diff --git a/examples/micelle/in.micelle b/examples/micelle/in.micelle index 2abdd18734..34bc9ad359 100644 --- a/examples/micelle/in.micelle +++ b/examples/micelle/in.micelle @@ -58,7 +58,7 @@ pair_coeff 1 4 1.0 1.0 1.12246 pair_coeff 2 3 1.0 0.88 1.12246 pair_coeff 2 4 1.0 0.75 1.12246 -thermo 1000 +thermo 50 #dump 1 all atom 2000 dump.micelle @@ -69,4 +69,4 @@ thermo 1000 #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 +run 1000 diff --git a/examples/micelle/in.micelle-rigid b/examples/micelle/in.micelle-rigid new file mode 100644 index 0000000000..93cb2655f8 --- /dev/null +++ b/examples/micelle/in.micelle-rigid @@ -0,0 +1,87 @@ +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle +special_bonds fene + +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 500 + +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 50 + +#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 +group solvent molecule 0 +group solute subtract all solvent +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 +fix 4 all enforce2d +run 500 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule +fix 4 all enforce2d +run 500 diff --git a/examples/micelle/log.28Feb2019.micelle.g++.1 b/examples/micelle/log.28Feb2019.micelle.g++.1 deleted file mode 100644 index c2bbc7cde4..0000000000 --- a/examples/micelle/log.28Feb2019.micelle.g++.1 +++ /dev/null @@ -1,259 +0,0 @@ -LAMMPS (28 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) - 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 CPU = 0.000394821 secs - read_data CPU = 0.00212336 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.00018549 secs - -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 0.113919 on 1 procs for 1000 steps with 1200 atoms - -Performance: 3792167.464 tau/day, 8778.165 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 | 0.076825 | 0.076825 | 0.076825 | 0.0 | 67.44 -Bond | 0.0041864 | 0.0041864 | 0.0041864 | 0.0 | 3.67 -Neigh | 0.017061 | 0.017061 | 0.017061 | 0.0 | 14.98 -Comm | 0.0019042 | 0.0019042 | 0.0019042 | 0.0 | 1.67 -Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.15 -Modify | 0.011218 | 0.011218 | 0.011218 | 0.0 | 9.85 -Other | | 0.002551 | | | 2.24 - -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 -1.9727644 0.05860769 -1.4645317 1.9982326 - 2000 0.46143408 -1.9889684 0.058103225 -1.4698156 1.7806269 - 3000 0.44459291 -1.9997961 0.068724164 -1.4868496 1.4369618 - 4000 0.46939549 -2.0330437 0.073499424 -1.4905399 1.3780016 - 5000 0.44411088 -2.0339936 0.05862049 -1.5316323 1.2544164 - 6000 0.44034597 -2.0265475 0.066481992 -1.5200864 1.2362891 - 7000 0.45097378 -2.0331083 0.058467565 -1.5240428 1.2762333 - 8000 0.45797632 -2.0330255 0.060048036 -1.5153828 1.3862396 - 9000 0.45297811 -2.0383417 0.067056519 -1.5186845 1.2762554 - 10000 0.45 -2.0628269 0.065650067 -1.5475518 1.0566213 - 11000 0.44466757 -2.0593977 0.06190999 -1.5531907 1.1452469 - 12000 0.46743534 -2.0684295 0.061056278 -1.5403274 1.0824225 - 13000 0.45601091 -2.0689708 0.054868536 -1.5584713 0.96703283 - 14000 0.44111882 -2.0553174 0.058249816 -1.5563164 1.0986427 - 15000 0.43894405 -2.0866829 0.064117804 -1.5839869 0.90031836 - 16000 0.43856814 -2.0879319 0.056024166 -1.593705 0.96387323 - 17000 0.45977841 -2.103188 0.058097306 -1.5856955 0.83352919 - 18000 0.43423341 -2.0813151 0.066623991 -1.5808196 0.98157638 - 19000 0.44245939 -2.0851261 0.057637655 -1.5853978 0.84228341 - 20000 0.43144678 -2.0895403 0.06536727 -1.5930858 0.88177768 - 21000 0.45014968 -2.106686 0.059137572 -1.5977739 0.89408935 - 22000 0.4575126 -2.1024115 0.063013023 -1.5822672 0.84886734 - 23000 0.45 -2.10897 0.06724784 -1.5920971 0.66205013 - 24000 0.43055602 -2.0894725 0.061566464 -1.5977089 0.81764789 - 25000 0.4366384 -2.0926743 0.059609321 -1.5967905 0.85549875 - 26000 0.4521714 -2.0963996 0.062031863 -1.5825731 0.80137118 - 27000 0.45734834 -2.1060987 0.061712636 -1.5874188 0.82899415 - 28000 0.44803467 -2.0859226 0.061871856 -1.5763894 0.97007526 - 29000 0.45 -2.1106243 0.063825481 -1.5971738 0.63798376 - 30000 0.44932806 -2.1006036 0.053053934 -1.598596 0.63907113 - 31000 0.44713779 -2.1096164 0.066470416 -1.5963808 0.66832708 - 32000 0.4373357 -2.0941237 0.058871613 -1.5982808 0.78176106 - 33000 0.44030485 -2.105644 0.058804306 -1.6069017 0.66286458 - 34000 0.43781175 -2.1233209 0.064611206 -1.6212628 0.56342584 - 35000 0.45670132 -2.1059408 0.053049584 -1.5965705 0.73992396 - 36000 0.45555427 -2.1149877 0.057627709 -1.6021854 0.85854939 - 37000 0.44134236 -2.1106202 0.064444306 -1.6052013 0.74674603 - 38000 0.44812623 -2.1003681 0.057266258 -1.5953491 0.78239359 - 39000 0.44167062 -2.11141 0.055354 -1.6147534 0.7066385 - 40000 0.46103176 -2.1166687 0.062155412 -1.5938657 0.73620955 - 41000 0.44537102 -2.0993898 0.05631213 -1.5980778 0.87348756 - 42000 0.44752506 -2.1115212 0.057506521 -1.6068625 0.72999561 - 43000 0.4483886 -2.1184719 0.066943915 -1.6035131 0.78112063 - 44000 0.45944897 -2.0916657 0.055242781 -1.5773568 0.98660473 - 45000 