diff --git a/examples/melt/log.5Oct16.melt.g++.1 b/examples/melt/log.27Nov18.melt.g++.1
similarity index 66%
rename from examples/melt/log.5Oct16.melt.g++.1
rename to examples/melt/log.27Nov18.melt.g++.1
index b4aefdceb4519b38eb8a35876278faac190d501a..69b39e6011259af3612506b1580c884d21d35981 100644
--- a/examples/melt/log.5Oct16.melt.g++.1
+++ b/examples/melt/log.27Nov18.melt.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
@@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
+ Time spent = 0.000645638 secs
mass 1 1.0
velocity all create 3.0 87287
@@ -35,13 +37,18 @@ fix 1 all nve
thermo 50
run 250
Neighbor list info ...
- 1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 12 12 12
-Memory usage per processor = 2.19271 Mbytes
+ binsize = 1.4, bins = 12 12 12
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
@@ -49,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
-Loop time of 0.724365 on 1 procs for 250 steps with 4000 atoms
+Loop time of 0.729809 on 1 procs for 250 steps with 4000 atoms
-Performance: 149096.106 tau/day, 345.130 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 147983.915 tau/day, 342.555 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.61654 | 0.61654 | 0.61654 | 0.0 | 85.11
-Neigh | 0.081313 | 0.081313 | 0.081313 | 0.0 | 11.23
-Comm | 0.010941 | 0.010941 | 0.010941 | 0.0 | 1.51
-Output | 9.4891e-05 | 9.4891e-05 | 9.4891e-05 | 0.0 | 0.01
-Modify | 0.012401 | 0.012401 | 0.012401 | 0.0 | 1.71
-Other | | 0.003077 | | | 0.42
+Pair | 0.60661 | 0.60661 | 0.60661 | 0.0 | 83.12
+Neigh | 0.092198 | 0.092198 | 0.092198 | 0.0 | 12.63
+Comm | 0.013581 | 0.013581 | 0.013581 | 0.0 | 1.86
+Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.02
+Modify | 0.014395 | 0.014395 | 0.014395 | 0.0 | 1.97
+Other | | 0.002878 | | | 0.39
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/melt/log.5Oct16.melt.g++.4 b/examples/melt/log.27Nov18.melt.g++.4
similarity index 66%
rename from examples/melt/log.5Oct16.melt.g++.4
rename to examples/melt/log.27Nov18.melt.g++.4
index 0335725187ffc59849a0d4d4f3cba24804635147..927895b1cd34a26c93275912afb57ed8fd8407d9 100644
--- a/examples/melt/log.5Oct16.melt.g++.4
+++ b/examples/melt/log.27Nov18.melt.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
@@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
+ Time spent = 0.00041604 secs
mass 1 1.0
velocity all create 3.0 87287
@@ -35,13 +37,18 @@ fix 1 all nve
thermo 50
run 250
Neighbor list info ...
- 1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 12 12 12
-Memory usage per processor = 2.10344 Mbytes
+ binsize = 1.4, bins = 12 12 12
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
@@ -49,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
-Loop time of 0.210997 on 4 procs for 250 steps with 4000 atoms
+Loop time of 0.223329 on 4 procs for 250 steps with 4000 atoms
-Performance: 511855.365 tau/day, 1184.850 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 483592.231 tau/day, 1119.426 timesteps/s
+97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.15475 | 0.16099 | 0.1682 | 1.2 | 76.30
-Neigh | 0.020829 | 0.021108 | 0.021522 | 0.2 | 10.00
-Comm | 0.01674 | 0.024412 | 0.030987 | 3.3 | 11.57
-Output | 0.00011587 | 0.0001238 | 0.00013185 | 0.1 | 0.06
-Modify | 0.0031242 | 0.0031361 | 0.0031476 | 0.0 | 1.49
-Other | | 0.001227 | | | 0.58
+Pair | 0.15881 | 0.16314 | 0.16859 | 0.9 | 73.05
+Neigh | 0.02472 | 0.025218 | 0.025828 | 0.3 | 11.29
+Comm | 0.025185 | 0.030091 | 0.034351 | 1.9 | 13.47
+Output | 0.00015163 | 0.00019169 | 0.00030899 | 0.0 | 0.09
+Modify | 0.0037532 | 0.0038366 | 0.0040054 | 0.2 | 1.72
+Other | | 0.00085 | | | 0.38
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
diff --git a/examples/micelle/log.27Nov18.micelle.g++.1 b/examples/micelle/log.27Nov18.micelle.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..30a965e0417753c41046b5a41ee63c1ac11e6e98
--- /dev/null
+++ b/examples/micelle/log.27Nov18.micelle.g++.1
@@ -0,0 +1,255 @@
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
+# 2d micelle simulation
+
+dimension 2
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+atom_style bond
+
+# Soft potential push-off
+
+read_data data.micelle
+ orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 1200 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 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
+Neighbor list info ...
