Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/examples/ASPHERE/tri/log.tri.srd.10Sep13
d9b19cf6ba16lammm-devel

Last Change
Raw File

log.tri.srd.10Sep13
View Options

LAMMPS (9 Sep 2013)
# 3d Lennard-Jones melt
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
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:438)
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:2737)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2761)
# 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 = 112.926 Mbytes
Step 1 tsmall 2[9] Temp Press
0 0 1.4405441 0 0 -0.15917996
1000 1.0535509 1.1241378 0.030778612 0 0.15526438
2000 2.4635987 1.0240667 0.031199432 0 0.011069846
3000 3.1093028 1.0070585 0.0412299 0 0.34124887
4000 2.9091229 1.0109332 0.042413338 0 -0.43067212
5000 3.143486 1.007502 0.047871105 0 0.44935703
6000 3.3117859 1.0031975 0.060884331 0 -0.17753945
7000 3.7329968 0.99472569 0.071341886 0 1.4727109
8000 4.0314822 1.0148882 0.089434073 0 6.3915959
9000 6.3667017 1.0144773 0.10558433 0 14.945841
10000 14.065219 1.0159965 0.11784659 0 131.62736
Loop time of 229.245 on 8 procs for 10000 steps with 16271 atoms
Pair time (%) = 142.296 (62.0717)
Neigh time (%) = 33.5162 (14.6203)
Comm time (%) = 44.4642 (19.396)
Outpt time (%) = 0.822778 (0.358909)
Other time (%) = 8.14531 (3.55311)
Nlocal: 2033.88 ave 2131 max 1886 min
Histogram: 1 0 0 1 0 1 2 1 1 1
Nghost: 2777.38 ave 2813 max 2734 min
Histogram: 2 0 1 0 0 0 2 0 0 3
Neighs: 30097.6 ave 35599 max 25702 min
Histogram: 3 0 0 1 0 1 0 1 1 1
Total # of neighbors = 240781
Ave neighs/atom = 14.7982
Neighbor list builds = 500
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:2737)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2761)
# of rescaled SRD velocities = 2
ave/max small velocity = 16.086 40
ave/max big velocity = 1.89008 7.06443
Memory usage per processor = 67.8409 Mbytes
Step 1 tsmall 2[9] Temp Press
10000 14.065219 1.0159841 0 0 125.62369
11000 15.89949 1.1021294 0.13432606 0 79.756722
12000 13.591974 1.0986468 0.14491966 0 69.017912
13000 10.672662 1.0974608 0.13980161 0 68.47417
14000 10.433124 1.0970815 0.13358543 0 63.921726
15000 11.350239 1.0919622 0.13501392 0 56.434986
16000 9.9440024 1.0909392 0.13733839 0 60.312203
17000 8.8069504 1.0862993 0.1331224 0 60.673373
18000 9.7454087 1.0874377 0.14030315 0 55.359223
19000 8.7467828 1.0955594 0.13826168 0 58.135899
20000 9.094869 1.0853936 0.13980748 0 54.918577
21000 8.1769632 1.0877609 0.13527913 0 59.779335
22000 8.4802311 1.0874158 0.14097292 0 55.518841
23000 8.5085635 1.0938995 0.13479334 0 52.444531
24000 7.7708574 1.093106 0.13843648 0 53.619874
25000 7.5891864 1.0892977 0.1309956 0 50.959157
26000 7.1595504 1.0943558 0.1313863 0 50.73602
27000 6.4924522 1.0932486 0.13264833 0 50.620315
28000 6.8555436 1.0956448 0.1395996 0 53.675344
29000 7.0391394 1.0867312 0.14199161 0 53.493952
30000 7.9245188 1.0927432 0.13348801 0 50.474831
31000 8.1045132 1.0932086 0.13605758 0 48.830305
32000 8.3316171 1.0984609 0.13978578 0 48.671107
33000 7.3537207 1.0866232 0.13800293 0 49.619075
34000 7.5646404 1.0762414 0.1282765 0 48.104248
35000 7.6598613 1.0988043 0.1399969 0 48.344193
36000 8.2985234 1.0927025 0.13712115 0 51.995955
37000 7.8266025 1.0986061 0.13590656 0 55.526454
38000 8.1374325 1.0908854 0.1356955 0 51.766017
39000 7.1742247 1.0867582 0.13871443 0 54.475644
40000 7.1327095 1.0873612 0.13361669 0 53.584849
41000 7.4393759 1.083626 0.13678989 0 52.190793
42000 7.1145295 1.0867999 0.13910883 0 56.760468
43000 7.1195706 1.1052677 0.14404153 0 58.427514
44000 7.9713656 1.0931625 0.13568773 0 58.026623
45000 7.9875631 1.0928839 0.13617383 0 60.495025
46000 8.7377452 1.0927309 0.14312311 0 62.011464
47000 8.5499453 1.0941412 0.13203028 0 64.3929
48000 8.6633515 1.0929638 0.14189189 0 58.671573
49000 8.6567883 1.0832134 0.1353634 0 54.667636
50000 7.9400691 1.0942958 0.13789637 0 58.089009
Loop time of 1633.43 on 8 procs for 40000 steps with 16271 atoms
Pair time (%) = 1201.96 (73.5851)
Neigh time (%) = 184.862 (11.3174)
Comm time (%) = 188.22 (11.523)
Outpt time (%) = 3.30344 (0.202239)
Other time (%) = 55.0837 (3.37226)
Nlocal: 2033.88 ave 2156 max 1952 min
Histogram: 2 1 0 1 1 0 2 0 0 1
Nghost: 2752.38 ave 2941 max 2567 min
Histogram: 1 0 1 0 2 2 0 1 0 1
Neighs: 30128.1 ave 38439 max 23335 min
Histogram: 1 0 1 2 2 1 0 0 0 1
Total # of neighbors = 241025
Ave neighs/atom = 14.8132
Neighbor list builds = 2002
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
c4science · Help