0.46238513 -2.1163075 0.0530031 -1.6013046 0.74416054 - 46000 0.45979064 -2.1165545 0.060657581 -1.5964895 0.63516974 - 47000 0.45936546 -2.1140678 0.049931919 -1.6051532 0.76425182 - 48000 0.45424613 -2.1122681 0.061885599 -1.5965149 0.71981142 - 49000 0.44449524 -2.1147361 0.06626748 -1.6043438 0.78720467 - 50000 0.4641185 -2.1114668 0.055104874 -1.5926302 0.70195865 - 51000 0.44220655 -2.1075773 0.0589109 -1.6068283 0.73806859 - 52000 0.43097906 -2.1189493 0.061502241 -1.6268271 0.69622593 - 53000 0.45 -2.137688 0.053631829 -1.6344311 0.48269158 - 54000 0.43777118 -2.1089246 0.047098534 -1.6244197 0.70423814 - 55000 0.46061985 -2.1129502 0.062520353 -1.5901938 0.72492307 - 56000 0.4524841 -2.1195648 0.06580089 -1.6016569 0.52709892 - 57000 0.44914574 -2.1041993 0.061040876 -1.594387 0.7979988 - 58000 0.46446286 -2.1181238 0.055741995 -1.598306 0.51009146 - 59000 0.4632674 -2.1169321 0.050672678 -1.6033781 0.83110911 - 60000 0.46340478 -2.122846 0.058485209 -1.6013422 0.69966471 -Loop time of 8.01683 on 1 procs for 60000 steps with 1200 atoms - -Performance: 3233199.903 tau/day, 7484.259 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 | 5.4027 | 5.4027 | 5.4027 | 0.0 | 67.39 -Bond | 0.23585 | 0.23585 | 0.23585 | 0.0 | 2.94 -Neigh | 1.5188 | 1.5188 | 1.5188 | 0.0 | 18.95 -Comm | 0.14452 | 0.14452 | 0.14452 | 0.0 | 1.80 -Output | 0.00060487 | 0.00060487 | 0.00060487 | 0.0 | 0.01 -Modify | 0.56352 | 0.56352 | 0.56352 | 0.0 | 7.03 -Other | | 0.1508 | | | 1.88 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 395 ave 395 max 395 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 9652 ave 9652 max 9652 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 9652 -Ave neighs/atom = 8.04333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 4886 -Dangerous builds = 0 -Total wall time: 0:00:08 diff --git a/examples/micelle/log.28Feb2019.micelle.g++.4 b/examples/micelle/log.28Feb2019.micelle.g++.4 deleted file mode 100644 index 6af9051ed2..0000000000 --- a/examples/micelle/log.28Feb2019.micelle.g++.4 +++ /dev/null @@ -1,259 +0,0 @@ -LAMMPS (28 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) - 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 CPU = 0.000130415 secs - read_data CPU = 0.00132132 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 4.76837e-05 secs - -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 0.0377742 on 4 procs for 1000 steps with 1200 atoms - -Performance: 11436375.633 tau/day, 26473.092 timesteps/s -96.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.016871 | 0.017299 | 0.018185 | 0.4 | 45.80 -Bond | 0.0010128 | 0.0010633 | 0.001116 | 0.1 | 2.81 -Neigh | 0.004832 | 0.0048565 | 0.0048807 | 0.0 | 12.86 -Comm | 0.0066509 | 0.0077528 | 0.0084352 | 0.8 | 20.52 -Output | 0.00022054 | 0.00028259 | 0.00046587 | 0.0 | 0.75 -Modify | 0.0035386 | 0.0036086 | 0.0036943 | 0.1 | 9.55 -Other | | 0.002912 | | | 7.71 - -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 -1.9727652 0.058608073 -1.4645321 1.9982444 - 2000 0.44428815 -1.9902282 0.064240544 -1.4820698 1.7051263 - 3000 0.46641766 -1.9856844 0.065017468 -1.4546379 1.6939772 - 4000 0.45734058 -2.0242583 0.070494626 -1.4968042 1.3474276 - 5000 0.44904747 -2.0086954 0.058801142 -1.501221 1.4632351 - 6000 0.44961405 -2.0334509 0.05721299 -1.5269985 1.3093586 - 7000 0.45474928 -2.0453645 0.064725006 -1.5262692 1.1581035 - 8000 0.44274767 -2.0375379 0.062216035 -1.5329431 1.312914 - 9000 0.46176571 -2.0473031 0.065581966 -1.5203402 1.2013868 - 10000 0.45046977 -2.0540466 0.065402724 -1.5385495 0.95819581 - 11000 0.45016671 -2.0610028 0.056993955 -1.5542172 1.0433435 - 12000 0.43823039 -2.073155 0.065171939 -1.5701178 1.1400059 - 13000 0.44482161 -2.0678338 0.063901045 -1.5594819 0.97993813 - 14000 0.45 -2.0892562 0.061753632 -1.5778776 0.89841778 - 15000 0.44328626 -2.0859346 0.059956258 -1.5830615 0.90664821 - 16000 0.45666508 -2.0859262 0.059582346 -1.5700593 0.9702235 - 17000 0.44832038 -2.0762124 0.059153394 -1.5691122 0.93020504 - 18000 0.4555831 -2.0844959 0.057986324 -1.5713062 0.87398232 - 19000 0.45257867 -2.0671736 0.062190389 -1.5527816 0.89208496 - 20000 0.44010419 -2.1020944 0.062053708 -1.6003033 0.84140973 - 21000 0.45239369 -2.0820308 0.060981799 -1.5690323 0.98502522 - 22000 0.44607468 -2.0820602 0.051731316 -1.5846259 0.86120529 - 23000 0.45088473 -2.0865286 0.05727778 -1.5787418 1.1479844 - 24000 0.45526919 -2.1086678 0.057378327 -1.5963997 0.86944138 - 25000 0.46536624 -2.1055425 0.05665328 -1.5839108 0.72895438 - 26000 0.46716668 -2.1035267 0.057498747 -1.5792505 0.85105386 - 27000 0.44374699 -2.0932213 0.060937242 -1.5889069 0.93200759 - 28000 0.45944001 -2.0968869 0.053052954 -1.5847768 0.78909249 - 29000 0.4543632 -2.10493 0.061511018 -1.5894345 0.85862527 - 30000 0.44987776 -2.0942536 0.062431086 -1.5823197 0.7349894 - 31000 0.43829016 -2.0951259 0.060245682 -1.5969553 0.86702973 - 32000 0.45416601 -2.0991679 0.055978905 -1.5894015 0.75777153 - 33000 0.4605079 -2.1118364 