update logfiles and adjust some example inputs to be consistent
This commit is contained in:
Axel Kohlmeyer
81
examples/rigid/in.rigid.nve
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81
examples/rigid/in.rigid.nve
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# Simple rigid body system
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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read_data data.rigid
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velocity all create 100.0 4928459
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# unconnected bodies
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group clump1 id <> 1 9
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group clump2 id <> 10 18
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group clump3 id <> 19 27
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group clump4 id <> 28 36
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group clump5 id <> 37 45
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group clump6 id <> 46 54
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group clump7 id <> 55 63
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group clump8 id <> 64 72
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group clump9 id <> 73 81
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fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 &
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clump6 clump7 clump8 clump9
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# 1 chain of connected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 36 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
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# clump6 clump7 clump8 clump9
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# 2 chains of connected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 37 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#fix 1 all poems group clump1 clump2 clump3 clump4
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#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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#dump 1 all atom 50 dump.rigid
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#dump 2 all image 100 image.*.jpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 100 movie.mpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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timestep 0.0001
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thermo 50
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run 10000
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338
examples/rigid/log.20Apr18.rigid.atomfile.g++.1
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338
examples/rigid/log.20Apr18.rigid.atomfile.g++.1
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@ -0,0 +1,338 @@
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LAMMPS (20 Apr 2018)
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using 1 OpenMP thread(s) per MPI task
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# Simple rigid body system
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units lj
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atom_style atomic
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atom_modify map array
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pair_style lj/cut 2.5
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read_data data.rigid
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orthogonal box = (-12 -12 -12) to (12 12 12)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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81 atoms
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velocity all create 100.0 4928459
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# unconnected bodies
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group clump1 id <> 1 9
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9 atoms in group clump1
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group clump2 id <> 10 18
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9 atoms in group clump2
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group clump3 id <> 19 27
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9 atoms in group clump3
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group clump4 id <> 28 36
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9 atoms in group clump4
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group clump5 id <> 37 45
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9 atoms in group clump5
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group clump6 id <> 46 54
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9 atoms in group clump6
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group clump7 id <> 55 63
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9 atoms in group clump7
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group clump8 id <> 64 72
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9 atoms in group clump8
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group clump9 id <> 73 81
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9 atoms in group clump9
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variable bodies atomfile bodies.txt
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fix 1 all rigid custom v_bodies
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9 rigid bodies with 81 atoms
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# 1 chain of connected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 36 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
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# 2 chains of connected bodies
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#group clump1 id <> 1 9
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#group clump2 id <> 9 18
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#group clump3 id <> 18 27
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#group clump4 id <> 27 36
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#group clump5 id <> 37 45
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#group clump6 id <> 45 54
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#group clump7 id <> 54 63
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#group clump8 id <> 63 72
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#group clump9 id <> 72 81
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#fix 1 all poems group clump1 clump2 clump3 clump4
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#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
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neigh_modify exclude group clump1 clump1
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neigh_modify exclude group clump2 clump2
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neigh_modify exclude group clump3 clump3
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neigh_modify exclude group clump4 clump4
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neigh_modify exclude group clump5 clump5
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neigh_modify exclude group clump6 clump6
