参照先URL
分子動力学計算の実践講習 −溶融塩とイオン液体−
amorphous.tf.chiba-u.jp
作業ログ
$ mkdir argon_melt_ini_coords_240724_230
$ cd argon_melt_ini_coords_240724_230/
$ pwd
~/argon_melt_ini_coords_240724_230初期構造の作成
Arの密度からセルを作る。ポテンシャル関数の変数も定義する。
$ touch Ar.data
$ cat Ar.data
Liquid Ar (rho=1.374g/cm3), Phys. Rev. 136, A405 (1964)
1 atoms
1 atom types
0 3.6412664191749493 xlo xhi
0 3.6412664191749493 ylo yhi
0 3.6412664191749493 zlo zhi
Masses
1 39.948
Pair Coeffs # lj/cut
1 0.23846475655872523 3.4
Atoms
1 1 0.0 0.0 0.0平衡計算と動径分布関数と平均自乗変位の計算
- 10x10x10のセル(1000個のAr)としNVT(94.4K)とする。
- 3 psの計算で平衡状態を得る。
- 30 psの計算で動径分布関数と平均自乗変位を計算する。
- 動径分布関数は12 Åまで計算する。
- 平均自乗変位は1 ps毎に計算する。
$ touch Ar_nvt.in
$ cat Ar_nvt.in
# Correlations in the Motion of Atoms in Liquid Argon
# A. Rahman, Phys. Rev. 136, A405 (1964)
# 単位の指定(E:kcal/mol, time:fs, distance:Ang., mass:g/mol, P:atmospheres)
units real
# ポテンシャル関数とcutoff距離 (# https://lammps.sandia.gov/doc/pair_lj.html)
pair_style lj/cut 7.65
# simulation boxとポテンシャル関数の係数をAr.dataから読む
read_data Ar.data
# 10x10x10のスーパーセルを生成, 10*10*10=1,000個のAr
replicate 10 10 10
# 熱力データを出力頻度(10ステップ毎)と出力パラメータ
thermo 10
thermo_style custom step temp etotal press vol density
# 粒子に与える温度(初期速度)と乱数用のseed
velocity all create 94.4 777
# NVTアンサンブルで温度は94.4K
fix 1 all nvt temp 94.4 94.4 100
# 100step毎に粒子の座標をAr.lammpstrjに記録
dump 1 all custom 1 Ar_nvt.lammpstrj id element x y z
# 原子番号でsortして元素記号を付したlammpstrjを保存
dump_modify 1 element Ar sort id
# 計算の時間刻み 1 fs
timestep 10
# 300ステップ=3ps実行して系を平衡にする
run 300
# 平衡になったら動径分布関数と平均自乗変位の計算
comm_modify cutoff 14
compute a all rdf 240 * * cutoff 12
fix 2 all ave/time 1 100 100 c_a[*] file Ar_nvt.gr mode vector
compute b all msd
fix 3 all ave/time 1 1 100 c_b[*] file Ar_nvt.msd title1 "#dt=10fs"
run 3000
# 最後の座標をlj.xyzファイルに出力
write_dump all xyz lj.xyz$ ls -CF
Ar.data Ar_nvt.in計算を実行します。
$ mpirun -np 4 ~/lammps-2Aug2023/src/lmp_mpi -in Ar_nvt.in -log Ar_nvt.log
LAMMPS (2 Aug 2023 - Update 2)
Reading data file ...
orthogonal box = (0 0 0) to (3.6412664 3.6412664 3.6412664)
1 by 2 by 2 MPI processor grid
reading atoms ...
1 atoms
read_data CPU = 0.003 seconds
Replication is creating a 10x10x10 = 1000 times larger system...
