From b6b101f29af3c18df6bc223c5e12aa2e8e0fb376 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 9 Apr 2021 09:54:47 -0400 Subject: [PATCH] update melt example to use velocity with loop geom for consistent velocities --- examples/melt/in.melt | 2 +- examples/melt/log.27Nov18.melt.g++.4 | 85 ------------------- ...Nov18.melt.g++.1 => log.8Apr21.melt.g++.1} | 50 +++++------ examples/melt/log.8Apr21.melt.g++.4 | 85 +++++++++++++++++++ 4 files changed, 111 insertions(+), 111 deletions(-) delete mode 100644 examples/melt/log.27Nov18.melt.g++.4 rename examples/melt/{log.27Nov18.melt.g++.1 => log.8Apr21.melt.g++.1} (51%) create mode 100644 examples/melt/log.8Apr21.melt.g++.4 diff --git a/examples/melt/in.melt b/examples/melt/in.melt index 8431a4344e..f169dc2ffc 100644 --- a/examples/melt/in.melt +++ b/examples/melt/in.melt @@ -9,7 +9,7 @@ create_box 1 box create_atoms 1 box mass 1 1.0 -velocity all create 3.0 87287 +velocity all create 3.0 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 diff --git a/examples/melt/log.27Nov18.melt.g++.4 b/examples/melt/log.27Nov18.melt.g++.4 deleted file mode 100644 index 927895b1cd..0000000000 --- a/examples/melt/log.27Nov18.melt.g++.4 +++ /dev/null @@ -1,85 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# 3d Lennard-Jones melt - -units lj -atom_style atomic - -lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 -region box block 0 10 0 10 0 10 -create_box 1 box -Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 4000 atoms - Time spent = 0.00041604 secs -mass 1 1.0 - -velocity all create 3.0 87287 - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify every 20 delay 0 check no - -fix 1 all nve - -#dump id all atom 50 dump.melt - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -thermo 50 -run 250 -Neighbor list info ... - update every 20 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 12 12 12 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 3 -6.7733681 0 -2.2744931 -3.7033504 - 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 - 100 1.6503357 -4.756014 0 -2.2811293 5.8050524 - 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 - 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 - 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 -Loop time of 0.223329 on 4 procs for 250 steps with 4000 atoms - -Performance: 483592.231 tau/day, 1119.426 timesteps/s -97.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.15881 | 0.16314 | 0.16859 | 0.9 | 73.05 -Neigh | 0.02472 | 0.025218 | 0.025828 | 0.3 | 11.29 -Comm | 0.025185 | 0.030091 | 0.034351 | 1.9 | 13.47 -Output | 0.00015163 | 0.00019169 | 0.00030899 | 0.0 | 0.09 -Modify | 0.0037532 | 0.0038366 | 0.0040054 | 0.2 | 1.72 -Other | | 0.00085 | | | 0.38 - -Nlocal: 1000 ave 1010 max 982 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 2703.75 ave 2713 max 2689 min -Histogram: 1 0 0 0 0 0 0 2 0 1 -Neighs: 37915.5 ave 39239 max 36193 min -Histogram: 1 0 0 0 0 1 1 0 0 1 - -Total # of neighbors = 151662 -Ave neighs/atom = 37.9155 -Neighbor list builds = 12 -Dangerous builds not checked -Total wall time: 0:00:00 diff --git a/examples/melt/log.27Nov18.melt.g++.1 b/examples/melt/log.8Apr21.melt.g++.1 similarity index 51% rename from examples/melt/log.27Nov18.melt.g++.1 rename to examples/melt/log.8Apr21.melt.g++.1 index 69b39e6011..a3b6d003db 100644 --- a/examples/melt/log.27Nov18.melt.g++.1 +++ b/examples/melt/log.8Apr21.melt.