diff --git a/cmake/Modules/generate_lmpgitversion.cmake b/cmake/Modules/generate_lmpgitversion.cmake index 8aead88f5f..a4aa59b262 100644 --- a/cmake/Modules/generate_lmpgitversion.cmake +++ b/cmake/Modules/generate_lmpgitversion.cmake @@ -5,15 +5,15 @@ set(temp_git_describe "(unknown)") set(temp_git_info "false") if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git) set(temp_git_info "true") - execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse HEAD + execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD OUTPUT_VARIABLE temp_git_commit ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) - execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse --abbrev-ref HEAD + execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD OUTPUT_VARIABLE temp_git_branch ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) - execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git describe --dirty=-modified + execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified OUTPUT_VARIABLE temp_git_describe ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) diff --git a/doc/Makefile b/doc/Makefile index 044e358bd5..5c679440b8 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -116,6 +116,13 @@ mobi: epub @echo "Conversion finished. The MOBI manual file is created." pdf: $(OBJECTS) $(ANCHORCHECK) + @(\ + cd src/Developer; \ + pdflatex developer; \ + pdflatex developer; \ + mv developer.pdf ../../Developer.pdf; \ + cd ../../; \ + ) @(\ . $(VENV)/bin/activate ;\ cp -r src/* $(RSTDIR)/ ;\ @@ -135,14 +142,7 @@ pdf: $(OBJECTS) $(ANCHORCHECK) make && \ make && \ mv LAMMPS.pdf ../Manual.pdf && \ - cd ../; - @(\ - cd src/Developer; \ - pdflatex developer; \ - pdflatex developer; \ - mv developer.pdf ../../Developer.pdf; \ - cd ../../; \ - ) + cd ../; @rm -rf latex/_sources @rm -rf latex/PDF @rm -rf latex/USER diff --git a/examples/micelle/data.micelle b/examples/micelle/data.micelle index e4805bceee..5ff6196bc6 100644 --- a/examples/micelle/data.micelle +++ b/examples/micelle/data.micelle @@ -49,7 +49,7 @@ 22 0 1 25.100 0.000 0.000 23 0 1 26.295 0.000 0.000 24 110 2 27.490 0.000 0.000 - 25 128 2 28.685 0.000 0.000 + 25 128 2 28.685 35.85686 0.000 26 0 1 29.881 0.000 0.000 27 0 1 31.076 0.000 0.000 28 0 1 32.271 0.000 0.000 @@ -175,7 +175,7 @@ 148 0 1 32.271 4.781 0.000 149 0 1 33.466 4.781 0.000 150 0 1 34.662 4.781 0.000 - 151 53 2 0.000 5.976 0.000 + 151 53 2 35.85686 5.976 0.000 152 0 1 1.195 5.976 0.000 153 0 1 2.390 5.976 0.000 154 0 1 3.586 5.976 0.000 @@ -655,7 +655,7 @@ 628 0 1 32.271 23.905 0.000 629 0 1 33.466 23.905 0.000 630 0 1 34.662 23.905 0.000 - 631 148 2 0.000 25.100 0.000 + 631 148 2 35.85686 25.100 0.000 632 0 1 1.195 25.100 0.000 633 0 1 2.390 25.100 0.000 634 0 1 3.586 25.100 0.000 @@ -976,7 +976,7 @@ 949 25 3 0.677 33.143 0.000 950 25 4 1.353 32.819 0.000 951 26 3 35.071 18.557 0.000 - 952 26 4 35.480 19.186 0.000 + 952 26 4 35.48000 19.186 0.000 953 27 3 29.131 15.504 0.000 954 27 4 28.382 15.470 0.000 955 28 3 23.456 33.395 0.000 @@ -1096,7 +1096,7 @@ 1069 85 3 33.021 33.461 0.000 1070 85 4 33.771 33.455 0.000 1071 86 3 0.552 18.315 0.000 - 1072 86 4 35.766 18.701 0.000 + 1072 86 4 -0.09086 18.701 0.000 1073 87 3 28.026 32.796 0.000 1074 87 4 28.562 33.321 0.000 1075 88 3 24.351 29.925 0.000 @@ -1112,7 +1112,7 @@ 1085 93 3 26.170 16.278 0.000 1086 93 4 