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neigh_modify exclude group clump7 clump7
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neigh_modify exclude group clump8 clump8
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neigh_modify exclude group clump9 clump9
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thermo 100
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#dump 1 all atom 50 dump.rigid
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#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 5
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#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 5
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timestep 0.0001
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thermo 50
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run 10000
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 18 18 18
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.109 | 4.109 | 4.109 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 115.29439 5235.9179 0 5272.2142 -2.7403788
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50 14910.685 571.71558 0 5265.82 32.006171
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100 16298.442 136.66184 0 5267.653 16.444229
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150 16682.606 17.490511 0 5269.4219 14.900344
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200 16733.929 1.372872 0 5269.4617 14.569267
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250 16738.853 -0.15252816 0 5269.4864 14.496404
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300 16738.588 -0.055171335 0 5269.5002 14.496025
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350 16738.492 -0.017444677 0 5269.5077 14.496446
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400 16738.464 -0.0060102023 0 5269.5104 14.496618
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450 16738.455 -0.0012713351 0 5269.5124 14.496701
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500 16738.455 -0.00081068621 0 5269.5128 14.496709
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550 16738.455 -0.00083203497 0 5269.5129 14.496707
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600 16738.455 -0.00058355356 0 5269.5131 14.496709
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650 16738.455 -0.00047226704 0 5269.5131 14.496708
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700 16738.455 0 0 5269.5136 14.496713
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750 16738.455 0 0 5269.5136 14.49671
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800 16738.455 0 0 5269.5137 14.496709
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850 16738.455 0 0 5269.5137 14.49671
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900 16738.456 0 0 5269.5138 14.496713
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950 16738.462 -0.0035323872 0 5269.5122 14.496671
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1000 16738.586 -0.051135144 0 5269.5036 14.496229
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1050 16737.358 0.32995057 0 5269.4981 14.525763
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1100 16737.892 0.16210246 0 5269.4984 14.531983
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1150 16738.703 -0.089235095 0 5269.5025 14.509899
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1200 16738.466 -0.0075446243 0 5269.5096 14.510615
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|
1250 16738.456 0 0 5269.514 14.510704
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|
1300 16738.457 0 0 5269.5141 14.510701
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|
1350 16738.457 0 0 5269.5141 14.510699
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|
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
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|
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
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|
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
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|
1550 16738.457 0 0 5269.5143 14.51071
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|
1600 16738.457 0 0 5269.5144 14.510712
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|
1650 16738.457 0 0 5269.5144 14.510712
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|
1700 16738.458 0 0 5269.5144 14.51071
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|
1750 16738.458 0 0 5269.5145 14.510708
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|
1800 16738.458 0 0 5269.5145 14.510706
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|
1850 16738.458 0 0 5269.5146 14.510705
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|
1900 16738.458 0 0 5269.5146 14.510706
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|
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
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|
2000 16738.491 -0.013255268 0 5269.5117 14.510532
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|
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
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|
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||||
|
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
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|
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||||
|
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||||
|
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||||
|
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||||
|
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||||
|
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||||
|
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||||
|
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
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|
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
|
||||||
|
2650 16733.017 1.705148 0 5269.5067 14.596295
|
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|
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||||
|
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||||
|
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||||
|
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||||
|
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||||
|
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||||
|
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||||
|
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||||
|
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||||
|
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||||
|
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||||
|
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||||
|
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||||
|
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||||
|
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||||
|
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||||
|
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||||
|
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||||
|
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||||
|
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||||
|
3700 16738.602 -0.070934367 0 5269.4889 12.025288
|
||||||
|
