forked from lijiext/lammps
243 lines
12 KiB
Groff
243 lines
12 KiB
Groff
LAMMPS (27 Nov 2018)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# 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 bond
|
|
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 bond/types 1 extra/bond/per/atom 6
|
|
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
|
|
Time spent = 0.00067687 secs
|
|
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
|
|
|
|
bond_style harmonic
|
|
bond_coeff 1 10.0 1.2
|
|
|
|
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
|
|
|
|
special_bonds lj/coul 0 1 1
|
|
0 = max # of 1-2 neighbors
|
|
1 = max # of special neighbors
|
|
create_bonds many all all 1 1.0 1.5
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 10 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
|
|
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
|
(1) command create_bonds, occasional
|
|
attributes: full, newton on
|
|
pair build: full/bin
|
|
stencil: full/bin/2d
|
|
bin: standard
|
|
(2) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/2d/newton
|
|
bin: standard
|
|
Added 1014 bonds, new total = 1014
|
|
6 = max # of 1-2 neighbors
|
|
6 = max # of special neighbors
|
|
|
|
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
|
|
comm_modify cutoff 10.0 # because bonds stretch a long ways
|
|
fix 10 all balance 50 0.9 rcb
|
|
|
|
#compute 1 all property/atom proc
|
|
#variable p atom (c_1%10)+1
|
|
#dump 2 all custom 50 tmp.dump id v_p x y z
|
|
|
|
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # 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 ...
|
|
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 = 10
|
|
binsize = 1.4, bins = 42 29 1
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/2d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 5.122 | 5.141 | 5.174 Mbytes
|
|
Step Temp E_pair Press f_10[3] f_10
|
|
0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
|
|
100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102
|
|
200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906
|
|
300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906
|
|
400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102
|
|
500 37.154928 -24.096946 3.2656177 1.3296399 1.0304709
|
|
600 35.059873 -21.524223 2.3729526 1.3296399 1.0083102
|
|
700 36.735117 -22.012675 3.266197 1.3296399 1.0083102
|
|
800 39.218223 -25.076176 4.7162461 1.4182825 1.0193906
|
|
900 38.003628 -24.598176 3.4651756 1.4958449 1.0083102
|
|
1000 37.599298 -25.117714 4.6714491 1.2963989 1.0193906
|
|
1100 35.587211 -24.476201 4.8766816 1.2077562 1.0083102
|
|
1200 33.05745 -21.457847 4.7304313 1.2188366 1.0193906
|
|
1300 35.505899 -20.103017 7.0543469 1.1523546 1.0193906
|
|
1400 32.687958 -18.411286 2.8022421 1.1523546 1.0083102
|
|
1500 30.681103 -13.979491 1.5780815 1.1523546 1.0083102
|
|
1600 28.134276 -12.408217 1.4370834 1.2188366 1.0193906
|
|
1700 29.150676 -12.486223 1.7118526 1.1745152 1.0083102
|
|
