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log.lammps
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LAMMPS (16 Feb 2016)
# set up our simulation environment
dimension 3
units lj
atom_style hybrid sphere dipole
boundary p p p
#input data file
read_data "/Users/joelforster/Projects/np-toolkit/data/sp_data.data"
orthogonal box = (-24.7314 -24.8449 -100) to (24.7314 24.8449 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
2925 atoms
reading velocities ...
2925 velocities
#group particles according to their types
group mem type 1
2900 atoms in group mem
group vehicle type 2
1 atoms in group vehicle
group ligand type 3:26
24 atoms in group ligand
group np type 2:26
25 atoms in group np
#give our particle a small kick towards the membrane
velocity np set 0 0 -2
#membrane parameters (see Yuan 2011)
variable rc equal 2.6
variable rmin equal 1.122462
variable rclus equal 2.0
variable mu equal 3
variable zeta equal 4
variable eps equal 4.34
variable sigma equal 1.00
variable theta0_11 equal 0
variable memsize equal "count(mem)"
# nanoparticle parameters
variable peps equal 25.0
# set up additional variables to be computed during the simulation (see lammps wiki for full explainations)
#compute 1 all pair lj/cut epair
compute cls all cluster/atom ${rclus}
compute cls all cluster/atom 2
compute ct all temp/sphere
compute_modify ct extra ${memsize}
compute_modify ct extra 2900
# set up the pair style for the membrane
pair_style hybrid membrane ${rc} lj/cut 5.04
pair_style hybrid membrane 2.6 lj/cut 5.04
# membrane-nanoparticle interactions, each is set separately so any distribution of ligand strengths is possible
pair_coeff * * lj/cut 0.0 0.0 0.0
pair_coeff 1 2 lj/cut 100 4.0 4.45
pair_coeff 1 3 lj/cut ${peps} 1 1.8
pair_coeff 1 3 lj/cut 25 1 1.8
pair_coeff 1 4 lj/cut ${peps} 1 1.8
pair_coeff 1 4 lj/cut 25 1 1.8
pair_coeff 1 5 lj/cut ${peps} 1 1.8
pair_coeff 1 5 lj/cut 25 1 1.8
pair_coeff 1 6 lj/cut ${peps} 1 1.8
pair_coeff 1 6 lj/cut 25 1 1.8
pair_coeff 1 7 lj/cut ${peps} 1 1.8
pair_coeff 1 7 lj/cut 25 1 1.8
pair_coeff 1 8 lj/cut ${peps} 1 1.8
pair_coeff 1 8 lj/cut 25 1 1.8
pair_coeff 1 9 lj/cut ${peps} 1 1.8
pair_coeff 1 9 lj/cut 25 1 1.8
pair_coeff 1 10 lj/cut ${peps} 1 1.8
pair_coeff 1 10 lj/cut 25 1 1.8
pair_coeff 1 11 lj/cut ${peps} 1 1.8
pair_coeff 1 11 lj/cut 25 1 1.8
pair_coeff 1 12 lj/cut ${peps} 1 1.8
pair_coeff 1 12 lj/cut 25 1 1.8
pair_coeff 1 13 lj/cut ${peps} 1 1.8
pair_coeff 1 13 lj/cut 25 1 1.8
pair_coeff 1 14 lj/cut ${peps} 1 1.8
pair_coeff 1 14 lj/cut 25 1 1.8
pair_coeff 1 15 lj/cut ${peps} 1 1.8
pair_coeff 1 15 lj/cut 25 1 1.8
pair_coeff 1 16 lj/cut ${peps} 1 1.8
pair_coeff 1 16 lj/cut 25 1 1.8
pair_coeff 1 17 lj/cut ${peps} 1 1.8
pair_coeff 1 17 lj/cut 25 1 1.8
pair_coeff 1 18 lj/cut ${peps} 1 1.8
pair_coeff 1 18 lj/cut 25 1 1.8
pair_coeff 1 19 lj/cut ${peps} 1 1.8
pair_coeff 1 19 lj/cut 25 1 1.8
pair_coeff 1 20 lj/cut ${peps} 1 1.8
pair_coeff 1 20 lj/cut 25 1 1.8
pair_coeff 1 21 lj/cut ${peps} 1 1.8
pair_coeff 1 21 lj/cut 25 1 1.8
pair_coeff 1 22 lj/cut ${peps} 1 1.8
