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lammps/examples/srd/log.srd.mixture.10Sep10.linux.4
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LAMMPS (1 Oct 2010)
# 2d SRD test: big + small particles
units lj
atom_style colloid
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)
2 by 2 by 1 processor grid
create_atoms 1 region box
Created 100 atoms
mass 1 1.0
mass 2 0.01
shape 1 1.0 1.0 1.0
shape 2 0.0 0.0 0.0
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
Memory usage per processor = 2.12925 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 0.61487657
Loop time of 0.032092 on 4 procs for 1000 steps with 100 atoms
Pair time (%) = 0.00402153 (12.5312)
Neigh time (%) = 0.000997305 (3.10764)
Comm time (%) = 0.0206033 (64.2007)
Outpt time (%) = 8.10027e-05 (0.252408)
Other time (%) = 0.0063889 (19.9081)
Nlocal: 25 ave 26 max 23 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 47 ave 48 max 46 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 114.75 ave 124 max 100 min
Histogram: 1 0 0 0 0 1 0 0 0 2
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
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
Deleted 6700 atoms, new total = 14716
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
communicate 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 100
dump 1 all atom 250 dump.srd.mixture
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
# of rescaled SRD velocities = 0
ave/max small velocity = 13.2944 24.262
ave/max big velocity = 1.69284 5.10989
Memory usage per processor = 4.74632 Mbytes
Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10]
0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487657 0 0 0 0 0 0 0 0 0
100 1.3582446 3969 0.0026789295 -0.95043087 0.39423126 0.73581726 7479 87 87 0 0 22500 2999 1.0285157 0
200 1.2572907 3969 0.0019616669 -0.95603884 0.28867891 0.62749376 7394 98 98 0 0 22500 2994 1.0253343 0
300 1.12798 3969 0.00057755533 -1.0317072 0.084993042 0.30262448 7311 88 88 0 0 22500 2997 1.022263 0
400 1.1466105 3969 0.00088785773 -1.0044873 0.13065714 0.40537124 7467 82 82 0 0 22500 2993 1.0139003 0
500 1.0151043 3969 -0.00021014381 -1.0358781 -0.030924763 0.19673928 7587 81 81 0 0 22500 2994 1.0145019 0
600 0.99210691 3969 -0.0002577968 -1.0201232 -0.037937377 0.2625174 7449 92 92 0 0 22500 2968 0.98574736 0
700 0.92572874 3969 -0.00067753277 -1.0161772 -0.099705722 0.19520999 7537 78 78 0 0 22500 2998 1.0064032 0
800 0.94627244 3969 -0.0003639106 -0.9903628 -0.053553084 0.22241336 7602 79 79 0 1 22500 3010 1.0134331 0
900 0.92523394 3969 -0.00080502966 -1.0344498 -0.11846816 0.18846804 7576 72 72 0 1 22500 3015 1.0136704 0
1000 1.0322972 3969 -0.00037569219 -1.0772611 -0.055286863 0.13263626 7601 88 88 0 0 22500 3000 1.0224061 0
1100 0.9726161 3969 -0.00041776377 -1.0243681 -0.061478117 0.3120931 7425 87 87 0 0 22500 2991 1.0216981 0
1200 0.9785542 3969 -0.00036217362 -1.0220661 -0.053297471 0.37956001 7634 94 94 0 0 22500 3022 1.0055215 0
1300 1.102684 3969 0.00056306573 -1.0087964 0.082860753 0.50039902 7380 94 94 0 0 22500 3011 1.0298198 0
1400 1.2416072 3969 0.0016380507 -0.98813558 0.24105553 0.6709785 7532 95 95 0 0 22500 3005 1.0272106 0
1500 1.1009579 3969 0.00041059416 -1.0295252 0.060423037 0.4271012 7443 86 86 0 0 22500 2990 1.0322439 0
1600 0.97932726 3969 -0.00044406974 -1.0348833 -0.065349303 0.23710215 7541 85 85 0 0 22500 3005 1.0504545 0
1700 1.07156 3969 0.0003309407 -1.0121432 0.048701233 0.32615222 7660 90 90 0 1 22500 3010 1.0192163 0
1800 0.94379054 3969 -0.00060529206 -1.0234274 -0.08907478 0.28437994 7706 92 92 0 0 22500 2983 1.0197247 0
1900 1.1935542 3969 0.001087796 -1.0215386 0.16008006 0.32082985 7633 102 102 0 0 22500 3026 1.0227294 0
2000 1.0794535 3969 0.00017035747 -1.0435892 0.025069805 0.12933714 7547 76 76 0 0 22500 3028 1.0339312 0