orthogonal box = (0 0 0) to (36.412664 36.412664 36.412664)
1 by 2 by 2 MPI processor grid
1000 atoms
replicate CPU = 0.000 seconds
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9.65
ghost atom cutoff = 9.65
binsize = 4.825, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 10
Per MPI rank memory allocation (min/avg/max) = 3.134 | 3.134 | 3.134 Mbytes
Step Temp TotEng Press Volume Density
0 94.4 -914.01993 560.79034 48278.9 1.374
10 58.785539 -899.11412 1348.9575 48278.9 1.374
20 65.932275 -866.54067 1477.6352 48278.9 1.374
30 94.550451 -824.37987 1240.3218 48278.9 1.374
40 111.38294 -813.93596 1031.639 48278.9 1.374
50 107.61911 -877.11585 698.2372 48278.9 1.374
60 92.473713 -928.70865 660.01965 48278.9 1.374
70 89.218982 -947.44092 614.95228 48278.9 1.374
80 95.448754 -941.2189 556.44633 48278.9 1.374
90 96.865133 -937.14909 573.19349 48278.9 1.374
100 93.499693 -943.80982 606.94586 48278.9 1.374
110 94.344842 -948.26519 569.26165 48278.9 1.374
120 94.076932 -950.93766 558.9755 48278.9 1.374
130 94.001562 -952.76573 553.39319 48278.9 1.374
140 94.167183 -952.19908 556.73153 48278.9 1.374
150 96.214156 -952.73452 515.98659 48278.9 1.374
160 93.148293 -960.22248 527.64273 48278.9 1.374
170 91.756665 -961.31298 554.23121 48278.9 1.374
180 97.491497 -952.11502 509.71667 48278.9 1.374
190 96.384051 -957.82048 486.55465 48278.9 1.374
200 91.155053 -970.95342 495.66567 48278.9 1.374
210 92.985875 -968.46979 482.65266 48278.9 1.374
220 95.710452 -957.22989 513.78868 48278.9 1.374
230 97.411739 -952.25038 525.86208 48278.9 1.374
240 95.947595 -964.57403 475.55679 48278.9 1.374
250 93.299305 -976.89218 438.392 48278.9 1.374
260 93.806804 -979.31879 401.82411 48278.9 1.374
270 93.075601 -976.67904 419.8749 48278.9 1.374
280 96.315745 -958.41675 478.64567 48278.9 1.374
290 96.364704 -952.77976 518.12723 48278.9 1.374
300 95.58332 -961.84683 495.80474 48278.9 1.374
Loop time of 0.187491 on 4 procs for 300 steps with 1000 atoms
Performance: 1382.469 ns/day, 0.017 hours/ns, 1600.080 timesteps/s, 1.600 Matom-step/s
96.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.02909 | 0.03083 | 0.033339 | 0.9 | 16.44
Neigh | 0.0051092 | 0.0052691 | 0.0053934 | 0.1 | 2.81
Comm | 0.014398 | 0.017089 | 0.019047 | 1.3 | 9.11
Output | 0.11784 | 0.12444 | 0.13095 | 1.4 | 66.37
Modify | 0.0020822 | 0.0022111 | 0.0023836 | 0.2 | 1.18
Other | | 0.007649 | | | 4.08
Nlocal: 250 ave 259 max 243 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 1374.5 ave 1392 max 1366 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 9458.75 ave 10113 max 8984 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 37835
Ave neighs/atom = 37.835
Neighbor list builds = 15
Dangerous builds = 0
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9.65
ghost atom cutoff = 14
binsize = 4.825, bins = 8 8 8
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
(2) compute rdf, occasional
attributes: half, newton on, cut 14
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 300
Time step : 10
Per MPI rank memory allocation (min/avg/max) = 5.517 | 5.518 | 5.519 Mbytes
Step Temp TotEng Press Volume Density
300 95.58332 -961.84683 495.80474 48278.9 1.374
310 90.96752 -968.35264 545.3815 48278.9 1.374
