LAMMPS (2 Jun 2022) KOKKOS mode is enabled (src/KOKKOS/kokkos.cpp:105) will use up to 1 GPU(s) per node using 1 OpenMP thread(s) per MPI task log 2.1_Initialize.out #------------------------------------------------------------------------------- # Stage 2.1: Initialize LAMMPS run for 3-d periodic #------------------------------------------------------------------------------- units real boundary p p p atom_style full atom_modify map array box tilt large read_data structure.dat Reading data file ... orthogonal box = (0 0 0) to (19.8868 19.8868 100) 1 by 1 by 1 MPI processor grid reading atoms ... 593 atoms Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 0 = max # of 1-2 neighbors 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.002 seconds pair_style reax/c NULL checkqeq no safezone 10.0 mincap 1000 pair_coeff * * parameters.dat C H O Si variable R equal 0.00198722 variable sysvol equal vol variable sysmass equal mass(all)/6.0221367e+23 variable sysdensity equal v_sysmass/v_sysvol/1.0e-24 variable coulomb equal ecoul+elong variable etotal equal etotal variable pe equal pe variable ke equal ke variable evdwl equal evdwl variable epair equal epair variable ebond equal ebond variable eangle equal eangle variable edihed equal edihed variable eimp equal eimp variable lx equal lx variable ly equal ly variable lz equal lz variable Nthermo equal 0 variable cella equal lx variable cellb equal sqrt(ly*ly+xy*xy) variable cellc equal sqrt(lz*lz+xz*xz+yz*yz) variable cellalpha equal acos((xy*xz+ly*yz)/(v_cellb*v_cellc)) variable cellbeta equal acos(xz/v_cellc) variable cellgamma equal acos(xy/v_cellb) variable p equal press variable pxx equal pxx variable pyy equal pyy variable pzz equal pzz variable pyz equal pyz variable pxz equal pxz variable pxy equal pxy variable sxx equal -pxx variable syy equal -pyy variable szz equal -pzz variable syz equal -pyz variable sxz equal -pxz variable sxy equal -pxy variable fmax equal fmax variable fnorm equal fnorm variable time equal step*dt+0.000001 variable surfacetension equal 0.5*v_lz*(0.5*(v_sxx+v_syy)-v_szz) thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo_modify flush yes # # Set up the fixed and movable groups # group movable union all 593 atoms in group movable group fixed subtract all movable 0 atoms in group fixed compute sum_f1 movable reduce sum fx fy fz variable sum_fx equal c_sum_f1[1] variable sum_fy equal c_sum_f1[2] variable sum_fz equal c_sum_f1[3] # # Subsets # group subset_thermoset id 1 2 3 4 5 6 7 8 9 10 10 atoms in group subset_thermoset group subset_thermoset id 11 12 13 14 15 16 17 18 19 20 20 atoms in group subset_thermoset group subset_thermoset id 21 22 23 24 25 26 27 28 29 30 30 atoms in group subset_thermoset group subset_thermoset id 31 32 33 34 35 36 37 38 39 40 40 atoms in group subset_thermoset group subset_thermoset id 41 42 43 44 45 46 47 48 49 50 50 atoms in group subset_thermoset group subset_thermoset id 51 52 53 54 55 56 57 58 59 60 60 atoms in group subset_thermoset group subset_thermoset id 61 62 63 64 65 66 67 68 69 70 70 atoms in group subset_thermoset group subset_thermoset id 71 72 73 74 75 76 77 78 79 80 80 atoms in group subset_thermoset group subset_thermoset id 81 82 83 84 85 86 87 88 89 90 90 atoms in group subset_thermoset group subset_thermoset id 91 92 93 94 95 96 97 98 99 100 100 atoms in group subset_thermoset group subset_thermoset id 101 102 103 104 105 106 107 108 109 110 110 atoms in group subset_thermoset group subset_thermoset id 111 112 113 114 115 116 117 118 119 120 120 atoms in group subset_thermoset group subset_thermoset id 121 122 123 124 125 126 127 128 129 130 130 atoms in group subset_thermoset group subset_thermoset id 131 132 133 134 135 136 137 138 139 140 140 atoms in group subset_thermoset group subset_thermoset id 141 142 143 144 145 146 147 148 149 150 150 atoms in group subset_thermoset group subset_thermoset id 151 152 153 154 155 156 157 158 159 160 160 atoms in group subset_thermoset group subset_thermoset id 161 162 163 164 165 166 167 168 169 170 170 atoms in group subset_thermoset group subset_thermoset id 171 172 173 174 175 176 177 178 179 180 180 atoms in group subset_thermoset group subset_thermoset id 181 182 183 184 185 186 187 188 189 190 190 atoms in group subset_thermoset group subset_thermoset id 191 192 193 194 195 196 197 198 199 200 200 atoms in group subset_thermoset