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||||
|
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||||
|
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||||
|
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||||
|
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||||
|
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||||
|
4050 16738.437 0 0 5269.5078 12.035454
|
||||||
|
4100 16738.437 0 0 5269.508 12.035435
|
||||||
|
4150 16738.438 0 0 5269.5081 12.035426
|
||||||
|
4200 16738.438 0 0 5269.5083 12.035432
|
||||||
|
4250 16738.439 0 0 5269.5085 12.035447
|
||||||
|
4300 16738.439 0 0 5269.5086 12.035463
|
||||||
|
4350 16738.44 0 0 5269.5087 12.035474
|
||||||
|
4400 16738.44 0 0 5269.5088 12.035478
|
||||||
|
4450 16738.44 0 0 5269.5089 12.035474
|
||||||
|
4500 16738.44 0 0 5269.509 12.035462
|
||||||
|
4550 16738.441 0 0 5269.5092 12.035449
|
||||||
|
4600 16738.441 0 0 5269.5093 12.035445
|
||||||
|
4650 16738.442 0 0 5269.5095 12.035451
|
||||||
|
4700 16738.442 0 0 5269.5096 12.03546
|
||||||
|
4750 16738.443 0 0 5269.5097 12.035465
|
||||||
|
4800 16738.443 0 0 5269.5098 12.035466
|
||||||
|
4850 16738.443 0 0 5269.51 12.035463
|
||||||
|
4900 16738.444 0 0 5269.5101 12.035456
|
||||||
|
4950 16738.444 0 0 5269.5102 12.035447
|
||||||
|
5000 16738.445 0 0 5269.5104 12.03544
|
||||||
|
5050 16738.445 0 0 5269.5105 12.035442
|
||||||
|
5100 16738.446 0 0 5269.5107 12.035455
|
||||||
|
5150 16738.446 0 0 5269.5108 12.03547
|
||||||
|
5200 16738.446 0 0 5269.5109 12.035479
|
||||||
|
5250 16738.447 0 0 5269.511 12.035479
|
||||||
|
5300 16738.447 0 0 5269.5111 12.03547
|
||||||
|
5350 16738.447 0 0 5269.5112 12.035454
|
||||||
|
5400 16738.448 0 0 5269.5113 12.035434
|
||||||
|
5450 16738.448 0 0 5269.5115 12.03542
|
||||||
|
5500 16738.449 0 0 5269.5117 12.035422
|
||||||
|
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||||
|
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||||
|
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||||
|
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||||
|
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||||
|
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||||
|
5850 16738.451 0 0 5269.5123 12.011709
|
||||||
|
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
|
||||||
|
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||||
|
6000 16738.452 0 0 5269.5128 12.011688
|
||||||
|
6050 16738.453 0 0 5269.513 12.011702
|
||||||
|
6100 16738.453 0 0 5269.5131 12.011716
|
||||||
|
6150 16738.454 0 0 5269.5132 12.011725
|
||||||
|
6200 16738.454 0 0 5269.5133 12.011728
|
||||||
|
6250 16738.454 0 0 5269.5134 12.011723
|
||||||
|
6300 16738.455 0 0 5269.5135 12.011712
|
||||||
|
6350 16738.455 0 0 5269.5137 12.0117
|
||||||
|
6400 16738.456 0 0 5269.5138 12.011697
|
||||||
|
6450 16738.456 0 0 5269.514 12.011704
|
||||||
|
6500 16738.456 0 0 5269.5141 12.011714
|
||||||
|
6550 16738.457 0 0 5269.5142 12.011719
|
||||||
|
6600 16738.457 0 0 5269.5143 12.011718
|
||||||
|
6650 16738.458 0 0 5269.5144 12.011713
|
||||||
|
6700 16738.458 0 0 5269.5146 12.011705
|
||||||
|
6750 16738.459 0 0 5269.5147 12.011696
|
||||||
|
6800 16738.459 0 0 5269.5149 12.01169
|
||||||
|
6850 16738.46 0 0 5269.515 12.011695
|
||||||
|
6900 16738.46 0 0 5269.5152 12.01171
|
||||||
|
6950 16738.46 0 0 5269.5153 12.011726
|
||||||
|
7000 16738.461 0 0 5269.5154 12.011736
|
||||||
|
7050 16738.461 0 0 5269.5155 12.011737
|
||||||
|
7100 16738.461 0 0 5269.5155 12.011728
|
||||||
|
7150 16738.461 0 0 5269.5156 12.011712
|
||||||
|
7200 16738.462 0 0 5269.5158 12.011691
|
||||||
|
7250 16738.463 0 0 5269.516 12.011676
|
||||||
|
7300 16738.463 0 0 5269.5162 12.011677
|
||||||
|
7350 16738.464 0 0 5269.5164 12.011693
|
||||||
|
7400 16738.464 0 0 5269.5165 12.011713
|
||||||
|
7450 16738.465 0 0 5269.5166 12.011729
|
||||||
|
7500 16738.465 0 0 5269.5167 12.011736
|
||||||
|
7550 16738.465 0 0 5269.5168 12.011734
|
||||||
|
7600 16738.465 0 0 5269.5168 12.011722
|
||||||
|
7650 16738.466 0 0 5269.517 12.011704
|
||||||
|
7700 16738.466 0 0 5269.5171 12.011687
|
||||||
|
7750 16738.467 0 0 5269.5173 12.011681
|
||||||
|
7800 16738.467 0 0 5269.5175 12.011687
|
||||||
|
7850 16738.468 0 0 5269.5176 12.0117
|
||||||
|
7900 16738.468 0 0 5269.5178 12.011712
|
||||||
|
7950 16738.469 0 0 5269.5179 12.011721
|
||||||
|
8000 16738.469 0 0 5269.518 12.011724
|
||||||
|
8050 16738.469 0 0 5269.5181 12.01172
|
||||||
|
8100 16738.47 0 0 5269.5182 12.011709
|
||||||
|
8150 16738.47 0 0 5269.5183 12.0117
|
||||||
|
8200 16738.47 0 0 5269.5185 12.0117
|
||||||
|
8250 16738.471 0 0 5269.5186 12.011709
|
||||||
|
8300 16738.471 0 0 5269.5187 12.011719
|
||||||
|
8350 16738.472 0 0 5269.5189 12.011723
|
||||||
|
8400 16738.472 0 0 5269.519 12.01172
|
||||||
|
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
|
||||||
|
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
|
||||||
|
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||||
|
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||||
|
8650 16738.474 0 0 5269.5197 12.011699
|
||||||
|
8700 16738.475 0 0 5269.5199 12.011715
|
||||||
|
8750 16738.475 0 0 5269.52 12.011732
|
||||||
|
8800 16738.475 0 0 5269.52 12.011743
|
||||||
|
8850 16738.476 0 0 5269.5201 12.011744
|
||||||
|
8900 16738.476 0 0 5269.5202 12.011735
|
||||||
|
8950 16738.476 0 0 5269.5203 12.011719
|
||||||
|
9000 16738.477 0 0 5269.5205 12.011698
|
||||||
|
9050 16738.477 0 0 5269.5206 12.011683
|
||||||
|
9100 16738.478 0 0 5269.5208 12.011684
|
||||||
|
9150 16738.479 0 0 5269.521 12.011701
|
||||||
|
9200 16738.479 0 0 5269.5212 12.011722
|
||||||
|
9250 16738.479 0 0 5269.5213 12.011738
|
||||||
|
9300 16738.48 0 0 5269.5214 12.011746
|
||||||
|
9350 16738.48 0 0 5269.5214 12.011744
|
||||||
|
9400 16738.48 0 0 5269.5215 12.011732
|
||||||
|
9450 16738.48 0 0 5269.5216 12.011715
|
||||||
|
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
|
||||||
|
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
|
||||||
|
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||||
|
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||||
|
9700 16735.041 1.0589893 0 5269.4979 12.062708
|
||||||
|
9750 16738.013 0.13550102 0 5269.5101 11.407246
|
||||||
|
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||||
|
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
|
||||||
|
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
|
||||||
|
9950 16738.49 0 0 5269.5245 11.395076
|
||||||
|
10000 16738.49 0 0 5269.5246 11.395075
|
||||||
|
Loop time of 0.13941 on 1 procs for 10000 steps with 81 atoms
|
||||||
|
|
||||||
|
Performance: 619755.656 tau/day, 71730.979 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 | 0.010763 | 0.010763 | 0.010763 | 0.0 | 7.72
|
||||||
|
Neigh | 0.037528 | 0.037528 | 0.037528 | 0.0 | 26.92
|
||||||
|
Comm | 0.0093656 | 0.0093656 | 0.0093656 | 0.0 | 6.72
|
||||||
|
Output | 0.0024004 | 0.0024004 | 0.0024004 | 0.0 | 1.72
|
||||||
|
Modify | 0.073635 | 0.073635 | 0.073635 | 0.0 | 52.82
|
||||||
|
Other | | 0.005718 | | | 4.10
|
||||||
|
|
||||||
|
Nlocal: 81 ave 81 max 81 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 84 ave 84 max 84 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