pair_coeff 1 22 lj/cut 25 1 1.8
pair_coeff 1 23 lj/cut ${peps} 1 1.8
pair_coeff 1 23 lj/cut 25 1 1.8
pair_coeff 1 24 lj/cut ${peps} 1 1.8
pair_coeff 1 24 lj/cut 25 1 1.8
pair_coeff 1 25 lj/cut ${peps} 1 1.8
pair_coeff 1 25 lj/cut 25 1 1.8
pair_coeff 1 26 lj/cut ${peps} 1 1.8
pair_coeff 1 26 lj/cut 25 1 1.8
#we set the interaction to zero at its cutoff distance, otherwise we will have a discontinuity
pair_modify pair lj/cut shift yes
#membrane-membrane interactions (these can be changed by messing with the variables at the top)
pair_coeff 1 1 membrane ${eps} ${sigma} ${rmin} ${rc} ${zeta} ${mu} ${theta0_11}
pair_coeff 1 1 membrane 4.34 ${sigma} ${rmin} ${rc} ${zeta} ${mu} ${theta0_11}
pair_coeff 1 1 membrane 4.34 1 ${rmin} ${rc} ${zeta} ${mu} ${theta0_11}
pair_coeff 1 1 membrane 4.34 1 1.122462 ${rc} ${zeta} ${mu} ${theta0_11}
pair_coeff 1 1 membrane 4.34 1 1.122462 2.6 ${zeta} ${mu} ${theta0_11}
pair_coeff 1 1 membrane 4.34 1 1.122462 2.6 4 ${mu} ${theta0_11}
pair_coeff 1 1 membrane 4.34 1 1.122462 2.6 4 3 ${theta0_11}
pair_coeff 1 1 membrane 4.34 1 1.122462 2.6 4 3 0
neigh_modify every 1 delay 1 exclude group np np
# we set up the integration parameters
fix fLANG all langevin 1.0 1.0 1.0 1000 zero yes omega yes
fix fNPH mem nph/sphere x 0.0 0.0 10.0 y 0.0 0.0 10.0 couple xy update dipole dilate all
fix_modify fNPH temp ct press thermo_press
fix fRIGID np rigid/nve group 1 np
1 rigid bodies with 25 atoms
#output settings, changing peps will change the output file name as well, change this by removing ${peps} from the dump file name
dump coords all custom 100 particle_${peps}_out.xyz id type x y z c_cls
dump coords all custom 100 particle_25_out.xyz id type x y z c_cls
dump_modify coords sort id
thermo_style custom step pe ke etotal
# set up our timestep and runtime
timestep 0.01
thermo 100
run 25000
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.75
ghost atom cutoff = 4.75
binsize = 2.375 -> bins = 21 21 85
Memory usage per processor = 6.32751 Mbytes
Step PotEng KinEng TotEng
0 -11.979473 0.0089504064 -11.970522
100 -12.438074 1.2493749 -11.188699
200 -12.165299 1.3752851 -10.790013
300 -11.995244 1.4549685 -10.540275
400 -12.008875 1.476094 -10.532781
500 -11.920048 1.5055621 -10.414486
600 -11.94646 1.5051026 -10.441357
700 -11.942104 1.4828098 -10.459294
800 -11.972992 1.487628 -10.485364
900 -11.963373 1.4865096 -10.476863
1000 -12.01014 1.4832402 -10.526899
1100 -11.946975 1.4860391 -10.460936
1200 -12.018074 1.4689037 -10.54917
1300 -12.145739 1.5224573 -10.623282
1400 -12.243577 1.5655835 -10.677994
1500 -12.303193 1.5643493 -10.738843
1600 -12.419288 1.5460142 -10.873273
1700 -12.422132 1.5047647 -10.917367
1800 -12.591209 1.4903664 -11.100843
1900 -12.640456 1.4969697 -11.143486
2000 -12.701437 1.517392 -11.184045
2100 -12.657062 1.5289995 -11.128062
2200 -12.766747 1.5300211 -11.236726
2300 -12.819472 1.4807048 -11.338767
2400 -12.781356 1.4988891 -11.282467
2500 -12.809809 1.5157123 -11.294097
2600 -12.878207 1.5318363 -11.346371
2700 -12.864842 1.5346847 -11.330157
