forked from lijiext/lammps
223 lines
10 KiB
Groff
223 lines
10 KiB
Groff
LAMMPS (27 Nov 2018)
|
|
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
|
|
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 = 0.000400782 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 0.38428256 0.0014168922 0.38569945 0.0020468171
|
|
2000 0.41372193 0.015263236 0.42898517 0.0029343462
|
|
3000 0.54844547 0.014870378 0.56331585 0.001978353
|
|
4000 0.73816048 0.031668204 0.76982869 0.0025939718
|
|
5000 0.84536165 0.011504649 0.8568663 0.0037990517
|
|
6000 0.73776478 0.14445932 0.8822241 0.0086538113
|
|
7000 0.52022565 0.069507637 0.58973329 0.0072098694
|
|
8000 0.72653213 0.12783367 0.85436581 0.023907185
|
|
9000 0.87685728 0.12398193 1.0008392 0.0064591005
|
|
10000 0.72509641 0.097241969 0.82233837 0.0012418726
|
|
11000 0.62314955 0.056042914 0.67919247 0.0018880786
|
|
12000 0.57157436 0.18187429 0.75344865 0.0096135623
|
|
13000 0.7489742 0.08262775 0.83160195 0.009183917
|
|
14000 0.78835138 0.18761048 0.97596186 0.023684357
|
|
15000 0.40408761 0.079431327 0.48351893 0.025285348
|
|
16000 0.4071013 0.13207058 0.53917188 0.02015488
|
|
17000 0.48417067 0.16699781 0.65116848 0.059188189
|
|
18000 0.60038567 0.18317457 0.78356024 -0.046456387
|
|
19000 0.73796958 0.064271521 0.8022411 0.090257204
|
|
20000 0.62508659 0.14486336 0.76994994 0.04948543
|
|
21000 0.5596837 0.10018831 0.65987201 0.044961962
|
|
22000 0.30731517 0.1386103 0.44592547 0.015096596
|
|
23000 0.34371843 0.1486761 0.49239453 0.026100892
|
|
24000 0.33484204 0.25428479 0.58912683 0.01974393
|
|
25000 0.48714744 0.32743616 0.8145836 0.037925893
|
|
26000 0.33255994 0.29851422 0.63107417 0.049419529
|
|
27000 0.21735889 0.18816203 0.40552093 0.050622152
|
|
28000 0.31911317 0.12559898 0.44471215 -0.0036236361
|
|
29000 0.53280161 0.055185441 0.58798705 0.083856225
|
|
30000 0.52916941 0.28697284 0.81614225 0.055873213
|
|
31000 0.47861645 0.21932568 0.69794214 0.02762301
|
|
32000 0.46786314 0.041856438 0.50971958 0.029923804
|
|
33000 0.69944716 0.039356744 0.7388039 0.028174645
|
|
34000 0.39964317 0.1027175 0.50236068 0.039495865
|
|
35000 0.70199237 0.10421859 0.80621095 0.015943417
|
|
36000 0.45053533 0.078626602 0.52916193 0.0073950287
|
|
37000 0.41587918 0.056551665 0.47243084 0.034091318
|
|
38000 0.58663473 0.039228671 0.6258634 0.033093641
|
|
39000 0.72480658 0.14792564 0.87273222 0.030903741
|
|
40000 0.51163285 0.13445292 0.64608577 -0.03114559
|
|
41000 0.56273761 0.16720374 0.72994135 0.027968528
|
|
42000 0.61850184 0.10584389 0.72434573 -0.036301799
|
|
43000 0.60039772 0.11984289 0.72024062 0.080894236
|
|
44000 0.57499839 0.068211092 0.64320948 0.049726122
|
|
45000 0.69937239 0.16287141 0.8622438 0.044921114
|
|
46000 0.23303785 0.2391726 0.47221045 0.021668935
|
|
47000 0.27051781 0.10690378 0.37742159 0.11963476
|
|
48000 0.408895 0.079919688 0.48881469 0.087484004
|
|
49000 0.74363181 0.040819422 0.78445123 0.011937456
|
|
50000 0.84482316 0.10205256 0.94687572 0.064133262
|
|
51000 0.84923574 0.089882984 0.93911872 0.062696388
|
|
52000 0.66278324 0.0331554 0.69593864 0.035150337
|
|
53000 0.64737251 0.039608076 0.68698058 0.057687461
|
|
54000 0.68931435 0.042661403 0.73197576 0.069664795
|
|
55000 0.84523308 0.10293275 0.94816583 0.047343755
|
|
56000 0.80033937 0.1534797 0.95381907 0.070206074