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 998
|
||||||
|
Dangerous builds = 997
|
||||||
|
Total wall time: 0:00:00
|
||||||
338
examples/rigid/log.20Apr18.rigid.atomfile.g++.4
Normal file
338
examples/rigid/log.20Apr18.rigid.atomfile.g++.4
Normal file
@ -0,0 +1,338 @@
|
|||||||
|
LAMMPS (20 Apr 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Simple rigid body system
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
atom_modify map array
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
|
||||||
|
read_data data.rigid
|
||||||
|
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
81 atoms
|
||||||
|
|
||||||
|
velocity all create 100.0 4928459
|
||||||
|
|
||||||
|
|
||||||
|
# unconnected bodies
|
||||||
|
|
||||||
|
group clump1 id <> 1 9
|
||||||
|
9 atoms in group clump1
|
||||||
|
group clump2 id <> 10 18
|
||||||
|
9 atoms in group clump2
|
||||||
|
group clump3 id <> 19 27
|
||||||
|
9 atoms in group clump3
|
||||||
|
group clump4 id <> 28 36
|
||||||
|
9 atoms in group clump4
|
||||||
|
group clump5 id <> 37 45
|
||||||
|
9 atoms in group clump5
|
||||||
|
group clump6 id <> 46 54
|
||||||
|
9 atoms in group clump6
|
||||||
|
group clump7 id <> 55 63
|
||||||
|
9 atoms in group clump7
|
||||||
|
group clump8 id <> 64 72
|
||||||
|
9 atoms in group clump8
|
||||||
|
group clump9 id <> 73 81
|
||||||
|
9 atoms in group clump9
|
||||||
|
|
||||||
|
variable bodies atomfile bodies.txt
|
||||||
|
fix 1 all rigid custom v_bodies
|
||||||
|
9 rigid bodies with 81 atoms
|
||||||
|
|
||||||
|
# 1 chain of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 36 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
# 2 chains of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 37 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||||
|
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
neigh_modify exclude group clump1 clump1
|
||||||
|
neigh_modify exclude group clump2 clump2
|
||||||
|
neigh_modify exclude group clump3 clump3
|
||||||
|
neigh_modify exclude group clump4 clump4
|
||||||
|
neigh_modify exclude group clump5 clump5
|
||||||
|
neigh_modify exclude group clump6 clump6
|
||||||
|
neigh_modify exclude group clump7 clump7
|
||||||
|
neigh_modify exclude group clump8 clump8
|
||||||
|
neigh_modify exclude group clump9 clump9
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.rigid
|
||||||
|
|
||||||
|
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
thermo 50
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 18 18 18
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.174 | 4.455 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||||
|
50 14910.685 571.71558 0 5265.82 32.006171
|
||||||
|
100 16298.442 136.66184 0 5267.653 16.444229
|
||||||
|
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||||
|
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||||
|
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||||
|
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||||
|
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||||
|
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||||
|
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||||
|
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||||
|
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||||
|
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||||
|
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||||
|
700 16738.455 0 0 5269.5136 14.496713
|
||||||
|
750 16738.455 0 0 5269.5136 14.49671
|
||||||
|
800 16738.455 0 0 5269.5137 14.496709
|
||||||
|
850 16738.455 0 0 5269.5137 14.49671
|
||||||
|
900 16738.456 0 0 5269.5138 14.496713
|
||||||
|
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||||
|
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||||
|
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||||
|
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||||
|
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||||
|
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||||
|
1250 16738.456 0 0 5269.514 14.510704
|
||||||
|
1300 16738.457 0 0 5269.5141 14.510701
|
||||||
|
1350 16738.457 0 0 5269.5141 14.510699
|
||||||
|
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||||
|
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||||
|
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||||
|
1550 16738.457 0 0 5269.5143 14.51071
|
||||||
|
1600 16738.457 0 0 5269.5144 14.510712
|
||||||
|
1650 16738.457 0 0 5269.5144 14.510712
|
||||||
|
1700 16738.458 0 0 5269.5144 14.51071
|
||||||
|
1750 16738.458 0 0 5269.5145 14.510708
|
||||||
|
1800 16738.458 0 0 5269.5145 14.510706
|
||||||
|
1850 16738.458 0 0 5269.5146 14.510705
|
||||||
|
1900 16738.458 0 0 5269.5146 14.510706
|
||||||
|
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||||
|
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||||
|
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||||
|
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||||
|
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||||
|
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||||
|
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||||
|
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||||
|
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||||
|
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||||
|
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||||
|
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||||
|
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||||
|
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
|
||||||
|
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||||
|
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||||
|
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||||
|
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||||
|
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||||
|
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||||
|
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||||
|
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||||
|
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||||
|
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||||
|
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||||
|
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||||
|
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||||
|
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||||
|
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||||
|
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||||
|
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||||
|
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||||
|
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||||
|
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||||
|
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||||
|
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||||
|
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||||
|
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||||
|
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||||
|
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||||
|
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||||
|
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||||
|
4050 16738.437 0 0 5269.5078 12.035454
|
