diff --git a/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.1 b/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.1 new file mode 100644 index 0000000000..cf7d851f64 --- /dev/null +++ b/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.1 @@ -0,0 +1,192 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# GayBerne ellipsoids in LJ background fluid + +units lj +atom_style ellipsoid +dimension 2 + +lattice sq 0.02 +Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 +region box block 0 20 0 20 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 400 atoms + Time spent = 0.000507116 secs + +set group all type/fraction 2 0.1 95392 + 45 settings made for type/fraction +set type 1 mass 1.0 + 355 settings made for mass +set type 2 mass 1.5 + 45 settings made for mass +set type 1 shape 1 1 1 + 355 settings made for shape +set type 2 shape 3 1 1 + 45 settings made for shape +set group all quat/random 18238 + 400 settings made for quat/random + +compute rot all temp/asphere +group spheroid type 1 +355 atoms in group spheroid +variable dof equal count(spheroid)+2 +compute_modify rot extra/dof ${dof} +compute_modify rot extra/dof 357 + +velocity all create 2.4 87287 loop geom + +pair_style gayberne 1.0 3.0 1.0 4.0 +pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5 +pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 +pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0 + +neighbor 0.8 bin + +thermo_style custom step c_rot epair etotal press vol +thermo 100 + +timestep 0.002 + +compute q all property/atom quatw quati quatj quatk + +#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] + +#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 + +#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 + +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +compute_modify 1_temp extra/dof ${dof} +compute_modify 1_temp extra/dof 357 + +# equilibrate to shrink box around dilute system + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.8 + ghost atom cutoff = 4.8 + binsize = 2.4, bins = 59 59 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gayberne, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.752 | 4.752 | 4.752 Mbytes +Step c_rot E_pair TotEng Press Volume + 0 2.2718861 0 2.394 0.04788 20000 + 100 1.7443419 0 1.8381003 0.035765442 20557.278 + 200 2.2768798 0 2.3992621 0.046544845 20618.928 + 300 1.8573086 0 1.9571389 0.04239709 18464.842 + 400 2.1707875 -0.00045989278 2.2870073 0.066725499 13701.839 + 500 1.9710982 -0.014545321 2.0486111 0.12205188 8490.5214 + 600 2.0818888 -0.21572832 1.8356955 0.22333255 4697.3035 + 700 2.1551458 -0.68175426 1.4003368 0.60385996 2541.157 + 800 1.8879651 -1.6357045 0.21794544 1.0826917 1444.4484 + 900 2.1993533 -3.0664068 -0.91036919 3.2142529 925.96691 + 1000 1.4285977 -4.3962037 -2.9651113 3.1830461 744.91324 + 1100 1.933074 -4.9398703 -3.0147256 1.4694937 715.30906 + 1200 2.0872875 -4.5711608 -2.4689861 1.4091154 757.68606 + 1300 1.8950043 -4.1568789 -2.2487345 0.19138859 846.69407 + 1400 2.1773467 -3.7905723 -1.6164698 0.55639059 930.77026 + 1500 1.934954 -3.5505876 -1.6187812 0.2572587 1020.2803 + 1600 2.083004 -3.2707357 -1.1794873 0.68661802 1088.5587 + 1700 1.9434093 -3.2434441 -1.3043926 0.72465776 1136.9866 + 1800 1.9731416 -3.2692426 -1.3364608 0.52887378 1162.1022 + 1900 2.0618126 -3.2264372 -1.162807 0.93455596 1155.8306 + 2000 1.894614 -3.3964158 -1.4932323 0.69021871 1125.7713 +Loop time of 0.950695 on 1 procs for 2000 steps with 400 atoms + +Performance: 363523.513 tau/day, 2103.724 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 | 0.72638 | 0.72638 | 0.72638 | 0.0 | 76.40 +Neigh | 0.015026 | 0.015026 | 0.015026 | 0.0 | 1.58 +Comm | 0.015169 | 0.015169 | 0.015169 | 0.0 | 1.60 +Output | 0.0004487 | 0.0004487 | 0.0004487 | 0.0 | 0.05 +Modify | 0.18921 | 0.18921 | 0.18921 | 0.0 | 19.90 +Other | | 0.004463 | | | 0.47 + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 247 ave 247 max 247 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3021 ave 3021 max 3021 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3021 +Ave neighs/atom = 7.5525 +Neighbor list builds = 137 +Dangerous builds = 80 + +# run dynamics on dense system + +unfix 1 +fix 1 all nve/asphere + +run 2000 +Per MPI rank memory allocation (min/avg/max) = 4.763 | 4.763 | 4.763 Mbytes +Step c_rot E_pair TotEng Press Volume + 2000 1.894614 -3.3964158 -1.4932323 0.69021871 1125.7713 + 2100 1.8880098 -3.3875135 -1.4857102 0.21017294 1125.7713 + 2200 1.9098636 -3.4103342 -1.5286928 0.58806422 1125.7713 + 2300 1.9069018 -3.4099451 -1.6100279 0.63472569 1125.7713 + 2400 1.9773111 -3.4856999 -1.5268537 0.68904663 1125.7713 + 2500 2.0027582 -3.5144592 -1.4900208 0.59925433 1125.7713 + 2600 1.9616623 -3.4744355 -1.5230915 0.26873349 1125.7713 + 2700 1.8601168 -3.3625754 -1.4872109 0.68399005 1125.7713 + 2800 1.8194253 -3.319084 -1.5148077 0.62537226 1125.7713 + 2900 1.8465082 -3.3451652 -1.5508026 0.60163613 1125.7713 + 3000 1.8894551 -3.3918005 -1.5180435 0.61243969 1125.7713 + 3100 1.866554 -3.3662479 -1.5275331 0.54334005 1125.7713 + 3200 1.8233715 -3.3204693 -1.5180055 0.82717864 1125.7713 + 3300 1.7945158 -3.2898507 -1.4976351 0.56745564 1125.7713 + 3400 1.8242025 -3.3242538 -1.5070312 1.0550995 1125.7713 + 3500 1.860405 -3.3595757 -1.5138968 0.56959347 1125.7713 + 3600 1.76951 -3.2635375 -1.5302852 0.47091998 1125.7713 + 3700 1.7874111 -3.2838743 -1.4858244 0.74507678 1125.7713 + 3800 1.8084002 -3.3081089 -1.5294313 0.63717641 1125.7713 + 3900 1.9201118 -3.4261733 -1.4874713 0.4111663 1125.7713 + 4000 1.9130445 -3.4170846 -1.49357 0.35783848 1125.7713 +Loop time of 1.05944 on 1 procs for 2000 steps with 400 atoms + +Performance: 326208.857 tau/day, 1887.783 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 | 0.91753 | 0.91753 | 0.91753 | 0.0 | 86.60 +Neigh | 0.0072479 | 0.0072479 | 0.0072479 | 0.0 | 0.68 +Comm | 0.016155 | 0.016155 | 0.016155 | 0.0 | 1.52 +Output | 0.00042105 | 0.00042105 | 0.00042105 | 0.0 | 0.04 +Modify | 0.11222 | 0.11222 | 0.11222 | 0.0 | 10.59 +Other | | 0.005868 | | | 0.55 + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 243 ave 243 max 243 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3073 ave 3073 max 3073 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3073 +Ave neighs/atom = 7.6825 +Neighbor list builds = 46 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:02 diff --git a/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.4 b/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.4 new file mode 100644 index 0000000000..e15ce8474f --- /dev/null +++ b/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.4 @@ -0,0 +1,192 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# GayBerne ellipsoids in LJ background fluid + +units lj +atom_style ellipsoid +dimension 2 + +lattice sq 0.02 +Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 +region box block 0 20 0 20 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 400 atoms + Time spent = 0.000466347 secs + +set group all type/fraction 2 0.1 95392 + 45 settings made for type/fraction +set type 1 mass 1.0 + 355 settings made for mass +set type 2 mass 1.5 + 45 settings made for mass +set type 1 shape 1 1 1 + 355 settings made for shape +set type 2 shape 3 1 1 + 45 settings made for shape +set group all quat/random 18238 + 400 settings made for quat/random + +compute rot all temp/asphere +group spheroid type 1 +355 atoms in group spheroid +variable