From 2bded3da5e166e543d245ff998e94ee4e35367db Mon Sep 17 00:00:00 2001 From: phankl Date: Wed, 31 Aug 2022 12:42:47 +0100 Subject: [PATCH] repeatable example --- examples/PACKAGES/mesont/in.film_mesocnt | 2 +- .../mesont/log.29Aug2022.film_mesocnt.g++.1 | 118 ---------------- .../mesont/log.29Aug2022.film_mesocnt.g++.4 | 118 ---------------- .../mesont/log.31Aug2022.film_mesocnt.g++.1 | 126 ++++++++++++++++++ .../mesont/log.31Aug2022.film_mesocnt.g++.4 | 126 ++++++++++++++++++ 5 files changed, 253 insertions(+), 237 deletions(-) delete mode 100644 examples/PACKAGES/mesont/log.29Aug2022.film_mesocnt.g++.1 delete mode 100644 examples/PACKAGES/mesont/log.29Aug2022.film_mesocnt.g++.4 create mode 100644 examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.1 create mode 100644 examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.4 diff --git a/examples/PACKAGES/mesont/in.film_mesocnt b/examples/PACKAGES/mesont/in.film_mesocnt index d05e7f9e48..ae8ee68eed 100644 --- a/examples/PACKAGES/mesont/in.film_mesocnt +++ b/examples/PACKAGES/mesont/in.film_mesocnt @@ -18,7 +18,7 @@ bond_coeff 1 C 10 10 10 angle_style mesocnt angle_coeff 1 buckling C 10 10 10 -pair_style mesocnt 30 chain +pair_style mesocnt 40 chain pair_coeff * * C_10_10.mesocnt 1 # output diff --git a/examples/PACKAGES/mesont/log.29Aug2022.film_mesocnt.g++.1 b/examples/PACKAGES/mesont/log.29Aug2022.film_mesocnt.g++.1 deleted file mode 100644 index d8269ecb28..0000000000 --- a/examples/PACKAGES/mesont/log.29Aug2022.film_mesocnt.g++.1 +++ /dev/null @@ -1,118 +0,0 @@ -LAMMPS (3 Aug 2022) -# initialisation - -units metal -dimension 3 -boundary p p s -atom_style full -special_bonds lj 1 1 1 -neigh_modify every 5 delay 0 check yes -newton on - -read_data data.film_mesocnt -Reading data file ... - orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 79596 atoms - scanning bonds ... - 1 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 79200 bonds - reading angles ... - 78804 angles -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 1 1 1 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.012 seconds - read_data CPU = 0.158 seconds - -# force field - -bond_style mesocnt -bond_coeff 1 C 10 10 10 - -angle_style mesocnt -angle_coeff 1 buckling C 10 10 10 - -pair_style mesocnt 30 chain -pair_coeff * * C_10_10.mesocnt 1 -Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12 - -# output - -thermo 100 - -compute epair all pe pair -compute ebond all pe bond -compute eangle all pe angle - -compute epair_atom all pe/atom pair -compute ebond_atom all pe/atom bond -compute eangle_atom all pe/atom angle - -fix angle_mesocnt_buckled all property/atom i_buckled ghost yes - -thermo_style custom step time cpu temp etotal ke pe c_ebond c_eangle c_epair -dump custom all custom 1000 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled - -# simulation setup - -velocity all create 600.0 2022 -timestep 0.01 -fix nvt all nvt temp 300.0 300.0 1 - -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 = 32 - ghost atom cutoff = 32 - binsize = 16, bins = 313 313 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair mesocnt, perpetual - attributes: full, newton on - pair build: full/bin - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 58.03 | 58.03 | 58.03 Mbytes - Step Time CPU Temp TotEng KinEng PotEng c_ebond c_eangle c_epair - 0 0 0 600 1355.9473 6173.0767 -4817.1294 28.668731 21.29199 -4867.0901 - 100 1 3.0380832 322.67058 1292.7084 3319.7837 -2027.0754 1107.8055 2092.5049 -5227.3858 -Loop time of 3.03811 on 1 procs for 100 steps with 79596 atoms - -Performance: 28.439 ns/day, 0.844 hours/ns, 32.915 timesteps/s -99.2% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.5683 | 