LAMMPS (7 Jan 2022)
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
pair_style tersoff
box tilt large
read_data structure.dat
Reading data file ...
orthogonal box = (0 0 0) to (30.6524 30.6524 100)
2 by 2 by 10 MPI processor grid
reading atoms ...
2050 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 = 0.001 seconds
read_data CPU = 0.009 seconds
pair_coeff * * parameters.dat O Si
newton on
variable R equal 0.00198722
variable sysvol equal vol
variable sysmass equal mass(all)/6.0221367e+023
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 fixed id 1 17 33 49 65 81 97 113 129 145
10 atoms in group fixed
group fixed id 161 177 193 209 225 241 257 273 289 305
20 atoms in group fixed
group fixed id 321 337 353 369 385 401 417 433 449 465
30 atoms in group fixed
group fixed id 481 497 513 529 545 561 577 593 609 625
40 atoms in group fixed
group fixed id 641 657 673 689 705 721 737 753 769 785
50 atoms in group fixed
group fixed id 801 817 833 849 865 881 897 913 929 945
60 atoms in group fixed
group fixed id 961 977 993 1009 1025 1041 1057 1073 1089 1105
70 atoms in group fixed
group fixed id 1121 1137 1153 1169 1185 1201 1217 1233 1249 1265
80 atoms in group fixed
group fixed id 1281 1297 1313 1329 1345 1361 1377 1393 1409 1425
90 atoms in group fixed
group fixed id 1441 1457 1473 1489 1505 1521 1537 1553 1569 1585
100 atoms in group fixed
group fixed id 1601 1617 1633 1649 1665 1681 1697 1713 1729 1745
110 atoms in group fixed
group fixed id 1761 1777 1793 1809 1825 1841 1857 1873 1889 1905
120 atoms in group fixed
group fixed id 1921 1937 1953 1969 1985 2001 2017 2033
128 atoms in group fixed
group movable subtract all fixed
1922 atoms in group movable
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]
uncompute thermo_temp
compute thermo_temp movable temp
#
# Subsets
#
group subset_thermostat id 3 5 7 10 12 14 16 19 21 23
10 atoms in group subset_thermostat
group subset_thermostat id 26 28 30 32 35 37 39 42 44 46
20 atoms in group subset_thermostat
group subset_thermostat id 48 51 53 55 58 60 62 64 67 69
30 atoms in group subset_thermostat
group subset_thermostat id 71 74 76 78 80 83 85 87 90 92
40 atoms in group subset_thermostat
group subset_thermostat id 94 96 99 101 103 106 108 110 112 115
50 atoms in group subset_thermostat
group subset_thermostat id 117 119 122 124 126 128 131 133 135 138
60 atoms in group subset_thermostat
group subset_thermostat id 140 142 144 147 149 151 154 156 158 160
70 atoms in group subset_thermostat
group subset_thermostat id 163 165 167 170 172 174 176 179 181 183
80 atoms in group subset_thermostat
group subset_thermostat id 186 188 190 192 195 197 199 202 204 206
90 atoms in group subset_thermostat
group subset_thermostat id 208 211 213 215 218 220 222 224 227 229
100 atoms in group subset_thermostat
group subset_thermostat id 231 234 236 238 240 243 245 247 250 252
110 atoms in group subset_thermostat
group subset_thermostat id 254 256 259 261 263 266 268 270 272 275
120 atoms in group subset_thermostat
group subset_thermostat id 277 279 282 284 286 288 291 293 295 298
130 atoms in group subset_thermostat
group subset_thermostat id 300 302 304 307 309 311 314 316 318 320
140 atoms in group subset_thermostat
group subset_thermostat id 323 325 327 330 332 334 336 339 341 343
150 atoms in group subset_thermostat
group subset_thermostat id 346 348 350 352 355 357 359 362 364 366
160 atoms in group subset_thermostat
group subset_thermostat id 368 371 373 375 378 380 382 384 387 389
170 atoms in group subset_thermostat
group subset_thermostat id 391 394 396 398 400 403 405 407 410 412
180 atoms in group subset_thermostat
group subset_thermostat id 414 416 419 421 423 426 428 430 432 435
190 atoms in group subset_thermostat
group subset_thermostat id 437 439 442 444 446 448 451 453 455 458
200 atoms in group subset_thermostat
group subset_thermostat id 460 462 464 467 469 471 474 476 478 480
210 atoms in group subset_thermostat
group subset_thermostat id 483 485 487 490 492 494 496 499 501 503
220 atoms in group subset_thermostat
group subset_thermostat id 506 508 510 512 515 517 519 522 524 526