dof equal count(spheroid)+2 +compute_modify rot extra/dof ${dof} +compute_modify rot extra/dof 357 + +velocity all create 2.4 87287 loop geom + +pair_style gayberne 1.0 3.0 1.0 4.0 +pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5 +pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 +pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0 + +neighbor 0.8 bin + +thermo_style custom step c_rot epair etotal press vol +thermo 100 + +timestep 0.002 + +compute q all property/atom quatw quati quatj quatk + +#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] + +#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 + +#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 + +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +compute_modify 1_temp extra/dof ${dof} +compute_modify 1_temp extra/dof 357 + +# equilibrate to shrink box around dilute system + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.8 + ghost atom cutoff = 4.8 + binsize = 2.4, bins = 59 59 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gayberne, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.738 | 4.738 | 4.738 Mbytes +Step c_rot E_pair TotEng Press Volume + 0 2.2718861 0 2.394 0.04788 20000 + 100 1.7443419 0 1.8381003 0.035765442 20557.278 + 200 2.2768798 0 2.3992621 0.046544845 20618.928 + 300 1.8573086 0 1.9571389 0.04239709 18464.842 + 400 2.1707875 -0.00045989278 2.2870073 0.066725499 13701.839 + 500 1.9710982 -0.014545321 2.0486111 0.12205188 8490.5214 + 600 2.0818888 -0.21572832 1.8356955 0.22333255 4697.3035 + 700 2.1551458 -0.68175426 1.4003368 0.60385996 2541.157 + 800 1.8879651 -1.6357045 0.21794544 1.0826917 1444.4484 + 900 2.1993533 -3.0664068 -0.91036919 3.2142529 925.96691 + 1000 1.4285977 -4.3962037 -2.9651113 3.1830461 744.91324 + 1100 1.933074 -4.9398703 -3.0147256 1.4694937 715.30906 + 1200 2.0872875 -4.5711608 -2.4689861 1.4091154 757.68606 + 1300 1.8950043 -4.1568789 -2.2487345 0.19138859 846.69407 + 1400 2.1773467 -3.7905723 -1.6164698 0.55639059 930.77026 + 1500 1.934954 -3.5505876 -1.6187812 0.2572587 1020.2803 + 1600 2.083004 -3.2707357 -1.1794873 0.68661802 1088.5587 + 1700 1.9434093 -3.2434441 -1.3043926 0.72465775 1136.9866 + 1800 1.9731416 -3.2692426 -1.3364608 0.52887379 1162.1022 + 1900 2.0618126 -3.2264372 -1.162807 0.93455596 1155.8306 + 2000 1.894614 -3.3964158 -1.4932323 0.69021875 1125.7713 +Loop time of 0.349687 on 4 procs for 2000 steps with 400 atoms + +Performance: 988313.640 tau/day, 5719.408 timesteps/s +95.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17051 | 0.19038 | 0.20513 | 3.1 | 54.44 +Neigh | 0.0039656 | 0.0043136 | 0.0049045 | 0.6 | 1.23 +Comm | 0.054327 | 0.071206 | 0.087044 | 4.9 | 20.36 +Output | 0.00043106 | 0.00062788 | 0.0012097 | 0.0 | 0.18 +Modify | 0.072846 | 0.077488 | 0.081302 | 1.2 | 22.16 +Other | | 0.005673 | | | 1.62 + +Nlocal: 100 ave 112 max 84 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 146.75 ave 156 max 137 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 755.25 ave 889 max 589 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 3021 +Ave neighs/atom = 7.5525 +Neighbor list builds = 137 +Dangerous builds = 80 + +# run dynamics on dense system + +unfix 1 +fix 1 all nve/asphere + +run 2000 +Per MPI rank memory allocation (min/avg/max) = 4.74 | 4.74 | 4.74 Mbytes +Step c_rot E_pair TotEng Press Volume + 2000 1.894614 -3.3964158 -1.4932323 0.69021875 1125.7713 + 2100 1.8880098 -3.3875135 -1.4857102 0.21017294 1125.7713 + 2200 1.9098636 -3.4103342 -1.5286928 0.58806421 1125.7713 + 2300 1.9069019 -3.4099452 -1.610028 0.63472573 1125.7713 + 2400 1.9773106 -3.4856993 -1.5268537 0.68904883 1125.7713 + 2500 2.0027578 -3.5144588 -1.4900205 0.59925475 1125.7713 + 2600 1.9616631 -3.4744364 -1.5230915 0.26873516 1125.7713 + 2700 1.8601136 -3.362572 -1.487211 0.68399725 1125.7713 + 2800 1.8194391 -3.3190986 -1.5148092 0.62533318 1125.7713 + 2900 1.846505 -3.3451617 -1.5508267 0.60156074 1125.7713 + 3000 1.8894747 -3.3918215 -1.5180241 0.61210219 1125.7713 + 3100 1.866832 -3.3665537 -1.5276291 0.54222093 1125.7713 + 3200 1.8233362 -3.320323 -1.5177672 0.82891257 1125.7713 + 3300 1.7946952 -3.2899252 -1.4974666 0.56782835 1125.7713 + 3400 1.8283468 -3.3286169 -1.5065958 1.0370934 1125.7713 + 3500 1.8538134 -3.3526037 -1.5116661 0.58945341 1125.7713 + 3600 1.7851382 -3.2811082 -1.5306837 0.462114 1125.7713 + 3700 1.7664573 -3.2622701 -1.4774432 0.86540402 1125.7713 + 3800 1.8574677 -3.3592552 -1.5196884 0.45146881 1125.7713 + 3900 1.9139087 -3.4196718 -1.5054647 0.79636137 1125.7713 + 4000 1.9081675 -3.4146407 -1.5285325 0.69377107 1125.7713 +Loop time of 0.379139 on 4 procs for 2000 steps with 400 atoms + +Performance: 911539.742 tau/day, 5275.114 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 | 0.20177 | 0.23758 | 0.28816 | 7.4 | 62.66 +Neigh | 0.0015984 | 0.001946 | 0.0022459 | 0.6 | 0.51 +Comm | 0.046169 | 0.093409 | 0.13456 | 11.9 | 24.64 +Output | 0.00048614 | 0.00087821 | 0.0016096 | 0.0 | 0.23 +Modify | 0.02563 | 0.029633 | 0.034698 | 2.0 | 7.82 +Other | | 0.01569 | | | 4.14 + +Nlocal: 100 ave 117 max 87 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Nghost: 152.5 ave 169 max 131 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 771.25 ave 988 max 612 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 3085 +Ave neighs/atom = 7.7125 +Neighbor list builds = 45 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/ellipse/log.27Nov18.ellipse.resquared.g++.1 b/examples/ellipse/log.27Nov18.ellipse.resquared.g++.1 new file mode 100644 index 0000000000..be1a711218 --- /dev/null +++ b/examples/ellipse/log.27Nov18.ellipse.resquared.g++.1 @@ -0,0 +1,189 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# RESquared ellipsoids in LJ background fluid + +units lj +atom_style ellipsoid +dimension 2 + +lattice sq 0.02 +Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 +region box block 0 20 0 20 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 400 atoms + Time spent = 0.000540733 secs + +set group all type/fraction 2 0.1 95392 + 45 settings made for type/fraction +set type 1 mass 1.0 + 355 settings made for mass +set type 2 mass 1.5 + 45 settings made for mass +set type 1 shape 1 1 1 + 355 settings made for shape +set type 2 shape 3 1 1 + 45 settings made for shape +set group all quat/random 18238 + 400 settings made for quat/random + +compute rot all temp/asphere +group spheroid type 1 +355 atoms in group spheroid +variable dof equal count(spheroid)+2 +compute_modify rot extra/dof ${dof} +compute_modify rot extra/dof 357 + +velocity all create 2.4 87287 loop geom + +pair_style resquared 4.0 +pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 +pair_coeff 1 2 3.0 1 1 1 1 0 0 0 +pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0 + +neighbor 0.8 bin + +thermo_style custom step c_rot epair etotal press vol +thermo 100 + +timestep 0.002 + +compute q all property/atom quatw quati quatj quatk + +#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] + +#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 + +#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 + +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +compute_modify 1_temp extra/dof ${dof} +compute_modify 1_temp extra/dof 357 + +# equilibrate to shrink box around dilute system + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.8 + ghost atom cutoff = 4.8 + binsize = 2.4, bins = 59 59 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair resquared, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.752 | 4.752 | 4.752 Mbytes +Step c_rot E_pair TotEng Press Volume + 0 2.2718861 0 2.394 0.04788 20000 + 100 1.7443419 0 1.8381003 0.035765442 20557.278 + 200 2.2768798 0 2.3992621 0.046544845 20618.928 + 300 1.8573086 0 1.9571389 0.04239709 18464.842 + 400 2.1706741 -2.5275641e-05 2.2873225 0.066771565 13701.864 + 500 2.012561 0.0079467721 2.063898 0.10816504 8501.4958 + 600 2.1428003 0.083982458 2.2020759 0.3340759 4786.6892 + 700 2.0449292 0.17309565 2.1718849 0.78086274 2774.9262 + 800 1.9528849 0.31804014 2.2520272 1.8059473 1826.0933 + 900 1.6296095 0.24347613 1.8589813 1.7120274 1518.1139 + 1000 1.9349826 0.13913538 2.1125467 1.3044646 1519.7133 + 1100 2.1040629 0.11218748 2.2384236 1.0097965 1751.5229 + 1200 1.7801858 0.051922127 1.8564589 0.54836207 2198.0187 + 1300 2.3147158 0.049339841 2.390002 0.48871848 2754.4057 + 1400 1.754921 0.025804182 1.785499 0.28804529 3305.8359 + 1500 2.3701432 0.070771258 2.4523449 0.42290556 3531.1976 + 1600 1.7628065 0.054682596 1.830609 0.36138713 3319.2576 + 1700 2.2969598 0.130209 2.454872 0.73541699 2721.9102 + 1800 1.8253139 0.23039663 2.0810243 1.2065009 2155.7953 + 1900 2.017999 0.16257657 2.1664889 1.1654021 1815.9914 + 2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751 +Loop time of 1.62265 on 1 procs for 2000 steps with 400 atoms + +Performance: 212984.850 tau/day, 1232.551 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.4048 | 1.4048 | 1.4048 | 0.0 | 86.57 +Neigh | 0.014643 | 0.014643 | 0.014643 | 0.0 | 0.90 +Comm | 0.011678 | 0.011678 | 0.011678 | 0.0 | 0.72 +Output | 0.00046086 | 0.00046086 | 0.00046086 | 0.0 | 0.03 +Modify | 0.18748 | 0.18748 | 0.18748 | 0.0 | 11.55 +Other | | 0.003623 | | | 0.22 + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 213 ave 213 max 213 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1884 ave 1884 max 1884 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1884 +Ave neighs/atom = 4.71 +Neighbor list builds = 177 +Dangerous builds = 144 + +# run dynamics on dense system + +unfix 1 +fix 1 all nve/asphere + +run 2000 +Per MPI rank memory allocation (min/avg/max) = 4.754 | 4.754 | 4.754 Mbytes +Step c_rot E_pair TotEng Press Volume + 2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751 + 2100 2.0234333 0.11888043 2.165674 1.056689 1669.0751 + 2200 1.9652317 0.18018588 2.1288332 1.3191509 1669.0751 + 2300 1.9982484 0.1453846 2.1438911 1.2670661 1669.0751 + 2400 1.9752559 0.16967804 2.1177286 1.3037679 1669.0751 + 2500 1.978203 0.16642164 2.1631435 1.2908362 1669.0751 + 2600 1.9587508 0.18695272 2.1506896 1.3513902 1669.0751 + 2700 1.9654455 0.17997217 2.1247901 1.3360491 1669.0751 + 2800 1.9870267 0.15716583 2.1207709 1.2045103 1669.0751 + 2900 1.923066 0.22448724 2.1353571 1.4964299 1669.0751 + 3000 2.0042113 0.13903206 2.1149788 1.2100652 1669.0751 + 3100 1.9543697 0.19149442 2.0984704 1.3409703 1669.0751 + 3200 1.9991114 0.14441985 2.1292353 1.175647 1669.0751 + 3300 1.9629782 0.18246606 2.1463675 1.3162684 1669.0751 + 3400 1.9403528 0.2063029 2.1687044 1.4952816 1669.0751 + 3500 1.9887416 0.15531264 2.1485278 1.2530419 1669.0751 + 3600 1.9732723 0.1717156 2.1755741 1.2958545 1669.0751 + 3700 2.0072829 0.13576753 2.1212377 1.1421359 1669.0751 + 3800 1.9581273 0.18762532 2.1743415 1.3711091 1669.0751 + 3900 1.9761639 0.16862987 2.1429576 1.3036491 1669.0751 + 4000 1.9615823 0.18390729 2.12447 1.4179639 1669.0751 +Loop time of 2.70201 on 1 procs for 2000 steps with 400 atoms + +Performance: 127904.684 tau/day, 740.189 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 | 2.563 | 2.563 | 2.563 | 0.0 | 94.85 +Neigh | 0.0056589 | 0.0056589 | 0.0056589 | 0.0 | 0.21 +Comm | 0.014635 | 0.014635 | 0.014635 | 0.0 | 0.54 +Output | 0.00045729 | 0.00045729 | 0.00045729 | 0.0 | 0.02 +Modify | 0.11246 | 0.11246 | 0.11246 | 0.0 | 4.16 +Other | | 0.00584 | | | 0.22 + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 206 ave 206 max 206 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1872 ave 1872 max 1872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1872 +Ave neighs/atom = 4.68 +Neighbor list builds = 50 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/ellipse/log.27Nov18.ellipse.resquared.g++.4 b/examples/ellipse/log.27Nov18.ellipse.resquared.g++.4 new file mode 100644 index 0000000000..c32aa28653 --- /dev/null +++ b/examples/ellipse/log.27Nov18.ellipse.resquared.g++.4 @@ -0,0 +1,189 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# RESquared ellipsoids in LJ background fluid + +units lj +atom_style ellipsoid +dimension 2 + +lattice sq 0.02 +Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 +region box block 0 20 0 20 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 400 atoms + Time spent = 0.00047946 secs + +set group all type/fraction 2 0.1 95392 + 45 settings made for type/fraction +set type 1 mass 1.0 + 355 settings made for mass +set type 2 mass 1.5 + 45 settings made for mass +set type 1 shape 1 1 1 + 355 settings made for shape +set type 2 shape 3 1 1 + 45 settings made for shape +set group all quat/random 18238 + 400 settings made for quat/random + +compute rot all temp/asphere +group spheroid type 1 +355 atoms in group spheroid +variable dof equal count(spheroid)+2 +compute_modify rot extra/dof ${dof} +compute_modify rot extra/dof 357 + +velocity all create 2.4 87287 loop geom + +pair_style resquared 4.0 +pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 +pair_coeff 1 2 3.0 1 1 1 1 0 0 0 +pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0 + +neighbor 0.8 bin + +thermo_style custom step c_rot epair etotal press vol +thermo 100 + +timestep 0.002 + +compute q all property/atom quatw quati quatj quatk + +#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] + +#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 + +#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 + +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +compute_modify 1_temp extra/dof ${dof} +compute_modify 1_temp extra/dof 357 + +# equilibrate to shrink box around dilute system + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.8 + ghost atom cutoff = 4.8 + binsize = 2.4, bins = 59 59 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair resquared, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.738 | 4.738 | 4.738 Mbytes +Step c_rot E_pair TotEng Press Volume + 0 2.2718861 0 2.394 0.04788 20000 + 100 1.7443419 0 1.8381003 0.035765442 20557.278 + 200 2.2768798 0 2.3992621 0.046544845 20618.928 + 300 1.8573086 0 1.9571389 0.04239709 18464.842 + 400 2.1706741 -2.5275641e-05 2.2873225 0.066771565 13701.864 + 500 2.012561 0.0079467721 2.063898 0.10816504 8501.4958 + 600 2.1428003 0.083982458 2.2020759 0.3340759 4786.6892 + 700 2.0449292 0.17309565 2.1718849 0.78086274 2774.9262 + 800 1.9528849 0.31804014 2.2520272 1.8059473 1826.0933 + 900 1.6296095 0.24347613 1.8589813 1.7120274 1518.1139 + 1000 1.9349826 0.13913538 2.1125467 1.3044646 1519.7133 + 1100 2.1040629 0.11218748 2.2384236 1.0097965 1751.5229 + 1200 1.7801858 0.051922127 1.8564589 0.54836207 2198.0187 + 1300 2.3147158 0.049339841 2.390002 0.48871848 2754.4057 + 1400 1.754921 0.025804182 1.785499 0.28804529 3305.8359 + 1500 2.3701432 0.070771258 2.4523449 0.42290556 3531.1976 + 1600 1.7628065 0.054682596 1.830609 0.36138713 3319.2576 + 1700 2.2969598 0.130209 2.454872 0.73541699 2721.9102 + 1800 1.8253139 0.23039663 2.0810243 1.2065009 2155.7953 + 1900 2.017999 0.16257657 2.1664889 1.1654021 1815.9914 + 2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751 +Loop time of 0.513811 on 4 procs for 2000 steps with 400 atoms + +Performance: 672620.799 tau/day, 3892.481 timesteps/s +97.