From 0bc1c3b2a28859c2b49c079a84595bd3eb92b820 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 Jun 2020 05:48:49 -0400 Subject: [PATCH] update example logs and inputs --- examples/USER/mesont/MESONT-TABTP_10_10.xrs | 1 + examples/USER/mesont/in.bundle | 3 +- examples/USER/mesont/in.film | 5 +- ...bundle.g++.1 => log.2Jun2020.bundle.g++.1} | 27 +++--- .../USER/mesont/log.2Jun2020.bundle.g++.4 | 90 +++++++++++++++++++ ...020.film.g++.1 => log.2Jun2020.film.g++.1} | 30 +++---- examples/USER/mesont/log.2Jun2020.film.g++.4 | 81 +++++++++++++++++ 7 files changed, 201 insertions(+), 36 deletions(-) create mode 120000 examples/USER/mesont/MESONT-TABTP_10_10.xrs rename examples/USER/mesont/{log.3Mar2020.bundle.g++.1 => log.2Jun2020.bundle.g++.1} (79%) create mode 100644 examples/USER/mesont/log.2Jun2020.bundle.g++.4 rename examples/USER/mesont/{log.3Mar2020.film.g++.1 => log.2Jun2020.film.g++.1} (73%) create mode 100644 examples/USER/mesont/log.2Jun2020.film.g++.4 diff --git a/examples/USER/mesont/MESONT-TABTP_10_10.xrs b/examples/USER/mesont/MESONT-TABTP_10_10.xrs new file mode 120000 index 0000000000..9325ee372f --- /dev/null +++ b/examples/USER/mesont/MESONT-TABTP_10_10.xrs @@ -0,0 +1 @@ +../../../potentials/MESONT-TABTP_10_10.xrs \ No newline at end of file diff --git a/examples/USER/mesont/in.bundle b/examples/USER/mesont/in.bundle index 56e42848f3..edcb2f6cb4 100644 --- a/examples/USER/mesont/in.bundle +++ b/examples/USER/mesont/in.bundle @@ -8,14 +8,13 @@ neigh_modify every 5 delay 0 check yes atom_style mesont # cut, path, BendingMode, TPMType -pair_style mesont/tpm 45.0 ../../../potentials/MESONT-TABTP_10_10.xrs 0 0 +pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0 read_data data.bundle pair_coeff * * velocity all create 6000.0 2019 timestep 0.005 fix 1 all nve -thermo_modify flush yes thermo 10 reset_timestep 0 diff --git a/examples/USER/mesont/in.film b/examples/USER/mesont/in.film index 2e59a4c436..d0a7a9fdad 100644 --- a/examples/USER/mesont/in.film +++ b/examples/USER/mesont/in.film @@ -7,14 +7,13 @@ neigh_modify every 5 delay 0 check yes atom_style mesont # cut, path, BendingMode, TPMType -pair_style mesont/tpm 30.0 ../../../potentials/MESONT-TABTP_10_10.xrs 1 0 +pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0 read_data data.film pair_coeff * * velocity all create 600.0 2019 timestep 0.01 fix 1 all nve -thermo_modify flush yes thermo 10 reset_timestep 0 @@ -26,4 +25,4 @@ compute B all property/atom buckling thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et #dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz -run 10 +run 20 diff --git a/examples/USER/mesont/log.3Mar2020.bundle.g++.1 b/examples/USER/mesont/log.2Jun2020.bundle.g++.1 similarity index 79% rename from examples/USER/mesont/log.3Mar2020.bundle.g++.1 rename to examples/USER/mesont/log.2Jun2020.bundle.g++.1 index 5c9a788167..997e248f42 100644 --- a/examples/USER/mesont/log.3Mar2020.bundle.g++.1 +++ b/examples/USER/mesont/log.2Jun2020.bundle.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (3 Mar 2020) - using 1 OpenMP thread(s) per MPI task +LAMMPS (5 May 2020) processors 1 1 * newton on units metal @@ -11,19 +10,18 @@ neigh_modify every 5 delay 0 check yes atom_style mesont # cut, path, BendingMode, TPMType -pair_style mesont/tpm 45.0 ../../../potentials/MESONT-TABTP_10_10.xrs 0 0 +pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0 read_data data.bundle orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220) 1 by 1 by 1 MPI processor grid reading atoms ... 77 atoms - read_data CPU = 0.025475 secs + read_data CPU = 0.000613213 secs pair_coeff * * velocity all create 6000.0 2019 timestep 0.005 fix 1 all nve -thermo_modify flush yes thermo 10 reset_timestep 0 @@ -33,7 +31,6 @@ compute Et all mesont etube compute B all property/atom buckling thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et -WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:708) #dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz run 100 @@ -62,20 +59,20 @@ Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et 80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807 90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032 100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977 -Loop time of 0.457417 on 1 procs for 100 steps with 77 atoms +Loop time of 0.419735 on 1 procs for 100 steps with 77 atoms -Performance: 94.443 ns/day, 0.254 hours/ns, 218.619 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 102.922 ns/day, 0.233 hours/ns, 238.245 