203 lines
11 KiB
Groff
203 lines
11 KiB
Groff
LAMMPS (26 Sep 2016)
|
|
# 2d circle of particles inside a box with LJ walls
|
|
|
|
variable b index 0
|
|
|
|
variable x index 50
|
|
variable y index 20
|
|
variable d index 20
|
|
variable v index 5
|
|
variable w index 2
|
|
|
|
units lj
|
|
dimension 2
|
|
atom_style atomic
|
|
boundary f f p
|
|
|
|
lattice hex 0.85
|
|
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
|
region box block 0 $x 0 $y -0.5 0.5
|
|
region box block 0 50 0 $y -0.5 0.5
|
|
region box block 0 50 0 20 -0.5 0.5
|
|
create_box 1 box
|
|
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
|
2 by 2 by 1 MPI processor grid
|
|
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
|
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
|
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
|
region circle sphere 11 6.7735026918962581988 0.0 10
|
|
create_atoms 1 region circle
|
|
Created 361 atoms
|
|
mass 1 1.0
|
|
|
|
velocity all create 0.5 87287 loop geom
|
|
velocity all set $v $w 0 sum yes
|
|
velocity all set 5 $w 0 sum yes
|
|
velocity all set 5 2 0 sum yes
|
|
|
|
pair_style lj/cut 2.5
|
|
pair_coeff 1 1 10.0 1.0 2.5
|
|
|
|
neighbor 0.3 bin
|
|
neigh_modify delay 0 every 1 check yes
|
|
|
|
fix 1 all nve
|
|
|
|
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
|
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
|
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
|
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
|
|
|
comm_style tiled
|
|
fix 10 all balance 50 0.9 rcb
|
|
|
|
#compute 1 all property/atom proc
|
|
#variable p atom c_1%10
|
|
#dump 2 all custom 50 tmp.dump id v_p x y z
|
|
|
|
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
|
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
|
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
|
|
|
thermo_style custom step temp epair press f_10[3] f_10
|
|
thermo 100
|
|
|
|
run 10000
|
|
Neighbor list info ...
|
|
1 neighbor list requests
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 2.8
|
|
ghost atom cutoff = 2.8
|
|
binsize = 1.4 -> bins = 42 29 1
|
|
Memory usage per processor = 2.48839 Mbytes
|
|
Step Temp E_pair Press f_10[3] f_10
|
|
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
|
|
100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
|
|
200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
|
|
300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906
|
|
400 26.522239 -29.965537 6.6787858 1.1855956 1.0193906
|
|
500 25.725591 -29.168034 0.67065285 1.2520776 1.0083102
|
|
600 26.247693 -29.692706 7.9887712 1.3074792 1.0083102
|
|
700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102
|
|
800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102
|
|
900 23.635295 -27.372963 9.029962 1.1634349 1.0083102
|
|
1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906
|
|
1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906
|
|
1200 17.214459 -20.726965 6.3578917 1.0304709 1.0193906
|
|
1300 16.424084 -19.757322 3.9028131 1.1191136 1.0083102
|
|