320 95.38972 -962.18159 487.68456 48278.9 1.374
330 94.155437 -962.81524 485.30315 48278.9 1.374
340 96.336556 -963.49957 428.52551 48278.9 1.374
350 94.746541 -978.30715 347.02667 48278.9 1.374
360 89.603629 -986.92318 382.28763 48278.9 1.374
370 94.908648 -975.21618 374.78203 48278.9 1.374
380 94.132722 -968.9245 446.49731 48278.9 1.374
390 94.792103 -961.08849 501.71097 48278.9 1.374
400 98.820393 -950.72737 496.86657 48278.9 1.374
410 92.966228 -968.20373 478.07534 48278.9 1.374
420 92.439883 -975.20795 434.70119 48278.9 1.374
430 94.787092 -970.42589 427.07328 48278.9 1.374
440 93.66443 -963.71363 504.34528 48278.9 1.374
450 99.632061 -949.54226 496.13654 48278.9 1.374
460 93.523069 -955.1562 572.78607 48278.9 1.374
470 89.614688 -972.79118 521.65515 48278.9 1.374
480 95.911619 -969.65789 401.18011 48278.9 1.374
490 94.447963 -970.61513 404.83786 48278.9 1.374
500 94.249954 -970.08127 416.75953 48278.9 1.374
510 94.554062 -970.51938 417.47767 48278.9 1.374
520 92.653328 -973.48667 428.53931 48278.9 1.374
530 95.224781 -967.96718 418.73334 48278.9 1.374
540 97.367097 -959.07166 449.96501 48278.9 1.374
550 94.206199 -966.86857 459.6081 48278.9 1.374
560 92.227917 -978.97027 413.22437 48278.9 1.374
570 94.556224 -979.18343 362.30812 48278.9 1.374
580 94.583239 -976.05221 380.75273 48278.9 1.374
590 94.312572 -967.56876 445.37766 48278.9 1.374
600 96.072316 -956.96994 483.42237 48278.9 1.374
610 98.201156 -958.51754 444.70118 48278.9 1.374
620 91.217356 -974.78484 464.06305 48278.9 1.374
630 93.30913 -971.74434 435.61306 48278.9 1.374
640 94.942655 -965.89579 441.76449 48278.9 1.374
650 95.533316 -965.35461 439.4076 48278.9 1.374
660 91.597664 -979.44025 412.72871 48278.9 1.374
670 89.968166 -989.03367 367.18999 48278.9 1.374
680 92.638114 -977.37413 413.47458 48278.9 1.374
690 92.954064 -966.44782 503.59368 48278.9 1.374
700 97.086707 -961.9187 455.61091 48278.9 1.374
710 95.438209 -972.56389 402.51297 48278.9 1.374
720 92.005475 -982.17807 385.44499 48278.9 1.374
730 93.185383 -978.56774 383.57875 48278.9 1.374
740 95.151399 -973.62882 377.90459 48278.9 1.374
750 95.187589 -974.76728 377.97667 48278.9 1.374
760 92.870124 -976.07833 416.15622 48278.9 1.374
770 95.271338 -971.40086 405.59562 48278.9 1.374
780 95.633843 -959.77586 485.60363 48278.9 1.374
790 101.15197 -946.93288 473.83877 48278.9 1.374
800 98.232722 -965.96249 390.92448 48278.9 1.374
810 91.738543 -978.77654 420.48024 48278.9 1.374
820 93.646674 -976.01019 402.719 48278.9 1.374
830 97.816092 -968.38078 376.83992 48278.9 1.374
840 91.980731 -978.07188 418.02158 48278.9 1.374
850 90.555186 -981.69421 411.02596 48278.9 1.374
860 97.231975 -961.30041 415.08798 48278.9 1.374
870 94.313594 -961.82698 467.97308 48278.9 1.374
880 94.2581 -962.86505 467.34364 48278.9 1.374
890 95.818901 -965.27964 419.57477 48278.9 1.374
900 92.097102 -982.04246 357.87309 48278.9 1.374
910 91.53652 -987.01667 321.10927 48278.9 1.374
920 94.160775 -977.03508 353.57238 48278.9 1.374
930 92.787233 -969.11224 454.74579 48278.9 1.374
940 96.651942 -964.66185 414.76738 48278.9 1.374
950 95.549337 -970.7424 399.67688 48278.9 1.374
960 90.13285 -979.22394 455.82507 48278.9 1.374
970 96.133124 -968.2919 424.34996 48278.9 1.374