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (27 Nov 2018) +LAMMPS (8 Apr 2021) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt @@ -6,17 +6,17 @@ units lj atom_style atomic lattice fcc 0.8442 -Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 region box block 0 10 0 10 0 10 create_box 1 box -Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms - Time spent = 0.000645638 secs + create_atoms CPU = 0.002 seconds mass 1 1.0 -velocity all create 3.0 87287 +velocity all create 3.0 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 @@ -48,38 +48,38 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.222 | 3.222 | 3.222 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 - 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 - 100 1.6458363 -4.7492704 0 -2.2811332 5.8691042 - 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 - 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 - 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 -Loop time of 0.729809 on 1 procs for 250 steps with 4000 atoms + 50 1.6842865 -4.8082494 0 -2.2824513 5.5666131 + 100 1.6712577 -4.7875609 0 -2.281301 5.6613913 + 150 1.6444751 -4.7471034 0 -2.2810074 5.8614211 + 200 1.6471542 -4.7509053 0 -2.2807916 5.8805431 + 250 1.6645597 -4.7774327 0 -2.2812174 5.7526089 +Loop time of 1.61045 on 1 procs for 250 steps with 4000 atoms -Performance: 147983.915 tau/day, 342.555 timesteps/s +Performance: 67062.020 tau/day, 155.236 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.60661 | 0.60661 | 0.60661 | 0.0 | 83.12 -Neigh | 0.092198 | 0.092198 | 0.092198 | 0.0 | 12.63 -Comm | 0.013581 | 0.013581 | 0.013581 | 0.0 | 1.86 -Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.02 -Modify | 0.014395 | 0.014395 | 0.014395 | 0.0 | 1.97 -Other | | 0.002878 | | | 0.39 +Pair | 1.3961 | 1.3961 | 1.3961 | 0.0 | 86.69 +Neigh | 0.13555 | 0.13555 | 0.13555 | 0.0 | 8.42 +Comm | 0.037732 | 0.037732 | 0.037732 | 0.0 | 2.34 +Output | 0.0003345 | 0.0003345 | 0.0003345 | 0.0 | 0.02 +Modify | 0.038016 | 0.038016 | 0.038016 | 0.0 | 2.36 +Other | | 0.002731 | | | 0.17 -Nlocal: 4000 ave 4000 max 4000 min +Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 5499 ave 5499 max 5499 min +Nghost: 5506.00 ave 5506 max 5506 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 151513 ave 151513 max 151513 min +Neighs: 151788.0 ave 151788 max 151788 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 151513 -Ave neighs/atom = 37.8783 +Total # of neighbors = 151788 +Ave neighs/atom = 37.947000 Neighbor list builds = 12 Dangerous builds not checked -Total wall time: 0:00:00 +Total wall time: 0:00:01 diff --git a/examples/melt/log.8Apr21.melt.g++.4 b/examples/melt/log.8Apr21.melt.g++.4 new file mode 100644 index 0000000000..1edbeac7aa --- /dev/null +++ b/examples/melt/log.8Apr21.melt.g++.4 @@ -0,0 +1,85 @@ +LAMMPS (8 Apr 2021) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms + create_atoms CPU = 0.001 seconds +mass 1 1.0 + +velocity all create 3.0 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +#dump id all atom 50 dump.melt + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.706 | 2.706 | 2.706 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6842865 -4.8082494 0 -2.2824513 5.5666131 + 100 1.6712577 -4.7875609 0 -2.281301 5.6613913 + 150 1.6444751 -4.7471034 0 -2.2810074 5.8614211 + 200 1.6471542 -4.7509053 0 -2.2807916 5.8805431 + 250 1.6645597 -4.7774327 0 -2.2812174 5.7526089 +Loop time of 0.490832 on 4 procs for 250 steps with 4000 atoms + +Performance: 220034.754 tau/day, 509.340 timesteps/s +96.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.35932 | 0.37256 | 0.38746 | 1.9 | 75.90 +Neigh | 0.035928 | 0.038449 | 0.042344 | 1.3 | 7.83 +Comm | 0.053452 | 0.068917 | 0.08485 | 5.3 | 14.04 +Output | 0.00015545 | 0.00023746 | 0.00047684 | 0.0 | 0.05 +Modify | 0.0096958 | 0.0097951 | 0.0098989 | 0.1 | 2.00 +Other | | 0.0008721 | | | 0.18 + +Nlocal: 1000.00 ave 1008 max 987 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 2711.25 ave 2728 max 2693 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 37947.0 ave 38966 max 37338 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 151788 +Ave neighs/atom = 37.947000 +Neighbor list builds = 12 +Dangerous builds not checked +Total wall time: 0:00:00