ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11410 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2014-01-30 22:49:40 +00:00
parent b2e58866c4
commit abdec3cb5d
122 changed files with 0 additions and 49863 deletions
Download Patch File Download Diff File Expand all files Collapse all files

209
examples/micelle/log.micelle.18Feb13.linux.1
View File

@ -1,209 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
1 = max bonds/atom
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
1200 atoms
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Memory usage per processor = 2.4798 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.16137 on 1 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.103494 (64.1344)
Bond time (%) = 0.00649524 (4.02506)
Neigh time (%) = 0.0191967 (11.8961)
Comm time (%) = 0.00400829 (2.48391)
Outpt time (%) = 0.000231028 (0.143166)
Other time (%) = 0.027945 (17.3174)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 1 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Memory usage per processor = 2.63239 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727753 0.058614052 -1.4645362 1.9980678
2000 0.45 -2.001583 0.074586381 -1.4773716 1.677722
3000 0.45 -2.01376 0.065369685 -1.4987654 1.5672632
4000 0.44978364 -2.0284623 0.069543994 -1.5095095 1.3255914
5000 0.4515788 -2.0213579 0.063453981 -1.5067015 1.2898067
6000 0.44084238 -2.0220208 0.059857725 -1.5216881 1.3664878
7000 0.45280746 -2.0465582 0.056091161 -1.538037 1.1247107
8000 0.45575503 -2.0556878 0.056250977 -1.5440615 1.2847641
9000 0.45541476 -2.0383734 0.062759047 -1.5205791 1.4205644
10000 0.43553889 -2.0491499 0.064724759 -1.5492492 1.2479479
11000 0.46199123 -2.0775949 0.05294824 -1.5630404 0.91003048
12000 0.45116812 -2.0484232 0.065204884 -1.5324262 1.1225658
13000 0.44686952 -2.0599878 0.049287713 -1.564203 1.1154998
14000 0.45212998 -2.0625951 0.058683349 -1.5521586 0.98441931
15000 0.4556105 -2.0756197 0.059200748 -1.5611881 0.95502443
16000 0.45043625 -2.0824009 0.064992475 -1.5673475 1.1101553
17000 0.44547914 -2.0937506 0.063134923 -1.5855078 1.0387966
18000 0.44560114 -2.0932092 0.063158377 -1.584821 0.92976825
19000 0.46409216 -2.0998691 0.063095466 -1.5730682 0.74222038
20000 0.43356947 -2.079761 0.058993704 -1.5875591 0.98809322
21000 0.43970509 -2.0772972 0.063415284 -1.5745433 1.1679023
22000 0.45439796 -2.0869643 0.060942539 -1.5720025 0.95309247
23000 0.46436648 -2.0865877 0.062283763 -1.5603244 0.82847808
24000 0.45179512 -2.099375 0.057554155 -1.5904022 0.81341216
25000 0.45 -2.1028977 0.053292072 -1.5999806 0.8167413
26000 0.44379478 -2.0953332 0.065257482 -1.5866508 0.79986647
27000 0.45233801 -2.0995326 0.060977813 -1.5865937 0.8732284
28000 0.45416333 -2.0995467 0.051944425 -1.5938174 0.84546945
29000 0.44235173 -2.0819112 0.063209787 -1.5767183 0.7973497
30000 0.463297 -2.1019723 0.052828108 -1.5862333 0.83736896
31000 0.46237603 -2.114332 0.059492046 -1.5928492 0.6791076
32000 0.46010313 -2.1067583 0.06500768 -1.5820309 0.73245227
33000 0.45581512 -2.106217 0.054623133 -1.5961586 0.77209258
34000 0.46132621 -2.1005582 0.063679478 -1.5759369 0.79365061
35000 0.44457465 -2.1009737 0.063096958 -1.5936726 0.77684088
36000 0.46892599 -2.1283119 0.063349886 -1.5964267 0.66757096
37000 0.43919893 -2.117133 0.061828288 -1.6164718 0.82728955
38000 0.46347483 -2.1095945 0.053697761 -1.5928082 0.6018967
39000 0.46560699 -2.134901 0.051889552 -1.6177925 0.61468453
