 79950
15 atoms in group deposition_atoms_TSA_1_2
delete_atoms group deposition_atoms_TSA_1_2
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 130359
molecule depositing_species_TSA_1_2 deposition_TSA_1_2.dat
Read molecule template depositing_species_TSA_1_2:
1 molecules
0 fragments
15 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_TSA_1_2 block EDGE EDGE EDGE EDGE 680 780 units box
group deposition_atoms_TSA_1_3 id 79951 79952 79953 79954 79955 79956 79957 79958
8 atoms in group deposition_atoms_TSA_1_3
group deposition_atoms_TSA_1_3 id 79959 79960 79961 79962 79963 79964 79965
15 atoms in group deposition_atoms_TSA_1_3
delete_atoms group deposition_atoms_TSA_1_3
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 130344
molecule depositing_species_TSA_1_3 deposition_TSA_1_3.dat
Read molecule template depositing_species_TSA_1_3:
1 molecules
0 fragments
15 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_TSA_1_3 block EDGE EDGE EDGE EDGE 680 780 units box
group deposition_atoms_TSA_1_4 id 79966 79967 79968 79969 79970 79971 79972 79973
8 atoms in group deposition_atoms_TSA_1_4
group deposition_atoms_TSA_1_4 id 79974 79975 79976 79977 79978 79979 79980
15 atoms in group deposition_atoms_TSA_1_4
delete_atoms group deposition_atoms_TSA_1_4
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 130329
molecule depositing_species_TSA_1_4 deposition_TSA_1_4.dat
Read molecule template depositing_species_TSA_1_4:
1 molecules
0 fragments
15 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_TSA_1_4 block EDGE EDGE EDGE EDGE 680 780 units box
region evaporation_region block EDGE EDGE EDGE EDGE 795 EDGE units box
group evaporation_group dynamic all region evaporation_region every 10000
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 10000 removed_fragments.out element H N Si terse yes
fix 3 all evaporate 10000 1000 evaporation_region 5081124 molecule yes
fix dlan subset_thermoset langevin 300 300 20.0 1 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 500 1 500 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_TSA_1_1_1 deposition_atoms_TSA_1_1 deposit 1000 0 5000 5081124 region deposition_region_TSA_1_1 mol depositing_species_TSA_1_1 vz -0.007992851132130014 -0.009769040272603351 vx -0.00031012945774107451 0.00031012945774107451 vy -0.00031012945774107451 0.00031012945774107451 near 1.50 id next units box
fix deposition_TSA_1_1_2 deposition_atoms_TSA_1_1 nve
fix deposition_TSA_1_2_1 deposition_atoms_TSA_1_2 deposit 1000 0 5000 44599028 region deposition_region_TSA_1_2 mol depositing_species_TSA_1_2 vz -0.007992851132130014 -0.009769040272603351 vx -0.00031012945774107451 0.00031012945774107451 vy -0.00031012945774107451 0.00031012945774107451 near 1.50 id next units box
fix deposition_TSA_1_2_2 deposition_atoms_TSA_1_2 nve
fix deposition_TSA_1_3_1 deposition_atoms_TSA_1_3 deposit 1000 0 5000 6818327 region deposition_region_TSA_1_3 mol depositing_species_TSA_1_3 vz -0.007992851132130014 -0.009769040272603351 vx -0.00031012945774107451 0.00031012945774107451 vy -0.00031012945774107451 0.00031012945774107451 near 1.50 id next units box
fix deposition_TSA_1_3_2 deposition_atoms_TSA_1_3 nve
fix deposition_TSA_1_4_1 deposition_atoms_TSA_1_4 deposit 1000 0 5000 84359 region deposition_region_TSA_1_4 mol depositing_species_TSA_1_4 vz -0.007992851132130014 -0.009769040272603351 vx -0.00031012945774107451 0.00031012945774107451 vy -0.00031012945774107451 0.00031012945774107451 near 1.50 id next units box
fix deposition_TSA_1_4_2 deposition_atoms_TSA_1_4 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_TSA_1_1 deposition_atoms_TSA_1_1 custom 50000 2.3.trajectory_1.xyz id mol type q xs ys zs
dump trj_TSA_1_2 deposition_atoms_TSA_1_2 custom 50000 2.3.trajectory_2.xyz id mol type q xs ys zs
dump trj_TSA_1_3 deposition_atoms_TSA_1_3 custom 50000 2.3.trajectory_3.xyz id mol type q xs ys zs
dump trj_TSA_1_4 deposition_atoms_TSA_1_4 custom 50000 2.3.trajectory_4.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 = 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
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