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.42246
+ ghost atom cutoff = 1.42246
+ binsize = 0.71123, bins = 51 51 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair soft, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 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 0.167265 on 1 procs for 1000 steps with 1200 atoms
+
+Performance: 2582728.958 tau/day, 5978.539 timesteps/s
+99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.096171 | 0.096171 | 0.096171 | 0.0 | 57.50
+Bond | 0.006212 | 0.006212 | 0.006212 | 0.0 | 3.71
+Neigh | 0.024826 | 0.024826 | 0.024826 | 0.0 | 14.84
+Comm | 0.0047672 | 0.0047672 | 0.0047672 | 0.0 | 2.85
+Output | 0.00029063 | 0.00029063 | 0.00029063 | 0.0 | 0.17
+Modify | 0.028771 | 0.028771 | 0.028771 | 0.0 | 17.20
+Other | | 0.006227 | | | 3.72
+
+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 2 all image 2000 image.*.jpg type type zoom 1.6
+#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+#dump 3 all movie 2000 movie.mpg type type zoom 1.6
+#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+reset_timestep 0
+run 60000
+Neighbor list info ...
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 26 26 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
+ 1000 0.45 -1.9727655 0.058608715 -1.4645318 1.9982298
+ 2000 0.46465361 -1.9897467 0.067008449 -1.4584719 1.5873463
+ 3000 0.46175071 -2.0129279 0.057865385 -1.4936966 1.41269
+ 4000 0.44386154 -2.0280304 0.067167835 -1.5173709 1.4022093
+ 5000 0.46127582 -2.0556041 0.068318674 -1.526394 1.1416711
+ 6000 0.45354052 -2.0463246 0.05461954 -1.5385425 1.1650258
+ 7000 0.44082313 -2.040263 0.060218047 -1.5395891 1.3258681
+ 8000 0.44353466 -2.0423792 0.061769402 -1.5374447 1.2696989
+ 9000 0.46192977 -2.0761348 0.064999109 -1.5495908 0.9205826
+ 10000 0.45278646 -2.0589872 0.059623919 -1.5469542 1.075581
+ 11000 0.45583355 -2.0661957 0.058197558 -1.5525445 1.127643
+ 12000 0.45881198 -2.0921508 0.066937896 -1.5667833 0.98383574
+ 13000 0.45339481 -2.079088 0.06292782 -1.5631432 1.0188637
+ 14000 0.43601312 -2.0624084 0.057999616 -1.568759 1.1452177
+ 15000 0.45941503 -2.0746606 0.062523373 -1.553105 0.86928343
+ 16000 0.45 -2.0743162 0.05517924 -1.569512 0.86849848
+ 17000 0.45603004 -2.0657683 0.058711872 -1.5514064 0.95544551
+ 18000 0.45320383 -2.1009711 0.060716634 -1.5874283 0.8343521
+ 19000 0.44072983 -2.0846408 0.062893297 -1.581385 0.90776246
+ 20000 0.44452441 -2.0921415 0.060341571 -1.587646 0.98180005
+ 21000 0.45964557 -2.0837047 0.054459432 -1.5699827 1.0213779
+ 22000 0.46351849 -2.1053613 0.058392027 -1.5838371 0.81579487
+ 23000 0.45576065 -2.1001888 0.057646538 -1.5871614 0.76090085
+ 24000 0.44671746 -2.0848717 0.058192801 -1.5803337 0.77003809
+ 25000 0.44371239 -2.0870872 0.054804981 -1.5889396 0.92295746
+ 26000 0.45381188 -2.097021 0.057195346 -1.586392 0.7743058
+ 27000 0.46158533 -2.1071056 0.061289644 -1.5846153 0.78981802
+ 28000 0.46534671 -2.1056151 0.054934755 -1.5857214 0.80778664
+ 29000 0.4505804 -2.0949318 0.065503451 -1.5792234 0.78274755
+ 30000 0.45730883 -2.1029161 0.063461968 -1.5825264 0.82507857
+ 31000 0.4620071 -2.1124989 0.059980378 -1.5908964 0.78583986
+ 32000 0.46934619 -2.1107818 0.056442616 -1.5853842 0.70535653
+ 33000 0.45800203 -2.1062502 0.054317859 -1.594312 0.726293
+ 34000 0.44634295 -2.110401 0.057764968 -1.606665 0.85401059
+ 35000 0.4431929 -2.1274759 0.062048133 -1.6226042 0.64243758
+ 36000 0.46049645 -2.1300979 0.068463634 -1.6015216 0.57252544
+ 37000 0.45366344 -2.0977407 0.053788554 -1.5906668 0.78046879
+ 38000 0.44155077 -2.1166674 0.056888683 -1.6185959 0.53429042
+ 39000 0.45631012 -2.096949 0.04860872 -1.5924104 0.86494908
+ 40000 0.44684402 -2.1229137 0.067190397 -1.6092516 0.65110818
+ 41000 0.4479377 -2.1105264 0.059375259 -1.6035867 0.79092862
+ 42000 0.46143191 -2.1174539 0.057418393 -1.5989882 0.69762908
