diff --git a/examples/USER/misc/mesocnt/cnt.in b/examples/USER/misc/mesocnt/cnt.in deleted file mode 100644 index 9c0cc85827..0000000000 --- a/examples/USER/misc/mesocnt/cnt.in +++ /dev/null @@ -1,37 +0,0 @@ -#Initialisation - -units nano -dimension 3 -boundary p p p -atom_style full -comm_modify vel no cutoff 33.0 -neighbor 7.80 bin -newton on - -#Read data - -read_data cnt.data - -#Force field - -bond_style harmonic -bond_coeff 1 268896.77 2.0 - -angle_style harmonic -angle_coeff 1 46562.17 180.0 - -pair_style mesocnt -pair_coeff * * 10_10.cnt - -#Output - -thermo 10000 -dump xyz all xyz 1000 cnt.xyz - -#Simulation setup - -timestep 1.0e-05 - -#Nose-Hoover thermostat -fix nvt all nvt temp 300 300 0.001 -run 100000 diff --git a/examples/USER/misc/mesocnt/in.cnt b/examples/USER/misc/mesocnt/in.cnt new file mode 100644 index 0000000000..e4cb32eff0 --- /dev/null +++ b/examples/USER/misc/mesocnt/in.cnt @@ -0,0 +1,38 @@ +#Initialisation + +units nano +dimension 3 +boundary p p p +atom_style full +comm_modify cutoff 11.0 +neighbor 7.80 bin +newton on + +#Read data + +read_data cnt.data +replicate 1 2 2 + +#Force field + +bond_style harmonic +bond_coeff 1 268896.77 2.0 + +angle_style harmonic +angle_coeff 1 46562.17 180.0 + +pair_style mesocnt +pair_coeff * * 10_10.cnt + +#Output + +thermo 1000 +dump xyz all xyz 1000 cnt.xyz + +#Simulation setup + +timestep 1.0e-05 + +#Nose-Hoover thermostat +fix nvt all nvt temp 300 300 0.001 +run 10000 diff --git a/examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.1 b/examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.1 new file mode 100644 index 0000000000..f9c476bb8f --- /dev/null +++ b/examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.1 @@ -0,0 +1,126 @@ +LAMMPS (09 Jan 2020) +#Initialisation + +units nano +dimension 3 +boundary p p p +atom_style full +comm_modify cutoff 11.0 +neighbor 7.80 bin +newton on + +#Read data + +read_data cnt.data + orthogonal box = (0 0 0) to (600 600 60) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 498 bonds + reading angles ... + 496 angles + 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 = 0.000180006 secs + read_data CPU = 0.00125766 secs +replicate 1 2 2 + orthogonal box = (0 0 0) to (600 1200 120) + 1 by 1 by 1 MPI processor grid + 2000 atoms + 1992 bonds + 1984 angles + 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 = 0.00054121 secs + replicate CPU = 0.000902414 secs + +#Force field + +bond_style harmonic +bond_coeff 1 268896.77 2.0 + +angle_style harmonic +angle_coeff 1 46562.17 180.0 + +pair_style mesocnt +pair_coeff * * 10_10.cnt +Reading potential file 10_10.cnt with DATE: 2020-01-13 + +#Output + +thermo 1000 +dump xyz all xyz 1000 cnt.xyz + +#Simulation setup + +timestep 1.0e-05 + +#Nose-Hoover thermostat +fix nvt all nvt temp 300 300 0.001 +run 10000 +WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.177 + ghost atom cutoff = 11 + binsize = 5.0885, bins = 118 236 24 + 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) = 11.21 | 11.21 | 11.21 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304 + 1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182 + 2000 300.43933 -28320.212 11980.296 -3902.0877 -0.0045324757 + 3000 300.4263 -36049.855 11338.405 -12274.161 -0.0018833539 + 4000 299.13368 -43471.21 11926.882 -19160.553 -0.00043030866 + 5000 293.77858 -50083.893 12334.927 -25586.884 -0.0015653738 + 6000 296.4851 -56330.135 12325.63 -31730.376 -0.0012795986 + 7000 298.20879 -62120.359 12582.297 -37192.574 -0.0013845796 + 8000 299.45547 -67881.692 13058.926 -42425.669 -0.00021100885 + 9000 301.82622 -73333.698 13598.257 -47240.197 -0.0006009197 + 10000 307.16873 -78292.306 13818.929 -51756.96 -0.0005609903 +Loop time of 4.0316 on 1 procs for 10000 steps with 2000 atoms + +Performance: 2143.072 ns/day, 0.011 hours/ns, 