0.058205688 -1.5935066 0.86041104 - 34000 0.43638213 -2.0925345 0.067533519 -1.5889825 0.85100425 - 35000 0.46912252 -2.1082718 0.051646432 -1.5878938 0.73613751 - 36000 0.45 -2.0966442 0.052507159 -1.5945121 0.88722487 - 37000 0.44970507 -2.1029685 0.065454263 -1.588184 0.76033821 - 38000 0.44910233 -2.097751 0.05767009 -1.5913528 0.95830923 - 39000 0.4322161 -2.1060426 0.062453704 -1.611733 0.74681695 - 40000 0.46143858 -2.1328575 0.057333011 -1.6144704 0.58326322 - 41000 0.43180549 -2.1070656 0.064150563 -1.6114694 0.82842684 - 42000 0.46738909 -2.1067947 0.058017036 -1.5817781 0.73292362 - 43000 0.43699124 -2.1171964 0.062817262 -1.6177521 0.73354741 - 44000 0.45262916 -2.1281307 0.055228619 -1.6206502 0.64167946 - 45000 0.43905419 -2.088789 0.055597999 -1.5945027 0.8002542 - 46000 0.44485569 -2.1035061 0.067828181 -1.5911929 0.71861494 - 47000 0.44496824 -2.0968296 0.0632326 -1.5889996 0.75202899 - 48000 0.46567244 -2.1235948 0.061032118 -1.5972783 0.64094556 - 49000 0.43202506 -2.0986097 0.053464022 -1.6134806 0.83857984 - 50000 0.45454698 -2.1263344 0.058119708 -1.6140465 0.67030037 - 51000 0.43702766 -2.1292347 0.074047424 -1.6185238 0.52896462 - 52000 0.46367081 -2.1177288 0.06726625 -1.5871781 0.74343227 - 53000 0.45 -2.1341074 0.062769314 -1.6217131 0.51130365 - 54000 0.44862492 -2.1272108 0.057723381 -1.6212364 0.54735429 - 55000 0.44926027 -2.1350444 0.066186625 -1.6199719 0.66821299 - 56000 0.4544227 -2.1325537 0.065298628 -1.6132111 0.63597556 - 57000 0.45697003 -2.1323238 0.053312855 -1.6224218 0.55572633 - 58000 0.45698902 -2.1043208 0.055835989 -1.5918766 0.63502658 - 59000 0.4425306 -2.1120353 0.056617261 -1.6132563 0.65681272 - 60000 0.44319296 -2.1171981 0.058330294 -1.6160442 0.63602511 -Loop time of 2.63918 on 4 procs for 60000 steps with 1200 atoms - -Performance: 9821248.084 tau/day, 22734.371 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 | 1.1742 | 1.278 | 1.3471 | 5.9 | 48.43 -Bond | 0.046621 | 0.06565 | 0.081322 | 5.1 | 2.49 -Neigh | 0.46642 | 0.46917 | 0.47105 | 0.3 | 17.78 -Comm | 0.47295 | 0.55928 | 0.67758 | 10.5 | 21.19 -Output | 0.00073624 | 0.00173 | 0.0047016 | 4.1 | 0.07 -Modify | 0.14511 | 0.15226 | 0.15887 | 1.5 | 5.77 -Other | | 0.1131 | | | 4.28 - -Nlocal: 300 ave 309 max 281 min -Histogram: 1 0 0 0 0 0 0 1 0 2 -Nghost: 232.75 ave 234 max 231 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Neighs: 2450.25 ave 2576 max 2179 min -Histogram: 1 0 0 0 0 0 0 0 1 2 - -Total # of neighbors = 9801 -Ave neighs/atom = 8.1675 -Ave special neighs/atom = 0.5 -Neighbor list builds = 4887 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/micelle/log.28Feb2019.micelle.rigid.g++.1 b/examples/micelle/log.28Feb2019.micelle.rigid.g++.1 deleted file mode 100644 index ec0079818d..0000000000 --- a/examples/micelle/log.28Feb2019.micelle.rigid.g++.1 +++ /dev/null @@ -1,290 +0,0 @@ -LAMMPS (28 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) - 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 CPU = 0.000271559 secs - read_data CPU = 0.00115585 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 8.39233e-05 secs - -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 0.107201 on 1 procs for 1000 steps with 1200 atoms - -Performance: 4029800.456 tau/day, 9328.242 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 | 0.072035 | 0.072035 | 0.072035 | 0.0 | 67.20 -Bond | 0.0039918 | 0.0039918 | 0.0039918 | 0.0 | 3.72 -Neigh | 0.016078 | 0.016078 | 0.016078 | 0.0 | 15.00 -Comm | 0.0018375 | 0.0018375 | 0.0018375 | 0.0 | 1.71 -Output | 0.00016379 | 0.00016379 | 0.00016379 | 0.0 | 0.15 -Modify | 0.010665 | 0.010665 | 0.010665 | 0.0 | 9.95 -Other | | 0.002429 | | | 2.27 - -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 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 20000 -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) = 5.274 | 5.274 | 5.274 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736 - 1000 0.46008168 -1.9040837 0.08808163 -1.4425691 0.93225457 - 2000 0.44520658 -1.9317253 0.08808163 -1.4822843 3.8192896 - 3000 0.43988556 -1.945898 0.08808163 -1.5007759 3.0371634 - 4000 0.4646519 -1.9753553 0.08808163 -1.5101312 -1.8041178 - 5000 0.4362993 -1.9763715 0.08808163 -1.5341603 1.5037284 - 6000 0.47007384 -1.9833154 0.08808163 -1.5136905 2.1227653 - 7000 0.44854623 -1.9914288 0.08808163 -1.5392772 3.9458099 - 8000 0.43841372 -1.9779603 0.08808163 -1.5340328 -4.5429769 - 9000 0.4518303 -1.9834387 0.08808163 -1.5286215 4.4230447 - 10000 0.43562904 -2.001471 0.08808163 -1.5598038 1.8919582 - 11000 0.44014575 -1.9820611 0.08808163 -1.5367278 -2.1189418 - 12000 0.44466956 -2.0134014 0.08808163 -1.5643963 -2.5218497 - 13000 0.45274369 -2.021443 0.08808163 -1.5658844 2.4795173 - 14000 0.44742645 -2.011108 0.08808163 -1.5598653 -0.74697767 - 15000 0.4674843 -2.024737 0.08808163 -1.5572139 -1.9539999 - 16000 0.45610154 -2.0401029 0.08808163 -1.5818189 -0.53082066 - 17000 0.44679292 -2.0365577 0.08808163 -1.5858291 -6.5040295 - 18000 