+ 43000 0.4356786 -2.085826 0.056534028 -1.5939764 0.89541946
+ 44000 0.45806826 -2.126423 0.060905733 -1.6078307 0.66389027
+ 45000 0.44343688 -2.1116384 0.065870114 -1.602701 0.83947585
+ 46000 0.43844672 -2.1096265 0.064158652 -1.6073865 0.77278902
+ 47000 0.45794928 -2.1142786 0.058919562 -1.5977914 0.62611933
+ 48000 0.45412335 -2.1106058 0.059153304 -1.5977076 0.66190677
+ 49000 0.45927883 -2.1197656 0.068354598 -1.5925149 0.56008845
+ 50000 0.44117285 -2.1020783 0.064763249 -1.5965099 0.85935147
+ 51000 0.45325398 -2.1125154 0.062295387 -1.5973438 0.80951782
+ 52000 0.43896579 -2.1039004 0.057475908 -1.6078245 0.84753768
+ 53000 0.45180671 -2.1092446 0.063528598 -1.5942857 0.67065038
+ 54000 0.4554341 -2.1185135 0.059603337 -1.6038556 0.76399618
+ 55000 0.43861159 -2.0986406 0.057733879 -1.6026606 0.77334084
+ 56000 0.45522991 -2.1207166 0.063287543 -1.6025785 0.78669598
+ 57000 0.46125513 -2.1150202 0.06026261 -1.5938868 0.78148646
+ 58000 0.45236938 -2.1088894 0.062678374 -1.5942186 0.75643518
+ 59000 0.43927269 -2.1274165 0.055355076 -1.6331548 0.63495311
+ 60000 0.45331102 -2.1336193 0.051244399 -1.6294416 0.56706921
+Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms
+
+Performance: 1859917.639 tau/day, 4305.365 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 9.2211 | 9.2211 | 9.2211 | 0.0 | 66.17
+Bond | 0.33763 | 0.33763 | 0.33763 | 0.0 | 2.42
+Neigh | 2.3772 | 2.3772 | 2.3772 | 0.0 | 17.06
+Comm | 0.37693 | 0.37693 | 0.37693 | 0.0 | 2.70
+Output | 0.0011795 | 0.0011795 | 0.0011795 | 0.0 | 0.01
+Modify | 1.2727 | 1.2727 | 1.2727 | 0.0 | 9.13
+Other | | 0.3493 | | | 2.51
+
+Nlocal: 1200 ave 1200 max 1200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 405 ave 405 max 405 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 9565 ave 9565 max 9565 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9565
+Ave neighs/atom = 7.97083
+Ave special neighs/atom = 0.5
+Neighbor list builds = 4876
+Dangerous builds = 0
+Total wall time: 0:00:14
diff --git a/examples/micelle/log.27Nov18.micelle.g++.4 b/examples/micelle/log.27Nov18.micelle.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c9509df4b230f9b33fcd55700f2d1412fa0ab15f
--- /dev/null
+++ b/examples/micelle/log.27Nov18.micelle.g++.4
@@ -0,0 +1,255 @@
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
+# 2d micelle simulation
+
+dimension 2
+
+neighbor 0.3 bin
+neigh_modify delay 5
+
+atom_style bond
+
+# Soft potential push-off
+
+read_data data.micelle
+ orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
+ 2 by 2 by 1 MPI processor grid
+ reading atoms ...
+ 1200 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 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
+Neighbor list info ...
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 1.42246
+ ghost atom cutoff = 1.42246
+ binsize = 0.71123, bins = 51 51 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair soft, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 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 0.0641922 on 4 procs for 1000 steps with 1200 atoms
+
+Performance: 6729792.131 tau/day, 15578.223 timesteps/s
+90.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.020663 | 0.021445 | 0.022477 | 0.5 | 33.41
+Bond | 0.0014422 | 0.0015128 | 0.001569 | 0.1 | 2.36
+Neigh | 0.0067129 | 0.0067645 | 0.0068202 | 0.1 | 10.54
+Comm | 0.018454 | 0.019275 | 0.020386 | 0.5 | 30.03
+Output | 0.00038171 | 0.00040019 | 0.00044632 | 0.0 | 0.62
+Modify | 0.010561 | 0.010904 | 0.011309 | 0.3 | 16.99
+Other | | 0.003891 | | | 6.06
+
+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 2 all image 2000 image.*.jpg type type zoom 1.6
+#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+#dump 3 all movie 2000 movie.mpg type type zoom 1.6
+#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+reset_timestep 0
+run 60000
+Neighbor list info ...
