diff --git a/examples/meam/log.5Oct16.meam.icc.1 b/examples/meam/log.19May17.meam.g++.1 similarity index 68% copy from examples/meam/log.5Oct16.meam.icc.1 copy to examples/meam/log.19May17.meam.g++.1 index 200da68e0..a98de97f8 100644 --- a/examples/meam/log.5Oct16.meam.icc.1 +++ b/examples/meam/log.19May17.meam.g++.1 @@ -1,84 +1,95 @@ -LAMMPS (5 Oct 2016) +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task # Test of MEAM potential for SiC system units metal boundary p p p atom_style atomic read_data data.meam orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232) 1 by 1 by 1 MPI processor grid reading atoms ... 128 atoms pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C Reading potential file library.meam with DATE: 2012-06-29 Reading potential file SiC.meam with DATE: 2007-06-11 neighbor 0.3 bin neigh_modify delay 10 fix 1 all nve thermo 10 timestep 0.001 #dump 1 all atom 50 dump.meam #dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 #dump_modify 2 pad 3 element Si C #dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 #dump_modify 3 pad 3 element Si C run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 - binsize = 2.15 -> bins = 6 6 6 -Memory usage per processor = 7.39054 Mbytes + binsize = 2.15, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -636.38121 0 -636.38121 -76571.819 10 1807.8862 -666.21959 0 -636.54126 -150571.49 20 1932.4467 -668.2581 0 -636.53498 -120223.52 30 1951.3652 -668.58139 0 -636.54771 -100508.4 40 2172.5974 -672.22715 0 -636.5617 -110753.34 50 2056.9149 -670.33108 0 -636.56468 -105418.07 60 1947.9564 -668.52788 0 -636.55015 -111413.04 70 1994.7712 -669.28849 0 -636.54225 -109645.76 80 2126.0903 -671.43755 0 -636.53557 -97475.831 90 2065.755 -670.4349 0 -636.52338 -95858.837 100 2051.4553 -670.20799 0 -636.53122 -107068.9 -Loop time of 0.094512 on 1 procs for 100 steps with 128 atoms +Loop time of 0.0864418 on 1 procs for 100 steps with 128 atoms -Performance: 91.417 ns/day, 0.263 hours/ns, 1058.067 timesteps/s -99.4% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 99.952 ns/day, 0.240 hours/ns, 1156.848 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 | 0.091268 | 0.091268 | 0.091268 | 0.0 | 96.57 -Neigh | 0.0021861 | 0.0021861 | 0.0021861 | 0.0 | 2.31 -Comm | 0.00059438 | 0.00059438 | 0.00059438 | 0.0 | 0.63 -Output | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 | 0.0 | 0.10 -Modify | 0.00024438 | 0.00024438 | 0.00024438 | 0.0 | 0.26 -Other | | 0.000128 | | | 0.14 +Pair | 0.082592 | 0.082592 | 0.082592 | 0.0 | 95.55 +Neigh | 0.0028124 | 0.0028124 | 0.0028124 | 0.0 | 3.25 +Comm | 0.00049043 | 0.00049043 | 0.00049043 | 0.0 | 0.57 +Output | 0.00014329 | 0.00014329 | 0.00014329 | 0.0 | 0.17 +Modify | 0.00025415 | 0.00025415 | 0.00025415 | 0.0 | 0.29 +Other | | 0.0001497 | | | 0.17 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 543 ave 543 max 543 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1526 ave 1526 max 1526 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3052 ave 3052 max 3052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3052 Ave neighs/atom = 23.8438 Neighbor list builds = 10 Dangerous builds = 10 Total wall time: 0:00:00 diff --git a/examples/meam/log.5Oct16.meam.icc.4 b/examples/meam/log.19May17.meam.g++.4 similarity index 68% copy from examples/meam/log.5Oct16.meam.icc.4 copy to examples/meam/log.19May17.meam.g++.4 index 51a6619e3..adc34d08a 100644 --- a/examples/meam/log.5Oct16.meam.icc.4 +++ b/examples/meam/log.19May17.meam.g++.4 @@ -1,84 +1,95 @@ -LAMMPS (5 Oct 2016) +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task # Test of MEAM potential for SiC system units metal boundary p p p atom_style atomic read_data data.meam orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232) 1 by 2 by 2 MPI processor grid reading atoms ... 128 atoms pair_style meam pair_coeff * * library.meam Si C SiC.meam Si C Reading potential file library.meam with DATE: 2012-06-29 Reading potential file SiC.meam with DATE: 2007-06-11 neighbor 0.3 bin neigh_modify delay 10 fix 1 all nve thermo 10 timestep 0.001 #dump 1 all atom 50 dump.meam #dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 #dump_modify 2 pad 3 element Si C #dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 #dump_modify 3 pad 3 element Si C run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 - binsize = 2.15 -> bins = 6 6 6 -Memory usage per processor = 7.319 Mbytes + binsize = 2.15, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -636.38121 0 -636.38121 -76571.819 10 1807.8862 -666.21959 0 -636.54126 -150571.49 20 1932.4467 -668.2581 0 -636.53498 -120223.52 30 1951.3652 -668.58139 0 -636.54771 -100508.4 40 2172.5974 -672.22715 0 -636.5617 -110753.34 50 2056.9149 -670.33108 0 -636.56468 -105418.07 60 1947.9564 -668.52788 0 -636.55015 -111413.04 70 1994.7712 -669.28849 0 -636.54225 -109645.76 80 2126.0903 -671.43755 0 -636.53557 -97475.831 90 2065.755 -670.4349 0 -636.52338 -95858.837 100 2051.4553 -670.20799 0 -636.53122 -107068.9 -Loop time of 0.0350628 on 4 procs for 100 steps with 128 atoms +Loop time of 0.0389078 on 4 procs for 100 steps with 128 atoms -Performance: 246.415 ns/day, 0.097 hours/ns, 2852.026 timesteps/s -98.