#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 500 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_TSA id 79921 79922 79923 79924 79925 79926 79927 79928
8 atoms in group deposition_atoms_TSA
group deposition_atoms_TSA id 79929 79930 79931 79932 79933 79934 79935
15 atoms in group deposition_atoms_TSA
delete_atoms group deposition_atoms_TSA
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 80025
molecule depositing_species_TSA deposition_TSA.dat
Read molecule template depositing_species_TSA:
1 molecules
0 fragments
15 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_TSA block EDGE EDGE EDGE EDGE 500 600 units box
group deposition_atoms_TSA_1 id 79936 79937 79938 79939 79940 79941 79942 79943
8 atoms in group deposition_atoms_TSA_1
group deposition_atoms_TSA_1 id 79944 79945 79946 79947 79948 79949 79950
15 atoms in group deposition_atoms_TSA_1
delete_atoms group deposition_atoms_TSA_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 80010
molecule depositing_species_TSA_1 deposition_TSA_1.dat
Read molecule template depositing_species_TSA_1:
1 molecules
0 fragments
15 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_TSA_1 block EDGE EDGE EDGE EDGE 500 600 units box
group deposition_atoms_TSA_1_1 id 79951 79952 79953 79954 79955 79956 79957 79958
8 atoms in group deposition_atoms_TSA_1_1
group deposition_atoms_TSA_1_1 id 79959 79960 79961 79962 79963 79964 79965
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 = 79995
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 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_TSA_1_1 block EDGE EDGE EDGE EDGE 500 600 units box
group deposition_atoms_TSA_1_1_1 id 79966 79967 79968 79969 79970 79971 79972 79973
8 atoms in group deposition_atoms_TSA_1_1_1
group deposition_atoms_TSA_1_1_1 id 79974 79975 79976 79977 79978 79979 79980
15 atoms in group deposition_atoms_TSA_1_1_1
delete_atoms group deposition_atoms_TSA_1_1_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 79980
molecule depositing_species_TSA_1_1_1 deposition_TSA_1_1_1.dat
Read molecule template depositing_species_TSA_1_1_1:
1 molecules
0 fragments
15 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_TSA_1_1_1 block EDGE EDGE EDGE EDGE 500 600 units box
group deposition_atoms_TSA_2 id 79981 79982 79983 79984 79985 79986 79987 79988
8 atoms in group deposition_atoms_TSA_2
group deposition_atoms_TSA_2 id 79989 79990 79991 79992 79993 79994 79995
15 atoms in group deposition_atoms_TSA_2
delete_atoms group deposition_atoms_TSA_2
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 79965
molecule depositing_species_TSA_2 deposition_TSA_2.dat
Read molecule template depositing_species_TSA_2:
1 molecules
0 fragments
15 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_TSA_2 block EDGE EDGE EDGE EDGE 500 600 units box
group deposition_atoms_TSA_1_2 id 79996 79997 79998 79999 80000 80001 80002 80003
8 atoms in group deposition_atoms_TSA_1_2
group deposition_atoms_TSA_1_2 id 80004 80005 80006 80007 80008 80009 80010
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 = 79950
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 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_TSA_1_2 block EDGE EDGE EDGE EDGE 500 600 units box
group deposition_atoms_TSA_1_1_2 id 80011 80012 80013 80014 80015 80016 80017 80018
8 atoms in group deposition_atoms_TSA_1_1_2
group deposition_atoms_TSA_1_1_2 id 80019 80020 80021 80022 80023 80024 80025
15 atoms in group deposition_atoms_TSA_1_1_2
delete_atoms group deposition_atoms_TSA_1_1_2
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 79935
molecule depositing_species_TSA_1_1_2 deposition_TSA_1_1_2.dat
Read molecule template depositing_species_TSA_1_1_2:
1 molecules
0 fragments
15 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_TSA_1_1_2 block EDGE EDGE EDGE EDGE 500 600 units box
group deposition_atoms_TSA_1_1_1_1 id 80026 80027 80028 80029 80030 80031 80032 80033
8 atoms in group deposition_atoms_TSA_1_1_1_1