|
|
57000 0.6214799 0.1174575 0.7389374 0.078530452
|
|
58000 0.64228495 0.088089896 0.73037485 0.060245994
|
|
59000 0.89376363 0.065171887 0.95893552 0.071658895
|
|
60000 0.90162992 0.016564761 0.91819468 0.089245946
|
|
61000 0.72439995 0.0076508835 0.73205083 0.031430213
|
|
62000 0.71590702 0.0046728326 0.72057986 0.10153514
|
|
63000 0.74491219 0.0046757926 0.74958798 0.077145851
|
|
64000 0.77173614 0.008265632 0.78000178 -0.049932265
|
|
65000 0.72789092 0.0053605745 0.73325149 0.27060389
|
|
66000 0.63001101 0.013871945 0.64388296 -0.17766692
|
|
67000 0.65887071 0.0069105692 0.66578128 0.31632918
|
|
68000 0.89042862 0.0026334652 0.89306209 -0.050495873
|
|
69000 0.83442374 0.0059232957 0.84034703 -0.21871692
|
|
70000 0.65149642 0.004885383 0.65638181 0.50428108
|
|
71000 0.66888808 0.01125057 0.68013865 -0.29575772
|
|
72000 0.74941609 0.0026616299 0.75207772 0.34800716
|
|
73000 0.7898844 0.0048982026 0.7947826 -0.096872644
|
|
74000 0.68823538 0.0021467794 0.69038216 0.12272852
|
|
75000 0.5238808 0.0046112795 0.52849208 0.25760316
|
|
76000 0.65512889 0.014567969 0.66969686 -0.24622674
|
|
77000 0.82292373 0.0092471048 0.83217083 0.4002304
|
|
78000 0.76305221 0.01101937 0.77407158 -0.10704945
|
|
79000 0.66279814 0.0090486405 0.67184678 0.037466134
|
|
80000 0.65808885 0.010000569 0.66808942 0.31742291
|
|
81000 0.91357798 0.046226814 0.95980479 -0.20945693
|
|
82000 0.87611859 -0.016794871 0.85932372 0.31759733
|
|
83000 0.66285455 -0.017921021 0.64493353 0.27065273
|
|
84000 0.67460715 -0.0076174891 0.66698966 -0.024772659
|
|
85000 0.77786135 0.0014316505 0.779293 -0.21635327
|
|
86000 0.83246393 0.087489797 0.91995372 -0.13431455
|
|
87000 0.62935573 0.045088823 0.67444455 0.037766395
|
|
88000 0.55264538 -0.024625272 0.52802011 0.18121213
|
|
89000 0.74171392 -0.012629926 0.729084 -0.27666424
|
|
90000 0.82542165 -0.02296567 0.80245598 -0.30497174
|
|
91000 0.72958657 -0.026275093 0.70331147 -0.27624518
|
|
92000 0.6319558 0.022568297 0.65452409 -0.33539318
|
|
93000 0.66685301 0.021889807 0.68874282 -0.39890762
|
|
94000 0.91243243 0.0078218509 0.92025428 -0.27213648
|
|
95000 0.81125179 -0.0096756295 0.80157616 -0.099802335
|
|
96000 0.63354907 -0.018329423 0.61521965 0.18199604
|
|
97000 0.66812347 -0.016650228 0.65147324 0.49878257
|
|
98000 0.81490013 -0.0049164866 0.80998365 -0.13473106
|
|
99000 0.82131147 0.0043198846 0.82563136 -0.3083957
|
|
100000 0.50880983 -0.010467027 0.4983428 0.060606332
|
|
Loop time of 4.3169 on 4 procs for 100000 steps with 32 atoms
|
|
|
|
Performance: 2001435.573 tau/day, 23164.764 timesteps/s
|
|
95.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 1.2078 | 1.3972 | 1.6653 | 15.1 | 32.36
|
|
Neigh | 0.0030954 | 0.003284 | 0.0034814 | 0.3 | 0.08
|
|
Comm | 1.074 | 1.3595 | 1.6003 | 16.2 | 31.49
|
|
Output | 0.001703 | 0.0030067 | 0.0068843 | 4.1 | 0.07
|
|
Modify | 1.2071 | 1.2647 | 1.3062 | 3.6 | 29.30
|
|
Other | | 0.2893 | | | 6.70
|
|
|
|
Nlocal: 8 ave 9 max 6 min
|
|
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
Nghost: 17.75 ave 20 max 16 min
|
|
Histogram: 1 0 1 0 0 1 0 0 0 1
|
|
Neighs: 14 ave 18 max 7 min
|
|
Histogram: 1 0 0 0 0 0 0 1 1 1
|
|
|
|
Total # of neighbors = 56
|
|
Ave neighs/atom = 1.75
|
|
Neighbor list builds = 1566
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:04
|