2100 1.11728 3969 0.001197717 -0.92985122 0.17625603 0.4877601 7424 88 88 0 0 22500 2986 1.0268223 0
2200 1.022726 3969 -0.00017383526 -1.0380804 -0.025581597 0.18522494 7414 92 92 0 0 22500 3004 1.0254694 0
2300 1.2289681 3969 0.0014918151 -0.99714295 0.21953551 0.56571933 7669 90 90 0 0 22500 3008 1.0265701 0
2400 1.0261081 3969 0.00016550325 -0.99149158 0.024355459 0.53332928 7499 83 83 0 0 22500 3019 1.0160353 0
2500 1.0155015 3969 -0.00056230464 -1.0880952 -0.082748751 0.22398562 7712 79 79 0 0 22500 3017 1.03801 0
2600 0.8756954 3969 -0.0014956069 -1.087032 -0.22009351 0.10400097 7542 85 85 0 0 22500 2985 1.024091 0
2700 0.97964461 3969 -0.00075911535 -1.0815596 -0.11171141 0.27927544 7449 86 86 0 0 22500 2993 1.0166909 0
2800 0.97102332 3969 -0.00081115436 -1.0806826 -0.11936948 0.36647698 7662 85 85 0 0 22500 3014 1.0148134 0
2900 1.1405082 3969 0.00078035444 -1.0142661 0.11483696 0.73653576 7451 82 82 0 0 22500 3007 1.0296379 0
3000 1.0460256 3969 -0.00031837206 -1.082417 -0.046851633 0.25310003 7494 83 83 0 0 22500 3013 1.043192 0
3100 1.128752 3969 0.00043203186 -1.0538867 0.063577808 0.37101933 7458 89 89 0 1 22500 2981 1.0082866 0
3200 1.0546223 3969 0.00023156986 -1.0099982 0.034077821 0.66191884 7451 92 92 0 0 22500 2988 1.0254862 0
3300 1.0859707 3969 -5.4375056e-05 -1.0831128 -0.0080018333 0.3552947 7441 74 74 0 0 22500 2978 1.0252244 0
3400 0.90831095 3969 -0.0011506108 -1.0685517 -0.16932389 0.26027658 7478 76 76 0 0 22500 2997 1.0306308 0
3500 1.0971397 3969 0.00047675241 -1.0160094 0.070158884 0.39394719 7510 87 87 0 0 22500 2999 1.0303505 0
3600 1.0758592 3969 5.1451605e-05 -1.057529 0.0075716182 0.23217468 7505 98 98 0 0 22500 3022 1.0133265 0
3700 0.99184036 3969 -0.00051911023 -1.0583142 -0.076392262 0.2659259 7566 104 104 0 0 22500 3006 1.0284719 0
3800 0.86950687 3969 -0.0014525295 -1.074566 -0.21375425 0.27380224 7552 80 80 0 0 22500 3013 1.0351337 0
3900 0.86286132 3969 -0.0010595017 -1.010149 -0.15591627 0.56043933 7547 104 104 0 0 22500 2992 1.0313609 0
4000 0.76083626 3969 -0.0014009914 -0.9593978 -0.2061699 0.64813923 7448 101 101 0 0 22500 3032 1.0109258 0
4100 1.0071575 3969 -0.00018734554 -1.0246557 -0.027569769 0.55964495 7489 76 76 0 0 22500 3016 1.0175384 0
4200 0.88374612 3969 -0.0010981928 -1.0365187 -0.16161005 0.41352036 7481 92 92 0 0 22500 2995 1.0123735 0
4300 0.98819505 3969 -0.00066821798 -1.0766481 -0.098334958 0.41489158 7557 79 79 0 0 22500 2998 1.0400745 0
4400 1.1772685 3969 0.0010725317 -1.007662 0.15783376 0.7912903 7522 76 76 0 0 22500 2991 1.0176624 0
4500 1.0836741 3969 0.00021867511 -1.0406572 0.032180229 0.58489302 7800 93 93 0 0 22500 2997 1.0023484 0
4600 1.0334731 3969 -0.00015378918 -1.04577 -0.022631616 0.53872329 7542 94 94 0 0 22500 2996 0.98823241 0
4700 1.2126127 3969 0.0011423373 -1.0323802 0.16810636 0.49583696 7387 81 81 0 0 22500 3001 1.0425378 0
4800 1.1593219 3969 0.0010239969 -0.99703726 0.15069139 0.37192735 7374 80 80 0 1 22500 2988 1.0278368 0
4900 0.87223689 3969 -0.00099601272 -1.0100878 -0.14657323 0.11585542 7448 89 89 0 0 22500 3000 1.0267238 0
5000 0.87426493 3969 -0.0010817587 -1.0247139 -0.15919161 0.15322481 7587 100 100 0 0 22500 2988 1.0030228 0
Loop time of 1.93728 on 4 procs for 5000 steps with 14716 atoms
Pair time (%) = 0.0232192 (1.19854)
Neigh time (%) = 0.0877846 (4.53133)
Comm time (%) = 0.182241 (9.40704)
Outpt time (%) = 0.381904 (19.7134)
Other time (%) = 1.26213 (65.1497)
Nlocal: 3679 ave 3872 max 3379 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 48.25 ave 51 max 45 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 118 ave 167 max 87 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 472
Ave neighs/atom = 0.0320739
Neighbor list builds = 250
Dangerous builds = 0
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