2.5683 | 2.5683 | 0.0 | 84.53 -Bond | 0.2957 | 0.2957 | 0.2957 | 0.0 | 9.73 -Neigh | 0.057597 | 0.057597 | 0.057597 | 0.0 | 1.90 -Comm | 0.0020917 | 0.0020917 | 0.0020917 | 0.0 | 0.07 -Output | 0.00011104 | 0.00011104 | 0.00011104 | 0.0 | 0.00 -Modify | 0.10993 | 0.10993 | 0.10993 | 0.0 | 3.62 -Other | | 0.004415 | | | 0.15 - -Nlocal: 79596 ave 79596 max 79596 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1935 ave 1935 max 1935 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 659576 ave 659576 max 659576 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 659576 -Ave neighs/atom = 8.2865471 -Ave special neighs/atom = 5.9402985 -Neighbor list builds = 2 -Dangerous builds = 0 -Total wall time: 0:00:04 diff --git a/examples/PACKAGES/mesont/log.29Aug2022.film_mesocnt.g++.4 b/examples/PACKAGES/mesont/log.29Aug2022.film_mesocnt.g++.4 deleted file mode 100644 index beaeb886c1..0000000000 --- a/examples/PACKAGES/mesont/log.29Aug2022.film_mesocnt.g++.4 +++ /dev/null @@ -1,118 +0,0 @@ -LAMMPS (3 Aug 2022) -# initialisation - -units metal -dimension 3 -boundary p p s -atom_style full -special_bonds lj 1 1 1 -neigh_modify every 5 delay 0 check yes -newton on - -read_data data.film_mesocnt -Reading data file ... - orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 79596 atoms - scanning bonds ... - 1 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 79200 bonds - reading angles ... - 78804 angles -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 1 1 1 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.005 seconds - read_data CPU = 0.154 seconds - -# force field - -bond_style mesocnt -bond_coeff 1 C 10 10 10 - -angle_style mesocnt -angle_coeff 1 buckling C 10 10 10 - -pair_style mesocnt 30 chain -pair_coeff * * C_10_10.mesocnt 1 -Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12 - -# output - -thermo 100 - -compute epair all pe pair -compute ebond all pe bond -compute eangle all pe angle - -compute epair_atom all pe/atom pair -compute ebond_atom all pe/atom bond -compute eangle_atom all pe/atom angle - -fix angle_mesocnt_buckled all property/atom i_buckled ghost yes - -thermo_style custom step time cpu temp etotal ke pe c_ebond c_eangle c_epair -dump custom all custom 1000 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled - -# simulation setup - -velocity all create 600.0 2022 -timestep 0.01 -fix nvt all nvt temp 300.0 300.0 1 - -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 = 32 - ghost atom cutoff = 32 - binsize = 16, bins = 313 313 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair mesocnt, perpetual - attributes: full, newton on - pair build: full/bin - stencil: full/bin/3d - bin: standard -Per MPI rank memory allocation (min/avg/max) = 21.56 | 21.57 | 21.6 Mbytes - Step Time CPU Temp TotEng KinEng PotEng c_ebond c_eangle c_epair - 0 0 0 600 1355.9473 6173.0767 -4817.1294 28.668731 21.29199 -4867.0901 - 100 1 0.92993546 322.71889 1293.8436 3320.2808 -2026.4371 1107.7962 2093.0006 -5227.234 -Loop time of 0.929957 on 4 procs for 100 steps with 79596 atoms - -Performance: 92.908 ns/day, 0.258 hours/ns, 107.532 timesteps/s -98.0% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.58144 | 0.67551 | 0.78613 | 9.0 | 72.64 -Bond | 0.072245 | 0.077166 | 0.085344 | 1.8 | 8.30 -Neigh | 0.016299 | 0.016303 | 0.016308 | 0.0 | 1.75 -Comm | 0.011498 | 0.13156 | 0.23472 | 22.2 | 14.15 -Output | 6.3584e-05 | 6.9594e-05 | 8.0167e-05 | 0.0 | 0.01 -Modify | 0.020663 | 0.026031 | 0.028517 | 1.9 | 2.80 -Other | | 0.003318 | | | 0.36 - -Nlocal: 19899 ave 21952 max 18667 min -Histogram: 1 1 0 1 0 0 0 0 0 1 -Nghost: 1000.75 ave 1070 max 947 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: 164894 ave 187180 