||||||
|
4100 16738.437 0 0 5269.508 12.035435
|
||||||
|
4150 16738.438 0 0 5269.5081 12.035426
|
||||||
|
4200 16738.438 0 0 5269.5083 12.035432
|
||||||
|
4250 16738.439 0 0 5269.5085 12.035447
|
||||||
|
4300 16738.439 0 0 5269.5086 12.035463
|
||||||
|
4350 16738.44 0 0 5269.5087 12.035474
|
||||||
|
4400 16738.44 0 0 5269.5088 12.035478
|
||||||
|
4450 16738.44 0 0 5269.5089 12.035474
|
||||||
|
4500 16738.44 0 0 5269.509 12.035462
|
||||||
|
4550 16738.441 0 0 5269.5092 12.035449
|
||||||
|
4600 16738.441 0 0 5269.5093 12.035445
|
||||||
|
4650 16738.442 0 0 5269.5095 12.035451
|
||||||
|
4700 16738.442 0 0 5269.5096 12.03546
|
||||||
|
4750 16738.443 0 0 5269.5097 12.035465
|
||||||
|
4800 16738.443 0 0 5269.5098 12.035466
|
||||||
|
4850 16738.443 0 0 5269.51 12.035463
|
||||||
|
4900 16738.444 0 0 5269.5101 12.035456
|
||||||
|
4950 16738.444 0 0 5269.5102 12.035447
|
||||||
|
5000 16738.445 0 0 5269.5104 12.03544
|
||||||
|
5050 16738.445 0 0 5269.5105 12.035442
|
||||||
|
5100 16738.446 0 0 5269.5107 12.035455
|
||||||
|
5150 16738.446 0 0 5269.5108 12.03547
|
||||||
|
5200 16738.446 0 0 5269.5109 12.035479
|
||||||
|
5250 16738.447 0 0 5269.511 12.035479
|
||||||
|
5300 16738.447 0 0 5269.5111 12.03547
|
||||||
|
5350 16738.447 0 0 5269.5112 12.035454
|
||||||
|
5400 16738.448 0 0 5269.5113 12.035434
|
||||||
|
5450 16738.448 0 0 5269.5115 12.03542
|
||||||
|
5500 16738.449 0 0 5269.5117 12.035422
|
||||||
|
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||||
|
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||||
|
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||||
|
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||||
|
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||||
|
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||||
|
5850 16738.451 0 0 5269.5123 12.011709
|
||||||
|
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||||
|
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||||
|
6000 16738.452 0 0 5269.5128 12.011688
|
||||||
|
6050 16738.453 0 0 5269.513 12.011702
|
||||||
|
6100 16738.453 0 0 5269.5131 12.011716
|
||||||
|
6150 16738.454 0 0 5269.5132 12.011725
|
||||||
|
6200 16738.454 0 0 5269.5133 12.011728
|
||||||
|
6250 16738.454 0 0 5269.5134 12.011723
|
||||||
|
6300 16738.455 0 0 5269.5135 12.011712
|
||||||
|
6350 16738.455 0 0 5269.5137 12.0117
|
||||||
|
6400 16738.456 0 0 5269.5138 12.011697
|
||||||
|
6450 16738.456 0 0 5269.514 12.011704
|
||||||
|
6500 16738.456 0 0 5269.5141 12.011714
|
||||||
|
6550 16738.457 0 0 5269.5142 12.011719
|
||||||
|
6600 16738.457 0 0 5269.5143 12.011718
|
||||||
|
6650 16738.458 0 0 5269.5144 12.011713
|
||||||
|
6700 16738.458 0 0 5269.5146 12.011705
|
||||||
|
6750 16738.459 0 0 5269.5147 12.011696
|
||||||
|
6800 16738.459 0 0 5269.5149 12.01169
|
||||||
|
6850 16738.46 0 0 5269.515 12.011695
|
||||||
|
6900 16738.46 0 0 5269.5152 12.01171
|
||||||
|
6950 16738.46 0 0 5269.5153 12.011726
|
||||||
|
7000 16738.461 0 0 5269.5154 12.011736
|
||||||
|
7050 16738.461 0 0 5269.5155 12.011737
|
||||||
|
7100 16738.461 0 0 5269.5155 12.011728
|
||||||
|
7150 16738.461 0 0 5269.5156 12.011712
|
||||||
|
7200 16738.462 0 0 5269.5158 12.011691
|
||||||
|
7250 16738.463 0 0 5269.516 12.011676
|
||||||
|
7300 16738.463 0 0 5269.5162 12.011677
|
||||||
|
7350 16738.464 0 0 5269.5164 12.011693
|
||||||
|
7400 16738.464 0 0 5269.5165 12.011713
|
||||||
|
7450 16738.465 0 0 5269.5166 12.011729
|
||||||
|
7500 16738.465 0 0 5269.5167 12.011736
|
||||||
|
7550 16738.465 0 0 5269.5168 12.011734
|
||||||
|
7600 16738.465 0 0 5269.5168 12.011722
|
||||||
|
7650 16738.466 0 0 5269.517 12.011704
|
||||||
|
7700 16738.466 0 0 5269.5171 12.011687
|
||||||
|
7750 16738.467 0 0 5269.5173 12.011681
|
||||||
|
7800 16738.467 0 0 5269.5175 12.011687
|
||||||
|
7850 16738.468 0 0 5269.5176 12.0117
|
||||||
|
7900 16738.468 0 0 5269.5178 12.011712
|
||||||
|
7950 16738.469 0 0 5269.5179 12.011721
|
||||||
|
8000 16738.469 0 0 5269.518 12.011724
|
||||||
|
8050 16738.469 0 0 5269.5181 12.01172
|
||||||
|
8100 16738.47 0 0 5269.5182 12.011709
|
||||||
|
8150 16738.47 0 0 5269.5183 12.0117
|
||||||
|
8200 16738.47 0 0 5269.5185 12.0117
|
||||||
|
8250 16738.471 0 0 5269.5186 12.011709
|
||||||
|
8300 16738.471 0 0 5269.5187 12.011719
|
||||||
|
8350 16738.472 0 0 5269.5189 12.011723
|
||||||
|
8400 16738.472 0 0 5269.519 12.01172
|
||||||
|
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||||
|
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||||
|
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||||
|
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||||||
|
8650 16738.474 0 0 5269.5197 12.011699
|
||||||
|
8700 16738.475 0 0 5269.5199 12.011715
|
||||||
|
8750 16738.475 0 0 5269.52 12.011732
|
||||||
|
8800 16738.475 0 0 5269.52 12.011743
|
||||||
|
8850 16738.476 0 0 5269.5201 12.011744
|
||||||
|
8900 16738.476 0 0 5269.5202 12.011735
|
||||||
|
8950 16738.476 0 0 5269.5203 12.011719
|
||||||
|
9000 16738.477 0 0 5269.5205 12.011698
|
||||||
|
9050 16738.477 0 0 5269.5206 12.011683
|
||||||
|
9100 16738.478 0 0 5269.5208 12.011684
|
||||||
|
9150 16738.479 0 0 5269.521 12.011701
|
||||||
|
9200 16738.479 0 0 5269.5212 12.011722
|
||||||
|
9250 16738.479 0 0 5269.5213 12.011738
|
||||||
|
9300 16738.48 0 0 5269.5214 12.011746
|
||||||
|
9350 16738.48 0 0 5269.5214 12.011744
|
||||||
|
9400 16738.48 0 0 5269.5215 12.011732
|
||||||
|
9450 16738.48 0 0 5269.5216 12.011715
|
||||||
|
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
|
||||||
|
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
|
||||||
|
9600 16738.549 -0.026814369 0 5269.5163 12.011415
|
||||||
|
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||||
|
9700 16735.041 1.0589887 0 5269.4979 12.062708
|
||||||
|
9750 16738.013 0.135501 0 5269.5101 11.407245
|
||||||
|
9800 16738.512 -0.011620329 0 5269.5201 11.394973
|
||||||
|
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
|
||||||
|
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
|
||||||
|
9950 16738.49 0 0 5269.5245 11.395076
|
||||||
|
10000 16738.49 0 0 5269.5246 11.395075
|
||||||
|
Loop time of 0.202573 on 4 procs for 10000 steps with 81 atoms
|
||||||
|
|
||||||
|
Performance: 426512.281 tau/day, 49364.847 timesteps/s
|
||||||
|
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0024269 | 0.0037646 | 0.0050037 | 1.5 | 1.86
|
||||||
|
Neigh | 0.011164 | 0.012023 | 0.014231 | 1.2 | 5.94
|
||||||
|
Comm | 0.08759 | 0.090238 | 0.091749 | 0.5 | 44.55
|
||||||
|
Output | 0.004354 | 0.0046349 | 0.0054095 | 0.7 | 2.29
|
||||||
|
Modify | 0.080237 | 0.081892 | 0.083034 | 0.4 | 40.43
|
||||||
|
Other | | 0.01002 | | | 4.95
|
||||||
|
|
||||||
|
Nlocal: 20.25 ave 38 max 3 min
|
||||||
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
|
Nghost: 27.25 ave 48 max 13 min
|
||||||
|
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 998
|
||||||
|
Dangerous builds = 997
|
||||||
|
Total wall time: 0:00:00
|
||||||
338
examples/rigid/log.20Apr18.rigid.atomvar.g++.1
Normal file
338
examples/rigid/log.20Apr18.rigid.atomvar.g++.1
Normal file
@ -0,0 +1,338 @@
|
|||||||
|
LAMMPS (20 Apr 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Simple rigid body system
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