40000 0.45486545 -2.1082829 0.05921023 -1.5945863 0.67314005
41000 0.46926414 -2.1056671 0.052918097 -1.5838759 0.72673846
42000 0.44801848 -2.1122598 0.053198288 -1.6114163 0.7515948
43000 0.44733537 -2.1143993 0.048691802 -1.6187449 0.64883126
44000 0.44330158 -2.0946395 0.063057453 -1.5886499 0.74170615
45000 0.44616358 -2.1212538 0.054840602 -1.6206214 0.72390736
46000 0.43298663 -2.0977927 0.063259619 -1.6019073 0.75151063
47000 0.45 -2.093575 0.062292347 -1.5816576 0.83230853
48000 0.43668769 -2.1011039 0.055608008 -1.6091721 0.81680002
49000 0.43402566 -2.1180572 0.0705711 -1.6138221 0.61733524
50000 0.45870183 -2.1234461 0.061839249 -1.6032873 0.71893984
51000 0.46897063 -2.1240109 0.056638825 -1.5987922 0.57223633
52000 0.44547026 -2.114712 0.066830872 -1.6027821 0.88042497
53000 0.45698191 -2.1088353 0.055900552 -1.5963336 0.73302935
54000 0.46105819 -2.1164732 0.053844244 -1.6019549 0.52305471
55000 0.46526131 -2.1168922 0.053629683 -1.5983889 0.74647219
56000 0.4610805 -2.1203778 0.060044544 -1.5996369 0.56764901
57000 0.43539083 -2.1162246 0.058878039 -1.6223185 0.63599171
58000 0.45613812 -2.1341668 0.059717309 -1.6186914 0.5752578
59000 0.45035503 -2.1066421 0.056509876 -1.6001524 0.69875083
60000 0.46528439 -2.1306197 0.058828427 -1.6068946 0.47995479
Loop time of 13.4627 on 1 procs for 60000 steps with 1200 atoms
Pair time (%) = 9.23657 (68.6086)
Bond time (%) = 0.391739 (2.90981)
Neigh time (%) = 1.90366 (14.1403)
Comm time (%) = 0.341246 (2.53475)
Outpt time (%) = 0.000712633 (0.00529339)
Other time (%) = 1.58877 (11.8013)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 450 ave 450 max 450 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9799 ave 9799 max 9799 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9799
Ave neighs/atom = 8.16583
Ave special neighs/atom = 0.5
Neighbor list builds = 4876
Dangerous builds = 0

209
examples/micelle/log.micelle.18Feb13.linux.4
View File

@ -1,209 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
1 = max bonds/atom
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
1200 atoms
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Memory usage per processor = 2.79958 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0598879 on 4 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.0267262 (44.6271)
Bond time (%) = 0.00173765 (2.90151)
Neigh time (%) = 0.00505728 (8.44456)
Comm time (%) = 0.0149809 (25.0149)
Outpt time (%) = 0.000514269 (0.858719)
Other time (%) = 0.0108716 (18.1532)
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 1 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Memory usage per processor = 2.79958 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727852 0.0586182 -1.464542 1.9980664
2000 0.46082446 -1.977605 0.057039794 -1.4601247 1.726013
3000 0.45 -2.0006402 0.05562923 -1.495386 1.511225
4000 0.4623338 -2.0091993 0.059138048 -1.4881127 1.3542907
5000 0.45 -2.0395585 0.061066034 -1.5288674 1.1830193
6000 0.45905159 -2.0634848 0.058991931 -1.5458239 1.1082099
7000 0.45 -2.0508705 0.061559594 -1.5396859 1.2020831
8000 0.44666556 -2.0397402 0.066632486 -1.5268144 1.2612013
9000 0.45034184 -2.03446 0.064174681 -1.5203188 1.1644088
10000 0.44920732 -2.0856804 0.059525789 -1.5773216 0.93583471
11000 0.45896474 -2.063989 0.064678373 -1.5407284 1.0732096
12000 0.45848122 -2.0752398 0.061533665 -1.555607 1.0281395
13000 0.46738009 -2.0629007 0.067132245 -1.5287778 0.96711354
14000 0.44988856 -2.062354 0.062693783 -1.5501466 1.0123189