980 96.500231 -958.96985 484.16531 48278.9 1.374
990 95.607035 -962.65816 477.81584 48278.9 1.374
1000 95.23881 -966.32753 453.76524 48278.9 1.374
1010 92.275955 -970.96072 460.86235 48278.9 1.374
1020 94.601645 -968.48708 428.8664 48278.9 1.374
1030 95.272176 -958.6796 490.09626 48278.9 1.374
1040 97.867701 -948.29654 521.24256 48278.9 1.374
1050 93.897762 -958.23331 538.47485 48278.9 1.374
1060 91.535726 -972.23918 494.43961 48278.9 1.374
1070 93.352448 -969.20755 491.05102 48278.9 1.374
1080 97.052859 -958.7117 495.09655 48278.9 1.374
1090 102.94642 -937.7276 536.11177 48278.9 1.374
1100 95.963017 -946.03772 610.92028 48278.9 1.374
1110 93.402581 -957.75827 579.16122 48278.9 1.374
1120 95.275905 -960.86856 516.57479 48278.9 1.374
1130 94.233465 -971.09918 450.27734 48278.9 1.374
1140 90.487318 -984.92387 411.42699 48278.9 1.374
1150 93.986625 -977.9549 388.29007 48278.9 1.374
1160 98.264618 -964.62459 399.03327 48278.9 1.374
1170 95.27361 -968.1499 428.53924 48278.9 1.374
1180 96.202311 -972.4076 373.63914 48278.9 1.374
1190 90.902395 -981.41534 400.52056 48278.9 1.374
1200 93.856303 -975.52254 377.86076 48278.9 1.374
1210 96.113535 -964.13446 416.1131 48278.9 1.374
1220 94.359872 -961.45667 479.51745 48278.9 1.374
1230 96.463489 -954.28661 499.6668 48278.9 1.374
1240 96.775145 -946.04323 561.82792 48278.9 1.374
1250 94.693221 -950.72716 576.69106 48278.9 1.374
1260 93.031457 -960.86388 530.72354 48278.9 1.374
1270 93.556039 -972.33789 427.31803 48278.9 1.374
1280 90.636449 -983.29867 401.0618 48278.9 1.374
1290 94.237882 -968.21607 437.16062 48278.9 1.374
1300 99.359887 -959.23039 399.02481 48278.9 1.374
1310 91.535189 -971.90306 446.48424 48278.9 1.374
1320 94.30307 -974.06709 384.28862 48278.9 1.374
1330 90.676368 -970.33075 501.95751 48278.9 1.374
1340 96.806708 -950.68379 531.21797 48278.9 1.374
1350 95.949039 -951.90492 514.88732 48278.9 1.374
1360 94.710489 -963.01299 447.40906 48278.9 1.374
1370 93.399823 -973.01649 399.877 48278.9 1.374
1380 92.352142 -973.60153 424.40213 48278.9 1.374
1390 94.281796 -968.03765 441.39596 48278.9 1.374
1400 95.648654 -967.79804 432.2782 48278.9 1.374
1410 95.01055 -972.38374 421.66764 48278.9 1.374
1420 93.233569 -980.47291 394.7943 48278.9 1.374
1430 93.015161 -986.31757 349.39175 48278.9 1.374
1440 91.35772 -990.06596 348.24457 48278.9 1.374
1450 94.271156 -978.81341 367.43504 48278.9 1.374
1460 96.330884 -967.51299 401.82746 48278.9 1.374
1470 92.705233 -967.43792 470.99811 48278.9 1.374
1480 96.215044 -957.88373 466.64534 48278.9 1.374
1490 101.6724 -947.82671 419.72596 48278.9 1.374
1500 96.346646 -970.10803 362.57349 48278.9 1.374
1510 92.537261 -976.11991 404.57153 48278.9 1.374
1520 94.343024 -970.55642 416.99343 48278.9 1.374
1530 95.996723 -963.17224 434.83969 48278.9 1.374
1540 94.744344 -962.34775 458.09696 48278.9 1.374
1550 96.147509 -970.07994 379.27817 48278.9 1.374
1560 91.235561 -984.84125 364.4347 48278.9 1.374
1570 93.646305 -981.92348 341.05848 48278.9 1.374
1580 93.138489 -969.7303 450.03898 48278.9 1.374
1590 95.602804 -956.19124 506.74966 48278.9 1.374
1600 96.169544 -959.06448 470.76835 48278.9 1.374
1610 94.25917 -968.49778 427.29843 48278.9 1.374
