#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 500 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_r_OMCTS id 23171 23172 23173 23174 23175 23176 23177 23178
8 atoms in group deposition_atoms_r_OMCTS
group deposition_atoms_r_OMCTS id 23179 23180 23181 23182 23183 23184 23185 23186
16 atoms in group deposition_atoms_r_OMCTS
group deposition_atoms_r_OMCTS id 23187 23188 23189 23190 23191 23192 23193 23194
24 atoms in group deposition_atoms_r_OMCTS
group deposition_atoms_r_OMCTS id 23195 23196 23197 23198 23199 23200 23201 23202
32 atoms in group deposition_atoms_r_OMCTS
group deposition_atoms_r_OMCTS id 23203 23204 23205 23206
36 atoms in group deposition_atoms_r_OMCTS
delete_atoms group deposition_atoms_r_OMCTS
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 36 atoms, new total = 23326
molecule depositing_species_r_OMCTS deposition_r_OMCTS.dat
Read molecule template depositing_species_r_OMCTS:
1 molecules
0 fragments
36 atoms with max type 5
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_r_OMCTS block EDGE EDGE EDGE EDGE 330 380 units box
group deposition_atoms_r_OMCTS_1 id 23207 23208 23209 23210 23211 23212 23213 23214
8 atoms in group deposition_atoms_r_OMCTS_1
group deposition_atoms_r_OMCTS_1 id 23215 23216 23217 23218 23219 23220 23221 23222
16 atoms in group deposition_atoms_r_OMCTS_1
group deposition_atoms_r_OMCTS_1 id 23223 23224 23225 23226 23227 23228 23229 23230
24 atoms in group deposition_atoms_r_OMCTS_1
group deposition_atoms_r_OMCTS_1 id 23231 23232 23233 23234 23235 23236 23237 23238
32 atoms in group deposition_atoms_r_OMCTS_1
group deposition_atoms_r_OMCTS_1 id 23239 23240 23241 23242
36 atoms in group deposition_atoms_r_OMCTS_1
delete_atoms group deposition_atoms_r_OMCTS_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 36 atoms, new total = 23290
molecule depositing_species_r_OMCTS_1 deposition_r_OMCTS_1.dat
Read molecule template depositing_species_r_OMCTS_1:
1 molecules
0 fragments
36 atoms with max type 5
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_r_OMCTS_1 block EDGE EDGE EDGE EDGE 330 380 units box
group deposition_atoms_r_OMCTS_2 id 23243 23244 23245 23246 23247 23248 23249 23250
8 atoms in group deposition_atoms_r_OMCTS_2
group deposition_atoms_r_OMCTS_2 id 23251 23252 23253 23254 23255 23256 23257 23258
16 atoms in group deposition_atoms_r_OMCTS_2
group deposition_atoms_r_OMCTS_2 id 23259 23260 23261 23262 23263 23264 23265 23266
24 atoms in group deposition_atoms_r_OMCTS_2
group deposition_atoms_r_OMCTS_2 id 23267 23268 23269 23270 23271 23272 23273 23274
32 atoms in group deposition_atoms_r_OMCTS_2
group deposition_atoms_r_OMCTS_2 id 23275 23276 23277 23278
36 atoms in group deposition_atoms_r_OMCTS_2
delete_atoms group deposition_atoms_r_OMCTS_2
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 36 atoms, new total = 23254
molecule depositing_species_r_OMCTS_2 deposition_r_OMCTS_2.dat
Read molecule template depositing_species_r_OMCTS_2:
1 molecules
0 fragments
36 atoms with max type 5
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_r_OMCTS_2 block EDGE EDGE EDGE EDGE 330 380 units box
group deposition_atoms_r_OMCTS_3 id 23279 23280 23281 23282 23283 23284 23285 23286
8 atoms in group deposition_atoms_r_OMCTS_3
group deposition_atoms_r_OMCTS_3 id 23287 23288 23289 23290 23291 23292 23293 23294