1800 29.456937 -11.386522 2.0484739 1.1966759 1.0193906
|
|
1900 28.029998 -11.168436 0.38519481 1.1080332 1.0193906
|
|
2000 29.476997 -12.337678 1.8878345 1.1523546 1.0083102
|
|
2100 30.113294 -12.201714 2.8003366 1.1634349 1.0193906
|
|
2200 31.599067 -13.710787 2.5654923 1.2188366 1.0083102
|
|
2300 31.333799 -12.269386 1.9573739 1.1412742 1.0193906
|
|
2400 28.587094 -10.98229 2.090581 1.1745152 1.0083102
|
|
2500 28.012332 -11.416553 2.3293146 1.1855956 1.0083102
|
|
2600 28.703189 -13.33369 2.7247345 1.1080332 1.0083102
|
|
2700 26.933934 -13.546384 0.71447362 1.0415512 1.0304709
|
|
2800 24.556936 -12.231427 0.012081842 1.0526316 1.0193906
|
|
2900 24.362943 -10.921093 -0.6063159 1.0858726 1.0193906
|
|
3000 24.583358 -10.025143 0.35975315 1.0637119 1.0083102
|
|
3100 26.119046 -10.124317 0.75140102 1.0415512 1.0193906
|
|
3200 27.665317 -11.418452 0.39942176 1.1301939 1.0083102
|
|
3300 27.771434 -9.9777413 0.94693011 1.1080332 1.0083102
|
|
3400 25.692188 -9.9016885 2.2582772 1.0415512 1.0083102
|
|
3500 27.009276 -10.504438 0.98279258 1.1301939 1.0083102
|
|
3600 26.082843 -9.4359595 -0.030819747 1.1301939 1.0083102
|
|
3700 23.956851 -8.4601884 -0.45748969 1.0858726 1.0304709
|
|
3800 24.92141 -8.3315871 -0.19512647 1.0969529 1.0083102
|
|
3900 26.048044 -9.6299934 0.40522014 1.0858726 1.0083102
|
|
4000 26.558961 -10.032084 0.56213613 1.1745152 1.0083102
|
|
4100 26.949686 -10.133598 1.0140825 1.0747922 1.0083102
|
|
4200 25.868196 -9.3971859 1.2758465 1.0969529 1.0083102
|
|
4300 24.563369 -9.5992996 0.17389949 1.1191136 1.0193906
|
|
4400 24.032818 -10.002668 0.10233743 1.0969529 1.0083102
|
|
4500 25.281577 -9.948799 0.7590423 1.1523546 1.0083102
|
|
4600 25.010901 -10.195479 -0.24424931 1.0747922 1.0193906
|
|
4700 25.062368 -9.2973021 1.1755931 1.0858726 1.0193906
|
|
4800 25.70912 -8.890895 1.0780397 1.1080332 1.0193906
|
|
4900 26.027757 -10.205469 1.0644859 1.1080332 1.0083102
|
|
5000 25.845739 -9.8511049 0.49059257 1.1301939 1.0193906
|
|
5100 25.614064 -9.0396911 0.40825814 1.0526316 1.0304709
|
|
5200 25.548135 -9.000613 0.81571441 1.1080332 1.0083102
|
|
5300 26.592601 -9.2385129 1.4983434 1.0637119 1.0193906
|
|
5400 26.230779 -9.8226036 1.0072462 1.0858726 1.0083102
|
|
5500 26.809887 -9.9569954 1.4074968 1.0415512 1.0083102
|
|
5600 25.722206 -10.240487 -0.5216434 1.0747922 1.0193906
|
|
5700 24.973866 -9.0820997 0.92104357 1.0193906 1.0083102
|
|
5800 24.257134 -9.5439897 -0.75290789 1.0858726 1.0083102
|
|
5900 25.524917 -8.9920216 1.2049479 1.1191136 1.0083102
|
|
6000 24.816532 -9.5865764 -0.66634446 1.0637119 1.0193906
|
|
6100 27.034385 -9.4017037 1.0769494 1.0969529 1.0083102
|
|
6200 24.19144 -8.2292864 0.97913204 1.0415512 1.0193906
|
|
6300 26.112877 -9.1531212 0.77578963 1.0526316 1.0193906
|
|
6400 25.820541 -9.9662231 -0.092724413 1.0969529 1.0193906
|
|
6500 26.181404 -9.5875764 -0.30106405 1.1634349 1.0083102
|
|
6600 27.770851 -8.8366116 0.94545206 1.0304709 1.0193906
|
|
6700 26.065489 -9.8223382 0.24640067 1.0526316 1.0193906