230 atoms in group subset_thermostat
group subset_thermostat id 528 531 533 535 538 540 542 544 547 549
240 atoms in group subset_thermostat
group subset_thermostat id 551 554 556 558 560 563 565 567 570 572
250 atoms in group subset_thermostat
group subset_thermostat id 574 576 579 581 583 586 588 590 592 595
260 atoms in group subset_thermostat
group subset_thermostat id 597 599 602 604 606 608 611 613 615 618
270 atoms in group subset_thermostat
group subset_thermostat id 620 622 624 627 629 631 634 636 638 640
280 atoms in group subset_thermostat
group subset_thermostat id 643 645 647 650 652 654 656 659 661 663
290 atoms in group subset_thermostat
group subset_thermostat id 666 668 670 672 675 677 679 682 684 686
300 atoms in group subset_thermostat
group subset_thermostat id 688 691 693 695 698 700 702 704 707 709
310 atoms in group subset_thermostat
group subset_thermostat id 711 714 716 718 720 723 725 727 730 732
320 atoms in group subset_thermostat
group subset_thermostat id 734 736 739 741 743 746 748 750 752 755
330 atoms in group subset_thermostat
group subset_thermostat id 757 759 762 764 766 768 771 773 775 778
340 atoms in group subset_thermostat
group subset_thermostat id 780 782 784 787 789 791 794 796 798 800
350 atoms in group subset_thermostat
group subset_thermostat id 803 805 807 810 812 814 816 819 821 823
360 atoms in group subset_thermostat
group subset_thermostat id 826 828 830 832 835 837 839 842 844 846
370 atoms in group subset_thermostat
group subset_thermostat id 848 851 853 855 858 860 862 864 867 869
380 atoms in group subset_thermostat
group subset_thermostat id 871 874 876 878 880 883 885 887 890 892
390 atoms in group subset_thermostat
group subset_thermostat id 894 896 899 901 903 906 908 910 912 915
400 atoms in group subset_thermostat
group subset_thermostat id 917 919 922 924 926 928 931 933 935 938
410 atoms in group subset_thermostat
group subset_thermostat id 940 942 944 947 949 951 954 956 958 960
420 atoms in group subset_thermostat
group subset_thermostat id 963 965 967 970 972 974 976 979 981 983
430 atoms in group subset_thermostat
group subset_thermostat id 986 988 990 992 995 997 999 1002 1004 1006
440 atoms in group subset_thermostat
group subset_thermostat id 1008 1011 1013 1015 1018 1020 1022 1024 1027 1029
450 atoms in group subset_thermostat
group subset_thermostat id 1031 1034 1036 1038 1040 1043 1045 1047 1050 1052
460 atoms in group subset_thermostat
group subset_thermostat id 1054 1056 1059 1061 1063 1066 1068 1070 1072 1075
470 atoms in group subset_thermostat
group subset_thermostat id 1077 1079 1082 1084 1086 1088 1091 1093 1095 1098
480 atoms in group subset_thermostat
group subset_thermostat id 1100 1102 1104 1107 1109 1111 1114 1116 1118 1120
490 atoms in group subset_thermostat
group subset_thermostat id 1123 1125 1127 1130 1132 1134 1136 1139 1141 1143
500 atoms in group subset_thermostat
group subset_thermostat id 1146 1148 1150 1152 1155 1157 1159 1162 1164 1166
510 atoms in group subset_thermostat
group subset_thermostat id 1168 1171 1173 1175 1178 1180 1182 1184 1187 1189
520 atoms in group subset_thermostat
group subset_thermostat id 1191 1194 1196 1198 1200 1203 1205 1207 1210 1212
530 atoms in group subset_thermostat
group subset_thermostat id 1214 1216 1219 1221 1223 1226 1228 1230 1232 1235
540 atoms in group subset_thermostat
group subset_thermostat id 1237 1239 1242 1244 1246 1248 1251 1253 1255 1258
550 atoms in group subset_thermostat
group subset_thermostat id 1260 1262 1264 1267 1269 1271 1274 1276 1278 1280
560 atoms in group subset_thermostat
group subset_thermostat id 1283 1285 1287 1290 1292 1294 1296 1299 1301 1303
570 atoms in group subset_thermostat
group subset_thermostat id 1306 1308 1310 1312 1315 1317 1319 1322 1324 1326
580 atoms in group subset_thermostat
group subset_thermostat id 1328 1331 1333 1335 1338 1340 1342 1344 1347 1349
590 atoms in group subset_thermostat
group subset_thermostat id 1351 1354 1356 1358 1360 1363 1365 1367 1370 1372
600 atoms in group subset_thermostat