atom_modify map array
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
|
||||||
|
read_data data.rigid
|
||||||
|
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
81 atoms
|
||||||
|
|
||||||
|
velocity all create 100.0 4928459
|
||||||
|
|
||||||
|
|
||||||
|
# unconnected bodies
|
||||||
|
|
||||||
|
group clump1 id <> 1 9
|
||||||
|
9 atoms in group clump1
|
||||||
|
group clump2 id <> 10 18
|
||||||
|
9 atoms in group clump2
|
||||||
|
group clump3 id <> 19 27
|
||||||
|
9 atoms in group clump3
|
||||||
|
group clump4 id <> 28 36
|
||||||
|
9 atoms in group clump4
|
||||||
|
group clump5 id <> 37 45
|
||||||
|
9 atoms in group clump5
|
||||||
|
group clump6 id <> 46 54
|
||||||
|
9 atoms in group clump6
|
||||||
|
group clump7 id <> 55 63
|
||||||
|
9 atoms in group clump7
|
||||||
|
group clump8 id <> 64 72
|
||||||
|
9 atoms in group clump8
|
||||||
|
group clump9 id <> 73 81
|
||||||
|
9 atoms in group clump9
|
||||||
|
|
||||||
|
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
|
||||||
|
fix 1 all rigid custom v_bodies
|
||||||
|
9 rigid bodies with 81 atoms
|
||||||
|
|
||||||
|
# 1 chain of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 36 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
# 2 chains of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 37 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||||
|
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
neigh_modify exclude group clump1 clump1
|
||||||
|
neigh_modify exclude group clump2 clump2
|
||||||
|
neigh_modify exclude group clump3 clump3
|
||||||
|
neigh_modify exclude group clump4 clump4
|
||||||
|
neigh_modify exclude group clump5 clump5
|
||||||
|
neigh_modify exclude group clump6 clump6
|
||||||
|
neigh_modify exclude group clump7 clump7
|
||||||
|
neigh_modify exclude group clump8 clump8
|
||||||
|
neigh_modify exclude group clump9 clump9
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.rigid
|
||||||
|
|
||||||
|
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
thermo 50
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 18 18 18
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.984 | 3.984 | 3.984 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||||
|
50 14910.685 571.71558 0 5265.82 32.006171
|
||||||
|
100 16298.442 136.66184 0 5267.653 16.444229
|
||||||
|
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||||
|
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||||
|
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||||
|
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||||
|
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||||
|
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||||
|
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||||
|
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||||
|
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||||
|
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||||
|
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||||
|
700 16738.455 0 0 5269.5136 14.496713
|
||||||
|
750 16738.455 0 0 5269.5136 14.49671
|
||||||
|
800 16738.455 0 0 5269.5137 14.496709
|
||||||
|
850 16738.455 0 0 5269.5137 14.49671
|
||||||
|
900 16738.456 0 0 5269.5138 14.496713
|
||||||
|
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||||
|
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||||
|
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||||
|
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||||
|
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||||
|
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||||
|
1250 16738.456 0 0 5269.514 14.510704
|
||||||
|
1300 16738.457 0 0 5269.5141 14.510701
|
||||||
|
1350 16738.457 0 0 5269.5141 14.510699
|
||||||
|
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||||
|
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||||
|
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||||
|
1550 16738.457 0 0 5269.5143 14.51071
|
||||||
|
1600 16738.457 0 0 5269.5144 14.510712
|
||||||
|
1650 16738.457 0 0 5269.5144 14.510712
|
||||||
|
1700 16738.458 0 0 5269.5144 14.51071
|
||||||
|
1750 16738.458 0 0 5269.5145 14.510708
|
||||||
|
1800 16738.458 0 0 5269.5145 14.510706
|
||||||
|
1850 16738.458 0 0 5269.5146 14.510705
|
||||||
|
1900 16738.458 0 0 5269.5146 14.510706
|
||||||
|
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||||
|
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||||
|
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||||
|
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||||
|
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||||
|
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||||
|
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||||
|
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||||
|
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||||
|
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||||
|
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||||
|
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||||
|
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||||
|
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
|
||||||
|
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||||
|
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||||
|
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||||
|
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||||
|
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||||
|
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||||
|
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||||
|
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||||
|
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||||
|
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||||
|
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||||
|
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||||
|
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||||
|
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||||
|
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||||
|
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||||
|
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||||
|
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||||
|
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||||
|
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||||
|
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||||
|
3700 16738.602 -0.070934367 0 5269.4889 12.025288
|
||||||
|
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||||
|
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||||
|
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||||
|
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||||
|
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||||
|
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||||
|
4050 16738.437 0 0 5269.5078 12.035454
|
||||||
|
4100 16738.437 0 0 5269.508 12.035435
|
||||||
|
4150 16738.438 0 0 5269.5081 12.035426
|
||||||
|
4200 16738.438 0 0 5269.5083 12.035432
|
||||||
|
4250 16738.439 0 0 5269.5085 12.035447
|
||||||
|
4300 16738.439 0 0 5269.5086 12.035463
|
||||||
|
4350 16738.44 0 0 5269.5087 12.035474
|
||||||
|
4400 16738.44 0 0 5269.5088 12.035478
|
||||||
|
4450 16738.44 0 0 5269.5089 12.035474