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.3553 | 0.36778 | 0.37737 | 1.4 | 71.58 +Neigh | 0.0039301 | 0.0040173 | 0.004127 | 0.1 | 0.78 +Comm | 0.056627 | 0.065564 | 0.076112 | 3.0 | 12.76 +Output | 0.00041318 | 0.00061768 | 0.0012202 | 0.0 | 0.12 +Modify | 0.070257 | 0.072503 | 0.074547 | 0.6 | 14.11 +Other | | 0.003331 | | | 0.65 + +Nlocal: 100 ave 108 max 96 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Nghost: 123.5 ave 125 max 122 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 471 ave 518 max 433 min +Histogram: 1 0 1 0 0 1 0 0 0 1 + +Total # of neighbors = 1884 +Ave neighs/atom = 4.71 +Neighbor list builds = 177 +Dangerous builds = 144 + +# run dynamics on dense system + +unfix 1 +fix 1 all nve/asphere + +run 2000 +Per MPI rank memory allocation (min/avg/max) = 4.739 | 4.739 | 4.739 Mbytes +Step c_rot E_pair TotEng Press Volume + 2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751 + 2100 2.0234333 0.11888043 2.165674 1.056689 1669.0751 + 2200 1.9652317 0.18018588 2.1288332 1.3191509 1669.0751 + 2300 1.9982484 0.1453846 2.1438911 1.2670661 1669.0751 + 2400 1.9752559 0.16967804 2.1177286 1.303768 1669.0751 + 2500 1.978203 0.16642165 2.1631435 1.2908362 1669.0751 + 2600 1.9587508 0.18695271 2.1506896 1.3513902 1669.0751 + 2700 1.9654455 0.17997218 2.1247901 1.3360492 1669.0751 + 2800 1.9870267 0.15716584 2.1207709 1.2045104 1669.0751 + 2900 1.9230662 0.22448703 2.1353571 1.4964289 1669.0751 + 3000 2.0042113 0.13903204 2.1149787 1.210065 1669.0751 + 3100 1.9543694 0.19149467 2.0984705 1.3409714 1669.0751 + 3200 1.9991114 0.14441984 2.1292354 1.1756471 1669.0751 + 3300 1.9629781 0.18246618 2.1463676 1.3162687 1669.0751 + 3400 1.940353 0.20630269 2.1687038 1.4952819 1669.0751 + 3500 1.9887413 0.15531296 2.1485274 1.2530446 1669.0751 + 3600 1.9732704 0.17171758 2.1755757 1.295861 1669.0751 + 3700 2.0072863 0.13576402 2.1212392 1.1421254 1669.0751 + 3800 1.9581337 0.18761851 2.1743384 1.3710796 1669.0751 + 3900 1.9761519 0.16864273 2.142963 1.3037308 1669.0751 + 4000 1.9615865 0.18390288 2.1244667 1.4179575 1669.0751 +Loop time of 0.846017 on 4 procs for 2000 steps with 400 atoms + +Performance: 408502.313 tau/day, 2364.018 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.63647 | 0.67097 | 0.74711 | 5.4 | 79.31 +Neigh | 0.0015061 | 0.0015807 | 0.0017054 | 0.2 | 0.19 +Comm | 0.058258 | 0.1341 | 0.16808 | 12.1 | 15.85 +Output | 0.00045156 | 0.00077933 | 0.0016997 | 0.0 | 0.09 +Modify | 0.028721 | 0.029793 | 0.03152 | 0.6 | 3.52 +Other | | 0.0088 | | | 1.04 + +Nlocal: 100 ave 106 max 97 min +Histogram: 1 1 1 0 0 0 0 0 0 1 +Nghost: 114 ave 117 max 111 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 468 ave 528 max 431 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 1872 +Ave neighs/atom = 4.68 +Neighbor list builds = 50 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.1 b/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.1 deleted file mode 100644 index ad23b08f43..0000000000 --- a/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.1 +++ /dev/null @@ -1,185 +0,0 @@ -LAMMPS (5 Oct 2016) -# GayBerne ellipsoids in LJ background fluid - -units lj -atom_style ellipsoid -dimension 2 - -lattice sq 0.02 -Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 -region box block 0 20 0 20 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 400 atoms - -set group all type/fraction 2 0.1 95392 - 45 settings made for type/fraction -set type 1 mass 1.0 - 355 settings made for mass -set type 2 mass 1.5 - 45 settings made for mass -set type 1 shape 1 1 1 - 355 settings made for shape -set type 2 shape 3 1 1 - 45 settings made for shape -set group all quat/random 18238 - 400 settings made for quat/random - -compute rot all temp/asphere -group spheroid type 1 -355 atoms in group spheroid -variable dof equal count(spheroid)+2 -compute_modify rot extra ${dof} -compute_modify rot extra 357 - -velocity all create 2.4 87287 loop geom - -pair_style gayberne 1.0 3.0 1.0 4.0 -pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5 -pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 -pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0 - -neighbor 0.8 bin - -thermo_style custom step c_rot epair etotal press vol -thermo 100 - -timestep 0.002 - -compute q all property/atom quatw quati quatj quatk - -#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] - -#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 - -#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 - -fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 -fix 2 all enforce2d - -compute_modify 1_temp extra ${dof} -compute_modify 1_temp extra 357 - -# equilibrate to shrink box around dilute system - -run 2000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.8 - ghost atom cutoff = 4.8 - binsize = 2.4 -> bins = 59 59 3 -Memory usage per processor = 4.17878 Mbytes -Step c_rot E_pair TotEng Press Volume - 0 2.2718861 0 2.394 0.04788 20000 - 100 1.7443002 0 1.8380563 0.03576216 20558.672 - 200 2.2770454 0 2.3994366 0.046545139 20620.298 - 300 1.8573283 0 1.9571597 0.04240689 18460.771 - 400 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473 - 500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548 - 600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955 - 700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873 - 800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961 - 900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895 - 1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136 - 1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574 - 1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454 - 1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577 - 1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639 - 1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387 - 1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271 - 1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473 - 1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051 - 1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372 - 2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026 -Loop time of 1.01022 on 1 procs for 2000 steps with 400 atoms - -Performance: 342102.068 tau/day, 1979.757 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.80465 | 0.80465 | 0.80465 | 0.0 | 79.65 -Neigh | 0.014326 | 0.014326 | 0.014326 | 0.0 | 1.42 -Comm | 0.011179 | 0.011179 | 0.011179 | 0.0 | 1.11 -Output | 0.00032926 | 0.00032926 | 0.00032926 | 0.0 | 0.03 -Modify | 0.17561 | 0.17561 | 0.17561 | 0.0 | 17.38 -Other | | 0.004126 | | | 0.41 - -Nlocal: 400 ave 400 max 400 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 249 ave 249 max 249 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3031 ave 3031 max 3031 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3031 -Ave neighs/atom = 7.5775 -Neighbor list builds = 140 -Dangerous builds = 80 - -# run dynamics on dense system - -unfix 1 -fix 1 all nve/asphere - -run 2000 -Memory usage per processor = 4.18892 Mbytes -Step c_rot E_pair TotEng Press Volume - 2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026 - 2100 2.0067383 -3.4164295 -1.402453 0.63163512 1121.7026 - 