+ update every 1 steps, delay 5 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 26 26 1
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
+ 1000 0.45 -1.9727661 0.05860859 -1.4645325 1.9982402
+ 2000 0.45146247 -1.9766043 0.059408886 -1.4661092 1.7398826
+ 3000 0.43338517 -2.0028125 0.059884381 -1.5099041 1.4716488
+ 4000 0.46674519 -2.0200954 0.066548679 -1.4871905 1.2506693
+ 5000 0.45 -2.0207125 0.055926205 -1.5151613 1.3047457
+ 6000 0.45447759 -2.0585234 0.068004883 -1.5364197 1.1859762
+ 7000 0.43183018 -2.0170545 0.060800296 -1.5247839 1.3074223
+ 8000 0.46657547 -2.053224 0.063224367 -1.523813 1.1785643
+ 9000 0.45 -2.0691221 0.054959029 -1.564538 1.1833657
+ 10000 0.4428252 -2.0473987 0.054306905 -1.5506356 1.181794
+ 11000 0.45407036 -2.0746151 0.065849667 -1.5550734 1.1008545
+ 12000 0.46061944 -2.0580809 0.063129643 -1.5347156 1.0206491
+ 13000 0.45159068 -2.0640832 0.060059758 -1.5528091 1.0813494
+ 14000 0.44141594 -2.0467255 0.062785088 -1.5428923 1.1465772
+ 15000 0.454361 -2.0908595 0.057471037 -1.5794061 0.84297781
+ 16000 0.44061091 -2.0521452 0.064644196 -1.5472573 1.1478647
+ 17000 0.45118383 -2.081348 0.058660999 -1.5718791 1.0101404
+ 18000 0.44664866 -2.0845745 0.060435731 -1.5778623 0.96142277
+ 19000 0.45515339 -2.0914006 0.062174016 -1.5744525 0.87623323
+ 20000 0.45624408 -2.0837697 0.059263054 -1.5686428 0.92810644
+ 21000 0.46791657 -2.1062007 0.067355929 -1.5713181 0.88318793
+ 22000 0.43907391 -2.1005271 0.065885144 -1.5959339 0.77211644
+ 23000 0.43967354 -2.0723459 0.057613471 -1.5754253 1.0371548
+ 24000 0.45716384 -2.0987126 0.055157377 -1.5867723 0.89670061
+ 25000 0.45828285 -2.1041616 0.057736138 -1.5885245 0.79952286
+ 26000 0.45 -2.0743463 0.072455519 -1.5522658 0.88260204
+ 27000 0.46581599 -2.0804974 0.058113258 -1.5569564 0.93053891
+ 28000 0.46904194 -2.0920124 0.059748792 -1.5636125 0.79359618
+ 29000 0.46093196 -2.118556 0.063942334 -1.5940659 0.67707604
+ 30000 0.45733724 -2.1197827 0.066939064 -1.5958875 0.66886075
+ 31000 0.44580762 -2.0977175 0.056969121 -1.5953123 0.81042562
+ 32000 0.44403029 -2.1032264 0.063465127 -1.596101 0.71796412
+ 33000 0.45834072 -2.0934132 0.066035391 -1.569419 0.77873998
+ 34000 0.44981563 -2.0910902 0.07138738 -1.5702621 0.75679805
+ 35000 0.45383392 -2.0926654 0.067553478 -1.5716562 0.9064517
+ 36000 0.44447198 -2.1107114 0.062718917 -1.6038909 0.8538349
+ 37000 0.45838527 -2.1166464 0.062442606 -1.5962005 0.7300635
+ 38000 0.45014075 -2.1096258 0.059293718 -1.6005665 0.73988246
+ 39000 0.44377026 -2.080309 0.063545781 -1.5733628 0.99775641
+ 40000 0.44577324 -2.1134607 0.065271179 -1.6027878 0.64113168
+ 41000 0.45 -2.0937983 0.060881377 -1.5832919 0.78849829
+ 42000 0.46866695 -2.1142283 0.056417605 -1.5895343 0.73788436
+ 43000 0.43211727 -2.0819893 0.061463358 -1.5887688 0.95853724
+ 44000 0.44138397 -2.0921314 0.059643895 -1.5914713 0.89486208
+ 45000 0.45 -2.117209 0.054804331 -1.6127797 0.78564885
+ 46000 0.44285245 -2.1090975 0.057629006 -1.6089851 0.64549424
+ 47000 0.45537009 -2.1164296 0.068582324 -1.5928567 0.73629413
+ 48000 0.45046732 -2.1006362 0.057249591 -1.5932947 0.74317593
+ 49000 0.45425966 -2.1191703 0.064247719 -1.6010414 0.70962368
+ 50000 0.45506149 -2.1184671 0.064911797 -1.5988731 0.69958156
+ 51000 0.46047417 -2.1019719 0.058468259 -1.5834132 0.87219271
+ 52000 0.43808317 -2.092294 0.057280941 -1.597295 0.84156893
+ 53000 0.45012337 -2.1175234 0.064002667 -1.6037725 0.64562439
+ 54000 0.43854679 -2.1236444 0.061316257 -1.6241468 0.72478117
+ 55000 0.46382438 -2.1016563 0.060724666 -1.5774938 0.83311209
+ 56000 0.44951533 -2.0946157 0.055075217 -1.5903998 0.90066109