1620 94.763404 -978.81686 342.59388 48278.9 1.374
1630 89.636957 -984.36169 400.15103 48278.9 1.374
1640 96.759835 -969.61058 383.39829 48278.9 1.374
1650 93.20538 -967.08219 484.29223 48278.9 1.374
1660 95.815455 -963.35597 458.51276 48278.9 1.374
1670 95.741201 -968.91076 416.65845 48278.9 1.374
1680 91.186135 -981.42461 411.65571 48278.9 1.374
1690 92.71053 -977.04796 411.64668 48278.9 1.374
1700 96.64044 -963.87237 426.34724 48278.9 1.374
1710 97.169797 -965.80461 403.75193 48278.9 1.374
1720 92.748978 -971.95347 446.62758 48278.9 1.374
1730 95.745196 -970.63687 391.20027 48278.9 1.374
1740 93.466438 -977.90851 374.35612 48278.9 1.374
1750 89.280276 -986.8083 387.51891 48278.9 1.374
1760 96.615806 -970.92258 365.9485 48278.9 1.374
1770 95.981052 -969.21526 397.61846 48278.9 1.374
1780 92.021645 -973.35784 458.81546 48278.9 1.374
1790 95.421124 -966.89051 445.15226 48278.9 1.374
1800 97.355548 -961.5031 444.42277 48278.9 1.374
1810 92.931536 -976.68488 411.05891 48278.9 1.374
1820 90.142673 -984.24661 399.33107 48278.9 1.374
1830 96.562216 -973.06911 354.80507 48278.9 1.374
1840 96.021703 -971.55569 385.58393 48278.9 1.374
1850 90.432271 -979.35677 443.84351 48278.9 1.374
1860 92.218307 -975.75104 431.95359 48278.9 1.374
1870 97.557758 -957.96817 449.44698 48278.9 1.374
1880 95.942135 -963.96231 441.14435 48278.9 1.374
1890 90.579194 -972.09735 480.83169 48278.9 1.374
1900 96.007444 -964.00056 433.77323 48278.9 1.374
1910 95.325237 -962.18182 467.42988 48278.9 1.374
1920 91.096478 -975.89663 450.95418 48278.9 1.374
1930 91.232538 -983.35121 382.16562 48278.9 1.374
1940 96.113493 -972.51542 347.55161 48278.9 1.374
1950 97.349718 -967.23703 355.71172 48278.9 1.374
1960 88.300264 -980.22161 428.84653 48278.9 1.374
1970 92.517844 -979.58888 363.10568 48278.9 1.374
1980 95.595437 -960.59159 465.60506 48278.9 1.374
1990 96.194049 -959.60718 485.38279 48278.9 1.374
2000 93.090363 -968.47524 488.60499 48278.9 1.374
2010 91.401865 -967.9078 520.0807 48278.9 1.374
2020 96.775686 -952.90527 517.75297 48278.9 1.374
2030 93.742204 -952.79727 574.1522 48278.9 1.374
2040 96.361049 -952.76363 526.80282 48278.9 1.374
2050 90.608915 -959.96374 586.18179 48278.9 1.374
2060 96.766503 -951.40435 524.91824 48278.9 1.374
2070 101.43544 -948.82538 453.19139 48278.9 1.374
2080 93.252152 -965.44579 492.84205 48278.9 1.374
2090 95.045201 -966.77007 440.12134 48278.9 1.374
2100 92.788008 -967.05746 461.64262 48278.9 1.374
2110 95.408375 -959.22361 461.37761 48278.9 1.374
2120 97.364614 -950.46986 499.37186 48278.9 1.374
2130 95.811397 -955.85627 497.12695 48278.9 1.374
2140 91.51097 -975.60449 433.56328 48278.9 1.374
2150 93.550593 -975.65143 387.58802 48278.9 1.374
2160 94.351661 -968.86841 416.50661 48278.9 1.374
2170 96.672479 -958.00851 456.6422 48278.9 1.374
2180 98.729644 -943.88734 528.95622 48278.9 1.374
2190 98.305529 -951.08752 490.4237 48278.9 1.374
2200 93.254719 -969.66166 457.89136 48278.9 1.374
2210 91.564377 -968.24231 495.57642 48278.9 1.374
2220 98.824027 -956.74975 441.49728 48278.9 1.374
2230 94.226887 -964.9803 467.59462 48278.9 1.374
2240 92.698698 -972.99244 425.10867 48278.9 1.374
2250 93.633019 -972.12662 401.546 48278.9 1.374
2260 95.582687 -963.92237 444.1423 48278.9 1.374