max 151353 min -Histogram: 1 0 2 0 0 0 0 0 0 1 - -Total # of neighbors = 659576 -Ave neighs/atom = 8.2865471 -Ave special neighs/atom = 5.9402985 -Neighbor list builds = 2 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.1 b/examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.1 new file mode 100644 index 0000000000..2ec221f98c --- /dev/null +++ b/examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.1 @@ -0,0 +1,126 @@ +LAMMPS (3 Aug 2022) +# initialisation + +units metal +dimension 3 +boundary p p s +atom_style full +special_bonds lj 1 1 1 +neigh_modify every 5 delay 0 check yes +newton on + +read_data data.film_mesocnt +Reading data file ... + orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 79596 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 79200 bonds + reading angles ... + 78804 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.012 seconds + read_data CPU = 0.160 seconds + +# force field + +bond_style mesocnt +bond_coeff 1 C 10 10 10 + +angle_style mesocnt +angle_coeff 1 buckling C 10 10 10 + +pair_style mesocnt 40 chain +pair_coeff * * C_10_10.mesocnt 1 +Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12 + +# output + +compute epair all pe pair +compute ebond all pe bond +compute eangle all pe angle + +compute epair_atom all pe/atom pair +compute ebond_atom all pe/atom bond +compute eangle_atom all pe/atom angle + +fix angle_mesocnt_buckled all property/atom i_buckled ghost yes + +thermo_style custom step temp etotal ke pe c_ebond c_eangle c_epair +thermo 10 +#dump custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled + +# simulation setup + +velocity all create 600.0 2022 loop geom +timestep 0.01 +fix nvt all nvt temp 300.0 300.0 1 + +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 = 42 + ghost atom cutoff = 42 + binsize = 21, bins = 239 239 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mesocnt, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 49.89 | 49.89 | 49.89 Mbytes + Step Temp TotEng KinEng PotEng c_ebond c_eangle c_epair + 0 600 1355.8735 6173.0767 -4817.2032 28.668731 21.29199 -4867.1639 + 10 389.92732 1373.1839 4011.7521 -2638.5683 848.77485 1387.6166 -4874.9597 + 20 311.7468 1388.0161 3207.3949 -1819.3788 1211.534 1868.6817 -4899.5945 + 30 291.75586 1385.2114 3001.7189 -1616.5075 1184.1423 2133.2088 -4933.8586 + 40 320.42607 1364.2644 3296.6912 -1932.4267 951.62534 2088.33 -4972.382 + 50 341.37701 1346.0547 3512.2441 -2166.1894 956.59158 1891.9196 -5014.7005 + 60 333.15461 1337.5518 3427.6483 -2090.0965 1137.7331 1825.9946 -5053.8242 + 70 324.47061 1328.7153 3338.3033 -2009.588 1133.3639 1953.8288 -5096.7807 + 80 324.39487 1315.4948 3337.5241 -2022.0293 979.16213 2141.4697 -5142.6611 + 90 323.39973 1302.3471 3327.2856 -2024.9385 972.70286 2185.7686 -5183.41 + 100 322.73067 1289.0538 3320.402 -2031.3482 1100.1024 2088.3804 -5219.831 +Loop time of 4.1637 on 1 procs for 100 steps with 79596 atoms + +Performance: 20.751 ns/day, 1.157 hours/ns, 24.017 timesteps/s +99.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.705 | 3.705 | 3.705 | 0.0 | 88.98 +Bond | 0.29317 | 0.29317 | 0.29317 | 0.0 | 7.04 +Neigh | 0.078491 | 0.078491 | 0.078491 | 0.0 | 1.89 +Comm | 0.0019462 | 0.0019462 | 0.0019462 | 0.0 | 0.05 +Output | 0.00099817 | 0.00099817 | 0.00099817 | 0.0 | 0.02 +Modify | 0.079874 | 0.079874 | 0.079874 | 0.0 | 1.92 +Other | | 0.004224 | | | 0.10 + +Nlocal: 79596 ave 79596 max 79596 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2567 ave 2567 max 2567 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.1337e+06 ave 1.1337e+06 max 1.1337e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1133696 +Ave neighs/atom = 14.243128 +Ave special neighs/atom = 5.9402985 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.4 b/examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.4 new file mode 100644 index 0000000000..7158f62819 --- /dev/null +++ b/examples/PACKAGES/mesont/log.31Aug2022.film_mesocnt.