2800 -12.886142 1.5120276 -11.374115
2900 -12.960454 1.5005686 -11.459886
3000 -12.939714 1.4729028 -11.466811
3100 -12.966117 1.4606929 -11.505424
3200 -13.007708 1.4874879 -11.52022
3300 -13.014457 1.5382875 -11.476169
3400 -12.915995 1.4649298 -11.451065
3500 -12.947422 1.4685058 -11.478916
3600 -13.032544 1.5150753 -11.517469
3700 -12.994599 1.4651855 -11.529414
3800 -13.061574 1.4988955 -11.562678
3900 -13.021956 1.5298974 -11.492058
4000 -13.001988 1.5464347 -11.455554
4100 -12.967599 1.5095842 -11.458015
4200 -13.026024 1.5123582 -11.513666
4300 -13.000591 1.5042622 -11.496329
4400 -13.074669 1.4907732 -11.583896
4500 -13.02824 1.4799424 -11.548298
4600 -12.98493 1.4836518 -11.501278
4700 -13.109259 1.4758328 -11.633426
4800 -13.06852 1.4823224 -11.586197
4900 -13.071364 1.4977709 -11.573593
5000 -13.098155 1.5041452 -11.59401
5100 -13.033813 1.5189567 -11.514856
5200 -13.045535 1.5322431 -11.513292
5300 -13.029852 1.5118951 -11.517956
5400 -13.086187 1.4903465 -11.595841
5500 -13.057463 1.5148199 -11.542644
5600 -13.060693 1.5307718 -11.529921
5700 -13.08443 1.4991336 -11.585296
5800 -13.116853 1.4638785 -11.652975
5900 -13.095696 1.4950763 -11.60062
6000 -13.08626 1.4920372 -11.594223
6100 -13.078875 1.5448776 -11.533998
6200 -13.028455 1.4927454 -11.53571
6300 -13.053427 1.5026392 -11.550787
6400 -13.041659 1.5120365 -11.529622
6500 -13.106435 1.4847378 -11.621697
6600 -13.119468 1.49356 -11.625908
6700 -13.108193 1.4750546 -11.633139
6800 -13.149286 1.4833633 -11.665923
6900 -13.07339 1.4798865 -11.593504
7000 -13.110519 1.497019 -11.6135
7100 -13.083491 1.4717238 -11.611767
7200 -13.102538 1.486252 -11.616286
7300 -13.045978 1.5076978 -11.53828
7400 -13.013054 1.4778971 -11.535156
7500 -13.089346 1.4954663 -11.593879
7600 -13.119921 1.4893469 -11.630574
7700 -13.036075 1.4756231 -11.560452
7800 -13.054175 1.5050442 -11.549131
7900 -13.111694 1.4729803 -11.638714
8000 -13.086707 1.504793 -11.581914
8100 -13.102838 1.5023358 -11.600502
8200 -13.096375 1.4874008 -11.608974
8300 -13.13206 1.5371575 -11.594902
8400 -13.072264 1.5108974 -11.561367
8500 -13.08603 1.5196573 -11.566372
8600 -13.049409 1.470045 -11.579364
8700 -13.068505 1.5381629 -11.530342
8800 -13.059603 1.5039593 -11.555644
8900 -13.124089 1.4934637 -11.630625
9000 -13.05722 1.4815115 -11.575708
9100 -13.052045 1.4824765 -11.569568
9200 -13.082027 1.4698752 -11.612152
9300 -13.054194 1.4914982 -11.562696
9400 -13.091423 1.5199087 -11.571515
9500 -13.077608 1.4948683 -11.582739
9600 -13.089721 1.4932885 -11.596432
9700 -13.096152 1.4742071 -11.621945
9800 -13.095994 1.5019747 -11.594019
9900 -13.05872 1.505116 -11.553604
10000 -13.085709 1.5007962 -11.584913
10100 -13.097351 1.4756461 -11.621705
10200 -13.140464 1.5120386 -11.628425
10300 -13.141586 1.4652177 -11.676368
10400 -13.119295 1.4389935 -11.680301
10500 -13.159966 1.4934245 -11.666541
10600 -13.053627 1.4899691 -11.563657
10700 -13.116701 1.5044275 -11.612273
10800 -13.080862 1.5082156 -11.572647
10900 -13.09989 1.4772657 -11.622624
11000 -13.109301 1.5060464 -11.603254