+ 57000 0.45937401 -2.0983442 0.061558996 -1.577794 0.58606161
+ 58000 0.446669 -2.1146838 0.062385166 -1.6060019 0.73443388
+ 59000 0.43847747 -2.1197461 0.060460257 -1.6211738 0.7230937
+ 60000 0.45294215 -2.1258513 0.061895006 -1.6113915 0.70722168
+Loop time of 4.56226 on 4 procs for 60000 steps with 1200 atoms
+
+Performance: 5681397.232 tau/day, 13151.382 timesteps/s
+97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 2.2114 | 2.2527 | 2.3592 | 4.1 | 49.38
+Bond | 0.083713 | 0.09234 | 0.10244 | 2.3 | 2.02
+Neigh | 0.72491 | 0.7277 | 0.72957 | 0.2 | 15.95
+Comm | 0.79464 | 0.90036 | 0.94957 | 6.5 | 19.74
+Output | 0.0014119 | 0.0024976 | 0.0057502 | 3.8 | 0.05
+Modify | 0.33757 | 0.35202 | 0.36946 | 2.1 | 7.72
+Other | | 0.2346 | | | 5.14
+
+Nlocal: 300 ave 306 max 289 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Nghost: 227.25 ave 250 max 216 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+Neighs: 2373.25 ave 2489 max 2283 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 9493
+Ave neighs/atom = 7.91083
+Ave special neighs/atom = 0.5
+Neighbor list builds = 4888
+Dangerous builds = 0
+Total wall time: 0:00:04
diff --git a/examples/micelle/log.5Oct16.micelle.g++.1 b/examples/micelle/log.5Oct16.micelle.g++.1
deleted file mode 100644
index 5dfc652d68abf2d7c2a47232aab81f056a71ed05..0000000000000000000000000000000000000000
--- a/examples/micelle/log.5Oct16.micelle.g++.1
+++ /dev/null
@@ -1,244 +0,0 @@
-LAMMPS (5 Oct 2016)
-# 2d micelle simulation
-
-dimension 2
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-atom_style bond
-
-# Soft potential push-off
-
-read_data data.micelle
- orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 1200 atoms
- scanning bonds ...
- 1 = max bonds/atom
- reading bonds ...
- 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
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 5 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 1.42246
- ghost atom cutoff = 1.42246
- binsize = 0.71123 -> bins = 51 51 1
-Memory usage per processor = 3.45296 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 0.192637 on 1 procs for 1000 steps with 1200 atoms
-
-Performance: 2242560.228 tau/day, 5191.112 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.13348 | 0.13348 | 0.13348 | 0.0 | 69.29
-Bond | 0.0066328 | 0.0066328 | 0.0066328 | 0.0 | 3.44
-Neigh | 0.023894 | 0.023894 | 0.023894 | 0.0 | 12.40
-Comm | 0.0032849 | 0.0032849 | 0.0032849 | 0.0 | 1.71
-Output | 0.00019765 | 0.00019765 | 0.00019765 | 0.0 | 0.10
-Modify | 0.020029 | 0.020029 | 0.020029 | 0.0 | 10.40
-Other | | 0.005115 | | | 2.66
-
-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 2 all image 2000 image.*.jpg type type zoom 1.6
-#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
-
-#dump 3 all movie 2000 movie.mpg type type zoom 1.6
-#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
-
-reset_timestep 0
-run 60000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 5 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 26 26 1
-Memory usage per processor = 3.45296 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
- 1000 0.45 -1.9727655 0.058608718 -1.4645318 1.9982299
- 2000 0.4661092 -1.9963233 0.067084121 -1.4635184 1.5676107
- 3000 0.44946688 -2.0126501 0.070702998 -1.4928548 1.5636132
- 4000 0.45269674 -1.9944702 0.05825464 -1.4838961 1.6015127
- 5000 0.46281924 -2.0302807 0.058318349 -1.5095288 1.3929421
- 6000 0.45409991 -2.0339156 0.061724414 -1.5184697 1.1978692
- 7000 0.44058968 -2.0436374 0.060141133 -1.5432738 1.1877802
- 8000 0.4429781 -2.0508103 0.061300632 -1.5469007 1.1825472