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 222.063 ns/day, 0.108 hours/ns, 2570.177 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.030952 | 0.031776 | 0.032203 | 0.3 | 90.63 -Neigh | 0.00058937 | 0.00061423 | 0.00063896 | 0.1 | 1.75 -Comm | 0.0018125 | 0.0022421 | 0.0030777 | 1.1 | 6.39 -Output | 0.00018525 | 0.00019765 | 0.00021911 | 0.1 | 0.56 -Modify | 8.0585e-05 | 9.0539e-05 | 9.7752e-05 | 0.1 | 0.26 -Other | | 0.0001422 | | | 0.41 +Pair | 0.031958 | 0.033267 | 0.034691 | 0.6 | 85.50 +Neigh | 0.00079155 | 0.00086409 | 0.00098801 | 0.0 | 2.22 +Comm | 0.0025704 | 0.0041765 | 0.005573 | 1.9 | 10.73 +Output | 0.0002749 | 0.00029588 | 0.00033569 | 0.0 | 0.76 +Modify | 9.4891e-05 | 0.00010347 | 0.00011587 | 0.0 | 0.27 +Other | | 0.000201 | | | 0.52 Nlocal: 32 ave 36 max 30 min Histogram: 1 2 0 0 0 0 0 0 0 1 Nghost: 293.75 ave 305 max 285 min Histogram: 2 0 0 0 0 0 0 1 0 1 Neighs: 381.5 ave 413 max 334 min Histogram: 1 0 0 0 1 0 0 0 0 2 FullNghs: 763 ave 866 max 678 min Histogram: 1 0 1 0 0 1 0 0 0 1 Total # of neighbors = 3052 Ave neighs/atom = 23.8438 Neighbor list builds = 10 Dangerous builds = 10 Total wall time: 0:00:00 diff --git a/examples/meam/log.5Oct16.meam.shear.icc.1 b/examples/meam/log.19May17.meam.shear.g++.1 similarity index 55% rename from examples/meam/log.5Oct16.meam.shear.icc.1 rename to examples/meam/log.19May17.meam.shear.g++.1 index 57f48d5ee..77b968845 100644 --- a/examples/meam/log.5Oct16.meam.shear.icc.1 +++ b/examples/meam/log.19May17.meam.shear.g++.1 @@ -1,196 +1,207 @@ -LAMMPS (5 Oct 2016) +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation units metal boundary s s p atom_style atomic lattice fcc 3.52 Lattice spacing in x,y,z = 3.52 3.52 3.52 region box block 0 16.0 0 10.0 0 2.828427 create_box 3 box Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606) 1 by 1 by 1 MPI processor grid lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 Lattice spacing in x,y,z = 3.52 4.97803 4.97803 create_atoms 1 box Created 1912 atoms pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 neighbor 0.3 bin neigh_modify delay 5 region lower block INF INF INF 0.9 INF INF region upper block INF INF 6.1 INF INF INF group lower region lower 264 atoms in group lower group upper region upper 264 atoms in group upper group boundary union lower upper 528 atoms in group boundary group mobile subtract all boundary 1384 atoms in group mobile set group lower type 2 264 settings made for type set group upper type 3 264 settings made for type # void #region void cylinder z 8 5 2.5 INF INF #delete_atoms region void # temp controllers compute new3d mobile temp compute new2d mobile temp/partial 0 1 1 # equilibrate velocity mobile create 300.0 5812775 temp new3d fix 1 all nve fix 2 boundary setforce 0.0 0.0 0.0 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) timestep 0.001 run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 - binsize = 2.15 -> bins = 27 17 5 -Memory usage per processor = 8.55725 Mbytes + binsize = 2.15, bins = 27 17 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02 25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02 50 300 -8149.7654 0 -8096.1353 10633.141 19684.382 75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745 100 300 -8173.6884 0 -8120.0584 5952.521 19886.589 -Loop time of 1.72323 on 1 procs for 100 steps with 1912 atoms +Loop time of 1.58103 on 1 procs for 100 steps with 1912 atoms -Performance: 5.014 ns/day, 4.787 hours/ns, 58.031 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 5.465 ns/day, 4.392 hours/ns, 63.250 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 | 1.7026 | 1.7026 | 1.7026 | 0.0 | 98.80 -Neigh | 0.014496 | 0.014496 | 0.014496 | 0.0 | 0.84 -Comm | 0.0015783 | 0.0015783 | 0.0015783 | 0.0 | 0.09 -Output | 6.0081e-05 | 6.0081e-05 | 6.0081e-05 | 0.0 | 0.00 -Modify | 0.0034628 | 0.0034628 | 0.0034628 | 0.0 | 0.20 -Other | | 0.00101 | | | 0.06 +Pair | 1.5561 | 1.5561 | 1.5561 | 0.0 | 98.42 +Neigh | 0.018544 | 0.018544 | 0.018544 | 0.0 | 1.17 +Comm | 0.0013864 | 0.0013864 | 0.0013864 | 0.0 | 0.09 +Output | 0.00011396 | 0.00011396 | 0.00011396 | 0.0 | 0.01 +Modify | 0.0038245 | 0.0038245 | 0.0038245 | 0.0 | 0.24 +Other | | 0.001096 | | | 0.07 Nlocal: 1912 ave 1912 max 1912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1672 ave 1672 max 1672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23806 ave 23806 max 23806 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47612 ave 47612 max 47612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47612 Ave neighs/atom = 24.9017 Neighbor list builds = 5 Dangerous builds = 0 # shear velocity upper set 1.0 0 0 velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes unfix 3 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 fix_modify 3 temp new2d #dump 1 all atom 500 dump.meam.shear #dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 #dump_modify 2 pad 4 #dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 #dump_modify 3 pad 4 thermo 100 thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) reset_timestep 0 run 3000 -Memory usage per processor = 8.73384 Mbytes +Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300.39988 -8173.6884 0 -8137.8874 4992.9811 19894.297 100 292.06374 -8177.7096 0 -8142.9021 