26.046 17.017 0.000 1087 94 3 10.380 0.547 0.000 - 1088 94 4 10.003 35.755 0.000 + 1088 94 4 10.003 -0.10186 0.000 1089 95 3 0.419 29.308 0.000 1090 95 4 0.837 29.930 0.000 1091 96 3 13.712 28.191 0.000 diff --git a/examples/micelle/in.micelle.rigid b/examples/micelle/in.micelle.rigid new file mode 100644 index 0000000000..47d2f74950 --- /dev/null +++ b/examples/micelle/in.micelle.rigid @@ -0,0 +1,86 @@ +# 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 1000 + +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 +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 20000 +unfix 5 +unfix 4 +fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211 +fix 4 all enforce2d +run 20000 diff --git a/examples/micelle/log.27Nov18.micelle.g++.1 b/examples/micelle/log.27Nov18.micelle.g++.1 deleted file mode 100644 index 30a965e041..0000000000 --- a/examples/micelle/log.27Nov18.micelle.g++.1 +++ /dev/null @@ -1,255 +0,0 @@ -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 deleted file mode 100644 index c9509df4b2..0000000000 --- a/examples/micelle/log.27Nov18.micelle.g++.4 +++ /dev/null @@ -1,255 +0,0 @@ -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.28Feb2019.micelle.g++.1 b/examples/micelle/log.28Feb2019.micelle.g++.1 new file mode 100644 index 0000000000..c2bbc7cde4 --- /dev/null +++ b/examples/micelle/log.28Feb2019.micelle.g++.1 @@ -0,0 +1,259 @@ +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 new file mode 100644 index 0000000000..6af9051ed2 --- /dev/null +++ b/examples/micelle/log.28Feb2019.micelle.g++.4 @@ -0,0 +1,259 @@ +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 new file mode 100644 index 0000000000..ec0079818d --- /dev/null +++ b/examples/micelle/log.28Feb2019.micelle.rigid.g++.1 @@ -0,0 +1,290 @@ +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 new file mode 100644 index 0000000000..a6687a3c00 --- /dev/null +++ b/examples/micelle/log.28Feb2019.micelle.rigid.g++.4 @@ -0,0 +1,290 @@ +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/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 2e1f752dc1..7480703ce8 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -64,8 +64,10 @@ #include "input.h" #include "variable.h" +#if defined(LMP_KIM_CURL) #include #include +#endif using namespace LAMMPS_NS; diff --git a/src/domain.cpp b/src/domain.cpp index beaf5fc08e..86c4eb2c02 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -763,9 +763,9 @@ void Domain::image_check() continue; } - delx = unwrap[i][0] - unwrap[k][0]; - dely = unwrap[i][1] - unwrap[k][1]; - delz = unwrap[i][2] - unwrap[k][2]; + delx = fabs(unwrap[i][0] - unwrap[k][0]); + dely = fabs(unwrap[i][1] - unwrap[k][1]); + delz = fabs(unwrap[i][2] - unwrap[k][2]); if (xperiodic && delx > xprd_half) flag = 1; if (yperiodic && dely > yprd_half) flag = 1; diff --git a/src/modify.cpp b/src/modify.cpp index 0a03bb6804..7f43f035d2 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -28,6 +28,7 @@ #include "variable.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -1058,7 +1059,7 @@ int Modify::check_rigid_group_overlap(int groupbit) int n = 0; for (int ifix = 0; ifix < nfix; ifix++) { - if (strncmp("rigid",fix[ifix]->style,5) == 0) { + if (utils::strmatch(fix[ifix]->style,"^rigid")) { const int * const body = (const int *)fix[ifix]->extract("body",dim); if ((body == NULL) || (dim != 1)) break;