Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/examples/ASPHERE/tri/log.tri.srd.1Feb14
1514cff5c805lammm-master-deprecated

Last Change
Raw File

log.tri.srd.1Feb14
View Options

LAMMPS (1 Feb 2014)
# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles
units lj
atom_style tri
atom_modify first big
read_data data.tri.srd
orthogonal box = (-8.43734 -8.43734 -8.43734) to (8.43734 8.43734 8.43734)
2 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
1500 triangles
# add small particles as hi density lattice
lattice sc 0.4
Lattice spacing in x,y,z = 1.35721 1.35721 1.35721
region box block INF INF INF INF INF INF
lattice sc 20.0
Lattice spacing in x,y,z = 0.368403 0.368403 0.368403
create_atoms 2 region box
Created 91125 atoms
group big type 1
1500 atoms in group big
group small type 2
91125 atoms in group small
set group small mass 0.01
91125 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
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
delete_atoms overlap 1.5 small big
Deleted 76354 atoms, new total = 16271
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule big include big
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style tri/lj 3.5
pair_coeff 1 1 0.1 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
# if comment out, big particles won't see SRD particles
timestep 0.001
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
125 rigid bodies with 1500 atoms
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step f_1 c_tsmall f_2[9] temp press
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
run 10000
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 1.46014 0.436602
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 67 67 67
SRD grid size: request, actual (xyz) = 0.25, 0.251861 0.251861 0.251861
SRD per actual grid cell = 0.0647662
SRD viscosity = -1.09837
big/SRD mass density ratio = 24.668
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
# of rescaled SRD velocities = 0
ave/max small velocity = 19.9708 35.1504
ave/max big velocity = 0 0
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
Memory usage per processor = 116.135 Mbytes
Step 1 tsmall 2[9] Temp Press
0 0 1.4405441 0 0 -0.15917996
1000 1.0535509 1.1241378 1.1224038 0 0.15526438
2000 2.4635987 1.0240667 0.94231519 0 0.011069846
3000 3.1093028 1.0070585 1.0176028 0 0.34124888
4000 2.9524179 1.0101774 1.0311733 0 -0.22118101
5000 2.9175438 1.0109144 1.0284445 0 0.1839507
6000 3.3200928 0.99108983 0.95968219 0 1.0229339
7000 3.3020156 0.99661428 0.98000621 0 2.3333851
8000 4.1500999 0.99129645 0.99723707 0 4.3054414
9000 6.537028 1.0074533 1.0251098 0 18.782913
10000 16.233245 1.0145766 1.0219787 0 147.83787
Loop time of 228.558 on 8 procs for 10000 steps with 16271 atoms
Pair time (%) = 145.018 (63.4492)
Neigh time (%) = 32.6283 (14.2757)
Comm time (%) = 43.3283 (18.9572)
Outpt time (%) = 0.000848889 (0.00037141)
Other time (%) = 7.58254 (3.31755)
Nlocal: 2033.88 ave 2092 max 1902 min
Histogram: 1 0 0 0 1 1 0 1 1 3
Nghost: 2805 ave 2855 max 2751 min
Histogram: 1 0 2 1 0 0 0 2 1 1
Neighs: 30026.5 ave 38700 max 24367 min
Histogram: 1 0 2 1 3 0 0 0 0 1
Total # of neighbors = 240212
Ave neighs/atom = 14.7632
Neighbor list builds = 501
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
triclinic box = (-5.0624 -5.0624 -5.0624) to (5.0624 5.0624 5.0624) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 40000
SRD info:
SRD/big particles = 14771 1500
big particle diameter max/min = 1.46014 0.436602
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 40 40 40
SRD grid size: request, actual (xyz) = 0.25, 0.25312 0.25312 0.25312
SRD per actual grid cell = -1.93929
SRD viscosity = -0.36972
big/SRD mass density ratio = -0.836253
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
# of rescaled SRD velocities = 1
ave/max small velocity = 16.0639 40
ave/max big velocity = 2.05735 6.73052
Memory usage per processor = 65.2471 Mbytes
Step 1 tsmall 2[9] Temp Press
10000 16.233245 1.0144194 0 0 146.27032
11000 17.301043 1.0619209 1 0 84.226323
12000 13.481177 1.063945 1 0 80.42834
13000 12.616615 1.0536125 1 0 68.365053
14000 12.16592 1.0581344 1 0 59.709941
15000 10.811557 1.0650453 1 0 59.869798
16000 9.9303081 1.0641012 1 0 59.289126
17000 10.452639 1.0589904 1 0 52.680235
18000 9.2488947 1.0556713 1 0 51.044123
19000 8.7179788 1.0566791 1 0 50.927924
20000 7.8641299 1.0668891 1 0 53.961014
21000 8.4333975 1.0628003 1 0 54.677068
22000 8.554623 1.0591872 1 0 51.784737
23000 7.895462 1.0598512 1 0 53.26885
24000 7.7014869 1.055569 1 0 54.236941
25000 7.508138 1.0581539 1 0 53.297709
26000 8.0707381 1.0586451 1 0 51.411341
27000 8.224223 1.0585509 1 0 52.775784
28000 8.8720461 1.0648837 1 0 49.681447
29000 8.503895 1.0538278 1 0 52.478556
30000 8.2272425 1.0625583 1 0 52.795709
31000 8.4626161 1.0599557 1 0 52.905343
32000 7.7410527 1.0587681 1 0 57.464472
33000 7.2765481 1.0677531 1 0 59.46728
34000 7.036016 1.0640728 1 0 60.636828
35000 8.497203 1.0577458 1 0 55.257312
36000 8.9218761 1.0585038 1 0 55.668201
37000 8.0469115 1.0561193 1 0 58.711565
38000 8.6456966 1.0663818 1 0 53.691658
39000 8.566667 1.0616928 1 0 52.866468
40000 7.7081259 1.0577046 1 0 54.105829
41000 7.4051952 1.0570277 1 0 56.094997
42000 7.331432 1.0632261 1 0 55.661067
43000 7.5587053 1.0602077 1 0 54.30762
44000 7.4521497 1.0594391 1 0 52.993548
45000 7.6234559 1.0641992 1 0 53.352202
46000 8.0659693 1.0609367 1 0 50.302682
47000 7.5227882 1.0563543 1 0 50.43551
48000 8.0798684 1.0628968 1 0 48.419201
49000 7.130784 1.0594143 1 0 50.656081
50000 7.3219268 1.0608236 1 0 54.808358
Loop time of 1651.84 on 8 procs for 40000 steps with 16271 atoms
Pair time (%) = 1232.76 (74.6296)
Neigh time (%) = 171.893 (10.4061)
Comm time (%) = 193.625 (11.7218)
Outpt time (%) = 0.00338289 (0.000204795)
Other time (%) = 53.5578 (3.24231)
Nlocal: 2033.88 ave 2229 max 1953 min
Histogram: 2 1 2 2 0 0 0 0 0 1
Nghost: 2757.88 ave 2810 max 2692 min
Histogram: 1 1 1 0 1 0 0 1 1 2
Neighs: 30098.6 ave 37369 max 25592 min
Histogram: 1 3 0 1 0 1 1 0 0 1
Total # of neighbors = 240789
Ave neighs/atom = 14.7987
Neighbor list builds = 2007
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
c4science · Help