1400 15.026954 -18.109911 1.7623684 1.0858726 1.0193906
|
|
1500 13.640678 -16.740794 1.5347425 1.0858726 1.0193906
|
|
1600 13.618211 -16.610276 1.9480883 1.0747922 1.0083102
|
|
1700 13.266465 -16.300632 1.6890777 1.0637119 1.0193906
|
|
1800 12.178444 -15.175544 2.1018989 1.0304709 1.0083102
|
|
1900 12.131633 -15.075269 2.0174899 1.0526316 1.0193906
|
|
2000 12.290785 -15.185923 1.8747772 1.0415512 1.0193906
|
|
2100 12.02255 -14.947108 1.086185 1.0747922 1.0083102
|
|
2200 11.733238 -14.620414 0.93934447 1.0526316 1.0193906
|
|
2300 12.180779 -15.092283 1.1969416 1.0526316 1.0083102
|
|
2400 11.721247 -14.503377 1.3759878 1.1080332 1.0083102
|
|
2500 11.609116 -14.371603 2.0315139 1.0747922 1.0083102
|
|
2600 11.712503 -14.494711 1.7236598 1.0415512 1.0193906
|
|
2700 10.932816 -13.665751 1.2772732 1.0415512 1.0083102
|
|
2800 10.418752 -13.183889 1.2940564 1.0415512 1.0193906
|
|
2900 10.668297 -13.404525 0.90378659 1.0304709 1.0083102
|
|
3000 10.562215 -13.581566 1.0507999 1.0083102 1.0193906
|
|
3100 10.283188 -13.016565 1.0685664 1.0526316 1.0193906
|
|
3200 10.424678 -13.136756 1.4038511 1.0193906 1.0083102
|
|
3300 10.207304 -12.901323 1.3077174 1.0415512 1.0193906
|
|
3400 10.143301 -12.802915 1.2776266 1.0415512 1.0193906
|
|
3500 9.8449452 -12.507639 1.5455496 1.0637119 1.0083102
|
|
3600 9.5629038 -12.204164 0.84971204 1.0304709 1.0083102
|
|
3700 9.1851938 -11.809431 1.0102805 1.0304709 1.0193906
|
|
3800 9.3305969 -11.989086 0.69923461 1.0193906 1.0083102
|
|
3900 9.2415243 -11.880498 1.2471235 1.0637119 1.0193906
|
|
4000 8.8240051 -11.417696 0.60781901 1.0304709 1.0083102
|
|
4100 8.9126422 -11.503716 0.96900558 1.0083102 1.0083102
|
|
4200 8.3738185 -10.93925 0.84927158 1.0193906 1.0083102
|
|
4300 8.2401487 -10.90291 0.97775564 1.0083102 1.0083102
|
|
4400 8.061288 -10.722169 1.4106859 1.0193906 1.0193906
|
|
4500 7.8900038 -10.422818 0.67651486 1.0193906 1.0193906
|
|
4600 7.8306694 -10.363812 0.83437455 1.0193906 1.0193906
|
|
4700 8.1116499 -10.712008 0.58885383 1.0304709 1.0193906
|
|
4800 8.0508103 -10.576232 0.52562827 1.0193906 1.0083102
|
|
4900 7.8161815 -10.368333 0.89724847 1.0415512 1.0083102
|
|
5000 7.4940002 -9.9763835 1.215446 1.0304709 1.0083102
|
|
5100 7.9981403 -10.510786 1.0948502 1.0304709 1.0193906
|
|
5200 7.7674668 -10.259031 0.81850586 1.0304709 1.0193906
|
|
5300 7.9627913 -10.465018 0.75004253 1.0304709 1.0083102
|
|
5400 7.8093696 -10.371624 0.75451812 1.0193906 1.0083102
|
|
5500 8.1189569 -10.623288 0.91908416 1.0304709 1.0083102
|
|
5600 7.5970957 -10.070305 0.84265844 1.0415512 1.0083102
|
|
5700 7.4322203 -9.9176252 0.32608772 1.0304709 1.0083102
|
|
5800 7.8210607 -10.311444 0.95696619 1.0304709 1.0083102
|
|
5900 7.6181913 -10.111225 1.1341946 1.0193906 1.0083102
|
|
6000 7.2217555 -9.7122281 0.75858423 1.0637119 1.0083102
|
|
6100 7.3643302 -9.851242 0.5240439 1.0193906 1.0193906
|
|
6200 7.0281589 -9.4834454 0.59523945 1.0526316 1.0193906
|
|
6300 7.1383115 -9.6099868 0.87558078 1.0193906 1.0193906
|
|
6400 7.2136999 -9.6965877 0.88426542 1.0304709 1.0083102
|
|