- 9000 0.44909024 -2.0620769 0.063430248 -1.5499306 1.1841529
- 10000 0.44709728 -2.0337047 0.059176633 -1.5278033 1.1906481
- 11000 0.46222813 -2.0666276 0.053626157 -1.5511585 0.99322264
- 12000 0.45722371 -2.0527602 0.062728903 -1.5331886 1.1135813
- 13000 0.44844353 -2.0672473 0.07057216 -1.5486053 0.9416127
- 14000 0.44211202 -2.0804052 0.056164487 -1.5824971 0.99700319
- 15000 0.45659943 -2.0711771 0.059428792 -1.5555294 1.1123211
- 16000 0.45113626 -2.0895625 0.057848795 -1.5809534 1.0015991
- 17000 0.44423013 -2.0840859 0.06718595 -1.57304 0.92034012
- 18000 0.45279338 -2.0644167 0.058541719 -1.5534589 1.1560585
- 19000 0.44673847 -2.0729637 0.061474462 -1.565123 0.99627228
- 20000 0.44428193 -2.0937135 0.066588799 -1.583213 0.86154418
- 21000 0.45902797 -2.0821041 0.057286828 -1.5661718 0.76853595
- 22000 0.45733559 -2.0962718 0.064103239 -1.5752141 0.90967955
- 23000 0.44617227 -2.070896 0.061562573 -1.5635329 0.92864876
- 24000 0.45569898 -2.0843503 0.061015469 -1.5680156 0.90170833
- 25000 0.45952666 -2.0892064 0.058901296 -1.5711614 0.9123274
- 26000 0.44773853 -2.0896169 0.065994021 -1.5762575 0.8887526
- 27000 0.43541542 -2.0893237 0.060387783 -1.5938834 0.97604018
- 28000 0.44025187 -2.0937721 0.066174764 -1.5877124 0.98394478
- 29000 0.44695847 -2.0966733 0.064980967 -1.5851064 0.78278706
- 30000 0.44848319 -2.1017012 0.053308469 -1.6002833 0.85185298
- 31000 0.45215181 -2.0927324 0.057875178 -1.5830822 0.77068692
- 32000 0.44586981 -2.0962193 0.056970051 -1.593751 0.85672441
- 33000 0.43591379 -2.1069871 0.064934652 -1.6065019 0.87081371
- 34000 0.44153683 -2.0967535 0.061537811 -1.5940468 0.75497708
- 35000 0.45482946 -2.1045277 0.060250612 -1.5898266 0.80290163
- 36000 0.45 -2.1154856 0.052206018 -1.6136546 0.67520748
- 37000 0.44973679 -2.1076496 0.067371347 -1.5909163 0.83319072
- 38000 0.45549751 -2.1044983 0.061863351 -1.587517 0.6786145
- 39000 0.43927254 -2.1159446 0.057855173 -1.6191829 0.66483475
- 40000 0.43711657 -2.0941837 0.063039594 -1.5943918 0.90680301
- 41000 0.43992749 -2.0931285 0.063772204 -1.5897954 0.7538478
- 42000 0.44374588 -2.1029745 0.061963499 -1.5976349 0.74793466
- 43000 0.45 -2.0916744 0.055058096 -1.5869913 0.86069235
- 44000 0.45381626 -2.0984483 0.059995477 -1.5850147 0.74948091
- 45000 0.44547409 -2.1217483 0.058753101 -1.6178924 0.57348898
- 46000 0.43283033 -2.1054695 0.059343099 -1.6136567 0.77490901
- 47000 0.44310217 -2.1215687 0.066613901 -1.6122219 0.73014542
- 48000 0.44611257 -2.118313 0.05944897 -1.6131232 0.59077782
- 49000 0.44114725 -2.0911126 0.065639368 -1.5846936 0.78309201
- 50000 0.44572124 -2.0892024 0.065540869 -1.5783117 0.87647821
- 51000 0.4460699 -2.1142274 0.061090043 -1.6074391 0.61721581
- 52000 0.44799203 -2.1122931 0.056821256 -1.6078531 0.70734576
- 53000 0.44819437 -2.1098838 0.058117987 -1.6039449 0.71349136
- 54000 0.45 -2.1384776 0.051012047 -1.6378405 0.4810217
- 55000 0.43931842 -2.1053055 0.061275315 -1.6050778 0.58268948
- 56000 0.44126963 -2.1133637 0.057474037 -1.6149877 0.68063945
- 57000 0.45823746 -2.1205329 0.065224217 -1.5974531 0.73788456
- 58000 0.437031 -2.0998724 0.051717885 -1.6114877 0.86071379
- 59000 0.45070454 -2.1115874 0.053721754 -1.6075367 0.62358834
- 60000 0.44181643 -2.1243164 0.060489492 -1.6223786 0.6992428
-Loop time of 13.6136 on 1 procs for 60000 steps with 1200 atoms
-
-Performance: 1903978.372 tau/day, 4407.357 timesteps/s
-99.5% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 9.3684 | 9.3684 | 9.3684 | 0.0 | 68.82
-Bond | 0.39461 | 0.39461 | 0.39461 | 0.0 | 2.90
-Neigh | 2.211 | 2.211 | 2.211 | 0.0 | 16.24