|
|
6800 27.468165 -10.160923 2.7263738 1.0747922 1.0304709
|
|
6900 27.317955 -10.356911 1.131609 1.0526316 1.0304709
|
|
7000 26.343789 -9.9153453 1.0385354 1.0858726 1.0193906
|
|
7100 24.366577 -8.9243936 0.37685043 1.0526316 1.0193906
|
|
7200 25.570042 -8.9195237 0.44206575 1.0637119 1.0193906
|
|
7300 24.635046 -8.4524117 -0.20581694 1.0193906 1.0193906
|
|
7400 27.161863 -7.9885934 1.1323072 1.0858726 1.0193906
|
|
7500 26.8044 -9.5703931 0.69476535 1.0858726 1.0193906
|
|
7600 27.381006 -10.702178 -0.20230101 1.0526316 1.0083102
|
|
7700 26.507406 -9.828117 0.50115907 1.0415512 1.0193906
|
|
7800 25.945271 -8.9912842 0.89121191 1.0747922 1.0083102
|
|
7900 24.498681 -7.7193231 -0.63874494 1.0858726 1.0083102
|
|
8000 24.517408 -7.6046107 -0.91642337 1.0415512 1.0083102
|
|
8100 26.388387 -8.1883906 0.093136981 1.1080332 1.0193906
|
|
8200 26.261054 -8.7223732 -0.086859057 1.0747922 1.0083102
|
|
8300 26.287026 -9.2583895 0.79506804 1.0858726 1.0083102
|
|
8400 24.691375 -9.0701909 -0.40058151 1.0637119 1.0193906
|
|
8500 25.390612 -7.9499801 0.59874113 1.1412742 1.0193906
|
|
8600 26.84383 -8.5520984 0.37618599 1.0637119 1.0083102
|
|
8700 25.685137 -7.688836 0.035978149 1.0415512 1.0193906
|
|
8800 26.614591 -9.0444146 0.20671465 1.0193906 1.0083102
|
|
8900 25.782718 -8.2594705 0.54378816 1.0747922 1.0304709
|
|
9000 26.026886 -8.6777252 0.25418163 1.1191136 1.0083102
|
|
9100 27.246916 -9.0307861 1.211131 1.0526316 1.0193906
|
|
9200 27.282948 -9.180029 -0.0056269613 1.0747922 1.0083102
|
|
9300 27.029692 -8.7791461 0.35971649 1.0304709 1.0083102
|
|
9400 26.549013 -7.5083174 0.77607249 1.0969529 1.0193906
|
|
9500 25.533731 -9.2763668 0.28360762 1.0969529 1.0083102
|
|
9600 27.997538 -9.2766769 1.6968428 1.0637119 1.0083102
|
|
9700 26.977436 -9.21372 1.8007256 1.0637119 1.0083102
|
|
9800 25.547091 -9.1024445 -0.29158273 1.0969529 1.0193906
|
|
9900 26.378841 -8.7645665 1.0385835 1.1080332 1.0083102
|
|
10000 26.699368 -8.5450739 0.19591452 1.0526316 1.0193906
|
|
Loop time of 0.916576 on 4 procs for 10000 steps with 361 atoms
|
|
|
|
Performance: 4713193.307 tau/day, 10910.170 timesteps/s
|
|
92.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.10915 | 0.12374 | 0.14167 | 3.5 | 13.50
|
|
Bond | 0.047075 | 0.049849 | 0.054161 | 1.2 | 5.44
|
|
Neigh | 0.31176 | 0.3246 | 0.3384 | 1.7 | 35.41
|
|
Comm | 0.24271 | 0.26717 | 0.30549 | 4.9 | 29.15
|
|
Output | 0.0017068 | 0.0021075 | 0.0031145 | 1.3 | 0.23
|
|
Modify | 0.064639 | 0.065705 | 0.067641 | 0.5 | 7.17
|
|
Other | | 0.08341 | | | 9.10
|
|
|
|
Nlocal: 90.25 ave 92 max 89 min
|
|
Histogram: 1 0 0 2 0 0 0 0 0 1
|
|
Nghost: 248.25 ave 264 max 230 min
|
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
|
Neighs: 569.5 ave 657 max 519 min
|
|
Histogram: 2 0 0 0 1 0 0 0 0 1
|
|
|
|
Total # of neighbors = 2278
|
|
Ave neighs/atom = 6.31025
|
|
Ave special neighs/atom = 5.61773
|
|
Neighbor list builds = 4964
|
|
Dangerous builds = 14
|
|
Total wall time: 0:00:00
|