0.44279107 -2.0500326 0.08808163 -1.6025522 -0.051597102 - 19000 0.45603993 -2.0306289 0.08808163 -1.5723948 1.0986608 - 20000 0.44519606 -2.0412229 0.08808163 -1.5917904 -1.0406746 -Loop time of 3.68102 on 1 procs for 20000 steps with 1200 atoms - -Performance: 2347175.802 tau/day, 5433.277 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 | 1.7349 | 1.7349 | 1.7349 | 0.0 | 47.13 -Bond | 0.079483 | 0.079483 | 0.079483 | 0.0 | 2.16 -Neigh | 0.49063 | 0.49063 | 0.49063 | 0.0 | 13.33 -Comm | 0.049093 | 0.049093 | 0.049093 | 0.0 | 1.33 -Output | 0.00022578 | 0.00022578 | 0.00022578 | 0.0 | 0.01 -Modify | 1.273 | 1.273 | 1.273 | 0.0 | 34.58 -Other | | 0.05369 | | | 1.46 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 395 ave 395 max 395 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8915 ave 8915 max 8915 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8915 -Ave neighs/atom = 7.42917 -Ave special neighs/atom = 0.5 -Neighbor list builds = 1580 -Dangerous builds = 0 -unfix 5 -unfix 4 -fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211 - create bodies CPU = 0.00012517 secs -150 rigid bodies with 450 atoms - 1.04536 = max distance from body owner to body atom -fix 4 all enforce2d -run 20000 -Per MPI rank memory allocation (min/avg/max) = 8.633 | 8.633 | 8.633 Mbytes -Step Temp E_pair E_mol TotEng Press - 20000 0.44519606 -2.0412229 0.08808163 -1.5917904 1.3058893 - 21000 0.4353376 -2.0483342 0.08808163 -1.6069035 0.53023317 - 22000 0.44034324 -2.0416876 0.08808163 -1.5961941 4.0327077 - 23000 0.4685403 -2.05295 0.08808163 -1.5845698 3.6792349 - 24000 0.44872075 -2.0320623 0.08808163 -1.579769 -2.0476923 - 25000 0.46829594 -2.0671408 0.08808163 -1.5989589 2.180811 - 26000 0.45257544 -2.0418792 0.08808163 -1.5864572 3.3924018 - 27000 0.44269664 -2.0409905 0.08808163 -1.5935868 -0.17012673 - 28000 0.46961216 -2.0552479 0.08808163 -1.5859978 -7.2870888 - 29000 0.46683129 -2.0438334 0.08808163 -1.5768404 3.0583141 - 30000 0.44262228 -2.036737 0.08808163 -1.5893937 0.087520915 - 31000 0.43517227 -2.0479672 0.08808163 -1.6066708 -0.3426009 - 32000 0.44543779 -2.0538031 0.08808163 -1.6041744 -0.2093148 - 33000 0.44629079 -2.0409901 0.08808163 -1.5906691 3.310113 - 34000 0.43058831 -2.0713827 0.08808163 -1.6338069 0.14128843 - 35000 0.44546512 -2.0427068 0.08808163 -1.593056 -3.1386697 - 36000 0.42971129 -2.0527435 0.08808163 -1.6158795 -2.7334963 - 37000 0.44707969 -2.0461803 0.08808163 -1.595219 -3.8777678 - 38000 0.43150818 -2.0435276 0.08808163 -1.6052052 0.2905487 - 39000 0.44463343 -2.0522113 0.08808163 -1.6032355 3.543123 - 40000 0.44582593 -2.052213 0.08808163 -1.6022693 1.1486536 -Loop time of 3.69012 on 1 procs for 20000 steps with 1200 atoms - -Performance: 2341388.948 tau/day, 5419.882 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 | 1.756 | 1.756 | 1.756 | 0.0 | 47.59 -Bond | 0.079221 | 0.079221 | 0.079221 | 0.0 | 2.15 -Neigh | 0.49085 | 0.49085 | 0.49085 | 0.0 | 13.30 -Comm | 0.048317 | 0.048317 | 0.048317 | 0.0 | 1.31 -Output | 0.0002315 | 0.0002315 | 0.0002315 | 0.0 | 0.01 -Modify | 1.2616 | 1.2616 | 1.2616 | 0.0 | 34.19 -Other | | 0.05386 | | | 1.46 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 393 ave 393 max 393 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 9091 ave 9091 max 9091 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 9091 -Ave neighs/atom = 7.57583 -Ave special neighs/atom = 0.5 -Neighbor list builds = 1582 -Dangerous builds = 0 -Total wall time: 0:00:07 diff --git a/examples/micelle/log.28Feb2019.micelle.rigid.g++.4 b/examples/micelle/log.28Feb2019.micelle.rigid.g++.4 deleted file mode 100644 index a6687a3c00..0000000000 --- a/examples/micelle/log.28Feb2019.micelle.rigid.g++.4 +++ /dev/null @@ -1,290 +0,0 @@ -LAMMPS (28 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) - 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 CPU = 0.000175714 secs - read_data CPU = 0.00145626 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 7.22408e-05 secs - -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 0.0389124 on 4 procs for 1000 steps with 1200 atoms - -Performance: 11101855.138 tau/day, 25698.739 timesteps/s -95.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.016776 | 0.017405 | 0.018435 | 0.5 | 44.73 -Bond | 0.0010033 | 0.0011995 | 0.0015519 | 0.6 | 3.08 -Neigh | 0.0044944 | 0.0045093 | 0.0045218 | 0.0 | 11.59 -Comm | 0.0080328 | 0.0093863 | 0.010242 | 0.9 | 24.12 -Output | 0.00021577 | 0.00027579 | 0.00045323 | 0.0 | 0.71 -Modify | 0.0034575 | 0.0036355 | 0.0040002 | 0.4 | 9.34 -Other | | 0.002501 | | | 6.43 - -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 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 20000 -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) = 5.251 | 5.282 | 5.374 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736 - 1000 0.46008163 -1.9040835 0.08808163 -1.4425689 0.93225869 - 2000 0.44943348 -1.9355135 0.08808163 -1.4826417 3.8399671 - 3000 0.4448437 -1.9480307 