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This commit is contained in:
Joel Clemmer
2021-01-08 15:27:23 -07:00
parent 50be21902e
commit d5f34f6296
14 changed files with 1604 additions and 23 deletions
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LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.1
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
region box block 0 60 0 60 -0.5 0.5
create_box 5 box
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
#Roughly equally partition atoms between types 1-4
set group all type/fraction 2 0.500 23984
Setting atom values ...
1768 settings made for type/fraction
set group all type/fraction 3 0.333 43684
Setting atom values ...
1255 settings made for type/fraction
set group all type/fraction 4 0.250 87811
Setting atom values ...
927 settings made for type/fraction
# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
delete_atoms region sphere1
Deleted 289 atoms, new total = 3311
delete_atoms region sphere2
Deleted 287 atoms, new total = 3024
create_atoms 5 single 60.0 60.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
create_atoms 5 single 130.0 130.0 0.0 units box
Created 1 atoms
create_atoms CPU = 0.000 seconds
set type 1 mass 400
Setting atom values ...
753 settings made for mass
set type 2 mass 1
Setting atom values ...
722 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #/old
neigh_modify delay 0 multi/custom 2 1*4 5
comm_modify mode multi multi/reduce
# colloid potential
pair_style colloid 20.0
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 31
ghost atom cutoff = 31
binsize = 2, bins = 95 95 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair colloid, perpetual
attributes: half, newton on
pair build: half/multi/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.382 | 5.384 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395241 0.121 36000
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688
3000 1.8956738 -0.090814176 1.8042332 0.075557943 77825.289
4000 1.9570462 -0.072505537 1.8838939 0.072824365 90931.708
5000 2.0376745 -0.083247829 1.9537533 0.068496975 90055.295
6000 2.0744887 -0.085395371 1.9884077 0.0821927 78070.648
7000 2.1002183 -0.11654617 1.9829781 0.10523249 63934.448
8000 2.0818325 -0.13271654 1.948428 0.11909162 52636.484
9000 2.0693987 -0.16404154 1.9046733 0.14702552 44539.609
10000 2.0667772 -0.19779488 1.8682993 0.17245383 38822.542
11000 2.0640582 -0.22114917 1.842227 0.18083079 34788.927
12000 2.0308462 -0.20353105 1.8266441 0.20640739 31706.009
13000 2.0395895 -0.24217765 1.7967378 0.21832952 29152.654
14000 2.030848 -0.2586169 1.77156 0.26577748 27068.89
15000 2.0222966 -0.27554585 1.7460825 0.2777169 25272.786
16000 2.0398867 -0.31547563 1.723737 0.27763622 23666.792
17000 2.03026 -0.32453791 1.7050512 0.28099246 22272.809
18000 2.0345512 -0.35026242 1.6836164 0.36600779 21023.172
19000 2.0242864 -0.35813231 1.6654851 0.33415432 19941.244
20000 2.0132465 -0.36563904 1.6469422 0.403365 18979.884
21000 2.0280384 -0.4075867 1.6197815 0.37205362 18152.487
22000 2.0206494 -0.40600336 1.6139782 0.42704594 17370.812
23000 2.0395761 -0.45083258 1.5880695 0.40276343 16700.427
24000 2.017203 -0.44930293 1.5672335 0.43867313 16161.79
25000 2.0191846 -0.4672218 1.5512955 0.47031215 15622.756
26000 2.0131624 -0.46436088 1.5481363 0.51717944 15141.645
27000 2.0322461 -0.50659994 1.5249745 0.49218933 14627.657
28000 2.0169304 -0.50555565 1.5107082 0.55547935 14186.079
29000 2.024656 -0.52258414 1.5014028 0.59125812 13759.99
30000 2.0153725 -0.53585947 1.478847 0.57235811 13384.355
31000 2.0163261 -0.56383766 1.4518221 0.58232057 13098.196
32000 2.0109673 -0.56784395 1.4424588 0.58282178 12831.934
33000 2.0099169 -0.57625621 1.4329964 0.65139601 12479.442
34000 2.0238152 -0.60189607 1.4212503 0.62659152 12210.628
35000 2.0359989 -0.62654733 1.4087787 0.67574446 11972.725
36000 2.0222689 -0.62880837 1.3927923 0.66602146 11690.049
37000 1.9982569 -0.62746376 1.3701328 0.71326589 11433.825
38000 1.9969836 -0.63975181 1.3565719 0.72799891 11285.497
39000 2.0071087 -0.65781805 1.3486274 0.79121297 11107.469
40000 2.0243046 -0.6881221 1.3355135 0.77519099 10943.846
41000 2.0351657 -0.70309175 1.3314014 0.68815156 10742.515
42000 2.0224788 -0.70975664 1.3120538 0.80484619 10505.657
43000 2.0123135 -0.70818545 1.3034631 0.84204556 10353.024
44000 1.999883 -0.70981202 1.2894101 0.94070546 10212.224
45000 2.0127291 -0.73338075 1.2786832 0.82095205 10109.959
46000 2.0109037 -0.75130029 1.2589389 0.88538358 9953.4822
47000 1.9879175 -0.73152019 1.2557404 0.92089629 9832.892
48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453
49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918
50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268
Loop time of 7.28248 on 4 procs for 50000 steps with 3026 atoms
Performance: 2966022.789 tau/day, 6865.793 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1624 | 2.5918 | 2.9227 | 17.4 | 35.59
Neigh | 0.62508 | 0.7436 | 0.83321 | 9.2 | 10.21
Comm | 1.1035 | 1.5265 | 2.0746 | 29.3 | 20.96
Output | 0.050094 | 0.050233 | 0.05062 | 0.1 | 0.69
Modify | 1.8164 | 1.8966 | 1.9583 | 4.2 | 26.04
Other | | 0.4737 | | | 6.50
Nlocal: 756.500 ave 839 max 673 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 292.500 ave 307 max 282 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 6435.25 ave 7367 max 5493 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 25741
Ave neighs/atom = 8.5066094
Neighbor list builds = 4335
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:07