2568.3762 19871.53 200 306.69894 -8177.1357 0 -8140.584 874.24259 20047.24 300 295.68229 -8172.9213 0 -8137.6825 -1049.0836 20091.759 400 308.99958 -8169.6355 0 -8132.8096 -1785.9335 20121.698 500 303.85723 -8163.984 0 -8127.7709 -150.56268 20183.813 600 300 -8157.7632 0 -8122.0099 1492.5742 20279.887 700 300 -8148.1328 0 -8112.3794 3506.9234 20435.302 800 300 -8139.1821 0 -8103.4288 3628.3957 20509.519 900 305.03425 -8126.7734 0 -8090.4201 5316.2206 20638.992 - 1000 304.00321 -8112.1616 0 -8075.9311 7441.9639 20767.243 - 1100 304.14051 -8096.5041 0 -8060.2573 9646.698 20888.167 - 1200 302.78461 -8080.5931 0 -8044.5079 11516.21 20995.917 - 1300 308.67046 -8061.6724 0 -8024.8857 11496.487 21130.013 - 1400 309.83019 -8046.2701 0 -8009.3452 12926.847 21247.271 - 1500 300 -8035.0322 0 -7999.2789 15346.188 21370.637 - 1600 300 -8030.6678 0 -7994.9144 14802.342 21496.446 - 1700 300 -8024.5988 0 -7988.8454 13177.445 21611.262 - 1800 300 -8023.045 0 -7987.2916 10240.041 21740.735 - 1900 300 -8028.2797 0 -7992.5263 6912.1441 21866.544 - 2000 300 -8036.4487 0 -8000.6953 3561.8365 21977.695 - 2100 300 -8037.8249 0 -8002.0715 2879.2618 22109.611 - 2200 300 -8033.6682 0 -7997.9148 4936.3695 22224.427 - 2300 304.49349 -8033.4561 0 -7997.1673 5593.0915 22356.343 - 2400 300 -8033.2969 0 -7997.5436 7537.0891 22473.601 - 2500 300 -8033.1874 0 -7997.4341 11476.447 22598.189 - 2600 307.77395 -8026.9234 0 -7990.2436 15758.81 22720.333 - 2700 300 -8021.1736 0 -7985.4203 17948.896 22832.706 - 2800 300 -8017.0863 0 -7981.3329 17154.618 22957.293 - 2900 300 -8012.0514 0 -7976.298 13224.292 23089.209 - 3000 304.58031 -8008.1654 0 -7971.8661 8572.9227 23211.354 -Loop time of 55.136 on 1 procs for 3000 steps with 1912 atoms - -Performance: 4.701 ns/day, 5.105 hours/ns, 54.411 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads + 1000 304.00321 -8112.1616 0 -8075.9311 7441.9638 20767.243 + 1100 304.14047 -8096.5041 0 -8060.2573 9646.6976 20888.167 + 1200 302.78457 -8080.5931 0 -8044.5079 11516.209 20995.917 + 1300 308.67054 -8061.6724 0 -8024.8857 11496.479 21130.013 + 1400 309.8301 -8046.27 0 -8009.3452 12926.835 21247.271 + 1500 300 -8035.0321 0 -7999.2788 15346.455 21370.637 + 1600 300 -8030.6657 0 -7994.9123 14802.869 21496.446 + 1700 300 -8024.5251 0 -7988.7718 13176.923 21611.262 + 1800 300 -8022.9963 0 -7987.243 10260.665 21741.956 + 1900 300 -8028.0522 0 -7992.2988 6955.1367 21867.765 + 2000 300 -8037.2708 0 -8001.5175 3520.3749 21987.467 + 2100 300 -8035.9945 0 -8000.2412 3237.6121 22109.611 + 2200 300 -8036.1882 0 -8000.4348 4295.1386 22223.205 + 2300 300 -8032.7689 0 -7997.0155 6231.2346 22355.121 + 2400 300 -8034.6621 0 -7998.9088 8585.3799 22468.716 + 2500 300 -8031.7774 0 -7996.0241 11627.871 22587.196 + 2600 300 -8024.032 0 -7988.2786 16254.69 22716.669 + 2700 308.64215 -8017.407 0 -7980.6237 18440.226 22835.149 + 2800 300 -8015.7348 0 -7979.9814 17601.716 22957.293 + 2900 305.82558 -8013.7448 0 -7977.2972 14123.494 23089.209 + 3000 300 -8011.0289 0 -7975.2755 9957.2884 23205.247 +Loop time of 51.9315 on 1 procs for 3000 steps with 1912 atoms + +Performance: 4.991 ns/day, 4.808 hours/ns, 57.768 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 54.317 | 54.317 | 54.317 | -nan | 98.51 -Neigh | 0.63189 | 0.63189 | 0.63189 | 0.0 | 1.15 -Comm | 0.051245 | 0.051245 | 0.051245 | 0.0 | 0.09 -Output | 0.0005548 | 0.0005548 | 0.0005548 | 0.0 | 0.00 -Modify | 0.10452 | 0.10452 | 0.10452 | 0.0 | 0.19 -Other | | 0.03128 | | | 0.06 +Pair | 50.918 | 50.918 | 50.918 | 0.0 | 98.05 +Neigh | 0.81033 | 0.81033 | 0.81033 | 0.0 | 1.56 +Comm | 0.047331 | 0.047331 | 0.047331 | 0.0 | 0.09 +Output | 0.0011976 | 0.0011976 | 0.0011976 | 0.0 | 0.00 +Modify | 0.11889 | 0.11889 | 0.11889 | 0.0 | 0.23 +Other | | 0.03606 | | | 0.07 Nlocal: 1912 ave 1912 max 1912 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1667 ave 1667 max 1667 min +Nghost: 1672 ave 1672 max 1672 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 23365 ave 23365 max 23365 min +Neighs: 23557 ave 23557 max 23557 min Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 46730 ave 46730 max 46730 min +FullNghs: 47114 ave 47114 max 47114 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 46730 -Ave neighs/atom = 24.4404 +Total # of neighbors = 47114 +Ave neighs/atom = 24.6412 Neighbor list builds = 221 Dangerous builds = 0 -Total wall time: 0:00:56 +Total wall time: 0:00:53 diff --git a/examples/meam/log.5Oct16.meam.shear.icc.4 b/examples/meam/log.19May17.meam.shear.g++.4 similarity index 55% rename from examples/meam/log.5Oct16.meam.shear.icc.4 rename to examples/meam/log.19May17.meam.shear.g++.4 index 2f197de92..84cb94f4b 100644 --- a/examples/meam/log.5Oct16.meam.shear.icc.4 +++ b/examples/meam/log.19May17.meam.shear.g++.4 @@ -1,196 +1,207 @@ -LAMMPS (5 Oct 2016) +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation units metal boundary s s p atom_style atomic lattice fcc 3.52 Lattice spacing in x,y,z = 3.52 3.52 3.52 region box block 0 16.0 0 10.0 0 2.828427 create_box 3 box Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606) 2 by 2 by 1 MPI processor grid lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 Lattice spacing in x,y,z = 3.52 4.97803 4.97803 create_atoms 1 box Created 1912 