group subset_thermoset id 201 202 203 204 205 206 207 208 209 210 210 atoms in group subset_thermoset group subset_thermoset id 211 212 213 214 215 216 217 218 219 220 220 atoms in group subset_thermoset group subset_thermoset id 221 222 223 224 225 226 227 228 229 230 230 atoms in group subset_thermoset group subset_thermoset id 231 232 233 234 235 236 237 238 239 240 240 atoms in group subset_thermoset group subset_thermoset id 241 242 243 244 245 246 247 248 249 250 250 atoms in group subset_thermoset group subset_thermoset id 251 252 253 254 255 256 257 258 259 260 260 atoms in group subset_thermoset group subset_thermoset id 261 262 263 264 265 266 267 268 269 270 270 atoms in group subset_thermoset group subset_thermoset id 271 272 273 274 275 276 277 278 279 280 280 atoms in group subset_thermoset group subset_thermoset id 281 282 283 284 285 286 287 288 289 290 290 atoms in group subset_thermoset group subset_thermoset id 291 292 293 294 295 296 297 298 299 300 300 atoms in group subset_thermoset group subset_thermoset id 301 302 303 304 305 306 307 308 309 310 310 atoms in group subset_thermoset group subset_thermoset id 311 312 313 314 315 316 317 318 319 320 320 atoms in group subset_thermoset group subset_thermoset id 321 322 323 324 325 326 327 328 329 330 330 atoms in group subset_thermoset group subset_thermoset id 331 332 333 334 335 336 337 338 339 340 340 atoms in group subset_thermoset group subset_thermoset id 341 342 343 344 345 346 347 348 349 350 350 atoms in group subset_thermoset group subset_thermoset id 351 352 353 354 355 356 357 358 359 360 360 atoms in group subset_thermoset group subset_thermoset id 361 362 363 364 365 366 367 368 369 370 370 atoms in group subset_thermoset group subset_thermoset id 371 372 373 374 375 376 377 378 379 380 380 atoms in group subset_thermoset group subset_thermoset id 381 382 383 384 385 386 387 388 389 390 390 atoms in group subset_thermoset group subset_thermoset id 391 392 393 394 395 396 397 398 399 400 400 atoms in group subset_thermoset group subset_thermoset id 401 402 403 404 405 406 407 408 409 410 410 atoms in group subset_thermoset group subset_thermoset id 411 412 413 414 415 416 417 418 419 420 420 atoms in group subset_thermoset group subset_thermoset id 421 422 423 424 425 426 427 428 429 430 430 atoms in group subset_thermoset group subset_thermoset id 431 432 433 434 435 436 437 438 439 440 440 atoms in group subset_thermoset group subset_thermoset id 441 442 443 444 445 446 447 448 449 450 450 atoms in group subset_thermoset group subset_thermoset id 451 452 453 454 455 456 457 458 459 460 460 atoms in group subset_thermoset group subset_thermoset id 461 462 463 464 465 466 467 468 469 470 470 atoms in group subset_thermoset group subset_thermoset id 471 472 473 474 475 476 477 478 479 480 480 atoms in group subset_thermoset group subset_thermoset id 481 482 483 484 485 486 487 488 489 490 490 atoms in group subset_thermoset group subset_thermoset id 491 492 493 494 495 496 497 498 499 500 500 atoms in group subset_thermoset group subset_thermoset id 501 502 503 504 505 506 507 508 509 510 510 atoms in group subset_thermoset group subset_thermoset id 511 512 513 514 515 516 517 518 519 520 520 atoms in group subset_thermoset group subset_thermoset id 521 522 523 524 525 526 527 528 529 530 530 atoms in group subset_thermoset group subset_thermoset id 531 532 533 534 535 536 537 538 539 540 540 atoms in group subset_thermoset group subset_thermoset id 541 542 543 544 545 546 547 548 549 550 550 atoms in group subset_thermoset group subset_thermoset id 551 552 553 554 555 556 557 558 559 560 560 atoms in group subset_thermoset group subset_thermoset id 561 562 563 564 565 566 567 568 569 570 570 atoms in group subset_thermoset group subset_thermoset id 571 572 573 574 575 576 576 atoms in group subset_thermoset group subset_TMOS id 577 578 579 580 581 582 583 584 585 586 10 atoms in group subset_TMOS group subset_TMOS id 587 588 589 590 591 592 593 17 atoms in group subset_TMOS log 2.2_Velocities.out #------------------------------------------------------------------------------- # Stage 2.2: Set the initial velocities for $T #------------------------------------------------------------------------------- velocity movable create 300 72489 dist gaussian mom yes rot no log 2.3_Deposition.out #------------------------------------------------------------------------------- # Stage 