-Comm | 0.2552 | 0.2552 | 0.2552 | 0.0 | 1.87
-Output | 0.00065112 | 0.00065112 | 0.00065112 | 0.0 | 0.00
-Modify | 1.0819 | 1.0819 | 1.0819 | 0.0 | 7.95
-Other | | 0.3019 | | | 2.22
-
-Nlocal: 1200 ave 1200 max 1200 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 417 ave 417 max 417 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 9495 ave 9495 max 9495 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 9495
-Ave neighs/atom = 7.9125
-Ave special neighs/atom = 0.5
-Neighbor list builds = 4885
-Dangerous builds = 0
-Total wall time: 0:00:13
diff --git a/examples/micelle/log.5Oct16.micelle.g++.4 b/examples/micelle/log.5Oct16.micelle.g++.4
deleted file mode 100644
index 960489aad030d7ff518f558b6c40ab22cab7c106..0000000000000000000000000000000000000000
--- a/examples/micelle/log.5Oct16.micelle.g++.4
+++ /dev/null
@@ -1,244 +0,0 @@
-LAMMPS (5 Oct 2016)
-# 2d micelle simulation
-
-dimension 2
-
-neighbor 0.3 bin
-neigh_modify delay 5
-
-atom_style bond
-
-# Soft potential push-off
-
-read_data data.micelle
- orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
- 2 by 2 by 1 MPI processor grid
- reading atoms ...
- 1200 atoms
- scanning bonds ...
- 1 = max bonds/atom
- reading bonds ...
- 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
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 5 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 1.42246
- ghost atom cutoff = 1.42246
- binsize = 0.71123 -> bins = 51 51 1
-Memory usage per processor = 3.55365 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 0.0670803 on 4 procs for 1000 steps with 1200 atoms
-
-Performance: 6440046.660 tau/day, 14907.515 timesteps/s
-98.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.033971 | 0.034628 | 0.036162 | 0.5 | 51.62
-Bond | 0.001687 | 0.0017596 | 0.0018852 | 0.2 | 2.62
-Neigh | 0.0068789 | 0.0069902 | 0.0070932 | 0.1 | 10.42
-Comm | 0.011152 | 0.012883 | 0.013872 | 0.9 | 19.20
-Output | 0.00035501 | 0.00038034 | 0.00044274 | 0.2 | 0.57
-Modify | 0.0065997 | 0.0067009 | 0.0068605 | 0.1 | 9.99
-Other | | 0.003738 | | | 5.57
-
-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 2 all image 2000 image.*.jpg type type zoom 1.6
-#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
-
-#dump 3 all movie 2000 movie.mpg type type zoom 1.6
-#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
-
-reset_timestep 0
-run 60000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 5 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 26 26 1
-Memory usage per processor = 3.55365 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
- 1000 0.45 -1.9727663 0.058608449 -1.4645328 1.9982389
- 2000 0.45428051 -1.9704547 0.062434911 -1.4541178 1.7134222
- 3000 0.46748648 -2.0088544 0.065086237 -1.4766712 1.4648627
- 4000 0.45608936 -2.032563 0.057148422 -1.5197053 1.3833681
- 5000 0.46134038 -2.0250107 0.061983009 -1.5020718 1.3378201
- 6000 0.45254634 -2.0414745 0.071656389 -1.5176489 1.2670697
- 7000 0.46380932 -2.0463598 0.060057501 -1.5228795 1.1029258
- 8000 0.46495917 -2.0570216 0.058074076 -1.5343758 1.1187483
- 9000 0.45771237 -2.0510911 0.061803881 -1.5319563 1.1540073
- 10000 0.45 -2.0568306 0.06114562 -1.54606 1.128504
- 11000 0.43977142 -2.0442503 0.061128391 -1.543717 1.2268919
- 12000 0.4412548 -2.051046 0.065150223 -1.5450087 1.0681597
- 13000 0.46384147 -2.0657072 0.064678941 -1.5375734 0.99078604
- 14000 0.43330137 -2.0693058 0.06542588 -1.5709397 1.0252118
- 15000 0.44825078 -2.078972 0.059800283 -1.5712944 0.76305383
- 16000 0.45607271 -2.085101 0.058347214 -1.5710611 0.99903698
- 17000 0.45329523 -2.0865426 0.057674526 -1.5759505 0.90245709