group subset_thermostat id 1374 1376 1379 1381 1383 1386 1388 1390 1392 1395
610 atoms in group subset_thermostat
group subset_thermostat id 1397 1399 1402 1404 1406 1408 1411 1413 1415 1418
620 atoms in group subset_thermostat
group subset_thermostat id 1420 1422 1424 1427 1429 1431 1434 1436 1438 1440
630 atoms in group subset_thermostat
group subset_thermostat id 1443 1445 1447 1450 1452 1454 1456 1459 1461 1463
640 atoms in group subset_thermostat
group subset_thermostat id 1466 1468 1470 1472 1475 1477 1479 1482 1484 1486
650 atoms in group subset_thermostat
group subset_thermostat id 1488 1491 1493 1495 1498 1500 1502 1504 1507 1509
660 atoms in group subset_thermostat
group subset_thermostat id 1511 1514 1516 1518 1520 1523 1525 1527 1530 1532
670 atoms in group subset_thermostat
group subset_thermostat id 1534 1536 1539 1541 1543 1546 1548 1550 1552 1555
680 atoms in group subset_thermostat
group subset_thermostat id 1557 1559 1562 1564 1566 1568 1571 1573 1575 1578
690 atoms in group subset_thermostat
group subset_thermostat id 1580 1582 1584 1587 1589 1591 1594 1596 1598 1600
700 atoms in group subset_thermostat
group subset_thermostat id 1603 1605 1607 1610 1612 1614 1616 1619 1621 1623
710 atoms in group subset_thermostat
group subset_thermostat id 1626 1628 1630 1632 1635 1637 1639 1642 1644 1646
720 atoms in group subset_thermostat
group subset_thermostat id 1648 1651 1653 1655 1658 1660 1662 1664 1667 1669
730 atoms in group subset_thermostat
group subset_thermostat id 1671 1674 1676 1678 1680 1683 1685 1687 1690 1692
740 atoms in group subset_thermostat
group subset_thermostat id 1694 1696 1699 1701 1703 1706 1708 1710 1712 1715
750 atoms in group subset_thermostat
group subset_thermostat id 1717 1719 1722 1724 1726 1728 1731 1733 1735 1738
760 atoms in group subset_thermostat
group subset_thermostat id 1740 1742 1744 1747 1749 1751 1754 1756 1758 1760
770 atoms in group subset_thermostat
group subset_thermostat id 1763 1765 1767 1770 1772 1774 1776 1779 1781 1783
780 atoms in group subset_thermostat
group subset_thermostat id 1786 1788 1790 1792 1795 1797 1799 1802 1804 1806
790 atoms in group subset_thermostat
group subset_thermostat id 1808 1811 1813 1815 1818 1820 1822 1824 1827 1829
800 atoms in group subset_thermostat
group subset_thermostat id 1831 1834 1836 1838 1840 1843 1845 1847 1850 1852
810 atoms in group subset_thermostat
group subset_thermostat id 1854 1856 1859 1861 1863 1866 1868 1870 1872 1875
820 atoms in group subset_thermostat
group subset_thermostat id 1877 1879 1882 1884 1886 1888 1891 1893 1895 1898
830 atoms in group subset_thermostat
group subset_thermostat id 1900 1902 1904 1907 1909 1911 1914 1916 1918 1920
840 atoms in group subset_thermostat
group subset_thermostat id 1923 1925 1927 1930 1932 1934 1936 1939 1941 1943
850 atoms in group subset_thermostat
group subset_thermostat id 1946 1948 1950 1952 1955 1957 1959 1962 1964 1966
860 atoms in group subset_thermostat
group subset_thermostat id 1968 1971 1973 1975 1978 1980 1982 1984 1987 1989
870 atoms in group subset_thermostat
group subset_thermostat id 1991 1994 1996 1998 2000 2003 2005 2007 2010 2012
880 atoms in group subset_thermostat
group subset_thermostat id 2014 2016 2019 2021 2023 2026 2028 2030 2032 2035
890 atoms in group subset_thermostat
group subset_thermostat id 2037 2039 2042 2044 2046 2048
896 atoms in group subset_thermostat
group subset_O2 id 2049 2050
2 atoms in group subset_O2
log 2.2_Velocities.out
#-------------------------------------------------------------------------------
# Stage 2.2: Set the initial velocities for $T
#-------------------------------------------------------------------------------
velocity all create 300 72489 dist gaussian mom yes rot no
velocity fixed set 0.0 0.0 0.0
log 2.3_Deposition.out
#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 100000 with a timestep of 0.2
#-------------------------------------------------------------------------------
group deposition_atoms_O2 id 2049 2050
2 atoms in group deposition_atoms_O2
delete_atoms group deposition_atoms_O2