16 atoms in group deposition_atoms_r_OMCTS_3
group deposition_atoms_r_OMCTS_3 id 23295 23296 23297 23298 23299 23300 23301 23302
24 atoms in group deposition_atoms_r_OMCTS_3
group deposition_atoms_r_OMCTS_3 id 23303 23304 23305 23306 23307 23308 23309 23310
32 atoms in group deposition_atoms_r_OMCTS_3
group deposition_atoms_r_OMCTS_3 id 23311 23312 23313 23314
36 atoms in group deposition_atoms_r_OMCTS_3
delete_atoms group deposition_atoms_r_OMCTS_3
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 36 atoms, new total = 23218
molecule depositing_species_r_OMCTS_3 deposition_r_OMCTS_3.dat
Read molecule template depositing_species_r_OMCTS_3:
1 molecules
0 fragments
36 atoms with max type 5
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_r_OMCTS_3 block EDGE EDGE EDGE EDGE 330 380 units box
group deposition_atoms_r_TSA id 23315 23316 23317 23318 23319 23320 23321 23322
8 atoms in group deposition_atoms_r_TSA
group deposition_atoms_r_TSA id 23323 23324 23325 23326
12 atoms in group deposition_atoms_r_TSA
delete_atoms group deposition_atoms_r_TSA
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 12 atoms, new total = 23206
molecule depositing_species_r_TSA deposition_r_TSA.dat
Read molecule template depositing_species_r_TSA:
1 molecules
0 fragments
12 atoms with max type 5
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_r_TSA block EDGE EDGE EDGE EDGE 330 380 units box
group deposition_atoms_r_TSA_1 id 23327 23328 23329 23330 23331 23332 23333 23334
8 atoms in group deposition_atoms_r_TSA_1
group deposition_atoms_r_TSA_1 id 23335 23336 23337 23338
12 atoms in group deposition_atoms_r_TSA_1
delete_atoms group deposition_atoms_r_TSA_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 12 atoms, new total = 23194
molecule depositing_species_r_TSA_1 deposition_r_TSA_1.dat
Read molecule template depositing_species_r_TSA_1:
1 molecules
0 fragments
12 atoms with max type 5
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_r_TSA_1 block EDGE EDGE EDGE EDGE 330 380 units box
group deposition_atoms_r_TSA_2 id 23339 23340 23341 23342 23343 23344 23345 23346
8 atoms in group deposition_atoms_r_TSA_2
group deposition_atoms_r_TSA_2 id 23347 23348 23349 23350
12 atoms in group deposition_atoms_r_TSA_2
delete_atoms group deposition_atoms_r_TSA_2
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 12 atoms, new total = 23182
molecule depositing_species_r_TSA_2 deposition_r_TSA_2.dat
Read molecule template depositing_species_r_TSA_2:
1 molecules
0 fragments
12 atoms with max type 5
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_r_TSA_2 block EDGE EDGE EDGE EDGE 330 380 units box
group deposition_atoms_r_TSA_3 id 23351 23352 23353 23354 23355 23356 23357 23358
8 atoms in group deposition_atoms_r_TSA_3
group deposition_atoms_r_TSA_3 id 23359 23360 23361 23362
12 atoms in group deposition_atoms_r_TSA_3
delete_atoms group deposition_atoms_r_TSA_3
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 12 atoms, new total = 23170
molecule depositing_species_r_TSA_3 deposition_r_TSA_3.dat
Read molecule template depositing_species_r_TSA_3:
1 molecules
0 fragments
12 atoms with max type 5