0.08808163 -1.4988842 2.5506553 - 4000 0.46013872 -1.9783821 0.08808163 -1.5168212 -1.8963215 - 5000 0.45520233 -1.9659462 0.08808163 -1.5083921 1.9238897 - 6000 0.44942049 -1.9663403 0.08808163 -1.513479 3.0633512 - 7000 0.45975758 -1.988462 0.08808163 -1.5272105 4.8267309 - 8000 0.45125238 -1.9913522 0.08808163 -1.5370041 -4.6644852 - 9000 0.45863606 -1.9792375 0.08808163 -1.5188962 4.3655071 - 10000 0.46264541 -1.9864611 0.08808163 -1.5228656 2.2176464 - 11000 0.45048361 -1.9907235 0.08808163 -1.5369994 -0.055360699 - 12000 0.44536719 -2.012875 0.08808163 -1.5633037 -0.2583823 - 13000 0.44212663 -2.0060111 0.08808163 -1.55907 3.3616171 - 14000 0.44984353 -2.0335408 0.08808163 -1.5803361 -0.21585645 - 15000 0.44896672 -2.0385265 0.08808163 -1.5860335 -4.6186206 - 16000 0.46694997 -2.032795 0.08808163 -1.5657056 0.53443281 - 17000 0.43208201 -2.0272255 0.08808163 -1.5884373 -6.5239975 - 18000 0.43281873 -2.0331268 0.08808163 -1.5937406 -0.048319943 - 19000 0.44704527 -2.0286742 0.08808163 -1.5777408 1.6356417 - 20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -3.8337952 -Loop time of 1.71924 on 4 procs for 20000 steps with 1200 atoms - -Performance: 5025468.853 tau/day, 11633.030 timesteps/s -98.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.39864 | 0.40873 | 0.42192 | 1.6 | 23.77 -Bond | 0.02118 | 0.021816 | 0.022785 | 0.4 | 1.27 -Neigh | 0.13931 | 0.14031 | 0.14117 | 0.2 | 8.16 -Comm | 0.13974 | 0.15328 | 0.16884 | 3.3 | 8.92 -Output | 0.00026131 | 0.00044435 | 0.00099206 | 0.0 | 0.03 -Modify | 0.93275 | 0.94138 | 0.95072 | 0.7 | 54.76 -Other | | 0.05327 | | | 3.10 - -Nlocal: 300 ave 303 max 298 min -Histogram: 1 0 1 0 1 0 0 0 0 1 -Nghost: 218.5 ave 226 max 215 min -Histogram: 2 1 0 0 0 0 0 0 0 1 -Neighs: 2258.75 ave 2283 max 2216 min -Histogram: 1 0 0 0 0 0 1 0 1 1 - -Total # of neighbors = 9035 -Ave neighs/atom = 7.52917 -Ave special neighs/atom = 0.5 -Neighbor list builds = 1580 -Dangerous builds = 0 -unfix 5 -unfix 4 -fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211 - create bodies CPU = 5.43594e-05 secs -150 rigid bodies with 450 atoms - 0.916597 = max distance from body owner to body atom -fix 4 all enforce2d -run 20000 -Per MPI rank memory allocation (min/avg/max) = 8.568 | 8.6 | 8.691 Mbytes -Step Temp E_pair E_mol TotEng Press - 20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -1.033643 - 21000 0.4529129 -2.049461 0.08808163 -1.5937651 0.93160285 - 22000 0.45039188 -2.0530092 0.08808163 -1.5993595 -0.10608965 - 23000 0.45261583 -2.0336042 0.08808163 -1.5781494 -2.5769871 - 24000 0.4608331 -2.0404645 0.08808163 -1.57834 3.1931675 - 25000 0.43479001 -2.0617104 0.08808163 -1.6207242 2.8190122 - 26000 0.47009651 -2.0754873 0.08808163 -1.605844 -0.9158501 - 27000 0.45002704 -2.0782104 0.08808163 -1.6248568 0.98629661 - 28000 0.45126136 -2.0592619 0.08808163 -1.6049065 0.03305448 - 29000 0.44355328 -2.0572858 0.08808163 -1.6091868 -6.0797989 - 30000 0.45053899 -2.0530953 0.08808163 -1.5993261 0.38382951 - 31000 0.46931923 -2.0718827 0.08808163 -1.6028703 2.2346891 - 32000 0.45348857 -2.0744024 0.08808163 -1.6182393 4.5028966 - 33000 0.44767742 -2.0597127 0.08808163 -1.6082662 -2.8021641 - 34000 0.45287544 -2.0857303 0.08808163 -1.6300648 -5.384091 - 35000 0.44743898 -2.0927246 0.08808163 -1.6414717 1.4800508 - 36000 0.45627028 -2.0720546 0.08808163 -1.6136336 -2.9961696 - 37000 0.4641334 -2.0701098 0.08808163 -1.6053065 8.4186854 - 38000 0.45922901 -2.0962331 0.08808163 -1.6354106 0.38361763 - 39000 0.4692834 -2.0573815 0.08808163 -1.5883982 -2.2177345 - 40000 0.46206931 -2.057851 0.08808163 -1.5947231 -1.0405727 -Loop time of 1.25476 on 4 procs for 20000 steps with 1200 atoms - -Performance: 6885775.862 tau/day, 15939.296 timesteps/s -98.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.40627 | 0.43037 | 0.45515 | 2.6 | 34.30 -Bond | 0.020504 | 0.021573 | 0.022739 | 0.5 | 1.72 -Neigh | 0.14337 | 0.14438 | 0.1453 | 0.2 | 11.51 -Comm | 0.13776 | 0.16647 | 0.19351 | 5.0 | 13.27 -Output | 0.00025082 | 0.00052994 | 0.0013635 | 0.0 | 0.04 -Modify | 0.45467 | 0.45822 | 0.46259 | 0.5 | 36.52 -Other | | 0.03321 | | | 2.65 - -Nlocal: 300 ave 304 max 293 min -Histogram: 1 0 0 0 0 1 0 0 0 2 -Nghost: 215.25 ave 217 max 213 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Neighs: 2340 ave 2378 max 2290 min -Histogram: 1 0 0 1 0 0 0 0 0 2 - -Total # of neighbors = 9360 -Ave neighs/atom = 7.8 -Ave special neighs/atom = 0.5 -Neighbor list builds = 1579 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 new file mode 100644 index 0000000000..f1001e6cea --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 @@ -0,0 +1,260 @@ +LAMMPS (29 Mar 2019) + 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 CPU = 0.000473022 secs + read_data CPU = 0.0024147 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.00022316 secs + +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 500 +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 