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lammps/examples/srd/log.5Oct16.srd.mixture.g++.1
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log.5Oct16.srd.mixture.g++.1
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LAMMPS (5 Oct 2016)
# 2d SRD test: big + small particles
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with sigma 1.0
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
set type 1 mass 1.0
100 settings made for mass
set type 1 diameter 1.0
100 settings made for diameter
group big type 1
100 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
run 1000
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 = 12 12 2
Memory usage per processor = 3.60175 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.54272 0 0.88288 -0.041088
1000 1.8791467 -0.97185784 0 0.8884974 0.61487656
Loop time of 0.0151019 on 1 procs for 1000 steps with 100 atoms
Performance: 28605653.879 tau/day, 66216.791 timesteps/s
105.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0079689 | 0.0079689 | 0.0079689 | 0.0 | 52.77
Neigh | 0.0030537 | 0.0030537 | 0.0030537 | 0.0 | 20.22
Comm | 0.001416 | 0.001416 | 0.001416 | 0.0 | 9.38
Output | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 | 0.0 | 0.04
Modify | 0.001749 | 0.001749 | 0.001749 | 0.0 | 11.58
Other | | 0.0009084 | | | 6.01
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 88 ave 88 max 88 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 459 ave 459 max 459 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 459
Ave neighs/atom = 4.59
Neighbor list builds = 129
Dangerous builds = 0
unfix 1
unfix 2
# add small particles as hi density lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region plane block 0 10 0 10 -0.001 0.001
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 2 region plane
Created 21316 atoms
set type 2 mass 0.01
21316 settings made for mass
set type 2 diameter 0.0
21316 settings made for diameter
group small type 2
21316 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.5
delete_atoms overlap 0.5 small big
Neighbor list info ...
2 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 = 12 12 2
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:278)
Deleted 6700 atoms, new total = 14716
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
comm_modify mode multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip
fix 3 all enforce2d
# diagnostics
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
thermo 100
#dump 1 all atom 250 dump.srd.mixture
#dump 2 all image 250 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 4 adiam 1 1 adiam 2 0.2
#dump 3 all movie 250 movie.mpg type type zoom 1.6
#dump_modify 3 pad 4 adiam 1 1 adiam 2 0.2
run 5000
SRD info:
SRD/big particles = 14616 100
big particle diameter max/min = 0.88 0.88
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 63 63 1
SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
SRD per actual grid cell = 4.86648
SRD viscosity = 0.463448
big/SRD mass density ratio = 2.12808
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2884)
# of rescaled SRD velocities = 0
ave/max small velocity = 13.2944 24.262
ave/max big velocity = 1.69284 5.10989
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 = 12 12 2