atoms pair_style meam pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 Reading potential file library.meam with DATE: 2012-06-29 Reading potential file Ni.meam with DATE: 2007-06-11 neighbor 0.3 bin neigh_modify delay 5 region lower block INF INF INF 0.9 INF INF region upper block INF INF 6.1 INF INF INF group lower region lower 264 atoms in group lower group upper region upper 264 atoms in group upper group boundary union lower upper 528 atoms in group boundary group mobile subtract all boundary 1384 atoms in group mobile set group lower type 2 264 settings made for type set group upper type 3 264 settings made for type # void #region void cylinder z 8 5 2.5 INF INF #delete_atoms region void # temp controllers compute new3d mobile temp compute new2d mobile temp/partial 0 1 1 # equilibrate velocity mobile create 300.0 5812775 temp new3d fix 1 all nve fix 2 boundary setforce 0.0 0.0 0.0 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) timestep 0.001 run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 - binsize = 2.15 -> bins = 27 17 5 -Memory usage per processor = 7.74146 Mbytes + binsize = 2.15, bins = 27 17 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02 25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02 50 300 -8150.0685 0 -8096.4384 10317.407 19685.743 75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814 100 300 -8176.5141 0 -8122.884 4162.2559 19873.327 -Loop time of 0.469502 on 4 procs for 100 steps with 1912 atoms +Loop time of 0.482293 on 4 procs for 100 steps with 1912 atoms -Performance: 18.402 ns/day, 1.304 hours/ns, 212.992 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 17.914 ns/day, 1.340 hours/ns, 207.343 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.44052 | 0.45213 | 0.45813 | 1.0 | 96.30 -Neigh | 0.0036478 | 0.0037832 | 0.003854 | 0.1 | 0.81 -Comm | 0.0055377 | 0.011533 | 0.02316 | 6.5 | 2.46 -Output | 9.0837e-05 | 9.8228e-05 | 0.00011325 | 0.1 | 0.02 -Modify | 0.00098062 | 0.0010158 | 0.0010564 | 0.1 | 0.22 -Other | | 0.0009408 | | | 0.20 +Pair | 0.44374 | 0.45604 | 0.46922 | 1.4 | 94.56 +Neigh | 0.0047338 | 0.0049097 | 0.0051899 | 0.2 | 1.02 +Comm | 0.0054841 | 0.019044 | 0.031472 | 6.9 | 3.95 +Output | 0.00012755 | 0.00013644 | 0.00015831 | 0.0 | 0.03 +Modify | 0.0011139 | 0.0011852 | 0.0012643 | 0.2 | 0.25 +Other | | 0.0009753 | | | 0.20 Nlocal: 478 ave 492 max 465 min Histogram: 2 0 0 0 0 0 0 0 1 1 Nghost: 809 ave 822 max 795 min Histogram: 1 1 0 0 0 0 0 0 0 2 Neighs: 5916 ave 6133 max 5658 min Histogram: 1 0 0 1 0 0 0 0 1 1 FullNghs: 11832 ave 12277 max 11299 min Histogram: 1 0 0 1 0 0 0 0 1 1 Total # of neighbors = 47328 Ave neighs/atom = 24.7531 Neighbor list builds = 5 Dangerous builds = 0 # shear velocity upper set 1.0 0 0 velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes unfix 3 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 fix_modify 3 temp new2d #dump 1 all atom 500 dump.meam.shear #dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 #dump_modify 2 pad 4 #dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 #dump_modify 3 pad 4 thermo 100 thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) reset_timestep 0 run 3000 -Memory usage per processor = 7.78572 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 295.32113 -8176.5141 0 -8141.3183 3169.3113 19886.93 100 292.00251 -8176.5358 0 -8141.7356 -825.04802 19918.765 200 306.11682 -8176.7719 0 -8140.2895 -1370.6886 19948.877 300 300 -8172.6262 0 -8136.8729 -1735.9765 20085.714 400 306.88489 -8168.435 0 -8131.8611 -933.02058 20117.012 500 308.99003 -8166.2906 0 -8129.4658 -1049.3138 20198.256 600 304.23435 -8158.0946 0 -8121.8366 583.93595 20328.848 700 296.44479 -8149.7914 0 -8114.4618 1985.4155 20421.046 800 307.75738 -8139.1649 0 -8102.487 4319.078 20513.183 900 304.61422 -8126.9246 0 -8090.6214 6654.0963 20640.213 - 1000 300 -8113.8464 0 -8078.0931 7760.1242 20768.465 - 1100 300.17874 -8097.7469 0 -8061.9722 8438.1263 20874.731 - 1200 306.01444 -8083.3367 0 -8046.8665 10835.585 20994.432 + 1000 300 -8113.8464 0 -8078.0931 7760.1239 20768.465 + 1100 300.17873 -8097.7469 0 -8061.9722 8438.126 20874.731 + 1200 306.01441 -8083.3367 0 -8046.8665 10835.586 20994.432 1300 300 -8067.022 0 -8031.2686 11216.067 21126.348 - 1400 300 -8053.223 0 -8017.4697 10570.21 21253.378 - 1500 300 -8043.4848 0 -8007.7314 11360.829 21375.523 - 1600 300 -8034.6216 0 -7998.8683 11371.642 21498.889 - 1700 300 -8028.6774 0 -7992.924 9595.8772 21613.705 - 1800 300 -8033.0808 0 -7997.3274 8767.6261 21743.178 - 1900 303.30302 -8035.1958 0 -7999.0488 8059.5152 21859.215 - 2000 300 -8025.0857 0 -7989.3323 9308.9938 21980.138 - 2100 300 -8041.5796 0 -8005.8263 6656.0066 22108.39 - 2200 300 -8039.6315 0 -8003.8781 7532.9687 22226.87 - 2300 300 -8053.203 0 -8017.4497 8466.9094 22356.343 - 2400 300 -8050.9154 0 -8015.162 11784.136 22467.494 - 2500 300 -8037.6394 0 -8001.886 16464.786 22588.417 - 2600 300 -8030.9221 0 -7995.1688 16807.326 22719.112 - 2700 300 -8025.2102 0 -7989.4569 13729.61 22837.592 - 2800 300 -8014.5312 0 -7978.7779 6784.6283 22953.629 - 2900 300 -8007.4768 0 -7971.7234 1362.3131 23084.324 - 3000 300 -7994.5614 0 -7958.808 -1726.5273 23194.254 -Loop time of 14.8108 on 4 procs for 3000 steps with 1912 