222 lines
10 KiB
Groff
222 lines
10 KiB
Groff
LAMMPS (29 Jun 2018)
|
|
# 2d rounded polygon bodies
|
|
|
|
variable r index 4
|
|
variable steps index 100000
|
|
variable T index 0.5
|
|
variable P index 0.1
|
|
variable seed index 980411
|
|
|
|
units lj
|
|
dimension 2
|
|
|
|
atom_style body rounded/polygon 1 6
|
|
atom_modify map array
|
|
read_data data.squares
|
|
orthogonal box = (0 0 -0.5) to (12 12 0.5)
|
|
2 by 2 by 1 MPI processor grid
|
|
reading atoms ...
|
|
2 atoms
|
|
2 bodies
|
|
|
|
replicate $r $r 1
|
|
replicate 4 $r 1
|
|
replicate 4 4 1
|
|
orthogonal box = (0 0 -0.5) to (48 48 0.5)
|
|
2 by 2 by 1 MPI processor grid
|
|
32 atoms
|
|
Time spent = 0.000324011 secs
|
|
|
|
velocity all create $T ${seed} dist gaussian mom yes rot yes
|
|
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
|
|
velocity all create 0.5 980411 dist gaussian mom yes rot yes
|
|
|
|
variable cut_inner equal 0.5
|
|
variable k_n equal 100
|
|
variable k_na equal 2
|
|
variable c_n equal 1
|
|
variable c_t equal 1
|
|
variable mu equal 0.1
|
|
variable delta_ua equal 0.5
|
|
|
|
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
|
pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
|
pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
|
|
pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
|
|
pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
|
|
pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
|
|
pair_coeff * * ${k_n} ${k_na}
|
|
pair_coeff * * 100 ${k_na}
|
|
pair_coeff * * 100 2
|
|
|
|
comm_modify vel yes
|
|
|
|
neighbor 0.5 bin
|
|
neigh_modify every 1 delay 0 check yes
|
|
|
|
timestep 0.001
|
|
|
|
#fix 1 all nve/body
|
|
#fix 1 all nvt/body temp $T $T 1.0
|
|
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
|
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
|
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
|
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
|
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
|
|
|
|
fix 2 all enforce2d
|
|
|
|
#compute 1 all body/local id 1 2 3
|
|
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
|
|
|
thermo_style custom step ke pe etotal press
|
|
thermo 1000
|
|
|
|
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
|
|
#dump_modify 2 pad 6
|
|
|
|
run ${steps}
|
|
run 100000
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 6.15685
|
|
ghost atom cutoff = 6.15685
|
|
binsize = 3.07843, bins = 16 16 1
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair body/rounded/polygon, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/2d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 Mbytes
|
|
Step KinEng PotEng TotEng Press
|
|
0 0.484375 0.25 0.734375 0.0067274306
|
|
1000 0.39423376 0.0017918048 0.39602557 0.0021941612
|
|
2000 0.42284177 0.01346585 0.43630762 0.0029377883
|
|
3000 0.58154405 0.011321689 0.59286574 0.003667871
|
|
4000 0.73518304 0.034603175 0.76978621 0.0018689207
|
|
5000 0.84367476 0.025292163 0.86896692 0.0089161373
|
|
6000 0.70803236 0.0085631016 0.71659546 0.0045552895