2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026 - 2300 2.0418707 -3.4552616 -1.4277716 0.58834236 1121.7026 - 2400 2.0126621 -3.424202 -1.3839096 0.80723942 1121.7026 - 2500 1.9403964 -3.3489489 -1.3995215 0.79492719 1121.7026 - 2600 2.0459304 -3.4600931 -1.4229608 0.69699402 1121.7026 - 2700 2.0032293 -3.4126492 -1.429784 0.44210814 1121.7026 - 2800 1.9367905 -3.345688 -1.4171068 0.6872734 1121.7026 - 2900 1.9870908 -3.3983385 -1.4218501 0.42402247 1121.7026 - 3000 1.9654849 -3.3767671 -1.3835149 0.6611643 1121.7026 - 3100 1.9308462 -3.3343018 -1.3895992 0.45213534 1121.7026 - 3200 1.8924656 -3.2956948 -1.4157919 0.56524685 1121.7026 - 3300 1.8802888 -3.2822198 -1.4071878 0.86030365 1121.7026 - 3400 1.8847013 -3.2852796 -1.4162404 0.91660541 1121.7026 - 3500 1.9290452 -3.3332356 -1.3889879 0.70770119 1121.7026 - 3600 1.9223314 -3.32413 -1.3896278 0.56763748 1121.7026 - 3700 1.9185132 -3.3197222 -1.3913701 0.66889312 1121.7026 - 3800 1.877321 -3.2796045 -1.4050964 0.67335591 1121.7026 - 3900 1.9250447 -3.3313033 -1.3872185 0.64573122 1121.7026 - 4000 1.8574113 -3.2592142 -1.3807543 0.46117918 1121.7026 -Loop time of 1.13656 on 1 procs for 2000 steps with 400 atoms - -Performance: 304074.636 tau/day, 1759.691 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.0076 | 1.0076 | 1.0076 | 0.0 | 88.65 -Neigh | 0.0065663 | 0.0065663 | 0.0065663 | 0.0 | 0.58 -Comm | 0.011639 | 0.011639 | 0.011639 | 0.0 | 1.02 -Output | 0.00035858 | 0.00035858 | 0.00035858 | 0.0 | 0.03 -Modify | 0.10463 | 0.10463 | 0.10463 | 0.0 | 9.21 -Other | | 0.00581 | | | 0.51 - -Nlocal: 400 ave 400 max 400 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 219 ave 219 max 219 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3046 ave 3046 max 3046 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3046 -Ave neighs/atom = 7.615 -Neighbor list builds = 47 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:02 diff --git a/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.4 b/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.4 deleted file mode 100644 index 7217a863d3..0000000000 --- a/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.4 +++ /dev/null @@ -1,185 +0,0 @@ -LAMMPS (5 Oct 2016) -# GayBerne ellipsoids in LJ background fluid - -units lj -atom_style ellipsoid -dimension 2 - -lattice sq 0.02 -Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 -region box block 0 20 0 20 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) - 2 by 2 by 1 MPI processor grid -create_atoms 1 box -Created 400 atoms - -set group all type/fraction 2 0.1 95392 - 45 settings made for type/fraction -set type 1 mass 1.0 - 355 settings made for mass -set type 2 mass 1.5 - 45 settings made for mass -set type 1 shape 1 1 1 - 355 settings made for shape -set type 2 shape 3 1 1 - 45 settings made for shape -set group all quat/random 18238 - 400 settings made for quat/random - -compute rot all temp/asphere -group spheroid type 1 -355 atoms in group spheroid -variable dof equal count(spheroid)+2 -compute_modify rot extra ${dof} -compute_modify rot extra 357 - -velocity all create 2.4 87287 loop geom - -pair_style gayberne 1.0 3.0 1.0 4.0 -pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5 -pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 -pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0 - -neighbor 0.8 bin - -thermo_style custom step c_rot epair etotal press vol -thermo 100 - -timestep 0.002 - -compute q all property/atom quatw quati quatj quatk - -#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] - -#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 - -#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 - -fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 -fix 2 all enforce2d - -compute_modify 1_temp extra ${dof} -compute_modify 1_temp extra 357 - -# equilibrate to shrink box around dilute system - -run 2000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.8 - ghost atom cutoff = 4.8 - binsize = 2.4 -> bins = 59 59 3 -Memory usage per processor = 4.16784 Mbytes -Step c_rot E_pair TotEng Press Volume - 0 2.2718861 0 2.394 0.04788 20000 - 100 1.7443002 0 1.8380563 0.03576216 20558.672 - 200 2.2770454 0 2.3994366 0.046545139 20620.298 - 300 1.8573283 0 1.9571597 0.04240689 18460.771 - 400 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473 - 500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548 - 600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955 - 700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873 - 800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961 - 900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895 - 1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136 - 1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574 - 1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454 - 1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577 - 1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639 - 1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387 - 1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271 - 1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473 - 1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051 - 1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372 - 2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026 -Loop time of 0.348825 on 4 procs for 2000 steps with 400 atoms - -Performance: 990754.062 tau/day, 5733.530 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.18317 | 0.20567 | 0.22597 | 3.3 | 58.96 -Neigh | 0.0036285 | 0.0038322 | 0.0039773 | 0.2 | 1.10 -Comm | 0.043543 | 0.06339 | 0.085499 | 5.9 | 18.17 -Output | 0.00044894 | 0.00046825 | 0.00051665 | 0.1 | 0.13 -Modify | 0.069605 | 0.070677 | 0.071795 | 0.3 | 20.26 -Other | | 0.004791 | | | 1.37 - -Nlocal: 100 ave 113 max 85 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 149.75 ave 160 max 141 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Neighs: 757.75 ave 885 max 592 min -Histogram: 1 0 0 1 0 0 0 0 1 1 - -Total # of neighbors = 3031 -Ave neighs/atom = 7.5775 -Neighbor list builds = 140 -Dangerous builds = 80 - -# run dynamics on dense system - -unfix 1 -fix 1 all nve/asphere - -run 2000 -Memory usage per processor = 4.16867 Mbytes -Step c_rot E_pair TotEng Press Volume - 2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026 - 2100 2.0067383 -3.4164295 -1.402453 0.63163513 1121.7026 - 2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026 - 2300 2.0418708 -3.4552617 -1.4277716 0.58834191 1121.7026 - 2400 2.0126625 -3.4242024 -1.3839097 0.80723766 1121.7026 - 2500 1.9403968 -3.3489494 -1.3995212 0.79492647 1121.7026 - 2600 2.0459318 -3.4600945 -1.4229599 0.69698729 1121.7026 - 2700 2.0032338 -3.4126541 -1.4297892 0.44208354 1121.7026 - 2800 1.9367789 -3.3456765 -1.4171038 0.6873665 1121.7026 - 2900 1.9870979 -3.3983434 -1.4218523 0.42398659 1121.7026 - 3000 1.965491 -3.376773 -1.3835208 0.66112051 1121.7026 - 3100 1.9307633 -3.3342121 -1.3895745 0.45224657 1121.7026 - 3200 1.8918453 -3.2949278 -1.4157216 0.56825582 1121.7026 - 3300 1.8824584 -3.2844031 -1.4066487 0.85795659 1121.7026 - 3400 1.8871451 -3.2878452 -1.4156691 0.91410213 1121.7026 - 3500 1.9297625 -3.3340904 -1.3901995 0.6754809 1121.7026 - 3600 1.8994197 -3.3009141 -1.3964162 0.58676937 1121.7026 - 3700 1.9181765 -3.3204193 -1.3956433 0.54632736 1121.7026 - 3800 1.9278078 -3.3300748 -1.3999307 0.48904879 1121.7026 - 3900 1.888321 -3.2896024 -1.3848249 0.49521159 1121.7026 - 4000 1.8372182 -3.2347372 -1.4091759 0.61895915 1121.7026 -Loop time of 0.380732 on 4 procs for 2000 steps with 400 atoms - -Performance: 907726.114 tau/day, 5253.045 timesteps/s -98.