Memory usage per processor = 14.7783 Mbytes
Step Temp f_2[7] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10]
0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487656 0 0 0 0 0 0 0 0 0
100 1.1596877 3969 0.00179671 -0.88368701 0.26440385 0.85824547 7578 83 83 0 14 12996 3000 1.0041859 0
200 1.2193132 3969 0.0018345215 -0.93715187 0.26996819 0.70474845 7511 90 90 0 53 12996 3022 1.0188815 0
300 0.99431764 3969 -0.00029373076 -1.0275999 -0.043225419 0.17829084 7619 83 83 0 89 12996 3013 1.0200287 0
400 1.0357776 3969 0.00051788234 -0.94920826 0.076211565 0.43014085 7571 85 85 0 120 12996 3004 1.0370684 0
500 1.0481683 3969 0.0010184986 -0.88780442 0.14988225 0.70052984 7584 77 77 0 152 12996 3009 1.0142095 0
600 1.1928825 3969 0.00095759759 -1.0400336 0.14092006 0.21451332 7494 69 69 0 195 12996 2993 1.0228103 0
700 1.0524078 3969 0.00035360799 -0.9898468 0.052036951 0.42873114 7693 85 85 0 216 12996 3008 1.0054139 0
800 0.90603094 3969 -0.00092639686 -1.0332992 -0.13632856 0.25916674 7671 99 99 0 247 12996 2966 1.0361445 0
900 1.0636972 3969 0.00041617364 -0.99181615 0.061244113 0.58497843 7657 87 87 0 282 12996 2992 1.0161879 0
1000 1.0507488 3969 -0.0001556117 -1.0631411 -0.022899818 0.47566195 7465 94 94 0 326 12996 3030 0.99530538 0
1100 0.93006509 3969 -0.0003550828 -0.97301843 -0.052253985 0.77031309 7474 90 90 0 347 12996 3004 1.0214319 0
1200 1.0402459 3969 -0.00046600382 -1.0984205 -0.068577122 0.31255586 7396 78 78 0 385 12996 3010 1.0176572 0
1300 1.0520892 3969 -1.0354518e-06 -1.0417207 -0.00015237708 0.50280759 7529 81 81 0 415 12996 3000 1.0305024 0
1400 1.0166314 3969 -0.00076800379 -1.1194845 -0.11301944 0.25711665 7525 93 93 0 443 12996 3001 1.031584 0
1500 0.99218489 3969 -0.00098822242 -1.1276898 -0.14542681 0.25260367 7495 93 93 0 474 12996 2995 1.0242311 0
1600 1.1064178 3969 -0.00017916094 -1.121719 -0.026365324 0.47764294 7505 94 94 0 506 12996 3022 1.0136332 0
1700 1.1431125 3969 0.00094430031 -0.9927181 0.13896323 1.0995941 7474 88 88 0 539 12996 3003 1.0341733 0
1800 1.0222823 3969 -0.00059038783 -1.098941 -0.086881473 0.62506101 7310 87 87 0 586 12996 2981 1.0382713 0
1900 0.95084674 3969 -0.0015534806 -1.1699485 -0.22861021 0.2701615 7623 87 87 0 624 12996 3003 1.0181489 0
2000 1.0861079 3969 -0.00065855134 -1.1721593 -0.096912415 0.34276301 7470 90 90 0 660 12996 3015 1.0268618 0
2100 0.88345526 3969 -0.0016997139 -1.1247506 -0.2501299 0.43045597 7532 82 82 0 688 12996 3006 1.0124018 0
2200 0.92745839 3969 -0.0010657957 -1.0750263 -0.15684249 0.67080961 7508 84 84 0 719 12996 3010 1.0232807 0
2300 0.88367737 3969 -0.001454046 -1.088818 -0.21397742 0.63475334 7430 99 99 0 746 12996 2993 1.0344177 0
2400 0.87359171 3969 -0.0012946593 -1.0553779 -0.19052207 0.58406648 7454 96 96 0 780 12996 2981 1.0343798 0
2500 0.96618275 3969 -0.0010799782 -1.1154505 -0.1589296 0.32223081 7515 83 83 0 807 12996 3021 1.0142273 0
2600 0.86458041 3969 -0.0015382749 -1.0823071 -0.22637254 0.25396199 7489 91 91 0 828 12996 2980 1.0291839 0
2700 0.98390726 3969 -0.00079291155 -1.0907531 -0.11668486 0.30335914 7395 79 79 0 854 12996 3010 1.0120521 0
2800 1.0033122 3969 -0.0001965439 -1.0222025 -0.0289234 0.66093465 7387 68 68 0 888 12996 2980 1.0251477 0