11100 -13.137322 1.5201643 -11.617157
11200 -13.085027 1.466325 -11.618702
11300 -13.034829 1.5097961 -11.525033
11400 -13.119768 1.4982891 -11.621479
11500 -13.1467 1.4727413 -11.673959
11600 -13.077155 1.4987373 -11.578417
11700 -13.135778 1.4997317 -11.636047
11800 -13.143262 1.470052 -11.67321
11900 -13.110134 1.4332986 -11.676835
12000 -13.082556 1.4785566 -11.603999
12100 -13.11998 1.4759277 -11.644052
12200 -13.134201 1.4477602 -11.686441
12300 -13.153535 1.4629828 -11.690552
12400 -13.10449 1.5052633 -11.599226
12500 -13.071224 1.5027104 -11.568514
12600 -13.129766 1.5171531 -11.612613
12700 -13.118968 1.4847416 -11.634226
12800 -13.054313 1.4798776 -11.574435
12900 -13.104912 1.4932273 -11.611685
13000 -13.13163 1.5016579 -11.629972
13100 -13.036945 1.5104755 -11.526469
13200 -13.090952 1.4552776 -11.635674
13300 -13.123555 1.5080569 -11.615499
13400 -13.049734 1.4676348 -11.582099
13500 -13.05677 1.4886366 -11.568133
13600 -13.074781 1.483303 -11.591478
13700 -13.131389 1.5442924 -11.587096
13800 -13.054707 1.4871414 -11.567566
13900 -13.116313 1.5221518 -11.594161
14000 -13.097498 1.496624 -11.600874
14100 -13.167669 1.4868795 -11.680789
14200 -13.1374 1.5036186 -11.633781
14300 -13.179745 1.4766607 -11.703084
14400 -13.115298 1.4797796 -11.635519
14500 -13.106783 1.4669778 -11.639806
14600 -13.076006 1.4567448 -11.619262
14700 -13.132542 1.5093512 -11.623191
14800 -13.088388 1.5155722 -11.572816
14900 -13.077954 1.4915165 -11.586437
15000 -13.13065 1.4893577 -11.641292
15100 -13.099673 1.49902 -11.600653
15200 -13.02969 1.5155709 -11.514119
15300 -13.016399 1.51494 -11.501459
15400 -13.106255 1.5042263 -11.602029
15500 -13.078686 1.4880089 -11.590677
15600 -13.093926 1.4920248 -11.601901
15700 -13.098186 1.5047931 -11.593393
15800 -13.050572 1.480307 -11.570265
15900 -13.067727 1.5027654 -11.564961
16000 -13.100362 1.5363596 -11.564002
16100 -13.112512 1.5221029 -11.590409
16200 -13.143503 1.4984462 -11.645057
16300 -13.128675 1.5043022 -11.624373
16400 -13.052031 1.4884494 -11.563581
16500 -13.097728 1.492758 -11.60497
16600 -13.112877 1.5442381 -11.568639
16700 -13.075788 1.5065376 -11.56925
16800 -13.0923 1.5068285 -11.585472
16900 -13.12157 1.5179673 -11.603602
17000 -13.148689 1.5092078 -11.639481
17100 -13.100066 1.5005737 -11.599492
17200 -13.120726 1.51216 -11.608566
17300 -13.146627 1.5463572 -11.60027
17400 -13.115141 1.5336808 -11.58146
17500 -13.075696 1.5170702 -11.558626
17600 -13.146104 1.5337383 -11.612366
17700 -13.099008 1.4898127 -11.609195
17800 -13.148799 1.5021609 -11.646638
17900 -13.075707 1.5266317 -11.549076
18000 -13.065858 1.5068938 -11.558964
18100 -13.126828 1.4967618 -11.630066
18200 -13.121217 1.4775272 -11.64369
18300 -13.095168 1.4986229 -11.596545
18400 -13.06749 1.5076012 -11.559889
18500 -13.108274 1.5096844 -11.598589
18600 -13.081095 1.4901113 -11.590984
18700 -13.148721 1.4900923 -11.658629
18800 -13.142562 1.5071464 -11.635416
18900 -13.095359 1.4976566 -11.597703
19000 -13.098281 1.4754626 -11.622819
19100 -13.153037 1.4713062 -11.681731
