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