2900 1.222899 3969 0.0012034132 -1.0335757 0.17709428 0.65880933 7386 85 85 0 919 12996 3004 1.0162822 0
3000 1.002035 3969 -0.00054872208 -1.0727646 -0.080749941 0.34444254 7466 83 83 0 952 12996 3016 1.0122263 0
3100 1.206972 3969 0.0011369559 -1.0275879 0.16731443 0.51852441 7468 84 84 0 992 12996 3025 1.0099007 0
3200 1.0856646 3969 0.00014959203 -1.052794 0.022013964 0.3410219 7417 84 84 0 1032 12996 2976 1.0135289 0
3300 1.3331295 3969 0.0019856133 -1.0275953 0.29220285 0.47025792 7524 69 69 0 1062 12996 3018 1.0255776 0
3400 0.84929817 3969 -0.00098128795 -0.98521153 -0.14440633 0.36010527 7428 83 83 0 1101 12996 3014 1.0270963 0
3500 1.1302394 3969 0.00036763215 -1.0648363 0.054100747 0.1522826 7572 90 90 0 1119 12996 3012 1.0289088 0
3600 1.1936576 3969 0.00056858904 -1.0980475 0.083673563 0.23906343 7602 101 101 0 1158 12996 2995 1.0275146 0
3700 1.1286007 3969 0.0010142941 -0.96805122 0.14926351 0.72687935 7415 84 84 0 1198 12996 3018 1.0256527 0
3800 1.1244276 3969 0.00071868084 -1.0074222 0.10576107 0.44091142 7476 84 84 0 1231 12996 2984 1.0453126 0
3900 0.98213284 3969 -0.0008786738 -1.1016171 -0.12930564 0.069507795 7445 88 88 0 1267 12996 3017 1.0203869 0
4000 1.1632971 3969 0.00073199788 -1.0439433 0.10772081 0.50304552 7602 101 101 0 1301 12996 3021 1.0219416 0
4100 1.060029 3969 -0.00023302512 -1.0837207 -0.034291977 0.36492957 7538 77 77 0 1326 12996 2997 1.017007 0
4200 0.97057567 3969 -0.00052048968 -1.0374652 -0.076595262 0.3008083 7683 82 82 0 1363 12996 3010 1.0339142 0
4300 1.0562211 3969 -0.00040298636 -1.1049624 -0.059303473 0.12322043 7511 84 84 0 1386 12996 2991 1.035082 0
4400 0.97383798 3969 8.961738e-05 -0.95091151 0.013188094 0.68597762 7669 103 103 0 1420 12996 3010 1.0141431 0
4500 0.94750799 3969 -0.00086783826 -1.065744 -0.12771108 0.2109101 7739 96 96 0 1452 12996 3012 1.0244541 0
4600 1.1123048 3969 0.00016640454 -1.0766937 0.024488092 0.24736079 7615 75 75 0 1493 12996 3013 1.0013601 0
4700 1.0624886 3969 -1.2753265e-05 -1.0537404 -0.0018767705 0.29324615 7568 91 91 0 1524 12996 2997 1.019485 0
4800 1.2169028 3969 0.0010831546 -1.0453368 0.15939704 0.42728069 7444 80 80 0 1560 12996 2997 1.0300677 0
4900 0.90968786 3969 -0.0010022199 -1.0480777 -0.14748667 0.37681568 7563 88 88 0 1592 12996 2997 1.0257714 0
5000 1.0856525 3969 0.0001301746 -1.0556395 0.019156494 0.55496941 7439 78 78 0 1633 12996 3008 1.0343075 0
Loop time of 2.9124 on 1 procs for 5000 steps with 14716 atoms
Performance: 148331.176 tau/day, 1716.796 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041905 | 0.041905 | 0.041905 | 0.0 | 1.44
Neigh | 0.0063758 | 0.0063758 | 0.0063758 | 0.0 | 0.22
Comm | 0.027464 | 0.027464 | 0.027464 | 0.0 | 0.94
Output | 0.0026662 | 0.0026662 | 0.0026662 | 0.0 | 0.09
Modify | 2.7808 | 2.7808 | 2.7808 | 0.0 | 95.48
Other | | 0.0532 | | | 1.83
Nlocal: 14716 ave 14716 max 14716 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 86 ave 86 max 86 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 467 ave 467 max 467 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 467
Ave neighs/atom = 0.0317342
Neighbor list builds = 250
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03
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