6500 7.1710521 -9.7082917 1.2055959 1.0415512 1.0193906
|
|
6600 7.4150515 -9.9376614 0.48201097 1.0304709 1.0083102
|
|
6700 6.8701427 -9.3844769 0.72785561 1.0526316 1.0193906
|
|
6800 6.8486978 -9.3256413 0.93231327 1.0193906 1.0083102
|
|
6900 6.583533 -9.0068813 0.51281911 1.0193906 1.0193906
|
|
7000 6.7199396 -9.1773668 0.12636874 1.0193906 1.0083102
|
|
7100 6.5193695 -8.9553058 1.0423295 1.0083102 1.0193906
|
|
7200 6.4868896 -8.9090695 0.49867926 1.0083102 1.0193906
|
|
7300 6.2975635 -8.7775483 0.49072731 1.0415512 1.0083102
|
|
7400 6.4966155 -8.9410837 0.52952897 1.0193906 1.0083102
|
|
7500 6.7100139 -9.166691 0.82930078 1.0193906 1.0083102
|
|
7600 6.3569418 -8.7843554 0.93473251 1.0193906 1.0083102
|
|
7700 6.122789 -8.5434369 0.33725874 1.0526316 1.0083102
|
|
7800 6.0249595 -8.4453069 0.52784464 1.0193906 1.0083102
|
|
7900 6.6673238 -9.1166487 0.93753595 1.0193906 1.0083102
|
|
8000 6.4177253 -8.8896071 0.57421674 1.0193906 1.0193906
|
|
8100 5.965959 -8.3655023 0.42043964 1.0304709 1.0193906
|
|
8200 6.3325216 -8.758339 0.76723151 1.0193906 1.0193906
|
|
8300 6.4992751 -8.943922 0.86331769 1.0526316 1.0193906
|
|
8400 6.1834495 -8.6059885 0.43133079 1.0415512 1.0193906
|
|
8500 6.2567239 -8.6758815 0.8551113 1.0083102 1.0193906
|
|
8600 6.1232623 -8.5905174 0.6014726 1.0304709 1.0083102
|
|
8700 6.6650376 -9.0949995 0.46866086 1.0637119 1.0193906
|
|
8800 6.6103957 -9.0116868 0.84371859 1.0083102 1.0193906
|
|
8900 5.8867946 -8.3162884 0.64216189 1.0415512 1.0193906
|
|
9000 5.685369 -8.0652138 0.32067903 1.0304709 1.0083102
|
|
9100 6.2783881 -8.6826466 0.36419567 1.0415512 1.0304709
|
|
9200 6.0162211 -8.4584809 0.58707128 1.0083102 1.0083102
|
|
9300 5.9900511 -8.3949266 0.62037401 1.0304709 1.0193906
|
|
9400 6.2686573 -8.6713334 0.81204427 1.0415512 1.0083102
|
|
9500 6.0317917 -8.4325112 0.63221293 1.0304709 1.0193906
|
|
9600 5.8217003 -8.256407 0.816143 1.0304709 1.0083102
|
|
9700 5.6011023 -7.9966077 0.4114902 1.0304709 1.0193906
|
|
9800 5.6339982 -8.0317639 0.32315576 1.0083102 1.0083102
|
|
9900 5.8044743 -8.1942271 0.62892477 1.0193906 1.0083102
|
|
10000 6.1722678 -8.5642925 0.80423557 1.0304709 1.0083102
|
|
Loop time of 0.39332 on 4 procs for 10000 steps with 361 atoms
|
|
|
|
Performance: 10983420.832 tau/day, 25424.585 timesteps/s
|
|
98.9% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.067888 | 0.075593 | 0.091022 | 3.3 | 19.22
|
|
Neigh | 0.071147 | 0.075568 | 0.085203 | 2.1 | 19.21
|
|
Comm | 0.10841 | 0.12918 | 0.14463 | 4.0 | 32.84
|
|
Output | 0.0017445 | 0.001877 | 0.0022032 | 0.4 | 0.48
|
|
Modify | 0.038837 | 0.039568 | 0.040469 | 0.3 | 10.06
|
|
Other | | 0.07153 | | | 18.19
|
|
|
|
Nlocal: 90.25 ave 91 max 90 min
|
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
|
Nghost: 22.25 ave 27 max 16 min
|
|
Histogram: 1 0 0 0 0 0 2 0 0 1
|
|
Neighs: 268.25 ave 400 max 133 min
|
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
|
|
|
Total # of neighbors = 1073
|
|
Ave neighs/atom = 2.9723
|
|
Neighbor list builds = 3611
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:00
|