group deposition_atoms_TSA_1_1_1_1 id 80034 80035 80036 80037 80038 80039 80040
15 atoms in group deposition_atoms_TSA_1_1_1_1
delete_atoms group deposition_atoms_TSA_1_1_1_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 79920
molecule depositing_species_TSA_1_1_1_1 deposition_TSA_1_1_1_1.dat
Read molecule template depositing_species_TSA_1_1_1_1:
1 molecules
0 fragments
15 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_TSA_1_1_1_1 block EDGE EDGE EDGE EDGE 500 600 units box
region evaporation_region block EDGE EDGE EDGE EDGE 790 EDGE units box
group evaporation_group dynamic all region evaporation_region every 5000
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 5000 removed_fragments.out element H N O Si terse yes
fix 3 all evaporate 5000 1000 evaporation_region 229382 molecule yes
fix dlan subset_thermoset langevin 300 300 20.0 2453 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_TSA_1 deposition_atoms_TSA deposit 500 0 5000 229382 region deposition_region_TSA mol depositing_species_TSA vz -0.010592289334858541 -0.012946131409271552 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_TSA_2 deposition_atoms_TSA nve
fix deposition_TSA_1_1 deposition_atoms_TSA_1 deposit 500 0 5000 77 region deposition_region_TSA_1 mol depositing_species_TSA_1 vz -0.010592289334858541 -0.012946131409271552 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_TSA_1_2 deposition_atoms_TSA_1 nve
fix deposition_TSA_1_1_1 deposition_atoms_TSA_1_1 deposit 500 0 5000 7944 region deposition_region_TSA_1_1 mol depositing_species_TSA_1_1 vz -0.010592289334858541 -0.012946131409271552 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_TSA_1_1_2 deposition_atoms_TSA_1_1 nve
fix deposition_TSA_1_1_1_1 deposition_atoms_TSA_1_1_1 deposit 500 0 5000 1 region deposition_region_TSA_1_1_1 mol depositing_species_TSA_1_1_1 vz -0.010592289334858541 -0.012946131409271552 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_TSA_1_1_1_2 deposition_atoms_TSA_1_1_1 nve
fix deposition_TSA_2_1 deposition_atoms_TSA_2 deposit 500 0 5000 1 region deposition_region_TSA_2 mol depositing_species_TSA_2 vz -0.010592289334858541 -0.012946131409271552 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_TSA_2_2 deposition_atoms_TSA_2 nve
fix deposition_TSA_1_2_1 deposition_atoms_TSA_1_2 deposit 500 0 5000 1 region deposition_region_TSA_1_2 mol depositing_species_TSA_1_2 vz -0.010592289334858541 -0.012946131409271552 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_TSA_1_2_2 deposition_atoms_TSA_1_2 nve
fix deposition_TSA_1_1_2_1 deposition_atoms_TSA_1_1_2 deposit 500 0 5000 42758 region deposition_region_TSA_1_1_2 mol depositing_species_TSA_1_1_2 vz -0.010592289334858541 -0.012946131409271552 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_TSA_1_1_2_2 deposition_atoms_TSA_1_1_2 nve
fix deposition_TSA_1_1_1_1_1 deposition_atoms_TSA_1_1_1_1 deposit 500 0 5000 890 region deposition_region_TSA_1_1_1_1 mol depositing_species_TSA_1_1_1_1 vz -0.010592289334858541 -0.012946131409271552 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_TSA_1_1_1_1_2 deposition_atoms_TSA_1_1_1_1 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 deposition_atoms_TSA custom 50000 2.3.trajectory_1.xyz id mol type q xs ys zs
dump trj_TSA_1 deposition_atoms_TSA_1 custom 50000 2.3.trajectory_2.xyz id mol type q xs ys zs
dump trj_TSA_1_1 deposition_atoms_TSA_1_1 custom 50000 2.3.trajectory_3.xyz id mol type q xs ys zs
dump trj_TSA_1_1_1 deposition_atoms_TSA_1_1_1 custom 50000 2.3.trajectory_4.xyz id mol type q xs ys zs
dump trj_TSA_2 deposition_atoms_TSA_2 custom 50000 2.3.trajectory_5.xyz id mol type q xs ys zs
dump trj_TSA_1_2 deposition_atoms_TSA_1_2 custom 50000 2.3.trajectory_6.xyz id mol type q xs ys zs
dump trj_TSA_1_1_2 deposition_atoms_TSA_1_1_2 custom 50000 2.3.trajectory_7.xyz id mol type q xs ys zs
dump trj_TSA_1_1_1_1 deposition_atoms_TSA_1_1_1_1 custom 50000 2.3.trajectory_8.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/