forked from lijiext/lammps
233 lines
15 KiB
Groff
233 lines
15 KiB
Groff
|
LAMMPS (1 Feb 2014)
|
||
|
|
# 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
|
||
|
|
Memory usage per processor = 2.74778 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 0.0157461 on 1 procs for 1000 steps with 100 atoms
|
||
|
|
|
||
|
|
Pair time (%) = 0.00811386 (51.5293)
|
||
|
|
Neigh time (%) = 0.00263572 (16.7388)
|
||
|
|
Comm time (%) = 0.00207138 (13.1549)
|
||
|
|
Outpt time (%) = 7.86781e-06 (0.0499667)
|
||
|
|
Other time (%) = 0.00291729 (18.527)
|
||
|
|
|
||
|
|
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
|
||
|
|
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.cpp:439)
|
||
|
|
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:2875)
|
||
|
|
# 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 = 12.7948 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 0.61487656 0 0 0 0 0 0 0 0 0
|
||
|
|
100 1.1596877 3969 0.00179671 -0.88368702 0.26440384 0.85824544 7578 83 83 0 14 12996 3000 1.0041859 0
|
||
|
|
200 1.2193121 3969 0.001834514 -0.93715195 0.26996708 0.70474789 7511 90 90 0 53 12996 3022 1.0188814 0
|
||
|
|
300 0.99964232 3969 -0.00024687038 -1.0259753 -0.036329445 0.17545201 7647 91 91 0 84 12996 3012 1.0119139 0
|
||
|
|
400 1.0499322 3969 0.00055095426 -0.95835442 0.081078429 0.36186511 7386 108 108 0 111 12996 2998 1.0216118 0
|
||
|
|
500 1.0774128 3969 0.00085873911 -0.94026661 0.12637205 0.44079381 7472 85 85 0 138 12996 2996 1.0224021 0
|
||
|
|
600 1.0713454 3969 0.00045284139 -0.99399184 0.066640139 0.10369128 7656 83 83 0 159 12996 3007 1.030888 0
|
||
|
|
700 0.98148416 3969 0.00027332701 -0.93144651 0.040222802 0.40064794 7616 68 68 0 194 12996 2999 1.0156811 0
|
||
|
|
800 1.038835 3969 0.00026382768 -0.98962177 0.038824881 0.26546656 7518 100 100 0 217 12996 3018 1.0169426 0
|
||
|
|
900 1.0976069 3969 0.0005211042 -1.0099451 0.076685694 0.28307539 7658 91 91 0 243 12996 3028 1.037322 0
|
||
|
|
1000 1.0541417 3969 0.00060061674 -0.95521356 0.088386759 0.61226289 7577 78 78 0 285 12996 2996 1.019357 0
|
||
|
|
1100 1.0332458 3969 0.00050159758 -0.94909829 0.073815099 0.6685224 7581 79 79 0 317 12996 3000 1.0327932 0
|
||
|
|
1200 0.89438281 3969 -0.00096584613 -1.0275729 -0.14213392 0.37403554 7576 96 96 0 346 12996 2999 1.0185657 0
|
||
|
|
1300 1.0211539 3969 2.286332e-05 -1.0075778 0.0033645662 0.56342549 7660 94 94 0 385 12996 2994 1.019908 0
|
||
|
|
1400 0.99883891 3969 0.00024046091 -0.9534643 0.035386228 0.5689857 7634 82 82 0 416 12996 3022 1.0247654 0
|
||
|
|
1500 0.93938218 3969 -0.00014395945 -0.95117343 -0.021185072 0.53463026 7632 87 87 0 441 12996 3012 1.0411548 0
|
||
|
|
1600 1.2197277 3969 0.0011523527 -1.0379502 0.16958023 0.3478121 7659 82 82 0 466 12996 3011 1.0361286 0
|
||
|
|
1700 0.96932134 3969 -0.00064508306 -1.0545586 -0.094930423 0.29578009 7332 92 92 0 506 12996 2993 1.0361228 0
|
||
|
|
1800 1.0534784 3969 -4.2619236e-05 -1.0492155 -0.0062718467 0.42534773 7647 94 94 0 533 12996 3030 1.0252953 0
|
||
|
|
1900 1.1715618 3969 0.00031188504 -1.1139492 0.045897003 0.23182966 7624 78 78 0 557 12996 2987 1.0274073 0
|
||
|
|
2000 0.9840555 3969 -0.00078568321 -1.0898361 -0.11562114 0.24175316 7571 77 77 0 582 12996 3016 1.0207729 0
|
||
|
|
2100 0.91303589 3969 -0.001459571 -1.118696 -0.21479047 0.27799152 7668 84 84 0 599 12996 3022 1.024854 0
|
||
|
|
2200 0.97316562 3969 -0.00087469617 -1.0921543 -0.12872029 0.40701899 7422 96 96 0 634 12996 3003 1.030247 0
|
||
|
|
2300 1.1071289 3969 0.00055485995 -1.0144044 0.08165319 0.70028696 7242 86 86 0 659 12996 3013 1.0181269 0
|
||
|
|
2400 0.95313231 3969 -0.00066790967 -1.0418906 -0.098289587 0.56977108 7370 88 88 0 693 12996 3037 1.0174525 0
|
||
|
|
2500 1.0789299 3969 -0.00067288654 -1.1671626 -0.099021984 0.1320041 7485 84 84 0 723 12996 3011 1.0310304 0