2270 99.156489 -950.67766 493.65503 48278.9 1.374
2280 94.568016 -961.88159 493.87754 48278.9 1.374
2290 92.129159 -972.03198 452.50976 48278.9 1.374
2300 94.483217 -969.63278 424.36374 48278.9 1.374
2310 98.159379 -959.51802 433.77885 48278.9 1.374
2320 98.297858 -956.31377 456.05783 48278.9 1.374
2330 92.843794 -974.78169 421.25488 48278.9 1.374
2340 92.598471 -977.49843 393.25516 48278.9 1.374
2350 93.320116 -968.87119 439.81185 48278.9 1.374
2360 96.819222 -956.80519 473.07278 48278.9 1.374
2370 93.864558 -956.22231 537.03826 48278.9 1.374
2380 95.179395 -955.66205 514.5762 48278.9 1.374
2390 95.205524 -957.78272 483.16453 48278.9 1.374
2400 94.707027 -965.53173 424.46984 48278.9 1.374
2410 90.375781 -975.96635 430.74627 48278.9 1.374
2420 94.351636 -966.09763 426.91293 48278.9 1.374
2430 97.108183 -950.24641 486.1421 48278.9 1.374
2440 94.7209 -955.91116 494.51921 48278.9 1.374
2450 93.364852 -962.90426 474.0934 48278.9 1.374
2460 92.711183 -966.24442 457.74204 48278.9 1.374
2470 96.612616 -962.7591 401.7716 48278.9 1.374
2480 95.488487 -968.17378 378.77781 48278.9 1.374
2490 91.723232 -979.92771 362.95557 48278.9 1.374
2500 93.268749 -976.13963 361.09651 48278.9 1.374
2510 97.74122 -963.86192 378.60406 48278.9 1.374
2520 93.32059 -966.86951 456.98876 48278.9 1.374
2530 90.347824 -981.78001 412.65689 48278.9 1.374
2540 92.071446 -980.25135 391.18441 48278.9 1.374
2550 96.277168 -964.10469 435.30567 48278.9 1.374
2560 94.945612 -962.53553 479.84582 48278.9 1.374
2570 94.54791 -964.41043 480.7988 48278.9 1.374
2580 94.090387 -966.55985 470.94346 48278.9 1.374
2590 91.264807 -980.3158 424.47908 48278.9 1.374
2600 90.960866 -986.7932 369.39486 48278.9 1.374
2610 95.461668 -973.44122 372.04669 48278.9 1.374
2620 93.858024 -967.3785 443.59351 48278.9 1.374
2630 96.211452 -964.74996 401.80992 48278.9 1.374
2640 95.320311 -969.70398 365.47579 48278.9 1.374
2650 88.689537 -994.24138 312.14816 48278.9 1.374
2660 93.032156 -988.78111 275.04932 48278.9 1.374
2670 94.163301 -977.6994 337.24295 48278.9 1.374
2680 92.835033 -966.21883 453.64936 48278.9 1.374
2690 96.862954 -957.26173 453.10322 48278.9 1.374
2700 96.197916 -962.12607 430.45813 48278.9 1.374
2710 95.900828 -974.06985 349.03198 48278.9 1.374
2720 93.387863 -980.32774 351.3948 48278.9 1.374
2730 91.418938 -977.50904 418.50069 48278.9 1.374
2740 96.404906 -962.96178 440.61824 48278.9 1.374
2750 96.113926 -964.0512 449.94052 48278.9 1.374
2760 92.807037 -968.8016 482.85521 48278.9 1.374
2770 93.752986 -965.08069 485.73826 48278.9 1.374
2780 99.578273 -952.96562 464.18533 48278.9 1.374
2790 98.454882 -949.34117 512.8999 48278.9 1.374
2800 92.09702 -967.9241 489.21737 48278.9 1.374
2810 93.75996 -969.85063 430.22298 48278.9 1.374
2820 95.59728 -967.31366 418.72739 48278.9 1.374
2830 92.450012 -972.09475 468.50539 48278.9 1.374
2840 92.963844 -975.63999 442.22641 48278.9 1.374
2850 93.861937 -970.211 451.62059 48278.9 1.374
2860 96.327246 -957.46378 474.22023 48278.9 1.374
2870 95.876792 -956.14482 493.34718 48278.9 1.374
2880 91.247139 -971.15123 486.16744 48278.9 1.374
2890 92.105033 -978.45091 406.17981 48278.9 1.374
2900 96.022132 -969.49335 387.16012 48278.9 1.374
2910 98.560667 -949.21277 494.37529 48278.9 1.374