WARNING: Ignoring 'compress yes' for molecular system (../delete_atoms.cpp:126)
Deleted 2 atoms, new total = 2048
molecule depositing_species_O2 deposition_O2.dat
Read molecule template depositing_species_O2:
1 molecules
0 fragments
2 atoms with max type 1
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_O2 block EDGE EDGE EDGE EDGE 50 60 units box
region evaporation_region block EDGE EDGE EDGE EDGE 90 EDGE 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 (../output.cpp:888)
thermo ${Nthermo}
thermo 0
fix 1 movable nve
fix 2 all evaporate 1000 1000 evaporation_region 9828 molecule yes
fix dlan subset_thermostat langevin 300 300 20.0 352 tally yes
fix 3 movable ave/time 1 50000 50000 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 4 movable ave/time 50 1 50 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 deposition_O2_1 deposition_atoms_O2 deposit 50 0 10000 9828 region deposition_region_O2 mol depositing_species_O2 vz -0.06989574890928181 -0.085428137555788888 vx 0.0 0.0 vy 0.0 0.0 near 1.50 id next units box
fix deposition_O2_2 deposition_atoms_O2 nve
dump trj all custom 5000 2.3.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 5000 1 5000 v_etotal v_pe v_ke file 2.3.energies.txt
dump trj_O2 deposition_atoms_O2 custom 5000 2.3.trajectory_1.xyz id mol type q xs ys zs
compute chunk_1 deposition_atoms_O2 chunk/atom bin/1d z lower 1.0 units box
fix chunk_1 deposition_atoms_O2 ave/chunk 1 50000 50000 chunk_1 density/number norm sample file 2.3_distribution_O2_1.out
timestep 0.2
run 500000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4, bins = 13 13 42
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 0.2
Per MPI rank memory allocation (min/avg/max) = 7.02 | 7.592 | 8.167 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 3321.0139 93956.963 1.0165589 299.37531 0 0 0 0 -212361.64 0 0 0 -212361.64 1712.479
500000 100000 2395.05 93956.963 1.0431382 381.18831 0 0 0 0 -226058.66 0 0 0 -226058.66 2180.4636
Loop time of 190.832 on 40 procs for 500000 steps with 2142 atoms
Performance: 45.275 ns/day, 0.530 hours/ns, 2620.108 timesteps/s
98.0% CPU use with 40 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.035414 | 58.63 | 147.9 | 812.1 | 30.72
Bond | 0.01855 | 0.027219 | 0.042277 | 4.9 | 0.01
Neigh | 0.002072 | 0.17358 | 0.42995 | 43.5 | 0.09
Comm | 0.18763 | 28.96 | 94.63 | 617.0 | 15.18
Output | 0.043449 | 0.045847 | 0.048889 | 0.8 | 0.02
Modify | 25.582 | 101.36 | 188.89 | 733.9 | 53.11
Other | | 1.637 | | | 0.86
Nlocal: 53.55 ave 134 max 0 min
Histogram: 20 0 0 0 4 0 0 0 11 5
Nghost: 226.35 ave 525 max 0 min
Histogram: 16 0 0 4 4 0 3 1 4 8
Neighs: 0 ave 0 max 0 min
Histogram: 40 0 0 0 0 0 0 0 0 0
FullNghs: 1428.7 ave 3741 max 0 min
Histogram: 20 0 0 2 2 0 0 3 9 4
Total # of neighbors = 57148
Ave neighs/atom = 26.679739
Ave special neighs/atom = 0
Neighbor list builds = 2159
Dangerous builds = 0
write_dump all xyz final_2.3.xyz modify element O Si
undump trj
unfix trjE
undump trj_O2
write_dump deposition_atoms_O2 custom 2.3.deposited_1.xyz id mol type q xs ys zs
restart 0
dump sci all custom 500000 2.3.xyz id mol type q xs ys zs
run 0
Setting up Verlet run ...
Unit style : real
Current step : 500000
Time step : 0.2
Per MPI rank memory allocation (min/avg/max) = 6.9 | 7.622 | 8.047 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
500000 100000 2395.05 93956.963 1.0431382 381.18831 0 0 0 0 -226058.66 0 0 0 -226058.66 2180.4636
Loop time of 2.10392e-06 on 40 procs for 0 steps with 2142 atoms
95.1% CPU use with 40 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 | | 2.104e-06 | | |100.00
Nlocal: 53.55 ave 134 max 0 min
Histogram: 20 0 0 0 4 0 0 0 11 5
Nghost: 226.35 ave 525 max 0 min
Histogram: 16 0 0 4 4 0 3 1 4 8
Neighs: 0 ave 0 max 0 min
Histogram: 40 0 0 0 0 0 0 0 0 0
FullNghs: 1428.7 ave 3741 max 0 min
Histogram: 20 0 0 2 2 0 0 3 9 4
Total # of neighbors = 57148
Ave neighs/atom = 26.679739
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
undump sci
uncompute chunk_1
unfix chunk_1
unfix 1
unfix 2
unfix 3
unfix 4
unfix deposition_O2_1
unfix deposition_O2_2
unfix dlan
Total wall time: 0:03:10