atoms - -Performance: 17.501 ns/day, 1.371 hours/ns, 202.555 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads + 1400 300 -8053.223 0 -8017.4697 10570.206 21253.378 + 1500 300 -8043.4849 0 -8007.7315 11360.766 21375.523 + 1600 300 -8034.621 0 -7998.8676 11371.584 21498.889 + 1700 300 -8028.6783 0 -7992.925 9596.524 21613.705 + 1800 300 -8033.0818 0 -7997.3285 8767.2651 21743.178 + 1900 303.18912 -8035.194 0 -7999.0606 8059.9558 21859.215 + 2000 300 -8025.0327 0 -7989.2794 9305.7521 21980.138 + 2100 300 -8041.4626 0 -8005.7092 6623.8789 22108.39 + 2200 300 -8040.3133 0 -8004.5599 7512.9368 22225.648 + 2300 300 -8055.6567 0 -8019.9033 8281.354 22344.128 + 2400 304.05922 -8050.289 0 -8014.0518 11964.826 22476.044 + 2500 305.75646 -8037.0481 0 -8000.6087 16594.032 22595.746 + 2600 307.71105 -8031.2253 0 -7994.5529 18381.745 22708.119 + 2700 307.397 -8026.5338 0 -7989.8988 13944.653 22829.042 + 2800 309.3455 -8020.2305 0 -7983.3634 7037.4046 22954.851 + 2900 301.2859 -8010.4731 0 -7974.5665 3843.8972 23072.109 + 3000 303.29908 -8000.0395 0 -7963.8929 364.90172 23207.69 +Loop time of 14.5278 on 4 procs for 3000 steps with 1912 atoms + +Performance: 17.842 ns/day, 1.345 hours/ns, 206.500 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 14.05 | 14.237 | 14.332 | 2.9 | 96.12 -Neigh | 0.1592 | 0.16414 | 0.1671 | 0.8 | 1.11 -Comm | 0.26002 | 0.35589 | 0.54696 | 18.8 | 2.40 -Output | 0.00061679 | 0.00065172 | 0.0007441 | 0.2 | 0.00 -Modify | 0.02895 | 0.030174 | 0.03104 | 0.5 | 0.20 -Other | | 0.02338 | | | 0.16 - -Nlocal: 478 ave 509 max 448 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 799.25 ave 844 max 756 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 5813.25 ave 6081 max 5602 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -FullNghs: 11626.5 ave 12151 max 11205 min -Histogram: 1 1 0 0 0 0 1 0 0 1 - -Total # of neighbors = 46506 -Ave neighs/atom = 24.3232 -Neighbor list builds = 225 +Pair | 13.872 | 13.929 | 13.998 | 1.4 | 95.88 +Neigh | 0.20891 | 0.21114 | 0.21272 | 0.3 | 1.45 +Comm | 0.25364 | 0.32377 | 0.37706 | 8.9 | 2.23 +Output | 0.0011427 | 0.0012097 | 0.0013931 | 0.3 | 0.01 +Modify | 0.033687 | 0.033991 | 0.034694 | 0.2 | 0.23 +Other | | 0.02871 | | | 0.20 + +Nlocal: 478 ave 509 max 445 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 804 ave 845 max 759 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Neighs: 5827 ave 6177 max 5496 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +FullNghs: 11654 ave 12330 max 11039 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 46616 +Ave neighs/atom = 24.3808 +Neighbor list builds = 223 Dangerous builds = 0 Total wall time: 0:00:15 diff --git a/examples/meam/log.5Oct16.meam.icc.1 b/examples/meam/log.19May17.meamc.g++.1 similarity index 63% rename from examples/meam/log.5Oct16.meam.icc.1 rename to examples/meam/log.19May17.meamc.g++.1 index 200da68e0..4aa1f7bcc 100644 --- a/examples/meam/log.5Oct16.meam.icc.1 +++ b/examples/meam/log.19May17.meamc.g++.1 @@ -1,84 +1,95 @@ -LAMMPS (5 Oct 2016) +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task # Test of MEAM potential for SiC system units metal boundary p p p atom_style atomic read_data data.meam orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232) 1 by 1 by 1 MPI processor grid reading atoms ... 128 atoms -pair_style meam +pair_style meam/c pair_coeff * * library.meam Si C SiC.meam Si C Reading potential file library.meam with DATE: 2012-06-29 Reading potential file SiC.meam with DATE: 2007-06-11 neighbor 0.3 bin neigh_modify delay 10 fix 1 all nve thermo 10 timestep 0.001 #dump 1 all atom 50 dump.meam #dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 #dump_modify 2 pad 3 element Si C #dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 #dump_modify 3 pad 3 element Si C run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 - binsize = 2.15 -> bins = 6 6 6 -Memory usage per processor = 7.39054 Mbytes + binsize = 2.15, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/c, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/c, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -636.38121 0 -636.38121 -76571.819 10 1807.8862 -666.21959 0 -636.54126 -150571.49 20 1932.4467 -668.2581 0 -636.53498 -120223.52 30 1951.3652 -668.58139 0 -636.54771 -100508.4 40 2172.5974 -672.22715 0 -636.5617 -110753.34 50 2056.9149 -670.33108 0 -636.56468 -105418.07 60 1947.9564 -668.52788 0 -636.55015 -111413.04 70 1994.7712 -669.28849 0 -636.54225 -109645.76 - 80 2126.0903 -671.43755 0 -636.53557 -97475.831 - 90 2065.755 -670.4349 0 -636.52338 -95858.837 - 100 2051.4553 -670.20799 0 -636.53122 -107068.9 -Loop time of 0.094512 on 1 procs for 100 steps with 128 atoms + 80 2126.0903 -671.43755 0 -636.53557 -97475.832 + 90 2065.7549 -670.4349 0 -636.52338 -95858.836 + 100 2051.4553 -670.20799 0 -636.53122 -107068.89 +Loop time of 0.0778153 on 1 procs for 100 steps with 128 atoms -Performance: 91.417 ns/day, 0.263 hours/ns, 1058.067 timesteps/s -99.4% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 111.032 ns/day, 0.216 hours/ns, 1285.094 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.091268 | 0.091268 | 0.091268 | 0.0 | 96.57 -Neigh | 0.0021861 | 0.0021861 | 0.0021861 | 0.0 | 2.31 -Comm | 0.00059438 | 0.00059438 | 0.00059438 | 0.0 | 0.63 -Output | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 | 0.0 | 0.10 -Modify | 0.00024438 | 0.00024438 | 0.00024438 | 0.0 | 0.26 -Other | | 0.000128 | | | 0.14 +Pair | 0.073801 | 0.073801 | 0.073801 | 0.0 | 94.84 +Neigh | 0.0029731 | 0.0029731 | 0.0029731 | 0.0 | 3.82 +Comm | 0.00047708 | 0.00047708 | 0.00047708 | 0.0 | 0.61 +Output | 0.00015664 | 0.00015664 | 0.00015664 | 0.0 | 0.20 +Modify | 0.00025702 | 0.00025702 | 0.00025702 | 0.0 | 0.33 +Other | | 0.0001504 | | | 0.19 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 543 ave 543 max 543 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1526 ave 1526 max 1526 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3052 ave 3052 max 3052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3052 Ave neighs/atom = 23.8438 Neighbor list builds = 10 Dangerous builds = 10 Total wall time: 0:00:00 diff --git a/examples/meam/log.5Oct16.meam.icc.4 b/examples/meam/log.19May17.meamc.g++.4 similarity index 63% rename from examples/meam/log.5Oct16.meam.icc.4 rename to examples/meam/log.19May17.meamc.g++.4 index 51a6619e3..3701fb80d 100644 --- a/examples/meam/log.5Oct16.meam.icc.4 +++ b/examples/meam/log.19May17.meamc.g++.4 @@ -1,84 +1,95 @@ -LAMMPS (5 Oct 2016) +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task # Test of MEAM potential for SiC system units metal boundary p p p atom_style atomic read_data data.meam orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232) 1 by 2 by 2 MPI processor grid reading atoms ... 128 atoms -pair_style meam +pair_style meam/c pair_coeff * * library.meam Si C SiC.meam Si C Reading potential file library.meam with DATE: 2012-06-29 Reading potential file SiC.meam with DATE: 2007-06-11 neighbor 0.3 bin neigh_modify delay 10 fix 1 all nve thermo 10 timestep 0.001 #dump 1 all atom 50 dump.meam #dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 #dump_modify 2 pad 3 element Si C #dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 #dump_modify 3 pad 3 element Si C run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 - binsize = 2.15 -> bins = 6 6 6 -Memory usage per processor = 7.319 Mbytes + binsize = 2.15, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/c, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/c, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -636.38121 0 -636.38121 -76571.819 10 1807.8862 -666.21959 0 -636.54126 -150571.49 20 1932.4467 -668.2581 0 -636.53498 -120223.52 30 1951.3652 -668.58139 0 -636.54771 -100508.4 40 2172.5974 -672.22715 0 -636.5617 -110753.34 50 2056.9149 -670.33108 0 -636.56468 -105418.07 60 1947.9564 -668.52788 0 -636.55015 -111413.04 70 1994.7712 -669.28849 0 -636.54225 -109645.76 - 80 2126.0903 -671.43755 0 -636.53557 -97475.831 - 90 2065.755 -670.4349 0 -636.52338 -95858.837 - 100 2051.4553 -670.20799 0 -636.53122 -107068.9 -Loop time of 0.0350628 on 4 procs for 100 steps with 128 atoms + 80 2126.0903 -671.43755 0 -636.53557 -97475.832 + 90 2065.7549 -670.4349 0 -636.52338 -95858.836 + 100 2051.4553 -670.20799 0 -636.53122 -107068.89 +Loop time of 0.037066 on 4 procs for 100 steps with 128 atoms -Performance: 246.415 ns/day, 0.097 hours/ns, 2852.026 timesteps/s -98.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 233.097 ns/day, 0.103 hours/ns, 2697.887 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 | 0.030952 | 0.031776 | 0.032203 | 0.3 | 90.63 -Neigh | 0.00058937 | 0.00061423 | 0.00063896 | 0.1 | 1.75 -Comm | 0.0018125 | 0.0022421 | 0.0030777 | 1.1 | 6.39 -Output | 0.00018525 | 0.00019765 | 0.00021911 | 0.1 | 0.56 -Modify | 8.0585e-05 | 9.0539e-05 | 9.7752e-05 | 0.1 | 0.26 -Other | | 0.0001422 | | | 0.41 +Pair | 0.029985 | 0.031596 | 0.033021 | 0.8 | 85.24 +Neigh | 0.0007906 | 0.00085384 | 0.00088596 | 0.0 | 2.30 +Comm | 0.0025654 | 0.0040313 | 0.0057514 | 2.2 | 10.88 +Output | 0.00027013 | 0.00029153 | 0.00033426 | 0.0 | 0.79 +Modify | 9.5367e-05 | 0.00010639 | 0.00012016 | 0.0 | 0.29 +Other | | 0.0001866 | | | 0.50 Nlocal: 32 ave 36 max 30 min Histogram: 1 2 0 0 0 0 0 0 0 1 Nghost: 293.75 ave 305 max 285 min Histogram: 2 0 0 0 0 0 0 1 0 1 Neighs: 381.5 ave 413 max 334 min Histogram: 1 0 0 0 1 0 0 0 0 2 FullNghs: 763 ave 866 max 678 min Histogram: 1 0 1 0 0 1 0 0 0 1 Total # of neighbors = 3052 Ave neighs/atom = 23.8438 Neighbor list builds = 10 Dangerous builds = 10 Total wall time: 0:00:00 diff --git a/examples/meam/log.19May17.meamc.shear.g++.1 b/examples/meam/log.19May17.meamc.shear.g++.1 new file mode 100644 index 000000000..5eb06592d --- /dev/null +++ b/examples/meam/log.19May17.meamc.shear.g++.1 @@ -0,0 +1,207 @@ +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box +Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606) + 1 by 1 by 1 MPI processor grid + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 +Lattice spacing in x,y,z = 3.52 4.97803 4.97803 +create_atoms 1 box +Created 1912 atoms + +pair_style meam/c +pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 +Reading potential file library.meam with DATE: 2012-06-29 +Reading potential file Ni.meam with DATE: 2007-06-11 + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +264 atoms in group lower +group upper region upper +264 atoms in group