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms + +Performance: 2093802.885 tau/day, 4846.766 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21 +Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11 +Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64 +Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86 +Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17 +Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37 +Other | | 0.002726 | | | 2.64 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 197 ave 197 max 197 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3094 ave 3094 max 3094 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3094 +Ave neighs/atom = 2.57833 +Ave special neighs/atom = 0.5 +Neighbor list builds = 52 +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 50 + +#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 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 +150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +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) = 5.274 | 5.274 | 5.274 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 + 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 + 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 + 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 + 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 + 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 + 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 + 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 + 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 +Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms + +Performance: 1208012.705 tau/day, 2796.326 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17 +Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38 +Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92 +Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45 +Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10 +Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34 +Other | | 0.00293 | | | 1.64 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 416 ave 416 max 416 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8769 ave 8769 max 8769 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8769 +Ave neighs/atom = 7.3075 +Ave special neighs/atom = 0.5 +Neighbor list builds = 47 +Dangerous builds = 2 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 0.00015378 secs +150 rigid bodies with 450 atoms + 1.30435 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes +Step Temp E_pair E_mol TotEng Press + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 + 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 + 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 + 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 + 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 + 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 + 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 + 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 + 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 + 950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332 + 1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141 +Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms + +Performance: 1297278.008 tau/day, 3002.958 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51 +Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56 +Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83 +Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44 +Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11 +Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66 +Other | | 0.003141 | | | 1.89 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 415 ave 415 max 415 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8743 ave 8743 max 8743 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8743 +Ave neighs/atom = 7.28583 +Ave special neighs/atom = 0.5 +Neighbor list builds = 40 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 new file mode 100644 index 0000000000..e65f67a527 --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 @@ -0,0 +1,260 @@ +LAMMPS (29 Mar 2019) + 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 CPU = 0.000422001 secs + read_data CPU = 0.00473404 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000183344 secs + +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 500 +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 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms + +Performance: 5066547.720 tau/day, 11728.120 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16 +Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95 +Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95 +Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78 +Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62 +Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28 +Other | | 0.002669 | | | 6.26 + +Nlocal: 300 ave 304 max 292 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Nghost: 