2920 97.241598 -950.67629 515.07637 48278.9 1.374
2930 93.282386 -963.41704 484.63127 48278.9 1.374
2940 95.525207 -965.38898 421.24201 48278.9 1.374
2950 95.173473 -969.91466 395.5352 48278.9 1.374
2960 95.24655 -980.11899 311.71283 48278.9 1.374
2970 90.991477 -993.13609 294.11776 48278.9 1.374
2980 89.422512 -987.00241 372.05289 48278.9 1.374
2990 93.742351 -975.25822 377.35279 48278.9 1.374
3000 94.984981 -966.4663 424.75486 48278.9 1.374
3010 97.239002 -963.70069 413.63589 48278.9 1.374
3020 89.902843 -975.12398 472.91877 48278.9 1.374
3030 91.676494 -969.3587 475.09361 48278.9 1.374
3040 98.010639 -952.22223 471.02293 48278.9 1.374
3050 96.099933 -959.69372 450.12787 48278.9 1.374
3060 92.65454 -971.87366 427.80199 48278.9 1.374
3070 94.463093 -973.35526 385.13517 48278.9 1.374
3080 94.034215 -969.91555 414.18981 48278.9 1.374
3090 99.971256 -954.5995 412.81128 48278.9 1.374
3100 93.138201 -958.85065 521.67364 48278.9 1.374
3110 92.487943 -966.93472 492.21353 48278.9 1.374
3120 93.658414 -966.71178 483.51906 48278.9 1.374
3130 98.595328 -956.80136 471.38041 48278.9 1.374
3140 94.400544 -964.14393 502.73297 48278.9 1.374
3150 92.361317 -975.10569 463.32412 48278.9 1.374
3160 92.116827 -972.48329 479.40981 48278.9 1.374
3170 97.901545 -952.64367 514.42929 48278.9 1.374
3180 96.905988 -954.58547 526.95812 48278.9 1.374
3190 94.250733 -963.8504 509.63884 48278.9 1.374
3200 94.757996 -971.83179 428.52489 48278.9 1.374
3210 93.544548 -983.03811 357.25297 48278.9 1.374
3220 90.828513 -989.41405 354.96836 48278.9 1.374
3230 96.678637 -966.98474 403.16957 48278.9 1.374
3240 96.72713 -963.20603 434.0324 48278.9 1.374
3250 93.673325 -973.25119 416.67594 48278.9 1.374
3260 93.033005 -980.74159 371.18527 48278.9 1.374
3270 92.783243 -981.3281 380.42715 48278.9 1.374
3280 97.003427 -966.31303 424.18168 48278.9 1.374
3290 97.885829 -961.12602 451.31742 48278.9 1.374
3300 93.977877 -975.89832 416.89457 48278.9 1.374
Loop time of 3.97954 on 4 procs for 3000 steps with 1000 atoms
Performance: 651.331 ns/day, 0.037 hours/ns, 753.855 timesteps/s, 753.855 katom-step/s
97.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.32417 | 0.343 | 0.36124 | 2.3 | 8.62
Neigh | 0.063292 | 0.065544 | 0.066872 | 0.5 | 1.65
Comm | 0.21262 | 0.23245 | 0.25485 | 3.1 | 5.84
Output | 1.295 | 1.3452 | 1.3939 | 3.2 | 33.80
Modify | 1.9256 | 1.9282 | 1.9295 | 0.1 | 48.45
Other | | 0.06521 | | | 1.64
Nlocal: 250 ave 260 max 243 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 2623.25 ave 2647 max 2605 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 9450 ave 9679 max 9186 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 37800
Ave neighs/atom = 37.8
Neighbor list builds = 159
Dangerous builds = 0
Total wall time: 0:00:04$ ls -CF
Ar.data Ar_nvt.gr Ar_nvt.in Ar_nvt.lammpstrj Ar_nvt.log Ar_nvt.msd$ python3 grplot.py
$ python3 msdplot.py
$ ls -CF
Ar.data Ar_nvt.gr Ar_nvt.in Ar_nvt.lammpstrj Ar_nvt.log Ar_nvt.msd gr.jpg grplot.py lj.xyz msd.jpg msdplot.py融液からの結晶化
conv.pyを用いてLAMMPSの入力ファイル形式に変換
$ ~/phase0_2024.01/bin/conv.py --batch --input_type=xyz --output_type=LAMMPS_input --input_file=lj.xyz --output_file=config.atoms
atomic configuration converter utility.