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (3 Aug 2022) +# initialisation + +units metal +dimension 3 +boundary p p s +atom_style full +special_bonds lj 1 1 1 +neigh_modify every 5 delay 0 check yes +newton on + +read_data data.film_mesocnt +Reading data file ... + orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 79596 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 79200 bonds + reading angles ... + 78804 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.005 seconds + read_data CPU = 0.156 seconds + +# force field + +bond_style mesocnt +bond_coeff 1 C 10 10 10 + +angle_style mesocnt +angle_coeff 1 buckling C 10 10 10 + +pair_style mesocnt 40 chain +pair_coeff * * C_10_10.mesocnt 1 +Reading mesocnt potential file C_10_10.mesocnt with DATE: 2022-07-12 + +# output + +compute epair all pe pair +compute ebond all pe bond +compute eangle all pe angle + +compute epair_atom all pe/atom pair +compute ebond_atom all pe/atom bond +compute eangle_atom all pe/atom angle + +fix angle_mesocnt_buckled all property/atom i_buckled ghost yes + +thermo_style custom step temp etotal ke pe c_ebond c_eangle c_epair +thermo 10 +#dump custom all custom 100 film_mesocnt.lmp id mol type x y z c_ebond_atom c_eangle_atom c_epair_atom i_buckled + +# simulation setup + +velocity all create 600.0 2022 loop geom +timestep 0.01 +fix nvt all nvt temp 300.0 300.0 1 + +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 = 42 + ghost atom cutoff = 42 + binsize = 21, bins = 239 239 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair mesocnt, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 16.47 | 16.58 | 16.89 Mbytes + Step Temp TotEng KinEng PotEng c_ebond c_eangle c_epair + 0 600 1355.8735 6173.0767 -4817.2032 28.668731 21.29199 -4867.1639 + 10 389.92732 1373.1839 4011.7521 -2638.5683 848.77485 1387.6166 -4874.9597 + 20 311.7468 1388.0161 3207.3949 -1819.3788 1211.534 1868.6817 -4899.5945 + 30 291.75586 1385.2114 3001.7189 -1616.5075 1184.1423 2133.2088 -4933.8586 + 40 320.42607 1364.2644 3296.6912 -1932.4267 951.62534 2088.33 -4972.382 + 50 341.37701 1346.0547 3512.2441 -2166.1894 956.59158 1891.9196 -5014.7005 + 60 333.15461 1337.5518 3427.6483 -2090.0965 1137.7331 1825.9946 -5053.8242 + 70 324.47061 1328.7153 3338.3033 -2009.588 1133.3639 1953.8288 -5096.7807 + 80 324.39487 1315.4948 3337.5241 -2022.0293 979.16213 2141.4697 -5142.6611 + 90 323.39973 1302.3471 3327.2856 -2024.9385 972.70286 2185.7686 -5183.41 + 100 322.73067 1289.0538 3320.402 -2031.3482 1100.1024 2088.3804 -5219.831 +Loop time of 1.25052 on 4 procs for 100 steps with 79596 atoms + +Performance: 69.091 ns/day, 0.347 hours/ns, 79.967 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.87036 | 0.97558 | 1.1135 | 9.0 | 78.01 +Bond | 0.071751 | 0.076357 | 0.084244 | 1.7 | 6.11 +Neigh | 0.023232 | 0.023239 | 0.023244 | 0.0 | 1.86 +Comm | 0.0046002 | 0.15227 | 0.26319 | 24.1 | 12.18 +Output | 0.00032696 | 0.00037811 | 0.00045537 | 0.0 | 0.03 +Modify | 0.019263 | 0.020646 | 0.023155 | 1.1 | 1.65 +Other | | 0.00204 | | | 0.16 + +Nlocal: 19899 ave 21951 max 18670 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 1323.5 ave 1412 max 1255 min +Histogram: 1 0 1 0 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: 283424 ave 325466 max 258171 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 1133696 +Ave neighs/atom = 14.243128 +Ave special neighs/atom = 5.9402985 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:02