upper +group boundary union lower upper +528 atoms in group boundary +group mobile subtract all boundary +1384 atoms in group mobile + +set group lower type 2 + 264 settings made for type +set group upper type 3 + 264 settings made for type + +# void + +#region void cylinder z 8 5 2.5 INF INF +#delete_atoms region void + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) + +timestep 0.001 +run 100 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 27 17 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/c, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/c, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02 + 25 222.78953 -8188.1215 0 -8148.2941 9095.9003 19547.02 + 50 300 -8149.7654 0 -8096.1353 10633.139 19684.382 + 75 304.80657 -8163.4557 0 -8108.9665 7045.4555 19759.745 + 100 300 -8173.6884 0 -8120.0584 5952.5197 19886.589 +Loop time of 1.46986 on 1 procs for 100 steps with 1912 atoms + +Performance: 5.878 ns/day, 4.083 hours/ns, 68.034 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 | 1.445 | 1.445 | 1.445 | 0.0 | 98.31 +Neigh | 0.018564 | 0.018564 | 0.018564 | 0.0 | 1.26 +Comm | 0.0012956 | 0.0012956 | 0.0012956 | 0.0 | 0.09 +Output | 0.00012612 | 0.00012612 | 0.00012612 | 0.0 | 0.01 +Modify | 0.0038197 | 0.0038197 | 0.0038197 | 0.0 | 0.26 +Other | | 0.001095 | | | 0.07 + +Nlocal: 1912 ave 1912 max 1912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1672 ave 1672 max 1672 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 23806 ave 23806 max 23806 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 47612 ave 47612 max 47612 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 47612 +Ave neighs/atom = 24.9017 +Neighbor list builds = 5 +Dangerous builds = 0 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +#dump 1 all atom 500 dump.meam.shear + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 +#dump_modify 2 pad 4 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 +#dump_modify 3 pad 4 + +thermo 100 +thermo_modify temp new2d +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) + +reset_timestep 0 +run 3000 +Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300.39988 -8173.6884 0 -8137.8874 4992.9799 19894.297 + 100 292.06374 -8177.7096 0 -8142.9021 2568.3756 19871.53 + 200 306.69894 -8177.1357 0 -8140.584 874.24118 20047.24 + 300 295.68216 -8172.9213 0 -8137.6825 -1049.0799 20091.759 + 400 308.99955 -8169.6355 0 -8132.8096 -1785.9554 20121.698 + 500 303.85688 -8163.9842 0 -8127.7712 -150.60892 20183.813 + 600 300 -8157.7627 0 -8122.0093 1492.8514 20279.887 + 700 300 -8148.1314 0 -8112.3781 3507.1949 20435.297 + 800 300 -8139.1805 0 -8103.4272 3628.5908 20509.519 + 900 305.03217 -8126.7741 0 -8090.421 5313.7881 20638.992 + 1000 303.7648 -8112.1574 0 -8075.9554 7433.3181 20767.243 + 1100 302.39719 -8096.1399 0 -8060.1009 9681.7685 20888.167 + 1200 304.04919 -8080.7022 0 -8044.4663 11621.974 21011.532 + 1300 303.56395 -8062.0984 0 -8025.9203 11410.793 21125.127 + 1400 309.92338 -8046.0008 0 -8009.0648 12408.158 21246.05 + 1500 300 -8034.7094 0 -7998.956 14845.312 21363.308 + 1600 300 -8028.4585 0 -7992.7051 15120.908 21489.117 + 1700 308.23904 -8015.9618 0 -7979.2265 14714.73 21612.483 + 1800 300 -8013.5458 0 -7977.7924 11955.065 21737.07 + 1900 300 -8012.2984 0 -7976.545 6667.1353 21854.329 + 2000 300 -8025.6019 0 -7989.8485 2006.6545 21981.359 + 2100 300 -8027.6823 0 -7991.9289 16.47633 22109.611 + 2200 300 -8029.6905 0 -7993.9372 -603.98293 22224.427 + 2300 300 -8033.2663 0 -7997.513 -464.68645 22351.457 + 2400 300 -8040.6863 0 -8004.9329 -640.54641 22467.494 + 2500 300 -8037.0332 0 -8001.2799 1504.2444 22587.196 + 2600 300 -8036.0909 0 -8000.3375 4190.2052 22708.119 + 2700 308.97892 -8028.5269 0 -7991.7035 5755.7418 22832.706 + 2800 305.27189 -8023.8286 0 -7987.4469 2611.7551 22962.179 + 2900 301.94251 -8017.4523 0 -7981.4675 358.11928 23078.216 + 3000 305.67682 -8009.853 0 -7973.4231 -2345.487 23197.918 +Loop time of 48.351 on 1 procs for 3000 steps with 1912 atoms + +Performance: 5.361 ns/day, 4.477 hours/ns, 62.046 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 47.356 | 47.356 | 47.356 | 0.0 | 97.94 +Neigh | 0.79977 | 0.79977 | 0.79977 | 0.0 | 1.65 +Comm | 0.043133 | 0.043133 | 0.043133 | 0.0 | 0.09 +Output | 0.0011899 | 0.0011899 | 0.0011899 | 0.0 | 0.00 +Modify | 0.11648 | 0.11648 | 0.11648 | 0.0 | 0.24 +Other | | 0.03404 | | | 0.07 + +Nlocal: 1912 ave 1912 max 1912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1662 ave 1662 max 1662 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 23143 ave 23143 max 23143 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 46286 ave 46286 max 46286 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 46286 +Ave neighs/atom = 24.2082 +Neighbor list builds = 220 +Dangerous builds = 0 +Total wall time: 0:00:49 diff --git a/examples/meam/log.19May17.meamc.shear.g++.4 b/examples/meam/log.19May17.meamc.shear.g++.4 new file mode 100644 index 000000000..136459a44 --- /dev/null +++ b/examples/meam/log.19May17.meamc.shear.g++.4 @@ -0,0 +1,207 @@ +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box +Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606) + 2 by 2 by 1 MPI processor grid + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 +Lattice spacing in x,y,z = 3.52 4.97803 4.97803 +create_atoms 1 box +Created 1912 atoms + +pair_style meam/c +pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 +Reading potential file library.meam with DATE: 2012-06-29 +Reading potential file Ni.meam with DATE: 2007-06-11 + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +264 atoms in group lower +group upper region upper +264 atoms in group upper +group boundary union lower upper +528 atoms in group boundary +group mobile subtract all boundary +1384 atoms in group mobile + +set group lower type 2 + 264 settings made for type +set group upper type 3 + 264 settings made for type + +# void + +#region void cylinder z 8 5 2.5 INF INF +#delete_atoms region void + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) + +timestep 0.001 +run 100 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 27 17 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/c, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/c, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02 + 25 221.59546 -8187.6813 0 -8148.0673 9100.4505 19547.02 + 50 300 -8150.0685 0 -8096.4384 10317.406 19685.743 + 75 307.76021 -8164.6669 0 -8109.6496 6289.7123 19757.814 + 100 300 -8176.5141 0 -8122.884 4162.2548 19873.327 +Loop time of 0.435874 on 4 procs for 100 steps with 1912 atoms + +Performance: 19.822 ns/day, 1.211 hours/ns, 229.424 timesteps/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.4092 | 0.41563 | 0.42184 | 0.7 | 95.35 +Neigh | 0.0048575 | 0.004932 | 0.0049984 | 0.1 | 1.13 +Comm | 0.0069079 | 0.013151 | 0.019513 | 4.2 | 3.02 +Output | 0.00012398 | 0.00013405 | 0.00015688 | 0.0 | 0.03 +Modify | 0.0011275 | 0.0011509 | 0.0011735 | 0.1 | 0.26 +Other | | 0.0008795 | | | 0.20 + +Nlocal: 478 ave 492 max 465 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 809 ave 822 max 795 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 5916 ave 6133 max 5658 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +FullNghs: 11832 ave 12277 max 11299 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 47328 +Ave neighs/atom = 24.7531 +Neighbor list builds = 5 +Dangerous builds = 0 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +#dump 1 all atom 500 dump.meam.shear + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 +#dump_modify 2 pad 4 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 +#dump_modify 3 pad 4 + +thermo 100 +thermo_modify temp new2d +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) + +reset_timestep 0 +run 3000 +Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 295.32113 -8176.5141 0 -8141.3183 3169.3102 19886.93 + 100 292.0025 -8176.5358 0 -8141.7356 -825.04852 19918.765 + 200 306.11682 -8176.7718 0 -8140.2895 -1370.6881 19948.878 + 300 300 -8172.6262 0 -8136.8729 -1735.9794 20085.715 + 400 306.88504 -8168.4351 0 -8131.8612 -933.05532 20117.008 + 500 308.99111 -8166.2909 0 -8129.466 -1049.3442 20198.267 + 600 304.22555 -8158.0946 0 -8121.8377 583.69142 20328.753 + 700 296.41606 -8149.7777 0 -8114.4515 1986.7982 20421.032 + 800 307.88628 -8139.1709 0 -8102.4776 4311.4142 20513.183 + 900 303.37209 -8126.9382 0 -8090.7829 6712.7316 20640.213 + 1000 300 -8113.7973 0 -8078.044 7630.2594 20750.143 + 1100 300.07815 -8098.1383 0 -8062.3756 8423.7063 20879.616 + 1200 300 -8083.3163 0 -8047.563 10772.917 21000.539 + 1300 300 -8066.6741 0 -8030.9208 10834.336 21128.791 + 1400 300 -8050.8799 0 -8015.1265 10842.382 21257.043 + 1500 300 -8040.3206 0 -8004.5673 11852.589 21362.087 + 1600 300 -8033.2471 0 -7997.4937 11298.745 21492.782 + 1700 300 -8030.6375 0 -7994.8842 10850.43 21610.04 + 1800 300 -8035.1631 0 -7999.4097 9985.6107 21734.628 + 1900 308.56562 -8040.1954 0 -8003.4213 9865.7107 21859.215 + 2000 300 -8030.1651 0 -7994.4117 11817.502 21980.138 + 2100 300 -8031.6147 0 -7995.8613 12791.357 22101.061 + 2200 300 -8033.7793 0 -7998.0259 13823.043 22234.198 + 2300 300 -8040.5964 0 -8004.8431 16204.549 22350.236 + 2400 309.42867 -8045.9414 0 -8009.0644 18506.386 22465.051 + 2500 300 -8054.2629 0 -8018.5095 20099.612 22593.303 + 2600 300 -8054.9562 0 -8019.2028 20036.318 22721.555 + 2700 300 -8051.4788 0 -8015.7254 16993.437 22844.921 + 2800 300 -8050.6908 0 -8014.9374 9048.5896 22964.622 + 2900 309.90783 -8044.3096 0 -8007.3754 5017.0198 23080.659 + 3000 300 -8035.8165 0 -8000.0632 2084.8999 23207.69 +Loop time of 13.4901 on 4 procs for 3000 steps with 1912 atoms + +Performance: 19.214 ns/day, 1.249 hours/ns, 222.386 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.851 | 12.919 | 12.945 | 1.1 | 95.76 +Neigh | 0.20449 | 0.20777 | 0.21169 | 0.6 | 1.54 +Comm | 0.27479 | 0.30264 | 0.36667 | 6.8 | 2.24 +Output | 0.0010171 | 0.0010971 | 0.0012388 | 0.3 | 0.01 +Modify | 0.033248 | 0.033878 | 0.034567 | 0.3 | 0.25 +Other | | 0.02594 | | | 0.19 + +Nlocal: 478 ave 506 max 450 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 790.5 ave 822 max 751 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 5829.5 ave 6014 max 5672 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +FullNghs: 11659 ave 12027 max 11320 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 46636 +Ave neighs/atom = 24.3912 +Neighbor list builds = 220 +Dangerous builds = 0 +Total wall time: 0:00:13