Copyright (C) PHASE System Consortium
INFO: the number of frames defined in this XYZ file : 1
INFO: converting input file 'lj.xyz' (xyz file) to output file 'config.atoms' (LAMMPS_input file)
INFO: the number of frames to output : 1
INFO: ... done
INFO:$ head -15 config.atoms
LAMMPS input file generated by the PHASE I/O utility
# created on : 07/24/24 04:22:50
1000 atoms
1 atom types
Atoms
1 1 6.40199 0.842699 32.9623
2 1 2.34742 34.7032 35.1729
3 1 10.7366 0.0889766 2.03136
4 1 14.6903 36.1932 35.9774
5 1 9.27918 2.89455 29.3095
6 1 17.96 0.805663 34.8445
7 1 24.1784 2.27408 5.21755融液からの結晶化の計算条件ファイル作成
$ touch Ar_npt.in
$ cat Ar_npt.in
# LAMMPS input script for cooling Argon liquid to crystallize
units real
atom_style atomic
# Read initial configuration
read_data config.atoms
# Define interatomic potential
pair_style lj/cut 7.65
pair_coeff 1 1 0.23846475655872523 3.405
# Define groups
group all type 1
# Set initial velocities
velocity all create 94.4
# Define settings for NPT ensemble
fix 1 all npt temp 94.4 81.0 100 iso 1.0 1.0 1000.0
# Output settings
thermo 100
thermo_style custom step temp press pe ke etotal
dump 1 all atom 100 dump.argon
# Run the simulation
timestep 1.0
run 50000
# Unfix the NPT ensemble and switch to NVT for equilibration
unfix 1
fix 2 all nvt temp 100.0 100.0 100.0
# Continue the simulation for further equilibration
run 50000
# 最後の座標をlj.xyzファイルに出力
write_dump all xyz lj.xyz融液の結晶化計算と動径分布関数と平均自乗変位の計算
計算を実行します。
$ pwd
/home/morii-k/argon_melt_ini_coords_240724_230$ mpirun -np 4 ~/lammps-2Aug2023/src/lmp_mpi -in Ar_npt.in -log Ar_npt.log
LAMMPS (2 Aug 2023 - Update 2)
Reading data file ...
orthogonal box = (-0.5 -0.5 -0.5) to (0.5 0.5 0.5)
1 by 2 by 2 MPI processor grid
reading atoms ...
1000 atoms
read_data CPU = 0.011 seconds
1000 atoms in group all
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9.65
ghost atom cutoff = 9.65
binsize = 4.825, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:966)
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
[SurfaceLaptop-4:224420] *** Process received signal ***
[SurfaceLaptop-4:224420] Signal: Segmentation fault (11)
[SurfaceLaptop-4:224420] Signal code: Address not mapped (1)
[SurfaceLaptop-4:224420] Failing at address: 0x7f00b9797000
[SurfaceLaptop-4:224420] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f00c18e8520]
[SurfaceLaptop-4:224420] [ 1] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0x1623dc)[0x5649984f23dc]
[SurfaceLaptop-4:224420] [ 2] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0x1592df)[0x5649984e92df]
[SurfaceLaptop-4:224420] [ 3] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0x249e59)[0x5649985d9e59]
[SurfaceLaptop-4:224420] [ 4] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0x1e0c89)[0x564998570c89]
[SurfaceLaptop-4:224420] [ 5] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0xebfbc)[0x56499847bfbc]
[SurfaceLaptop-4:224420] [ 6] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0xec966)[0x56499847c966]
[SurfaceLaptop-4:224420] [ 7] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0xc4d01)[0x564998454d01]
[SurfaceLaptop-4:224420] [ 8] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f00c18cfd90]
[SurfaceLaptop-4:224420] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f00c18cfe40]
[SurfaceLaptop-4:224420] [10] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0xc6275)[0x564998456275]
[SurfaceLaptop-4:224420] *** End of error message ***
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[SurfaceLaptop-4:224421] *** Process received signal ***
[SurfaceLaptop-4:224421] Signal: Segmentation fault (11)
[SurfaceLaptop-4:224421] Signal code: Address not mapped (1)
[SurfaceLaptop-4:224421] Failing at address: 0x7fa2118f9000
[SurfaceLaptop-4:224421] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7fa219a28520]
[SurfaceLaptop-4:224421] [ 1] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0x1623dc)[0x55c27d3243dc]
[SurfaceLaptop-4:224421] [ 2] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0x1592df)[0x55c27d31b2df]
[SurfaceLaptop-4:224421] [ 3] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0x249e59)[0x55c27d40be59]
[SurfaceLaptop-4:224421] [ 4] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0x1e0c89)[0x55c27d3a2c89]
[SurfaceLaptop-4:224421] [ 5] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0xebfbc)[0x55c27d2adfbc]
[SurfaceLaptop-4:224421] [ 6] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0xec966)[0x55c27d2ae966]
[SurfaceLaptop-4:224421] [ 7] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0xc4d01)[0x55c27d286d01]
[SurfaceLaptop-4:224421] [ 8] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7fa219a0fd90]
[SurfaceLaptop-4:224421] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7fa219a0fe40]
[SurfaceLaptop-4:224421] [10] /home/morii-k/lammps-2Aug2023/src/lmp_mpi(+0xc6275)[0x55c27d288275]
[SurfaceLaptop-4:224421] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 0 on node SurfaceLaptop-4 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
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