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 | 0.45698 | 0.45698 | 0.45698 | 0.0 | 99.90 -Neigh | 5.6982e-05 | 5.6982e-05 | 5.6982e-05 | 0.0 | 0.01 -Comm | 4.4584e-05 | 4.4584e-05 | 4.4584e-05 | 0.0 | 0.01 -Output | 0.00019693 | 0.00019693 | 0.00019693 | 0.0 | 0.04 -Modify | 7.4863e-05 | 7.4863e-05 | 7.4863e-05 | 0.0 | 0.02 -Other | | 6.318e-05 | | | 0.01 +Pair | 0.41922 | 0.41922 | 0.41922 | 0.0 | 99.88 +Neigh | 5.8174e-05 | 5.8174e-05 | 5.8174e-05 | 0.0 | 0.01 +Comm | 7.0333e-05 | 7.0333e-05 | 7.0333e-05 | 0.0 | 0.02 +Output | 0.00017667 | 0.00017667 | 0.00017667 | 0.0 | 0.04 +Modify | 0.00011945 | 0.00011945 | 0.00011945 | 0.0 | 0.03 +Other | | 8.702e-05 | | | 0.02 Nlocal: 77 ave 77 max 77 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/USER/mesont/log.2Jun2020.bundle.g++.4 b/examples/USER/mesont/log.2Jun2020.bundle.g++.4 new file mode 100644 index 0000000000..bb6b7bcfc0 --- /dev/null +++ b/examples/USER/mesont/log.2Jun2020.bundle.g++.4 @@ -0,0 +1,90 @@ +LAMMPS (5 May 2020) +processors 1 1 * +newton on +units metal +lattice sc 1.0 +Lattice spacing in x,y,z = 1 1 1 +boundary fs fs p +neighbor 1.0 bin +neigh_modify every 5 delay 0 check yes + +atom_style mesont +# cut, path, BendingMode, TPMType +pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0 +read_data data.bundle + orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220) + 1 by 1 by 4 MPI processor grid + reading atoms ... + 77 atoms + read_data CPU = 0.000590563 secs +pair_coeff * * + +velocity all create 6000.0 2019 +timestep 0.005 +fix 1 all nve +thermo 10 +reset_timestep 0 + +compute Es all mesont estretch +compute Eb all mesont ebend +compute Et all mesont etube +compute B all property/atom buckling + +thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et +#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz + +run 100 +Neighbor list info ... + update every 5 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 46 + ghost atom cutoff = 46 + binsize = 23, bins = 7 7 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mesont/tpm, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.671 | 4.671 | 4.671 Mbytes +Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et + 0 0 6000 -201.86935 58.942626 -260.81198 0 0 -260.81198 + 10 0.05 5114.1875 -201.86234 50.240607 -252.10295 4.8334861 2.3998206 -259.33626 + 20 0.1 3437.2958 -201.8522 33.767207 -235.61941 11.42384 8.3426957 -255.38594 + 30 0.15 2430.6571 -201.85242 23.878219 -225.73064 10.346152 14.72688 -250.80367 + 40 0.2 2154.4755 -201.85683 21.165074 -223.0219 6.8146112 18.325709 -248.16222 + 50 0.25 2021.7899 -201.85503 19.861601 -221.71663 9.2972022 17.644143 -248.65798 + 60 0.3 2234.553 -201.85193 21.951737 -223.80367 13.541921 13.673721 -251.01931 + 70 0.35 3099.6503 -201.85721 30.450255 -232.30747 11.833679 9.0583807 -253.19953 + 80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807 + 90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032 + 100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977 +Loop time of 0.145545 on 4 procs for 100 steps with 77 atoms + +Performance: 296.815 ns/day, 0.081 hours/ns, 687.071 timesteps/s +95.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.046723 | 0.097529 | 0.14388 | 11.0 | 67.01 +Neigh | 2.5511e-05 | 2.8729e-05 | 3.171e-05 | 0.0 | 0.02 +Comm | 0.00058556 | 0.045174 | 0.098462 | 16.5 | 31.04 +Output | 0.0001483 | 0.0010182 | 0.002851 | 3.5 | 0.70 +Modify | 3.8147e-05 | 4.065e-05 | 4.4107e-05 | 0.0 | 0.03 +Other | | 0.001755 | | | 1.21 + +Nlocal: 19.25 ave 21 max 16 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 33.25 ave 40 max 28 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 555.5 ave 606 max 460 min +Histogram: 1 0 0 0 0 0 1 0 0 2 + +Total # of neighbors = 2222 +Ave neighs/atom = 28.8571 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/mesont/log.3Mar2020.film.g++.1 b/examples/USER/mesont/log.2Jun2020.film.g++.1 similarity index 73% rename from examples/USER/mesont/log.3Mar2020.film.g++.1 rename to examples/USER/mesont/log.2Jun2020.film.g++.1 index abf307a083..6b12acc18d 100644 --- a/examples/USER/mesont/log.3Mar2020.film.g++.1 +++ b/examples/USER/mesont/log.2Jun2020.film.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (3 Mar 2020) - using 1 OpenMP thread(s) per MPI task +LAMMPS (5 May 2020) newton on units metal lattice sc 1.0 @@ -10,19 +9,18 @@ neigh_modify every 5 delay 0 check yes atom_style mesont # cut, path, BendingMode, TPMType -pair_style mesont/tpm 30.0 ../../../potentials/MESONT-TABTP_10_10.xrs 1 0 +pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0 read_data data.film orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42) 1 by 1 by 1 MPI processor grid reading atoms ... 