2.3: NVE integration for Deposition for 1000 ps with a timestep of 0.2 fs #------------------------------------------------------------------------------- group deposition_atoms_TMOS id 577 578 579 580 581 582 583 584 8 atoms in group deposition_atoms_TMOS group deposition_atoms_TMOS id 585 586 587 588 589 590 591 592 16 atoms in group deposition_atoms_TMOS group deposition_atoms_TMOS id 593 17 atoms in group deposition_atoms_TMOS delete_atoms group deposition_atoms_TMOS WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140) Deleted 17 atoms, new total = 576 molecule depositing_species_TMOS deposition_TMOS.dat Read molecule template depositing_species_TMOS: 1 molecules 0 fragments 17 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_TMOS block EDGE EDGE EDGE EDGE 50 60 units box region evaporation_region block EDGE EDGE EDGE EDGE 90 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 C H O Si terse yes fix 3 all evaporate 1000 1000 evaporation_region 56 molecule yes fix dlan subset_thermoset langevin 300 300 20.0 39 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_TMOS_1 deposition_atoms_TMOS deposit 250 0 20000 56 region deposition_region_TMOS mol depositing_species_TMOS vz -0.0075482320826285908 -0.0092256169898793892 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box fix deposition_TMOS_2 deposition_atoms_TMOS 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_TMOS deposition_atoms_TMOS custom 50000 2.3.trajectory_1.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: - fix qeq/reaxff command: The log file lists these citations in BibTeX format. 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 = 2 2 9 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 Setting up Verlet run ... Unit style : real Current step : 0 Time step : 0.2 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) = 20.31 | 20.31 | 20.31 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 -26202.214 39548.481 0.48416308 298.11815 0 0 0 0 -70840.707 -11679.505 0 0 -82520.212 510.96431 5000000 1000000 504.59642 39548.481 0.62810449 304.93266 0 0 0 0 -111443.06 -17394.142 0 0 -128837.2 522.64414 Loop time of 70811.3 on 1 procs for 5000000 steps with 1001 atoms Performance: 1.220 ns/day, 19.670 hours/ns, 70.610 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32399 | 32399 | 32399 | 0.0 | 45.75 Bond | 0.6092 | 0.6092 | 0.6092 | 0.0 | 0.00 Neigh | 332.29 | 332.29 | 332.29 | 0.0 | 0.47 Comm | 87.892 | 87.892 | 87.892 | 0.0 | 0.12 Output | 0.075161 | 0.075161 | 0.075161 | 0.0 | 0.00 Modify | 37842 | 37842 | 37842 | 0.0 | 53.44 Other | | 149.1 | | | 0.21 Nlocal: 1001 ave 1001 max 1001 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5278 ave 5278 max 5278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 345254 ave 345254 max 345254 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 494298 ave 494298 max 494298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 494298 Ave neighs/atom = 493.8042 Ave special neighs/atom = 0 Neighbor list builds = 80250 Dangerous builds = 0 write_dump all xyz final_2.3.xyz modify element C H O Si undump trj unfix trjE undump trj_TMOS write_dump deposition_atoms_TMOS custom 2.3.deposited_1.xyz id mol type q xs ys zs restart 0 dump sci all custom 5000000 2.3.xyz id mol type q xs ys zs run 0 Setting up Verlet run ... Unit style : real Current step : 5000000 Time step : 0.2 Per MPI rank memory allocation (min/avg/max) = 65.5 | 65.5 | 65.5 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 5000000 1000000 504.66996 39548.481 0.62810449 304.93266 0 0 0 0 -111443.06 -17394.142 0 0 -128837.2 522.64414 Loop time of 0.00030682 on 1 procs for 0 steps with 1001 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Bond | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003068 | | |100.00 Nlocal: 1001 ave 1001 max 1001 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5278 ave 5278 max 5278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 345254 ave 345254 max 345254 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 494298 ave 494298 max 494298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 494298 Ave neighs/atom = 493.8042 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 undump sci unfix 1 unfix 2 unfix 3 unfix 4 unfix 5 unfix 6 unfix deposition_TMOS_1 unfix deposition_TMOS_2 unfix dlan Total wall time: 19:40:12