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_r_TSA_3 block EDGE EDGE EDGE EDGE 330 380 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_r_OMCTS langevin 300 300 20.0 1007 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_r_OMCTS_1 deposition_atoms_r_OMCTS deposit 1000 0 5000 7614 region deposition_region_r_OMCTS mol depositing_species_r_OMCTS vz -0.0084954386251807068 -0.010383313875220864 vx -0.016349479257106746 0.016349479257106746 vy -0.016349479257106746 0.016349479257106746 near 1.50 id next units box
fix deposition_r_OMCTS_2 deposition_atoms_r_OMCTS nve
fix deposition_r_OMCTS_1_1 deposition_atoms_r_OMCTS_1 deposit 500 0 5000 384670 region deposition_region_r_OMCTS_1 mol depositing_species_r_OMCTS_1 vz -0.0084954386251807068 -0.010383313875220864 vx -0.016349479257106746 0.016349479257106746 vy -0.016349479257106746 0.016349479257106746 near 1.50 id next units box
fix deposition_r_OMCTS_1_2 deposition_atoms_r_OMCTS_1 nve
fix deposition_r_OMCTS_2_1 deposition_atoms_r_OMCTS_2 deposit 500 0 5000 9 region deposition_region_r_OMCTS_2 mol depositing_species_r_OMCTS_2 vz -0.0084954386251807068 -0.010383313875220864 vx -0.016349479257106746 0.016349479257106746 vy -0.016349479257106746 0.016349479257106746 near 1.50 id next units box
fix deposition_r_OMCTS_2_2 deposition_atoms_r_OMCTS_2 nve
fix deposition_r_OMCTS_3_1 deposition_atoms_r_OMCTS_3 deposit 500 0 5000 5678 region deposition_region_r_OMCTS_3 mol depositing_species_r_OMCTS_3 vz -0.0084954386251807068 -0.010383313875220864 vx -0.016349479257106746 0.016349479257106746 vy -0.016349479257106746 0.016349479257106746 near 1.50 id next units box
fix deposition_r_OMCTS_3_2 deposition_atoms_r_OMCTS_3 nve
fix deposition_r_TSA_1 deposition_atoms_r_TSA deposit 500 0 5000 435704 region deposition_region_r_TSA mol depositing_species_r_TSA vz -0.013825090872112797 -0.016897333288137865 vx -0.026606399788617861 0.026606399788617861 vy -0.026606399788617861 0.026606399788617861 near 1.50 id next units box
fix deposition_r_TSA_2 deposition_atoms_r_TSA nve
fix deposition_r_TSA_1_1 deposition_atoms_r_TSA_1 deposit 500 0 5000 64079296 region deposition_region_r_TSA_1 mol depositing_species_r_TSA_1 vz -0.013825090872112797 -0.016897333288137865 vx -0.026606399788617861 0.026606399788617861 vy -0.026606399788617861 0.026606399788617861 near 1.50 id next units box
fix deposition_r_TSA_1_2 deposition_atoms_r_TSA_1 nve
fix deposition_r_TSA_2_1 deposition_atoms_r_TSA_2 deposit 500 0 5000 39278109 region deposition_region_r_TSA_2 mol depositing_species_r_TSA_2 vz -0.013825090872112797 -0.016897333288137865 vx -0.026606399788617861 0.026606399788617861 vy -0.026606399788617861 0.026606399788617861 near 1.50 id next units box
fix deposition_r_TSA_2_2 deposition_atoms_r_TSA_2 nve
fix deposition_r_TSA_3_1 deposition_atoms_r_TSA_3 deposit 500 0 5000 6711 region deposition_region_r_TSA_3 mol depositing_species_r_TSA_3 vz -0.013825090872112797 -0.016897333288137865 vx -0.026606399788617861 0.026606399788617861 vy -0.026606399788617861 0.026606399788617861 near 1.50 id next units box
fix deposition_r_TSA_3_2 deposition_atoms_r_TSA_3 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_r_OMCTS deposition_atoms_r_OMCTS custom 50000 2.3.trajectory_1.xyz id mol type q xs ys zs
dump trj_r_OMCTS_1 deposition_atoms_r_OMCTS_1 custom 50000 2.3.trajectory_2.xyz id mol type q xs ys zs
dump trj_r_OMCTS_2 deposition_atoms_r_OMCTS_2 custom 50000 2.3.trajectory_3.xyz id mol type q xs ys zs
dump trj_r_