|
||||||
|
4500 16738.44 0 0 5269.509 12.035462
|
||||||
|
4550 16738.441 0 0 5269.5092 12.035449
|
||||||
|
4600 16738.441 0 0 5269.5093 12.035445
|
||||||
|
4650 16738.442 0 0 5269.5095 12.035451
|
||||||
|
4700 16738.442 0 0 5269.5096 12.03546
|
||||||
|
4750 16738.443 0 0 5269.5097 12.035465
|
||||||
|
4800 16738.443 0 0 5269.5098 12.035466
|
||||||
|
4850 16738.443 0 0 5269.51 12.035463
|
||||||
|
4900 16738.444 0 0 5269.5101 12.035456
|
||||||
|
4950 16738.444 0 0 5269.5102 12.035447
|
||||||
|
5000 16738.445 0 0 5269.5104 12.03544
|
||||||
|
5050 16738.445 0 0 5269.5105 12.035442
|
||||||
|
5100 16738.446 0 0 5269.5107 12.035455
|
||||||
|
5150 16738.446 0 0 5269.5108 12.03547
|
||||||
|
5200 16738.446 0 0 5269.5109 12.035479
|
||||||
|
5250 16738.447 0 0 5269.511 12.035479
|
||||||
|
5300 16738.447 0 0 5269.5111 12.03547
|
||||||
|
5350 16738.447 0 0 5269.5112 12.035454
|
||||||
|
5400 16738.448 0 0 5269.5113 12.035434
|
||||||
|
5450 16738.448 0 0 5269.5115 12.03542
|
||||||
|
5500 16738.449 0 0 5269.5117 12.035422
|
||||||
|
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||||
|
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||||
|
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||||
|
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||||
|
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||||
|
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||||
|
5850 16738.451 0 0 5269.5123 12.011709
|
||||||
|
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
|
||||||
|
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||||
|
6000 16738.452 0 0 5269.5128 12.011688
|
||||||
|
6050 16738.453 0 0 5269.513 12.011702
|
||||||
|
6100 16738.453 0 0 5269.5131 12.011716
|
||||||
|
6150 16738.454 0 0 5269.5132 12.011725
|
||||||
|
6200 16738.454 0 0 5269.5133 12.011728
|
||||||
|
6250 16738.454 0 0 5269.5134 12.011723
|
||||||
|
6300 16738.455 0 0 5269.5135 12.011712
|
||||||
|
6350 16738.455 0 0 5269.5137 12.0117
|
||||||
|
6400 16738.456 0 0 5269.5138 12.011697
|
||||||
|
6450 16738.456 0 0 5269.514 12.011704
|
||||||
|
6500 16738.456 0 0 5269.5141 12.011714
|
||||||
|
6550 16738.457 0 0 5269.5142 12.011719
|
||||||
|
6600 16738.457 0 0 5269.5143 12.011718
|
||||||
|
6650 16738.458 0 0 5269.5144 12.011713
|
||||||
|
6700 16738.458 0 0 5269.5146 12.011705
|
||||||
|
6750 16738.459 0 0 5269.5147 12.011696
|
||||||
|
6800 16738.459 0 0 5269.5149 12.01169
|
||||||
|
6850 16738.46 0 0 5269.515 12.011695
|
||||||
|
6900 16738.46 0 0 5269.5152 12.01171
|
||||||
|
6950 16738.46 0 0 5269.5153 12.011726
|
||||||
|
7000 16738.461 0 0 5269.5154 12.011736
|
||||||
|
7050 16738.461 0 0 5269.5155 12.011737
|
||||||
|
7100 16738.461 0 0 5269.5155 12.011728
|
||||||
|
7150 16738.461 0 0 5269.5156 12.011712
|
||||||
|
7200 16738.462 0 0 5269.5158 12.011691
|
||||||
|
7250 16738.463 0 0 5269.516 12.011676
|
||||||
|
7300 16738.463 0 0 5269.5162 12.011677
|
||||||
|
7350 16738.464 0 0 5269.5164 12.011693
|
||||||
|
7400 16738.464 0 0 5269.5165 12.011713
|
||||||
|
7450 16738.465 0 0 5269.5166 12.011729
|
||||||
|
7500 16738.465 0 0 5269.5167 12.011736
|
||||||
|
7550 16738.465 0 0 5269.5168 12.011734
|
||||||
|
7600 16738.465 0 0 5269.5168 12.011722
|
||||||
|
7650 16738.466 0 0 5269.517 12.011704
|
||||||
|
7700 16738.466 0 0 5269.5171 12.011687
|
||||||
|
7750 16738.467 0 0 5269.5173 12.011681
|
||||||
|
7800 16738.467 0 0 5269.5175 12.011687
|
||||||
|
7850 16738.468 0 0 5269.5176 12.0117
|
||||||
|
7900 16738.468 0 0 5269.5178 12.011712
|
||||||
|
7950 16738.469 0 0 5269.5179 12.011721
|
||||||
|
8000 16738.469 0 0 5269.518 12.011724
|
||||||
|
8050 16738.469 0 0 5269.5181 12.01172
|
||||||
|
8100 16738.47 0 0 5269.5182 12.011709
|
||||||
|
8150 16738.47 0 0 5269.5183 12.0117
|
||||||
|
8200 16738.47 0 0 5269.5185 12.0117
|
||||||
|
8250 16738.471 0 0 5269.5186 12.011709
|
||||||
|
8300 16738.471 0 0 5269.5187 12.011719
|
||||||
|
8350 16738.472 0 0 5269.5189 12.011723
|
||||||
|
8400 16738.472 0 0 5269.519 12.01172
|
||||||
|
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
|
||||||
|
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
|
||||||
|
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||||
|
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||||
|
8650 16738.474 0 0 5269.5197 12.011699
|
||||||
|
8700 16738.475 0 0 5269.5199 12.011715
|
||||||
|
8750 16738.475 0 0 5269.52 12.011732
|
||||||
|
8800 16738.475 0 0 5269.52 12.011743
|
||||||
|
8850 16738.476 0 0 5269.5201 12.011744
|
||||||
|
8900 16738.476 0 0 5269.5202 12.011735
|
||||||
|
8950 16738.476 0 0 5269.5203 12.011719
|
||||||
|
9000 16738.477 0 0 5269.5205 12.011698
|
||||||
|
9050 16738.477 0 0 5269.5206 12.011683
|
||||||
|
9100 16738.478 0 0 5269.5208 12.011684
|
||||||
|
9150 16738.479 0 0 5269.521 12.011701
|
||||||
|
9200 16738.479 0 0 5269.5212 12.011722
|
||||||
|
9250 16738.479 0 0 5269.5213 12.011738
|
||||||
|
9300 16738.48 0 0 5269.5214 12.011746
|
||||||
|
9350 16738.48 0 0 5269.5214 12.011744
|
||||||
|
9400 16738.48 0 0 5269.5215 12.011732
|
||||||
|
9450 16738.48 0 0 5269.5216 12.011715
|
||||||
|
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
|
||||||
|
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
|
||||||
|
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||||
|
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||||
|
9700 16735.041 1.0589893 0 5269.4979 12.062708
|
||||||
|
9750 16738.013 0.13550102 0 5269.5101 11.407246
|
||||||
|
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||||
|
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
|
||||||
|
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
|
||||||
|
9950 16738.49 0 0 5269.5245 11.395076
|
||||||
|
10000 16738.49 0 0 5269.5246 11.395075
|
||||||
|
Loop time of 0.139487 on 1 procs for 10000 steps with 81 atoms
|
||||||
|
|
||||||
|
Performance: 619413.496 tau/day, 71691.377 timesteps/s
|
||||||
|
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.010553 | 0.010553 | 0.010553 | 0.0 | 7.57
|
||||||
|
Neigh | 0.036803 | 0.036803 | 0.036803 | 0.0 | 26.38
|
||||||
|
Comm | 0.0091739 | 0.0091739 | 0.0091739 | 0.0 | 6.58
|
||||||
|
Output | 0.0023518 | 0.0023518 | 0.0023518 | 0.0 | 1.69
|
||||||
|
Modify | 0.074784 | 0.074784 | 0.074784 | 0.0 | 53.61
|
||||||
|
Other | | 0.005822 | | | 4.17
|
||||||
|
|
||||||
|
Nlocal: 81 ave 81 max 81 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 84 ave 84 max 84 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
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 998
|
||||||
|
Dangerous builds = 997
|
||||||
|
Total wall time: 0:00:00
|
||||||
338
examples/rigid/log.20Apr18.rigid.atomvar.g++.4
Normal file
338
examples/rigid/log.20Apr18.rigid.atomvar.g++.4
Normal file
@ -0,0 +1,338 @@
|
|||||||
|
LAMMPS (20 Apr 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Simple rigid body system
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
atom_modify map array
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
|
||||||
|
read_data data.rigid
|
||||||
|
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
81 atoms
|
||||||
|
|
||||||
|
velocity all create 100.0 4928459
|
||||||
|
|
||||||
|
|
||||||
|
# unconnected bodies
|
||||||
|
|
||||||
|
group clump1 id <> 1 9
|
||||||
|