15000 0.45098377 -2.072531 0.051120563 -1.5708025 0.97044948
16000 0.45 -2.1017479 0.064909547 -1.5872134 0.90299146
17000 0.4552102 -2.0765865 0.056648474 -1.5651072 0.91280438
18000 0.44824933 -2.0828037 0.058978706 -1.5759492 0.92795752
19000 0.44079166 -2.0556475 0.059088524 -1.5561347 1.1454216
20000 0.44463382 -2.0859907 0.057486911 -1.5842405 0.92599126
21000 0.44406551 -2.0826296 0.056776522 -1.5821577 0.99925665
22000 0.44911834 -2.0711967 0.059641892 -1.5628107 0.95834342
23000 0.43655144 -2.0909928 0.062696368 -1.5921088 0.91119509
24000 0.44867934 -2.1018259 0.055592487 -1.597928 0.76348634
25000 0.45260844 -2.0937068 0.059149636 -1.5823259 0.89135412
26000 0.44898273 -2.1016995 0.066566046 -1.5865249 0.74284381
27000 0.43221936 -2.084773 0.062900549 -1.5900132 0.87821534
28000 0.46292457 -2.0965745 0.055816359 -1.5782193 0.74158202
29000 0.45 -2.1306418 0.063790424 -1.6172264 0.53967764
30000 0.44871717 -2.0907319 0.055486729 -1.586902 0.99873528
31000 0.46125755 -2.0755203 0.056517719 -1.5581294 0.9347469
32000 0.45941056 -2.0914092 0.057505763 -1.5748757 0.89468013
33000 0.46026614 -2.0984679 0.056646234 -1.5819391 0.80740251
34000 0.46916633 -2.1193229 0.054211886 -1.5963356 0.61039936
35000 0.43884901 -2.0922975 0.061924634 -1.5918896 0.79377862
36000 0.43947177 -2.0909805 0.053228588 -1.5986464 0.90484301
37000 0.45414812 -2.1030789 0.055686423 -1.5936228 0.87060399
38000 0.44280127 -2.0908535 0.058003408 -1.5904178 0.8046892
39000 0.45516585 -2.1008067 0.058183565 -1.5878366 0.6089312
40000 0.43067796 -2.0848319 0.062869447 -1.5916434 0.74412702
41000 0.44165418 -2.1259603 0.064019775 -1.6206544 0.6221064
42000 0.43982239 -2.1055547 0.064067567 -1.6020312 0.62130789
43000 0.46586098 -2.1382757 0.05819116 -1.6146118 0.54791918
44000 0.45469796 -2.1328327 0.066699087 -1.6118146 0.52752596
45000 0.45358824 -2.1251041 0.063138554 -1.6087553 0.64714368
46000 0.44191865 -2.1041137 0.059520035 -1.6030433 0.62417966
47000 0.45804456 -2.1075048 0.066124313 -1.5837176 0.82334648
48000 0.45700413 -2.1298865 0.065741607 -1.6075216 0.58174639
49000 0.45842123 -2.1362735 0.056849019 -1.6213852 0.51934277
50000 0.44239274 -2.1182037 0.053635135 -1.6225444 0.59636555
51000 0.45869721 -2.1176213 0.059785615 -1.5995207 0.62467419
52000 0.45 -2.1136347 0.062713868 -1.6012959 0.71773796
53000 0.44480469 -2.1070829 0.061995737 -1.6006531 0.72790523
54000 0.45834924 -2.1352139 0.056517736 -1.6207289 0.64257865
55000 0.44776128 -2.1167768 0.051321782 -1.6180669 0.52184371
56000 0.46087785 -2.1186123 0.059414538 -1.598704 0.72628855
57000 0.44514743 -2.1107461 0.062138072 -1.6038315 0.68847034
58000 0.44897344 -2.1218568 0.056966905 -1.6162906 0.66787759
59000 0.43532599 -2.1262526 0.062848971 -1.6284404 0.61398862
60000 0.44623012 -2.105934 0.05919675 -1.600879 0.73556885
Loop time of 4.45718 on 4 procs for 60000 steps with 1200 atoms
Pair time (%) = 2.33901 (52.4774)
Bond time (%) = 0.0977297 (2.19264)
Neigh time (%) = 0.49103 (11.0166)
Comm time (%) = 1.01247 (22.7155)
Outpt time (%) = 0.00150865 (0.0338477)
Other time (%) = 0.51543 (11.564)
Nlocal: 300 ave 320 max 287 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 218.75 ave 232 max 205 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 2461 ave 2617 max 2321 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 9844
Ave neighs/atom = 8.20333
Ave special neighs/atom = 0.5
Neighbor list builds = 4879
Dangerous builds = 0