|
|
7000 0.56206452 0.10453031 0.66659483 0.010255161
|
|
8000 0.64538994 0.088817673 0.73420761 0.0037633655
|
|
9000 0.90540819 0.063696004 0.96910419 0.0077673359
|
|
10000 0.68632042 0.093265016 0.77958544 0.0057864837
|
|
11000 0.59118074 0.025654748 0.61683549 0.012518759
|
|
12000 0.67522767 0.038176401 0.71340407 0.01741153
|
|
13000 0.7644843 0.10429844 0.86878274 0.013161339
|
|
14000 0.56152694 0.067836656 0.6293636 0.016852113
|
|
15000 0.41895505 0.019513353 0.43846841 0.015225696
|
|
16000 0.55799443 0.15645637 0.7144508 0.011703646
|
|
17000 0.59385248 0.03451986 0.62837234 0.025482966
|
|
18000 0.75902169 0.031103586 0.79012527 0.018263354
|
|
19000 0.64266826 0.12535314 0.76802141 0.014884119
|
|
20000 0.57836261 0.16581188 0.74417449 0.024667165
|
|
21000 0.78281936 0.11877527 0.90159464 -0.0090089213
|
|
22000 0.5312006 0.13300874 0.66420934 0.025797278
|
|
23000 0.56458861 0.084369128 0.64895774 0.024630917
|
|
24000 0.65126875 0.06122992 0.71249867 0.034377198
|
|
25000 0.55173441 0.15694886 0.70868327 0.021634086
|
|
26000 0.59121615 0.17071182 0.76192797 0.024758366
|
|
27000 0.6394843 0.17442949 0.81391378 0.034919937
|
|
28000 0.31144221 0.41243036 0.72387256 0.074115225
|
|
29000 0.13516917 0.3075419 0.44271107 0.023861298
|
|
30000 0.14094934 0.24407203 0.38502137 0.037030438
|
|
31000 0.26313749 0.087395422 0.35053291 0.042347005
|
|
32000 0.51602457 0.063012079 0.57903664 0.018550299
|
|
33000 0.55628829 0.200213 0.75650129 0.026507686
|
|
34000 0.97399408 0.082504517 1.0564986 0.037889878
|
|
35000 0.64710533 0.17662002 0.82372535 0.058295508
|
|
36000 0.45769083 0.08241194 0.54010277 0.014957415
|
|
37000 0.72850105 0.053874061 0.78237512 0.037194593
|
|
38000 0.44177995 0.28939498 0.73117493 0.045194029
|
|
39000 0.46828451 0.077630686 0.54591519 0.089849009
|
|
40000 0.46786451 0.092828423 0.56069294 0.028042052
|
|
41000 0.71861856 0.097085715 0.81570427 0.036473296
|
|
42000 0.74121021 0.10553127 0.84674148 0.054058843
|
|
43000 0.62945489 0.12770673 0.75716161 0.047267994
|
|
44000 0.49900638 0.085150056 0.58415644 0.054798793
|
|
45000 0.70199572 0.063415877 0.7654116 0.038363546
|
|
46000 0.49513142 0.10649384 0.60162526 0.059392561
|
|
47000 0.3858898 0.079458749 0.46534855 0.051825764
|
|
48000 0.62585854 0.028585902 0.65444444 0.054074424
|
|
49000 0.65934482 0.51865062 1.1779954 -0.035272836
|
|
50000 0.5420438 0.082056756 0.62410056 0.031187494
|
|
51000 0.36685223 0.14224019 0.50909241 0.073790397
|
|
52000 0.19044627 0.15368389 0.34413016 0.059034266
|
|
53000 0.26847678 0.075693324 0.3441701 0.032276915
|
|
54000 0.3593711 0.19034549 0.54971659 0.070827883
|
|
55000 0.21659198 0.1929074 0.40949939 0.035916364
|
|
56000 0.28242715 0.12313241 0.40555956 0.062083926
|
|
57000 0.34067475 0.14711992 0.48779467 0.059321458
|
|
58000 0.4842796 0.16143425 0.64571385 0.059048247
|
|
59000 0.84438871 0.076546849 0.92093556 0.048046901
|
|
60000 0.92794849 0.054331626 0.98228012 0.058392272
|
|
61000 0.6916736 0.076168342 0.76784194 0.058654987
|
|