|
||
|
|
2600 1.0013882 3969 -0.00086378434 -1.1184888 -0.1271145 0.31303314 7412 82 82 0 753 12996 2983 1.0183276 0
|
||
|
|
2700 0.99821888 3969 -0.00016681979 -1.0127859 -0.024549201 0.71198483 7543 93 93 0 788 12996 3025 1.0179264 0
|
||
|
|
2800 1.032743 3969 -0.00066018247 -1.119568 -0.097152452 0.34329585 7442 106 106 0 826 12996 2981 1.0218667 0
|
||
|
|
2900 1.158581 3969 0.00061952386 -1.055826 0.091169131 0.55199976 7462 85 85 0 853 12996 3022 1.0105531 0
|
||
|
|
3000 1.0890666 3969 -5.0289217e-05 -1.0855765 -0.0074005612 0.35916031 7412 77 77 0 886 12996 2994 1.0387853 0
|
||
|
|
3100 0.98273391 3969 -0.00062906795 -1.0654802 -0.09257364 0.32240559 7489 71 71 0 922 12996 3007 1.038908 0
|
||
|
|
3200 1.0182699 3969 -0.00092197839 -1.1437655 -0.13567834 0.060449966 7464 94 94 0 954 12996 3008 1.0137212 0
|
||
|
|
3300 0.92962276 3969 -0.0012252227 -1.1006303 -0.18030378 0.2692969 7449 98 98 0 985 12996 3011 1.0121446 0
|
||
|
|
3400 1.0270974 3969 -0.00078991522 -1.1330703 -0.11624392 0.28393475 7555 74 74 0 1013 12996 2981 1.0218996 0
|
||
|
|
3500 0.91276883 3969 -0.0012028955 -1.0806592 -0.1770181 0.48380351 7422 100 100 0 1045 12996 3019 1.0270228 0
|
||
|
|
3600 1.1604674 3969 0.00041287296 -1.0881043 0.060758384 0.4937285 7451 78 78 0 1084 12996 3001 1.021449 0
|
||
|
|
3700 0.92829756 3969 -0.0012843951 -1.1080262 -0.18901158 0.28403593 7502 80 80 0 1106 12996 3011 1.0140255 0
|
||
|
|
3800 0.99862294 3969 -0.00028587151 -1.0307056 -0.042068851 0.57880501 7353 84 84 0 1136 12996 3011 1.0238774 0
|
||
|
|
3900 1.0748889 3969 -0.00039644261 -1.1224805 -0.058340495 0.3117021 7199 95 95 0 1169 12996 2997 1.0141241 0
|
||
|
|
4000 1.1443251 3969 0.00073233367 -1.0251116 0.10777022 0.72975938 7478 90 90 0 1203 12996 3000 1.016123 0
|
||
|
|
4100 1.0573661 3969 -8.8349019e-05 -1.0597939 -0.013001442 0.62403315 7528 77 77 0 1235 12996 2993 1.0207081 0
|
||
|
|
4200 0.93387975 3969 -0.0012090318 -1.1024621 -0.17792112 0.50858912 7397 80 80 0 1285 12996 3007 1.0232781 0
|
||
|
|
4300 0.99747825 3969 -0.00050121316 -1.061262 -0.073758528 0.63526459 7355 90 90 0 1313 12996 3015 1.0210677 0
|
||
|
|
4400 0.91351004 3969 -0.0013423585 -1.1019164 -0.19754147 0.44962963 7448 94 94 0 1344 12996 3009 1.0203146 0
|
||
|
|
4500 1.112129 3969 -9.3639925e-05 -1.1147878 -0.013780051 0.5084257 7570 77 77 0 1375 12996 2993 1.0224154 0
|
||
|
|
4600 1.0070341 3969 -0.00044065884 -1.0618111 -0.064847355 0.50331376 7503 74 74 0 1406 12996 3001 1.0099788 0
|
||
|
|
4700 1.1678442 3969 0.00045268406 -1.0895488 0.066616986 0.46676039 7514 81 81 0 1436 12996 2983 1.0099861 0
|
||
|
|
4800 1.1647145 3969 0.00063121154 -1.0601783 0.092889091 0.52493522 7437 89 89 0 1467 12996 3016 1.0214313 0
|
||
|
|
4900 1.1545752 3969 -0.00015064108 -1.1651978 -0.022168341 0.098732178 7561 85 85 0 1490 12996 2999 1.0108506 0
|
||
|
|
5000 1.2758575 3969 0.0016719011 -1.017062 0.24603697 0.63374434 7283 77 77 0 1521 12996 2989 1.0136454 0
|
||
|
|
Loop time of 2.94861 on 1 procs for 5000 steps with 14716 atoms
|
||
|
|
|
||
|
|
Pair time (%) = 0.0425909 (1.44444)
|
||
|
|
Neigh time (%) = 0.207188 (7.02665)
|
||
|
|
Comm time (%) = 0.0410075 (1.39074)
|
||
|
|
Outpt time (%) = 0.00202203 (0.0685757)
|
||
|
|
Other time (%) = 2.6558 (90.0696)
|
||
|
|
|
||
|
|
Nlocal: 14716 ave 14716 max 14716 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Nghost: 80 ave 80 max 80 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
Neighs: 490 ave 490 max 490 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||
|
|
|
||
|
|
Total # of neighbors = 490
|
||
|
|
Ave neighs/atom = 0.0332971
|
||
|
|
Neighbor list builds = 250
|
||
|
|
Dangerous builds = 0
|
||
|
|
|
||
|
|
Please see the log.cite file for references relevant to this simulation
|
||
|
|
|