19200 -13.090202 1.5168443 -11.573357
19300 -13.08197 1.5198106 -11.56216
19400 -13.088065 1.4865135 -11.601552
19500 -13.119547 1.4755164 -11.644031
19600 -13.113334 1.4430126 -11.670321
19700 -13.11067 1.4781584 -11.632511
19800 -13.113534 1.4643761 -11.649158
19900 -13.152538 1.4633087 -11.689229
20000 -13.066238 1.4822991 -11.583939
20100 -13.101302 1.4879724 -11.613329
20200 -13.114751 1.4704343 -11.644317
20300 -13.147519 1.4828861 -11.664633
20400 -13.102646 1.4628862 -11.63976
20500 -13.07851 1.5184618 -11.560048
20600 -13.112935 1.4734474 -11.639488
20700 -13.088676 1.4774362 -11.61124
20800 -13.129706 1.5316771 -11.598029
20900 -13.117948 1.506782 -11.611166
21000 -13.057558 1.4855052 -11.572053
21100 -13.112495 1.4994262 -11.613069
21200 -13.10582 1.5043886 -11.601431
21300 -13.137186 1.5448665 -11.59232
21400 -13.167425 1.5206861 -11.646739
21500 -13.134415 1.4790413 -11.655374
21600 -13.163707 1.5262771 -11.63743
21700 -13.09104 1.5135929 -11.577447
21800 -13.111398 1.5287565 -11.582641
21900 -13.127287 1.4971231 -11.630164
22000 -13.101951 1.5177661 -11.584185
22100 -13.104459 1.5074939 -11.596965
22200 -13.12983 1.5488266 -11.581004
22300 -13.086572 1.5037959 -11.582776
22400 -13.026209 1.4966914 -11.529517
22500 -13.067651 1.4900987 -11.577552
22600 -13.065688 1.48754 -11.578148
22700 -13.10133 1.4971727 -11.604157
22800 -13.094352 1.4926585 -11.601693
22900 -13.124222 1.5309723 -11.593249
23000 -13.133323 1.5163371 -11.616986
23100 -13.173284 1.5207067 -11.652577
23200 -13.045518 1.4782677 -11.56725
23300 -13.123116 1.4890821 -11.634034
23400 -13.067929 1.4691087 -11.59882
23500 -13.099256 1.5038662 -11.59539
23600 -13.144024 1.4977574 -11.646267
23700 -13.122217 1.4380351 -11.684182
23800 -13.122519 1.4803844 -11.642134
23900 -13.114528 1.4884067 -11.626121
24000 -13.136937 1.5206854 -11.616251
24100 -13.100701 1.5375066 -11.563194
24200 -13.069032 1.4988665 -11.570166
24300 -13.076606 1.4610195 -11.615587
24400 -13.102146 1.4831261 -11.61902
24500 -13.128178 1.4721533 -11.656024
24600 -13.119937 1.4895052 -11.630432
24700 -13.14955 1.4894021 -11.660148
24800 -13.086654 1.5116515 -11.575002
24900 -13.002973 1.490776 -11.512197
25000 -13.058712 1.4913296 -11.567382
Loop time of 104.946 on 1 procs for 25000 steps with 2925 atoms
Performance: 205819.218 tau/day, 238.217 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 74.527 | 74.527 | 74.527 | 0.0 | 71.01
Neigh | 21.242 | 21.242 | 21.242 | 0.0 | 20.24
Comm | 0.6767 | 0.6767 | 0.6767 | 0.0 | 0.64
Output | 2.0104 | 2.0104 | 2.0104 | 0.0 | 1.92
Modify | 6.2001 | 6.2001 | 6.2001 | 0.0 | 5.91
Other | | 0.2902 | | | 0.28
Nlocal: 2925 ave 2925 max 2925 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1158 ave 1158 max 1158 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 43499 ave 43499 max 43499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 87086 ave 87086 max 87086 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 87086
Ave neighs/atom = 29.773
Neighbor list builds = 8716
Dangerous builds = 8
Total wall time: 0:01:45