- 18000 0.46719329 -2.076619 0.062698678 -1.5471164 0.95433376
- 19000 0.45253889 -2.0741652 0.06154596 -1.5604575 1.0606446
- 20000 0.43708811 -2.1005493 0.063453064 -1.6003723 0.65980174
- 21000 0.43630563 -2.0780131 0.05595505 -1.586116 0.86690426
- 22000 0.44050783 -2.0766368 0.057980992 -1.578515 0.99638367
- 23000 0.44657992 -2.0731942 0.058890194 -1.5680963 0.92620975
- 24000 0.45645869 -2.0957688 0.065464986 -1.5742255 0.88631971
- 25000 0.46007071 -2.0928226 0.058133397 -1.5750019 0.75468418
- 26000 0.46316546 -2.0945456 0.064110354 -1.5676557 0.84437166
- 27000 0.44780223 -2.0966995 0.063284428 -1.585986 0.89645525
- 28000 0.43945645 -2.0909433 0.062357411 -1.5894957 0.92336874
- 29000 0.44332217 -2.0885003 0.063832997 -1.5817146 0.86508766
- 30000 0.44865024 -2.0899642 0.057319345 -1.5843685 0.76862889
- 31000 0.45702135 -2.0941006 0.059669304 -1.5777908 0.76171188
- 32000 0.46630168 -2.1066612 0.051622888 -1.5891252 0.72214981
- 33000 0.44966822 -2.1086408 0.061298737 -1.5980486 0.7056562
- 34000 0.45599464 -2.11216 0.045835595 -1.6107098 0.75827582
- 35000 0.44021366 -2.1082791 0.066290667 -1.6021416 0.85079438
- 36000 0.46531913 -2.1228506 0.054779097 -1.6031402 0.60391389
- 37000 0.44777064 -2.1193684 0.062074675 -1.6098962 0.68654583
- 38000 0.46608897 -2.1243843 0.052889984 -1.6057938 0.6517974
- 39000 0.44921432 -2.1050268 0.059790015 -1.5963968 0.74248261
- 40000 0.44407222 -2.0930539 0.055687841 -1.5936639 0.69821332
- 41000 0.4377755 -2.0929451 0.056403441 -1.599131 0.90040574
- 42000 0.46403029 -2.1245032 0.058491534 -1.6023681 0.6984091
- 43000 0.45456147 -2.0966395 0.055922733 -1.5865341 0.86499812
- 44000 0.45619203 -2.1150101 0.054818604 -1.6043796 0.71197595
- 45000 0.44806278 -2.1067617 0.057539822 -1.6015324 0.7644258
- 46000 0.46326243 -2.1204997 0.060566953 -1.5970563 0.68822898
- 47000 0.43464277 -2.1257611 0.069053137 -1.6224273 0.60024032
- 48000 0.46986944 -2.1245871 0.058768355 -1.5963409 0.58191819
- 49000 0.4428734 -2.1203847 0.059089451 -1.6187909 0.60806508
- 50000 0.43813854 -2.12123 0.066218857 -1.6172377 0.42860822
- 51000 0.4514578 -2.1304644 0.057932769 -1.62145 0.62355123
- 52000 0.44155257 -2.1248047 0.062563155 -1.6210569 0.81276016
- 53000 0.4467801 -2.1254575 0.056774655 -1.6222751 0.6115287
- 54000 0.43972332 -2.1036785 0.061427338 -1.6028943 0.75225909
- 55000 0.44933771 -2.104883 0.058556755 -1.5973629 0.75480805
- 56000 0.45 -2.1212286 0.057392665 -1.614211 0.56759345
- 57000 0.43127001 -2.0978236 0.04986292 -1.61705 0.71828346
- 58000 0.43621486 -2.1097172 0.056706821 -1.617159 0.80497906
- 59000 0.44446312 -2.1103931 0.055606397 -1.610694 0.79904859
- 60000 0.43177211 -2.0985468 0.049687241 -1.6174473 0.81094066
-Loop time of 4.56204 on 4 procs for 60000 steps with 1200 atoms
-
-Performance: 5681665.051 tau/day, 13152.002 timesteps/s
-99.5% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 2.3705 | 2.4423 | 2.4948 | 2.9 | 53.54
-Bond | 0.084795 | 0.10292 | 0.11359 | 3.4 | 2.26
-Neigh | 0.63938 | 0.64418 | 0.64857 | 0.4 | 14.12
-Comm | 0.81947 | 0.8785 | 0.9618 | 5.7 | 19.26
-Output | 0.0012863 | 0.0013551 | 0.0015438 | 0.3 | 0.03
-Modify | 0.26717 | 0.27596 | 0.28816 | 1.5 | 6.05
-Other | | 0.2168 | | | 4.75
-
-Nlocal: 300 ave 305 max 293 min
-Histogram: 1 0 0 0 0 1 0 0 1 1
-Nghost: 211 ave 215 max 205 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-Neighs: 2448.75 ave 2531 max 2414 min
-Histogram: 2 1 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 9795
-Ave neighs/atom = 8.1625
-Ave special neighs/atom = 0.5
-Neighbor list builds = 4880
-Dangerous builds = 0
-Total wall time: 0:00:04