2480.408 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5955 | 2.5955 | 2.5955 | 0.0 | 64.38 +Bond | 1.1516 | 1.1516 | 1.1516 | 0.0 | 28.57 +Neigh | 0.001163 | 0.001163 | 0.001163 | 0.0 | 0.03 +Comm | 0.0019577 | 0.0019577 | 0.0019577 | 0.0 | 0.05 +Output | 0.020854 | 0.020854 | 0.020854 | 0.0 | 0.52 +Modify | 0.21637 | 0.21637 | 0.21637 | 0.0 | 5.37 +Other | | 0.04409 | | | 1.09 + +Nlocal: 2000 ave 2000 max 2000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 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: 13320 ave 13320 max 13320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13320 +Ave neighs/atom = 6.66 +Ave special neighs/atom = 5.952 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.4 b/examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.4 new file mode 100644 index 0000000000..fcac6d5583 --- /dev/null +++ b/examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (09 Jan 2020) +#Initialisation + +units nano +dimension 3 +boundary p p p +atom_style full +comm_modify cutoff 11.0 +neighbor 7.80 bin +newton on + +#Read data + +read_data cnt.data + orthogonal box = (0 0 0) to (600 600 60) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 500 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 498 bonds + reading angles ... + 496 angles + 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 = 0.000354767 secs + read_data CPU = 0.00286365 secs +replicate 1 2 2 + orthogonal box = (0 0 0) to (600 1200 120) + 1 by 4 by 1 MPI processor grid + 2000 atoms + 1992 bonds + 1984 angles + 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 = 0.00019598 secs + replicate CPU = 0.00055337 secs + +#Force field + +bond_style harmonic +bond_coeff 1 268896.77 2.0 + +angle_style harmonic +angle_coeff 1 46562.17 180.0 + +pair_style mesocnt +pair_coeff * * 10_10.cnt +Reading potential file 10_10.cnt with DATE: 2020-01-13 + +#Output + +thermo 1000 +dump xyz all xyz 1000 cnt.xyz + +#Simulation setup + +timestep 1.0e-05 + +#Nose-Hoover thermostat +fix nvt all nvt temp 300 300 0.001 +run 10000 +WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.177 + ghost atom cutoff = 11 + binsize = 5.0885, bins = 118 236 24 + 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) = 2.725 | 2.725 | 2.725 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304 + 1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182 + 2000 300.43861 -28320.205 11980.287 -3902.1202 -0.0045324738 + 3000 300.41076 -36049.308 11339.149 -12273.513 -0.0018848513 + 4000 299.13326 -43471.424 11927.668 -19159.998 -0.00042845101 + 5000 293.78857 -50083.216 12333.969 -25586.752 -0.0015664633 + 6000 296.45482 -56329.621 12326.419 -31730.328 -0.0012773686 + 7000 298.19097 -62119.086 12581.4 -37192.937 -0.0013862831 + 8000 299.46424 -67880.989 13057.62 -42425.908 -0.00020874264 + 9000 301.80677 -73332.208 13597.237 -47240.532 -0.00060074773 + 10000 307.17104 -78292.912 13818.889 -51757.51 -0.00056148282 +Loop time of 1.23665 on 4 procs for 10000 steps with 2000 atoms + +Performance: 6986.607 ns/day, 0.003 hours/ns, 8086.351 timesteps/s +96.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.66321 | 0.68439 | 0.71413 | 2.5 | 55.34 +Bond | 0.28561 | 0.29434 | 0.30976 | 1.7 | 23.80 +Neigh | 0.00043321 | 0.00043637 | 0.00043917 | 0.0 | 0.04 +Comm | 0.026656 | 0.05346 | 0.097228 | 12.7 | 4.32 +Output | 0.0070224 | 0.0073031 | 0.0081415 | 0.6 | 0.59 +Modify | 0.12769 | 0.15394 | 0.18743 | 6.5 | 12.45 +Other | | 0.04279 | | | 3.46 + +Nlocal: 500 ave 504 max 496 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 22 ave 24 max 20 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 3330 ave 3368 max 3292 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 13320 +Ave neighs/atom = 6.66 +Ave special neighs/atom = 5.952 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:02