103.5 ave 108 max 98 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 773.5 ave 792 max 735 min +Histogram: 1 0 0 0 0 0 0 0 2 1 + +Total # of neighbors = 3094 +Ave neighs/atom = 2.57833 +Ave special neighs/atom = 0.5 +Neighbor list builds = 52 +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 50 + +#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 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 +150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +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) = 5.251 | 5.282 | 5.374 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 + 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 + 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 + 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 + 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 + 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 + 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 + 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 + 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 +Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms + +Performance: 2434100.210 tau/day, 5634.491 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74 +Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30 +Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32 +Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30 +Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29 +Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73 +Other | | 0.002938 | | | 3.31 + +Nlocal: 300 ave 309 max 291 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 218.75 ave 223 max 216 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Neighs: 2192.25 ave 2251 max 2113 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 8769 +Ave neighs/atom = 7.3075 +Ave special neighs/atom = 0.5 +Neighbor list builds = 47 +Dangerous builds = 2 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 7.70092e-05 secs +150 rigid bodies with 450 atoms + 1.30435 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes +Step Temp E_pair E_mol TotEng Press + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 + 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 + 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 + 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 + 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 + 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 + 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 + 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 + 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 + 950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332 + 1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141 +Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms + +Performance: 3671840.233 tau/day, 8499.630 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47 +Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93 +Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98 +Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29 +Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42 +Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11 +Other | | 0.00224 | | | 3.81 + +Nlocal: 300 ave 303 max 295 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 219 ave 224 max 215 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 2185.75 ave 2244 max 2143 min +Histogram: 1 1 0 0 0 1 0 0 0 1 + +Total # of neighbors = 8743 +Ave neighs/atom = 7.28583 +Ave special neighs/atom = 0.5 +Neighbor list builds = 40 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle.g++.1 b/examples/micelle/log.29Mar2019.micelle.g++.1 new file mode 100644 index 0000000000..d482d6c890 --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle.g++.1 @@ -0,0 +1,218 @@ +LAMMPS (29 Mar 2019) + 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 CPU = 0.00037837 secs + read_data CPU = 0.00206876 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000177383 secs + +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 0.208895 on 1 procs for 1000 steps with 1200 atoms + +Performance: 2068027.282 tau/day, 4787.100 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14142 | 0.14142 | 0.14142 | 0.0 | 67.70 +Bond | 0.008441 | 0.008441 | 0.008441 | 0.0 | 4.04 +Neigh | 0.025716 | 0.025716 | 0.025716 | 0.0 | 12.31 +Comm | 0.0036864 | 0.0036864 | 0.0036864 | 0.0 | 1.76 +Output | 0.0003562 | 0.0003562 | 0.0003562 | 0.0 | 0.17 +Modify | 0.023699 | 0.023699 | 0.023699 | 0.0 | 11.35 +Other | | 0.00558 | | | 2.67 + +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 50 + +#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 1000 +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 + 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 + 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 + 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 + 200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655 + 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 + 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 + 350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532 + 400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066 + 450 0.47220236 -1.9468502 0.065625624 -1.4094157 2.0984288 + 500 0.4684673 -1.9444333 0.076696283 -1.3996601 2.0528682 + 550 0.47683128 -1.958676 0.070589719 -1.4116523 2.0856022 + 600 0.46851243 -1.9338267 0.07060548 -1.3950992 2.26405 + 650 0.46874142 -1.9462493 0.069134685 -1.4087638 2.1070263 + 700 0.46437384 -1.9309953 0.071977522 -1.3950309 2.2256923 + 750 0.47326225 -1.9484255 0.075435845 -1.4001218 2.0880254 + 800 0.45 -1.9646005 0.064159585 -1.4508159 2.0612696 + 850 0.46748307 -1.970559 0.060384874 -1.4430806 1.9472879 + 900 0.46909484 -1.953723 0.062470295 -1.4225488 2.0222909 + 950 0.45631531 -1.9387753 0.067536568 -1.4153037 2.0638421 + 1000 0.45 -1.9727646 0.058607721 -1.4645318 1.9982315 +Loop time of 0.252254 on 1 procs for 1000 steps with 1200 atoms + +Performance: 1712557.882 tau/day, 3964.254 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17177 | 0.17177 | 0.17177 | 0.0 | 68.09 +Bond | 0.0084555 | 0.0084555 | 0.0084555 | 0.0 | 3.35 +Neigh | 0.03991 | 0.03991 | 0.03991 | 0.0 | 15.82 +Comm | 0.0049119 | 0.0049119 | 0.0049119 | 0.0 | 1.95 +Output | 0.00039077 | 0.00039077 | 0.00039077 | 0.0 | 0.15 +Modify | 0.021131 | 0.021131 | 0.021131 | 0.0 | 8.38 +Other | | 0.005685 | | | 2.25 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 415 ave 415 max 415 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8586 ave 8586 max 8586 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8586 +Ave neighs/atom = 7.155 +Ave special neighs/atom = 0.5 +Neighbor list builds = 86 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle.g++.4 b/examples/micelle/log.29Mar2019.micelle.g++.4 new file mode 100644 index 0000000000..f3a54970cf --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle.g++.4 @@ -0,0 +1,218 @@ +LAMMPS (29 Mar 2019) + 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 CPU = 0.000413656 secs + read_data CPU = 0.00487924 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000178576 secs + +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 0.0906248 on 4 procs for 1000 steps with 1200 atoms + +Performance: 4766906.584 tau/day, 11034.506 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.036572 | 0.039266 | 0.041216 | 1.0 | 43.33 +Bond | 0.0023205 | 0.0024512 | 0.0025697 | 0.2 | 2.70 +Neigh | 0.0088909 | 0.0089301 | 0.0089679 | 0.0 | 9.85 +Comm | 0.022308 | 0.024047 | 0.027175 | 1.3 | 26.53 +Output | 0.00057411 | 0.00061274 | 0.00071025 | 0.0 | 0.68 +Modify | 0.0083182 | 0.0092374 | 0.0098341 | 0.6 | 10.19 +Other | | 0.006081 | | | 6.71 + +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 50 + +#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 1000 +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 + 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 + 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 + 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 + 200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655 + 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 + 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 + 350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532 + 400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066 + 450 0.47220236 -1.9468502 0.065625625 -1.4094157 2.0984288 + 500 0.4684673 -1.9444333 0.076696285 -1.3996601 2.0528682 + 550 0.47683128 -1.958676 0.070589721 -1.4116523 2.0856023 + 600 0.46851245 -1.9338267 0.070605469 -1.3950992 2.26405 + 650 0.46874143 -1.9462493 0.069134686 -1.4087638 2.1070262 + 700 0.4643739 -1.9309953 0.071977511 -1.3950309 2.225692 + 750 0.47326259 -1.9484258 0.075435808 -1.4001218 2.0880235 + 800 0.45 -1.9646003 0.06415956 -1.4508158 2.0612703 + 850 0.46748278 -1.9705588 0.06038513 -1.4430804 1.9472884 + 900 0.46909438 -1.9537221 0.062470305 -1.4225483 2.0223008 + 950 0.45631508 -1.9387742 0.067536066 -1.4153033 2.063854 + 1000 0.45 -1.9727651 0.058608085 -1.464532 1.9982447 +Loop time of 0.0878521 on 4 procs for 1000 steps with 1200 atoms + +Performance: 4917357.613 tau/day, 11382.772 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.043517 | 0.044455 | 0.046903 | 0.7 | 50.60 +Bond | 0.0020199 | 0.0022303 | 0.0024347 | 0.4 | 2.54 +Neigh | 0.012207 | 0.012335 | 0.012512 | 0.1 | 14.04 +Comm | 0.014938 | 0.018265 | 0.020068 | 1.5 | 20.79 +Output | 0.00061369 | 0.00064814 | 0.00073504 | 0.0 | 0.74 +Modify | 0.0052264 | 0.0053691 | 0.0055039 | 0.2 | 6.11 +Other | | 0.00455 | | | 5.18 + +Nlocal: 300 ave 305 max 296 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Nghost: 219.5 ave 228 max 214 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 2146.5 ave 2201 max 2114 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 8586 +Ave neighs/atom = 7.155 +Ave special neighs/atom = 0.5 +Neighbor list builds = 86 +Dangerous builds = 0 +Total wall time: 0:00:00