230 lines
11 KiB
Groff
230 lines
11 KiB
Groff
LAMMPS (28 Mar 2023 - Development)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# 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
|
|
Reading data file ...
|
|
orthogonal box = (0 0 -0.5) to (12 12 0.5)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
2 atoms
|
|
2 bodies
|
|
read_data CPU = 0.001 seconds
|
|
|
|
replicate $r $r 1
|
|
replicate 4 $r 1
|
|
replicate 4 4 1
|
|
Replication is creating a 4x4x1 = 16 times larger system...
|
|
orthogonal box = (0 0 -0.5) to (48 48 0.5)
|
|
1 by 1 by 1 MPI processor grid
|
|
32 atoms
|
|
replicate CPU = 0.001 seconds
|
|
|
|
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
|
|
|
|
change_box all boundary p f p
|
|
Changing box ...
|
|
|
|
variable cut_inner equal 0.5
|
|
variable k_n equal 100
|
|
variable k_na equal 2
|
|
variable c_n equal 0.1
|
|
variable c_t equal 0.1
|
|
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 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
|
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
|
|
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
|
|
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
|
|
pair_style body/rounded/polygon 0.1 0.1 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 fixedpoint 0 0 0
|
|
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
|
|
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
|
|
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
|
|
|
|
fix 2 all enforce2d
|
|
fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
|
|
|
|
#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
|
|
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 = 6.1568542
|
|
ghost atom cutoff = 6.1568542
|
|
binsize = 3.0784271, 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
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 5.376 | 5.376 | 5.376 Mbytes
|
|
Step KinEng PotEng TotEng Press
|
|
0 0.484375 0.25 0.734375 0.0067274306
|
|
1000 0.51464289 0.00099012638 0.51563301 0.013444625
|
|
2000 0.55653313 0.0040982283 0.56063136 0.0034505512
|
|
3000 0.75323998 0.023578898 0.77681887 0.0036652891
|
|
4000 0.70044978 0.092406287 0.79285607 0.0089262842
|
|
5000 0.54548803 0.096501313 0.64198934 0.0051379523
|
|
6000 0.48208829 0.097798861 0.57988715 0.015298049
|
|
7000 0.68219182 0.038843941 0.72103576 0.016842202
|
|
8000 0.53792445 0.012983807 0.55090825 0.0066797902
|
|
9000 0.49980359 0.029397948 0.52920154 0.0046731993
|
|
10000 0.48705779 0.10138799 0.58844578 -1.9696743e-05
|
|
11000 0.52151792 0.065893508 0.58741142 0.0049365175
|
|
12000 0.59066419 0.039261015 0.62992521 0.001420608
|
|
13000 0.46059009 0.07386532 0.53445541 0.005654565
|
|
14000 0.37899234 0.13421331 0.51320565 0.0097199047
|
|
15000 0.49566894 0.052006844 0.54767578 0.00053157628
|
|
16000 0.59294062 0.028393451 0.62133407 0.0057809461
|
|
17000 0.51260882 0.1266054 0.63921422 0.0021637817
|
|
18000 0.45603179 0.15710959 0.61314138 0.017707488
|
|
19000 0.52137969 0.1123825 0.63376219 0.015894031
|
|
20000 0.64553686 0.11579772 0.76133459 0.013239309
|
|
21000 0.38581837 0.17867419 0.56449256 0.0048572535
|
|
22000 0.42776514 0.12979071 0.55755585 0.008093469
|
|
23000 0.490055 0.14197765 0.63203265 -0.003575896
|
|
24000 0.57689881 0.10164831 0.67854712 0.022418321
|
|
25000 0.45630031 0.057905852 0.51420616 0.007959034
|
|
26000 0.59497685 0.193113 0.78808985 0.0076331679
|
|
27000 0.40943362 0.098595954 0.50802958 0.0016863757
|
|
28000 0.34512273 0.15696637 0.50208909 0.037435926
|
|
29000 0.59187862 0.1845377 0.77641632 0.014563665
|
|
30000 0.69204623 0.16392147 0.8559677 0.031708423
|
|
31000 0.40436029 0.34429435 0.74865464 0.073818847
|
|
32000 0.47580383 0.22708448 0.70288831 0.015795198
|
|
33000 0.48923447 0.23636413 0.72559861 0.025932606
|
|
34000 0.51960128 0.15145893 0.67106021 -0.00079607564
|
|
35000 0.44792834 0.19927109 0.64719943 -0.0063461505
|
|
36000 0.54265821 0.17924788 0.72190609 0.017916439
|
|
37000 0.56020344 0.24977507 0.80997851 0.057844411
|
|
38000 0.28874871 0.21399353 0.50274224 0.022675277
|
|
39000 0.39030236 0.30170176 0.69200411 0.037482614
|
|
