#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 500 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_TSA_1 id 109921 109922 109923 109924 109925 109926 109927 109928
8 atoms in group deposition_atoms_TSA_1
group deposition_atoms_TSA_1 id 109929 109930 109931 109932 109933 109934 109935
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 = 109965
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 560 780 units box
group deposition_atoms_TSA_2 id 109936 109937 109938 109939 109940 109941 109942 109943
8 atoms in group deposition_atoms_TSA_2
group deposition_atoms_TSA_2 id 109944 109945 109946 109947 109948 109949 109950
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 = 109950
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 560 780 units box
group deposition_atoms_TSA_3 id 109951 109952 109953 109954 109955 109956 109957 109958
8 atoms in group deposition_atoms_TSA_3
group deposition_atoms_TSA_3 id 109959 109960 109961 109962 109963 109964 109965
15 atoms in group deposition_atoms_TSA_3
delete_atoms group deposition_atoms_TSA_3
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 109935
molecule depositing_species_TSA_3 deposition_TSA_3.dat
Read molecule template depositing_species_TSA_3:
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_3 block EDGE EDGE EDGE EDGE 560 780 units box
group deposition_atoms_TSA_4 id 109966 109967 109968 109969 109970 109971 109972 109973
8 atoms in group deposition_atoms_TSA_4
group deposition_atoms_TSA_4 id 109974 109975 109976 109977 109978 109979 109980
15 atoms in group deposition_atoms_TSA_4
delete_atoms group deposition_atoms_TSA_4
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 15 atoms, new total = 109920
molecule depositing_species_TSA_4 deposition_TSA_4.dat
Read molecule template depositing_species_TSA_4:
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_4 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 1352020 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_TSA_1_1 deposition_atoms_TSA_1 deposit 500 0 5000 6 region deposition_region_TSA_1 mol depositing_species_TSA_1 vz -0.0035745116930957729 -0.0043688476248948342 vx -0.014822510278758307 0.014822510278758307 vy -0.014822510278758307 0.014822510278758307 near 1.50 id next units box
fix deposition_TSA_1_2 deposition_atoms_TSA_1 nve
fix deposition_TSA_2_1 deposition_atoms_TSA_2 deposit 500 0 5000 5684 region deposition_region_TSA_2 mol depositing_species_TSA_2 vz -0.0035745116930957729 -0.0043688476248948342 vx -0.014822510278758307 0.014822510278758307 vy -0.014822510278758307 0.014822510278758307 near 1.50 id next units box
fix deposition_TSA_2_2 deposition_atoms_TSA_2 nve
fix deposition_TSA_3_1 deposition_atoms_TSA_3 deposit 500 0 5000 289213 region deposition_region_TSA_3 mol depositing_species_TSA_3 vz -0.0035745116930957729 -0.0043688476248948342 vx -0.014822510278758307 0.014822510278758307 vy -0.014822510278758307 0.014822510278758307 near 1.50 id next units box
fix deposition_TSA_3_2 deposition_atoms_TSA_3 nve
fix deposition_TSA_4_1 deposition_atoms_TSA_4 deposit 500 0 5000 139175 region deposition_region_TSA_4 mol depositing_species_TSA_4 vz -0.0035745116930957729 -0.0043688476248948342 vx -0.014822510278758307 0.014822510278758307 vy -0.014822510278758307 0.014822510278758307 near 1.50 id next units box
fix deposition_TSA_4_2 deposition_atoms_TSA_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 deposition_atoms_TSA_1 custom 50000 2.3.trajectory_1.xyz id mol type q xs ys zs
dump trj_TSA_2 deposition_atoms_TSA_2 custom 50000 2.3.trajectory_2.xyz id mol type q xs ys zs
dump trj_TSA_3 deposition_atoms_TSA_3 custom 50000 2.3.trajectory_3.xyz id mol type q xs ys zs
dump trj_TSA_4 deposition_atoms_TSA_4 custom 50000 2.3.trajectory_4.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
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 communication, switching to classic exchange/border communication (src/KOKKOS/comm_kokkos.cpp:581)
Per MPI rank memory allocation (min/avg/max) = 1748 | 1748 | 1748 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 -776.68043 9829317.4 0.322