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.24119 | 0.25802 | 0.28318 | 3.0 | 67.77 -Neigh | 0.001538 | 0.0017161 | 0.0018811 | 0.3 | 0.45 -Comm | 0.055332 | 0.081399 | 0.098741 | 5.6 | 21.38 -Output | 0.0005157 | 0.00053984 | 0.00058794 | 0.1 | 0.14 -Modify | 0.026189 | 0.027282 | 0.029091 | 0.7 | 7.17 -Other | | 0.01177 | | | 3.09 - -Nlocal: 100 ave 106 max 92 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Nghost: 148 ave 152 max 145 min -Histogram: 1 1 0 0 0 1 0 0 0 1 -Neighs: 760.25 ave 815 max 713 min -Histogram: 1 1 0 0 0 0 1 0 0 1 - -Total # of neighbors = 3041 -Ave neighs/atom = 7.6025 -Neighbor list builds = 46 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/ellipse/log.5Oct16.ellipse.resquared.g++.1 b/examples/ellipse/log.5Oct16.ellipse.resquared.g++.1 deleted file mode 100644 index 51028b326e..0000000000 --- a/examples/ellipse/log.5Oct16.ellipse.resquared.g++.1 +++ /dev/null @@ -1,182 +0,0 @@ -LAMMPS (5 Oct 2016) -# RESquared ellipsoids in LJ background fluid - -units lj -atom_style ellipsoid -dimension 2 - -lattice sq 0.02 -Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 -region box block 0 20 0 20 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 400 atoms - -set group all type/fraction 2 0.1 95392 - 45 settings made for type/fraction -set type 1 mass 1.0 - 355 settings made for mass -set type 2 mass 1.5 - 45 settings made for mass -set type 1 shape 1 1 1 - 355 settings made for shape -set type 2 shape 3 1 1 - 45 settings made for shape -set group all quat/random 18238 - 400 settings made for quat/random - -compute rot all temp/asphere -group spheroid type 1 -355 atoms in group spheroid -variable dof equal count(spheroid)+2 -compute_modify rot extra ${dof} -compute_modify rot extra 357 - -velocity all create 2.4 87287 loop geom - -pair_style resquared 4.0 -pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 -pair_coeff 1 2 3.0 1 1 1 1 0 0 0 -pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0 - -neighbor 0.8 bin - -thermo_style custom step c_rot epair etotal press vol -thermo 100 - -timestep 0.002 - -compute q all property/atom quatw quati quatj quatk - -#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] - -#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 - -#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 - -fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 -fix 2 all enforce2d - -compute_modify 1_temp extra ${dof} -compute_modify 1_temp extra 357 - -# equilibrate to shrink box around dilute system - -run 2000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.8 - ghost atom cutoff = 4.8 - binsize = 2.4 -> bins = 59 59 3 -Memory usage per processor = 4.17878 Mbytes -Step c_rot E_pair TotEng Press Volume - 0 2.2718861 0 2.394 0.04788 20000 - 100 1.7443002 0 1.8380563 0.03576216 20558.672 - 200 2.2770454 0 2.3994366 0.046545139 20620.298 - 300 1.8573283 0 1.9571597 0.04240689 18460.771 - 400 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499 - 500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241 - 600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723 - 700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757 - 800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943 - 900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585 - 1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058 - 1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608 - 1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358 - 1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014 - 1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144 - 1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855 - 1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472 - 1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401 - 1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099 - 1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221 - 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587 -Loop time of 1.69003 on 1 procs for 2000 steps with 400 atoms - -Performance: 204492.823 tau/day, 1183.408 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.4827 | 1.4827 | 1.4827 | 0.0 | 87.73 -Neigh | 0.014216 | 0.014216 | 0.014216 | 0.0 | 0.84 -Comm | 0.0084538 | 0.0084538 | 0.0084538 | 0.0 | 0.50 -Output | 0.0003345 | 0.0003345 | 0.0003345 | 0.0 | 0.02 -Modify | 0.18062 | 0.18062 | 0.18062 | 0.0 | 10.69 -Other | | 0.003745 | | | 0.22 - -Nlocal: 400 ave 400 max 400 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 216 ave 216 max 216 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1929 ave 1929 max 1929 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1929 -Ave neighs/atom = 4.8225 -Neighbor list builds = 177 -Dangerous builds = 146 - -# run dynamics on dense system - -unfix 1 -fix 1 all nve/asphere - -run 2000 -Memory usage per processor = 4.18079 Mbytes -Step c_rot E_pair TotEng Press Volume - 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587 - 2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587 - 2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587 - 2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587 - 2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587 - 2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587 - 2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587 - 2700 1.9608664 0.18459944 2.1483889 1.3461095 1654.9587 - 2800 2.005755 0.13729992 2.1214078 1.1596182 1654.9587 - 2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587 - 3000 1.9606374 0.18480425 2.1301691 1.3280548 1654.9587 - 3100 1.9824235 0.16187644 2.1284432 1.2590072 1654.9587 - 3200 1.9389485 0.20774117 2.106322 1.4587341 1654.9587 - 3300 1.9849309 0.15929459 2.1301897 1.2415172 1654.9587 - 3400 1.9596863 0.18578944 2.1215072 1.3738214 1654.9587 - 3500 1.9671171 0.17804546 2.0934254 1.3147204 1654.9587 - 3600 1.9702641 0.17471582 2.1569255 1.3331099 1654.9587 - 3700 1.9103961 0.23792935 2.1305401 1.5832203 1654.9587 - 3800 1.9129619 0.23512654 2.1445946 1.5657403 1654.9587 - 3900 1.9868018 0.15725404 2.1658135 1.2582197 1654.9587 - 4000 2.0058784 0.13726837 2.1534352 1.1351359 1654.9587 -Loop time of 2.86686 on 1 procs for 2000 steps with 400 atoms - -Performance: 120550.133 tau/day, 697.628 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.7349 | 2.7349 | 2.7349 | 0.0 | 95.40 -Neigh | 0.0052247 | 0.0052247 | 0.0052247 | 0.0 | 0.18 -Comm | 0.011207 | 0.011207 | 0.011207 | 0.0 | 0.39 -Output | 0.00036931 | 0.00036931 | 0.00036931 | 0.0 | 0.01 -Modify | 0.10925 | 0.10925 | 0.10925 | 0.0 | 3.81 -Other | | 0.005949 | | | 0.21 - -Nlocal: 400 ave 400 max 400 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 204 ave 204 max 204 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1857 ave 1857 max 1857 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1857 -Ave neighs/atom = 4.6425 -Neighbor list builds = 48 -Dangerous builds = 0 -Total wall time: 0:00:04 diff --git a/examples/ellipse/log.5Oct16.ellipse.resquared.g++.4 b/examples/ellipse/log.5Oct16.ellipse.resquared.g++.4 deleted file mode 100644 index fa93b41fa3..0000000000 --- a/examples/ellipse/log.5Oct16.ellipse.resquared.g++.4 +++ /dev/null @@ -1,182 +0,0 @@ -LAMMPS (5 Oct 2016) -# RESquared ellipsoids in LJ background fluid - -units lj -atom_style ellipsoid -dimension 2 - -lattice sq 0.02 -Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 -region box block 0 20 0 20 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) - 2 by 2 by 1 MPI processor grid -create_atoms 1 box -Created 400 atoms - -set group all type/fraction 2 0.1 95392 - 45 settings made for type/fraction -set type 1 mass 1.0 - 355 settings made for mass -set type 2 mass 1.5 - 45 settings made for mass -set type 1 shape 1 1 1 - 355 settings made for shape -set type 2 shape 3 1 1 - 45 settings made for shape -set group all quat/random 18238 - 400 settings made for quat/random - -compute rot all temp/asphere -group spheroid type 1 -355 atoms in group spheroid -variable dof equal count(spheroid)+2 -compute_modify rot extra ${dof} -compute_modify rot extra 357 - -velocity all create 2.4 87287 loop geom - -pair_style resquared 4.0 -pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 -pair_coeff 1 2 3.0 1 1 1 1 0 0 0 -pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0 - -neighbor 0.8 bin - -thermo_style custom step c_rot epair etotal press vol -thermo 100 - -timestep 0.002 - -compute q all property/atom quatw quati quatj quatk - -#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] - -#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 - -#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 - -fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 -fix 2 all enforce2d - -compute_modify 1_temp extra ${dof} -compute_modify 1_temp extra 357 - -# equilibrate to shrink box around dilute system - -run 2000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.8 - ghost atom cutoff = 4.8 - binsize = 2.4 -> bins = 59 59 3 -Memory usage per processor = 4.16784 Mbytes -Step c_rot E_pair TotEng Press Volume - 0 2.2718861 0 2.394 0.04788 20000 - 100 1.7443002 0 1.8380563 0.03576216 20558.672 - 200 2.2770454 0 2.3994366 0.046545139 20620.298 - 300 1.8573283 0 1.9571597 0.04240689 18460.771 - 400 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499 - 500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241 - 600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723 - 700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757 - 800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943 - 900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585 - 1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058 - 1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608 - 1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358 - 1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014 - 1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144 - 1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855 - 1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472 - 1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401 - 1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099 - 1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221 - 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587 -Loop time of 0.529177 on 4 procs for 2000 steps with 400 atoms - -Performance: 653089.670 tau/day, 3779.454 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.36797 | 0.3809 | 0.38796 | 1.2 | 71.98 -Neigh | 0.0037003 | 0.0038002 | 0.0038807 | 0.1 | 0.72 -Comm | 0.057266 | 0.063631 | 0.076821 | 3.1 | 12.02 -Output | 0.00050998 | 0.00052881 | 0.00056648 | 0.1 | 0.10 -Modify | 0.075577 | 0.076514 | 0.078309 | 0.4 | 14.46 -Other | | 0.0038 | | | 0.72 - -Nlocal: 100 ave 108 max 95 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Nghost: 125.75 ave 128 max 123 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 482.25 ave 535 max 442 min -Histogram: 1 1 0 0 0 1 0 0 0 1 - -Total # of neighbors = 1929 -Ave neighs/atom = 4.8225 -Neighbor list builds = 177 -Dangerous builds = 146 - -# run dynamics on dense system - -unfix 1 -fix 1 all nve/asphere - -run 2000 -Memory usage per processor = 4.16867 Mbytes -Step c_rot E_pair TotEng Press Volume - 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587 - 2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587 - 2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587 - 2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587 - 2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587 - 2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587 - 2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587 - 2700 1.9608664 0.18459944 2.1483889 1.3461096 1654.9587 - 2800 2.005755 0.13729992 2.1214078 1.1596183 1654.9587 - 2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587 - 3000 1.9606373 0.18480426 2.1301691 1.3280548 1654.9587 - 3100 1.9824235 0.16187647 2.1284433 1.2590074 1654.9587 - 3200 1.9389485 0.20774113 2.1063219 1.4587339 1654.9587 - 3300 1.984931 0.15929453 2.1301897 1.2415169 1654.9587 - 3400 1.9596864 0.18578934 2.1215072 1.3738204 1654.9587 - 3500 1.9671165 0.17804604 2.0934256 1.3147236 1654.9587 - 3600 1.9702644 0.17471548 2.156925 1.3331072 1654.9587 - 3700 1.9104013 0.2379238 2.1305421 1.5831938 1654.9587 - 3800 1.9129623 0.23512612 2.1445951 1.565741 1654.9587 - 3900 1.9868116 0.15724371 2.1658058 1.2581725 1654.9587 - 4000 2.0058633 0.13728433 2.1534403 1.1352037 1654.9587 -Loop time of 0.822603 on 4 procs for 2000 steps with 400 atoms - -Performance: 420129.522 tau/day, 2431.305 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.67029 | 0.69125 | 0.73659 | 3.2 | 84.03 -Neigh | 0.0013115 | 0.0014372 | 0.0016122 | 0.3 | 0.17 -Comm | 0.046684 | 0.092118 | 0.1133 | 9.0 | 11.20 -Output | 0.00053906 | 0.00055629 | 0.00059342 | 0.1 | 0.07 -Modify | 0.026623 | 0.027991 | 0.029785 | 0.8 | 3.40 -Other | | 0.009251 | | | 1.12 - -Nlocal: 100 ave 103 max 96 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Nghost: 118 ave 122 max 115 min -Histogram: 1 0 1 0 1 0 0 0 0 1 -Neighs: 464.25 ave 489 max 449 min -Histogram: 2 0 0 0 1 0 0 0 0 1 - -Total # of neighbors = 1857 -Ave neighs/atom = 4.6425 -Neighbor list builds = 48 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/flow/log.5Oct16.flow.couette.g++.1 b/examples/flow/log.27Nov18.flow.couette.g++.1 similarity index 80% rename from examples/flow/log.5Oct16.flow.couette.g++.1 rename to examples/flow/log.27Nov18.flow.couette.g++.1 index a9d3a9929f..9045771f7c 100644 --- a/examples/flow/log.5Oct16.flow.couette.g++.1 +++ b/examples/flow/log.27Nov18.flow.couette.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2-d LJ flow simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.000395536 secs mass 1 1.0 mass 2 1.0 @@ -75,7 +77,7 @@ fix 4 all enforce2d timestep 0.003 thermo 500 thermo_modify temp mobile -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 500 dump.flow @@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 37 32 1 -Memory usage per processor = 2.47395 Mbytes + binsize = 0.71123, bins = 37 32 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.047 | 3.047 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 0 0 0.71190476 0.52314537 571.54286 500 1.0644427 -0.31382888 0 0.44395296 3.0013076 571.54286 @@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume 9000 1 -0.402333 0 0.30957177 2.4852035 571.54286 9500 0.99889786 -0.46870263 0 0.24241751 2.3763314 571.54286 10000 1 -0.43338695 0 0.27851782 2.405424 571.54286 -Loop time of 0.281614 on 1 procs for 10000 steps with 420 atoms +Loop time of 0.293461 on 1 procs for 10000 steps with 420 atoms -Performance: 9204085.735 tau/day, 35509.590 timesteps/s -100.