40000 0.4699469 0.20663643 0.67658333 -0.014082215
|
|
41000 0.50202447 0.21510708 0.71713155 -0.0063284222
|
|
42000 0.43029593 0.23511818 0.6654141 0.046478372
|
|
43000 0.41628842 0.21031596 0.62660438 -0.0053073644
|
|
44000 0.51101573 0.15862165 0.66963738 0.010251868
|
|
45000 0.56984114 0.18071709 0.75055823 0.021333409
|
|
46000 0.45510513 0.15385488 0.60896001 0.048441048
|
|
47000 0.41229547 0.20577222 0.61806769 0.027485704
|
|
48000 0.64114797 0.33672519 0.97787315 0.13522091
|
|
49000 0.44298056 0.27708867 0.72006923 0.026660315
|
|
50000 0.43250082 0.17778506 0.61028588 0.02714938
|
|
51000 0.59697891 0.25460003 0.85157894 0.026959715
|
|
52000 0.63110331 0.21528376 0.84638707 0.023157155
|
|
53000 0.46085491 0.25375607 0.71461099 0.024933391
|
|
54000 0.50772891 0.29280628 0.80053519 0.010621547
|
|
55000 0.67213557 0.2071375 0.87927307 0.061770903
|
|
56000 0.61184167 0.34686662 0.95870829 0.095262009
|
|
57000 0.42364554 0.29899934 0.72264488 -0.0080865129
|
|
58000 0.5033641 0.39810693 0.90147103 0.081474225
|
|
59000 0.61363438 0.25296035 0.86659472 0.041921315
|
|
60000 0.64600872 0.36997737 1.0159861 0.053833686
|
|
61000 0.43392277 0.29276613 0.7266889 0.054911225
|
|
62000 0.38910577 0.27714798 0.66625375 -0.0141031
|
|
63000 0.42343097 0.21637816 0.63980913 -1.6862315e-05
|
|
64000 0.52512516 0.38797726 0.91310242 0.03170217
|
|
65000 0.48930994 0.4863269 0.97563684 0.025108671
|
|
66000 0.68354817 0.3629732 1.0465214 0.066714362
|
|
67000 0.5361863 0.44003399 0.97622029 0.1063525
|
|
68000 0.3605148 0.40138904 0.76190383 0.03287684
|
|
69000 0.62747502 0.49229352 1.1197685 0.053648724
|
|
70000 0.51326037 0.36561885 0.87887922 0.070871008
|
|
71000 0.45429341 0.38458357 0.83887698 0.010485881
|
|
72000 0.55377877 0.36434231 0.91812107 0.10507819
|
|
73000 0.6857324 0.45242968 1.1381621 0.022470322
|
|
74000 0.46349397 0.39082798 0.85432196 0.067650912
|
|
75000 0.59216869 0.32893138 0.92110008 0.0196582
|
|
76000 0.42985327 0.40674342 0.83659669 0.025700762
|
|
77000 0.54319568 0.55627833 1.099474 0.067233159
|
|
78000 0.59244798 0.5121155 1.1045635 0.12063624
|
|
79000 0.61140864 0.45505083 1.0664595 0.088578795
|
|
80000 0.64308346 0.4143502 1.0574337 0.038537249
|
|
81000 0.55053046 0.43357659 0.98410705 0.053930256
|
|
82000 0.54049882 0.41354335 0.95404217 -0.036458392
|
|
83000 0.47517728 0.30128468 0.77646196 0.0019488841
|
|
84000 0.57452781 0.1949493 0.76947711 0.039244382
|
|
85000 0.7907368 0.51406164 1.3047984 0.12766082
|
|
86000 0.59488507 0.50084726 1.0957323 0.080232158
|
|
87000 0.43071262 0.4682738 0.89898642 0.1266876
|
|
88000 0.53305256 0.55941308 1.0924656 0.17062068
|
|
89000 0.60672487 0.64951209 1.256237 0.17194524
|
|
90000 0.7134227 0.57323404 1.2866567 0.074617282
|
|
91000 0.65670871 0.58567381 1.2423825 0.025281565
|
|
92000 0.72364891 0.59755693 1.3212058 0.092201188
|
|
93000 0.69254418 0.75766186 1.450206 0.16036111
|
|
94000 0.56326058 0.6398442 1.2031048 0.26280736
|
|
95000 0.47480145 0.57734551 1.052147 0.039940021
|
|
96000 0.56909151 0.73081903 1.2999105 0.030223516
|
|
97000 0.53198039 0.71808155 1.2500619 0.033191485
|
|
98000 0.63572731 0.86931519 1.5050425 0.20901135
|
|
99000 0.64477038 0.76771721 1.4124876 0.059732095
|
|
100000 0.71275398 0.66613673 1.3788907 0.020038364
|
|
Loop time of 2.21223 on 1 procs for 100000 steps with 32 atoms
|
|
|
|
Performance: 3905566.671 tau/day, 45203.318 timesteps/s, 1.447 Matom-step/s
|
|
96.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 1.1162 | 1.1162 | 1.1162 | 0.0 | 50.45
|
|
Neigh | 0.0049629 | 0.0049629 | 0.0049629 | 0.0 | 0.22
|
|
Comm | 0.045069 | 0.045069 | 0.045069 | 0.0 | 2.04
|
|
Output | 0.00060169 | 0.00060169 | 0.00060169 | 0.0 | 0.03
|
|
Modify | 1.0017 | 1.0017 | 1.0017 | 0.0 | 45.28
|
|
Other | | 0.04368 | | | 1.97
|
|
|
|
Nlocal: 32 ave 32 max 32 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 19 ave 19 max 19 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 59 ave 59 max 59 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 59
|
|
Ave neighs/atom = 1.84375
|
|
Neighbor list builds = 3214
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:02
|