79596 atoms - read_data CPU = 0.110827 secs + read_data CPU = 0.0860629 secs pair_coeff * * velocity all create 600.0 2019 timestep 0.01 fix 1 all nve -thermo_modify flush yes thermo 10 reset_timestep 0 @@ -32,10 +30,9 @@ compute Et all mesont etube compute B all property/atom buckling thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et -WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:708) #dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz -run 10 +run 20 Neighbor list info ... update every 5 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -52,20 +49,21 @@ Per MPI rank memory allocation (min/avg/max) = 37.43 | 37.43 | 37.43 Mbytes Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et 0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245 10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053 -Loop time of 5.41853 on 1 procs for 10 steps with 79596 atoms + 20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141 +Loop time of 10.2438 on 1 procs for 20 steps with 79596 atoms -Performance: 1.595 ns/day, 15.051 hours/ns, 1.846 timesteps/s -97.7% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 1.687 ns/day, 14.228 hours/ns, 1.952 timesteps/s +99.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.4022 | 5.4022 | 5.4022 | 0.0 | 99.70 +Pair | 10.226 | 10.226 | 10.226 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00052881 | 0.00052881 | 0.00052881 | 0.0 | 0.01 -Output | 0.00029206 | 0.00029206 | 0.00029206 | 0.0 | 0.01 -Modify | 0.012906 | 0.012906 | 0.012906 | 0.0 | 0.24 -Other | | 0.002562 | | | 0.05 +Comm | 0.00081086 | 0.00081086 | 0.00081086 | 0.0 | 0.01 +Output | 0.00046563 | 0.00046563 | 0.00046563 | 0.0 | 0.00 +Modify | 0.015165 | 0.015165 | 0.015165 | 0.0 | 0.15 +Other | | 0.001869 | | | 0.02 Nlocal: 79596 ave 79596 max 79596 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -80,4 +78,4 @@ Total # of neighbors = 642270 Ave neighs/atom = 8.06912 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:07 +Total wall time: 0:00:11 diff --git a/examples/USER/mesont/log.2Jun2020.film.g++.4 b/examples/USER/mesont/log.2Jun2020.film.g++.4 new file mode 100644 index 0000000000..7411b6d611 --- /dev/null +++ b/examples/USER/mesont/log.2Jun2020.film.g++.4 @@ -0,0 +1,81 @@ +LAMMPS (5 May 2020) +newton on +units metal +lattice sc 1.0 +Lattice spacing in x,y,z = 1 1 1 +boundary p p fs +neighbor 1.0 bin +neigh_modify every 5 delay 0 check yes + +atom_style mesont +# cut, path, BendingMode, TPMType +pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0 +read_data data.film + orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 79596 atoms + read_data CPU = 0.0704217 secs +pair_coeff * * + +velocity all create 600.0 2019 +timestep 0.01 +fix 1 all nve +thermo 10 +reset_timestep 0 + +compute Es all mesont estretch +compute Eb all mesont ebend +compute Et all mesont etube +compute B all property/atom buckling + +thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et +#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz + +run 20 +Neighbor list info ... + update every 5 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 31 + ghost atom cutoff = 31 + binsize = 15.5, bins = 323 323 26 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mesont/tpm, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 12.81 | 12.81 | 12.83 Mbytes +Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et + 0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245 + 10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053 + 20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141 +Loop time of 3.67186 on 4 procs for 20 steps with 79596 atoms + +Performance: 4.706 ns/day, 5.100 hours/ns, 5.447 timesteps/s +95.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.7317 | 3.1286 | 3.6556 | 18.8 | 85.20 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0036943 | 0.53094 | 0.92822 | 45.8 | 14.46 +Output | 0.00026512 | 0.00035298 | 0.00055647 | 0.0 | 0.01 +Modify | 0.010463 | 0.010884 | 0.011153 | 0.3 | 0.30 +Other | | 0.001109 | | | 0.03 + +Nlocal: 19899 ave 21951 max 18667 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 970.75 ave 1031 max 920 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 160568 ave 181723 max 147382 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 642270 +Ave neighs/atom = 8.06912 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:04