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 8832531.296 tau/day, 34076.124 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 | 0.12437 | 0.12437 | 0.12437 | 0.0 | 44.16 -Neigh | 0.062146 | 0.062146 | 0.062146 | 0.0 | 22.07 -Comm | 0.0076008 | 0.0076008 | 0.0076008 | 0.0 | 2.70 -Output | 0.00014687 | 0.00014687 | 0.00014687 | 0.0 | 0.05 -Modify | 0.067444 | 0.067444 | 0.067444 | 0.0 | 23.95 -Other | | 0.01991 | | | 7.07 +Pair | 0.11085 | 0.11085 | 0.11085 | 0.0 | 37.77 +Neigh | 0.059952 | 0.059952 | 0.059952 | 0.0 | 20.43 +Comm | 0.010563 | 0.010563 | 0.010563 | 0.0 | 3.60 +Output | 0.00021076 | 0.00021076 | 0.00021076 | 0.0 | 0.07 +Modify | 0.089026 | 0.089026 | 0.089026 | 0.0 | 30.34 +Other | | 0.02286 | | | 7.79 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/flow/log.5Oct16.flow.couette.g++.4 b/examples/flow/log.27Nov18.flow.couette.g++.4 similarity index 80% rename from examples/flow/log.5Oct16.flow.couette.g++.4 rename to examples/flow/log.27Nov18.flow.couette.g++.4 index 84bd03560d..01f1e81d46 100644 --- a/examples/flow/log.5Oct16.flow.couette.g++.4 +++ b/examples/flow/log.27Nov18.flow.couette.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2-d LJ flow simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.00031352 secs mass 1 1.0 mass 2 1.0 @@ -75,7 +77,7 @@ fix 4 all enforce2d timestep 0.003 thermo 500 thermo_modify temp mobile -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 500 dump.flow @@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 37 32 1 -Memory usage per processor = 2.47768 Mbytes + binsize = 0.71123, bins = 37 32 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.048 | 3.048 | 3.048 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 0 0 0.71190476 0.52314537 571.54286 500 1.0951876 -0.33403931 0 0.44562996 3.2502319 571.54286 @@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume 9000 1 -0.45171969 0 0.26018507 2.5525861 571.54286 9500 1.0322994 -0.40989898 0 0.32499991 2.6021234 571.54286 10000 1 -0.42489516 0 0.28700961 2.619505 571.54286 -Loop time of 0.134939 on 4 procs for 10000 steps with 420 atoms +Loop time of 0.172876 on 4 procs for 10000 steps with 420 atoms -Performance: 19208643.416 tau/day, 74107.421 timesteps/s -99.3% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 14993379.796 tau/day, 57844.829 timesteps/s +95.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.024453 | 0.030829 | 0.036954 | 3.5 | 22.85 -Neigh | 0.0152 | 0.016832 | 0.018415 | 1.2 | 12.47 -Comm | 0.040894 | 0.049385 | 0.058308 | 3.7 | 36.60 -Output | 0.00027037 | 0.00029039 | 0.0003438 | 0.2 | 0.22 -Modify | 0.017885 | 0.018734 | 0.019774 | 0.6 | 13.88 -Other | | 0.01887 | | | 13.98 +Pair | 0.024842 | 0.030136 | 0.036735 | 3.1 | 17.43 +Neigh | 0.014276 | 0.015892 | 0.017287 | 1.1 | 9.19 +Comm | 0.065952 | 0.075937 | 0.084912 | 3.2 | 43.93 +Output | 0.00034285 | 0.00042874 | 0.00067973 | 0.0 | 0.25 +Modify | 0.024682 | 0.026202 | 0.028216 | 1.0 | 15.16 +Other | | 0.02428 | | | 14.05 Nlocal: 105 ave 113 max 97 min Histogram: 2 0 0 0 0 0 0 0 0 2 diff --git a/examples/flow/log.5Oct16.flow.pois.g++.1 b/examples/flow/log.27Nov18.flow.pois.g++.1 similarity index 80% rename from examples/flow/log.5Oct16.flow.pois.g++.1 rename to examples/flow/log.27Nov18.flow.pois.g++.1 index 8a8748f984..45eed1d841 100644 --- a/examples/flow/log.5Oct16.flow.pois.g++.1 +++ b/examples/flow/log.27Nov18.flow.pois.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2-d LJ flow simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.000394583 secs mass 1 1.0 mass 2 1.0 @@ -75,7 +77,7 @@ fix 7 all enforce2d timestep 0.003 thermo 500 thermo_modify temp mobile -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 500 dump.flow @@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 37 32 1 -Memory usage per processor = 2.47395 Mbytes + binsize = 0.71123, bins = 37 32 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.047 | 3.047 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 0 0 0.71190476 0.52314537 571.54286 500 1.0990751 -0.36396768 0 0.41846911 2.522517 575.55806 @@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume 9000 1 -0.74461165 0 -0.032706889 2.574656 498.14523 9500 1.2047533 -0.75768848 0 0.09998113 2.4174997 501.8877 10000 1 -0.67361996 0 0.038284798 2.2310948 507.57444 -Loop time of 0.313724 on 1 procs for 10000 steps with 420 atoms +Loop time of 0.353337 on 1 procs for 10000 steps with 420 atoms -Performance: 8262038.165 tau/day, 31875.147 timesteps/s -100.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 7335771.903 tau/day, 28301.589 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 | 0.13662 | 0.13662 | 0.13662 | 0.0 | 43.55 -Neigh | 0.034956 | 0.034956 | 0.034956 | 0.0 | 11.14 -Comm | 0.0064242 | 0.0064242 | 0.0064242 | 0.0 | 2.05 -Output | 0.00014639 | 0.00014639 | 0.00014639 | 0.0 | 0.05 -Modify | 0.11616 | 0.11616 | 0.11616 | 0.0 | 37.03 -Other | | 0.01941 | | | 6.19 +Pair | 0.12053 | 0.12053 | 0.12053 | 0.0 | 34.11 +Neigh | 0.033673 | 0.033673 | 0.033673 | 0.0 | 9.53 +Comm | 0.00895 | 0.00895 | 0.00895 | 0.0 | 2.53 +Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.07 +Modify | 0.16577 | 0.16577 | 0.16577 | 0.0 | 46.92 +Other | | 0.02418 | | | 6.84 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/flow/log.5Oct16.flow.pois.g++.4 b/examples/flow/log.27Nov18.flow.pois.g++.4 similarity index 80% rename from examples/flow/log.5Oct16.flow.pois.g++.4 rename to examples/flow/log.27Nov18.flow.pois.g++.4 index 20c3293b82..6e0c58614a 100644 --- a/examples/flow/log.5Oct16.flow.pois.g++.4 +++ b/examples/flow/log.27Nov18.flow.pois.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2-d LJ flow simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.00031805 secs mass 1 1.0 mass 2 1.0 @@ -75,7 +77,7 @@ fix 7 all enforce2d timestep 0.003 thermo 500 thermo_modify temp mobile -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 500 dump.flow @@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 37 32 1 -Memory usage per processor = 2.47768 Mbytes + binsize = 0.71123, bins = 37 32 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.048 | 3.048 | 3.048 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 0 0 0.71190476 0.52314537 571.54286 500 1.0758737 -0.36090417 0 0.40501541 2.7822308 575.0659 @@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume 9000 1 -0.8200207 0 -0.10811593 2.6210027 502.60511 9500 1.2167146 -0.77385956 0 0.092325373 2.5938179 500.86068 10000 1 -0.73082779 0 -0.018923029 2.735112 505.69856 -Loop time of 0.225282 on 4 procs for 10000 steps with 420 atoms +Loop time of 0.208663 on 4 procs for 10000 steps with 420 atoms -Performance: 11505578.988 tau/day, 44388.808 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 12421919.467 tau/day, 47924.072 timesteps/s +95.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.032012 | 0.033154 | 0.035252 | 0.7 | 14.72 -Neigh | 0.0094411 | 0.0097138 | 0.010069 | 0.2 | 4.31 -Comm | 0.080785 | 0.085431 | 0.088782 | 1.0 | 37.92 -Output | 0.0003736 | 0.00039834 | 0.00046349 | 0.2 | 0.18 -Modify | 0.062812 | 0.064686 | 0.066481 | 0.6 | 28.71 -Other | | 0.0319 | | | 14.16 +Pair | 0.031368 | 0.032216 | 0.033688 | 0.5 | 15.44 +Neigh | 0.0093348 | 0.0097306 | 0.010144 | 0.3 | 4.66 +Comm | 0.059824 | 0.065823 | 0.07057 | 1.8 | 31.55 +Output | 0.00033283 | 0.00043827 | 0.00073981 | 0.0 | 0.21 +Modify | 0.067317 | 0.071492 | 0.075636 | 1.3 | 34.26 +Other | | 0.02896 | | | 13.88 Nlocal: 105 ave 106 max 103 min Histogram: 1 0 0 0 0 0 1 0 0 2