62000 0.63317965 0.094506389 0.72768604 0.061044719
|
|
63000 0.63317266 0.038785593 0.67195825 0.097236147
|
|
64000 0.81696668 0.121811 0.93877769 0.064935373
|
|
65000 0.82644758 0.25188344 1.078331 0.093352359
|
|
66000 0.64975019 0.17930857 0.82905876 0.058805254
|
|
67000 0.63487678 0.16877059 0.80364737 0.070254696
|
|
68000 0.79140717 0.11631004 0.9077172 0.064646394
|
|
69000 0.85687272 0.057835331 0.91470805 0.071057291
|
|
70000 0.67785976 0.040686768 0.71854653 0.074687222
|
|
71000 0.60594577 0.032193155 0.63813893 0.069349268
|
|
72000 0.77586745 0.024068533 0.79993598 0.083394193
|
|
73000 0.88877625 0.025746326 0.91452258 0.081511105
|
|
74000 0.73507888 0.036574786 0.77165367 0.075360233
|
|
75000 0.68787782 0.042098622 0.72997644 0.068651098
|
|
76000 0.72515745 0.04360868 0.76876613 0.069594624
|
|
77000 0.77580944 0.041826702 0.81763614 0.071937144
|
|
78000 0.76640394 0.039285046 0.80568899 0.074274921
|
|
79000 0.62504309 0.039593585 0.66463667 0.076443295
|
|
80000 0.60001642 0.043468215 0.64348464 0.094547719
|
|
81000 0.82175037 0.045608873 0.86735924 0.080186295
|
|
82000 0.85783276 0.042692576 0.90052534 0.081576548
|
|
83000 0.71367707 0.042172193 0.75584926 0.08256625
|
|
84000 0.68532406 0.044724759 0.73004882 0.083672013
|
|
85000 0.72576789 0.046982462 0.77275035 0.084789331
|
|
86000 0.75597701 0.04765086 0.80362787 0.085758056
|
|
87000 0.74190598 0.047629096 0.78953507 0.086679976
|
|
88000 0.60967704 0.049906172 0.65958321 0.085526191
|
|
89000 0.54490288 0.054768238 0.59967112 0.090604027
|
|
90000 0.75398341 0.057153453 0.81113686 0.091900858
|
|
91000 0.84577472 0.052753512 0.89852823 0.091913909
|
|
92000 0.7176235 0.050677427 0.76830093 0.092032507
|
|
93000 0.61699446 0.054097013 0.67109147 0.092071275
|
|
94000 0.76330752 0.057398618 0.82070614 0.092435043
|
|
95000 0.98754458 0.053801311 1.0413459 0.093526707
|
|
96000 0.7405897 0.052135628 0.79272533 0.095011929
|
|
97000 0.65587599 0.057011962 0.71288795 0.096692123
|
|
98000 0.72345634 0.060700171 0.78415651 0.097510345
|
|
99000 0.88283624 0.061795247 0.94463149 0.09799633
|
|
100000 0.86303812 0.058912988 0.92195111 0.09892993
|
|
Loop time of 2.80074 on 4 procs for 100000 steps with 32 atoms
|
|
|
|
Performance: 3084895.573 tau/day, 35704.810 timesteps/s
|
|
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.81169 | 0.89466 | 0.97669 | 8.4 | 31.94
|
|
Neigh | 0.0017524 | 0.0018129 | 0.0018773 | 0.1 | 0.06
|
|
Comm | 0.91307 | 0.99193 | 1.0691 | 7.3 | 35.42
|
|
Output | 0.00076914 | 0.00093722 | 0.0013936 | 0.0 | 0.03
|
|
Modify | 0.75335 | 0.75779 | 0.76346 | 0.4 | 27.06
|
|
Other | | 0.1536 | | | 5.48
|
|
|
|
Nlocal: 8 ave 10 max 4 min
|
|
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
Nghost: 17.25 ave 19 max 15 min
|
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
|
Neighs: 13.5 ave 21 max 5 min
|
|
Histogram: 1 0 0 0 1 0 1 0 0 1
|
|
|
|
Total # of neighbors = 54
|
|
Ave neighs/atom = 1.6875
|
|
Neighbor list builds = 1443
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:02
|