9 atoms in group clump1
|
||||||
|
group clump2 id <> 10 18
|
||||||
|
9 atoms in group clump2
|
||||||
|
group clump3 id <> 19 27
|
||||||
|
9 atoms in group clump3
|
||||||
|
group clump4 id <> 28 36
|
||||||
|
9 atoms in group clump4
|
||||||
|
group clump5 id <> 37 45
|
||||||
|
9 atoms in group clump5
|
||||||
|
group clump6 id <> 46 54
|
||||||
|
9 atoms in group clump6
|
||||||
|
group clump7 id <> 55 63
|
||||||
|
9 atoms in group clump7
|
||||||
|
group clump8 id <> 64 72
|
||||||
|
9 atoms in group clump8
|
||||||
|
group clump9 id <> 73 81
|
||||||
|
9 atoms in group clump9
|
||||||
|
|
||||||
|
variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
|
||||||
|
fix 1 all rigid custom v_bodies
|
||||||
|
9 rigid bodies with 81 atoms
|
||||||
|
|
||||||
|
# 1 chain of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 36 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
# 2 chains of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 37 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||||
|
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
neigh_modify exclude group clump1 clump1
|
||||||
|
neigh_modify exclude group clump2 clump2
|
||||||
|
neigh_modify exclude group clump3 clump3
|
||||||
|
neigh_modify exclude group clump4 clump4
|
||||||
|
neigh_modify exclude group clump5 clump5
|
||||||
|
neigh_modify exclude group clump6 clump6
|
||||||
|
neigh_modify exclude group clump7 clump7
|
||||||
|
neigh_modify exclude group clump8 clump8
|
||||||
|
neigh_modify exclude group clump9 clump9
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.rigid
|
||||||
|
|
||||||
|
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
thermo 50
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 18 18 18
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.955 | 4.049 | 4.33 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||||
|
50 14910.685 571.71558 0 5265.82 32.006171
|
||||||
|
100 16298.442 136.66184 0 5267.653 16.444229
|
||||||
|
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||||
|
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||||
|
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||||
|
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||||
|
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||||
|
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||||
|
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||||
|
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||||
|
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||||
|
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||||
|
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||||
|
700 16738.455 0 0 5269.5136 14.496713
|
||||||
|
750 16738.455 0 0 5269.5136 14.49671
|
||||||
|
800 16738.455 0 0 5269.5137 14.496709
|
||||||
|
850 16738.455 0 0 5269.5137 14.49671
|
||||||
|
900 16738.456 0 0 5269.5138 14.496713
|
||||||
|
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||||
|
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||||
|
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||||
|
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||||
|
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||||
|
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||||
|
1250 16738.456 0 0 5269.514 14.510704
|
||||||
|
1300 16738.457 0 0 5269.5141 14.510701
|
||||||
|
1350 16738.457 0 0 5269.5141 14.510699
|
||||||
|
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||||
|
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||||
|
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||||
|
1550 16738.457 0 0 5269.5143 14.51071
|
||||||
|
1600 16738.457 0 0 5269.5144 14.510712
|
||||||
|
1650 16738.457 0 0 5269.5144 14.510712
|
||||||
|
1700 16738.458 0 0 5269.5144 14.51071
|
||||||
|
1750 16738.458 0 0 5269.5145 14.510708
|
||||||
|
1800 16738.458 0 0 5269.5145 14.510706
|
||||||
|
1850 16738.458 0 0 5269.5146 14.510705
|
||||||
|
1900 16738.458 0 0 5269.5146 14.510706
|
||||||
|
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||||
|
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||||
|
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||||
|
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||||
|
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||||
|
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||||
|
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||||
|
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||||
|
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||||
|
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||||
|
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||||
|
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||||
|
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||||
|
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
|
||||||
|
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||||
|
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||||
|
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||||
|
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||||
|
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||||
|
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||||
|
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||||
|
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||||
|
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||||
|
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||||
|
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||||
|
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||||
|
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||||
|
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||||
|
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||||
|
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||||
|
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||||
|
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||||
|
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||||
|
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||||
|
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||||
|
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||||
|
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||||
|
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||||
|
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||||
|
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||||
|
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||||
|
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||||
|
4050 16738.437 0 0 5269.5078 12.035454
|
||||||
|
4100 16738.437 0 0 5269.508 12.035435
|
||||||
|
4150 16738.438 0 0 5269.5081 12.035426
|
||||||
|
4200 16738.438 0 0 5269.5083 12.035432
|
||||||
|
4250 16738.439 0 0 5269.5085 12.035447
|
||||||
|
4300 16738.439 0 0 5269.5086 12.035463
|
||||||
|
4350 16738.44 0 0 5269.5087 12.035474
|
||||||
|
4400 16738.44 0 0 5269.5088 12.035478
|
||||||
|
4450 16738.44 0 0 5269.5089 12.035474
|
||||||
|
4500 16738.44 0 0 5269.509 12.035462
|
||||||
|
4550 16738.441 0 0 5269.5092 12.035449
|
||||||
|
4600 16738.441 0 0 5269.5093 12.035445
|
||||||
|
4650 16738.442 0 0 5269.5095 12.035451
|
||||||
|
4700 16738.442 0 0 5269.5096 12.03546
|
||||||
|
4750 16738.443 0 0 5269.5097 12.035465
|
||||||
|
4800 16738.443 0 0 5269.5098 12.035466
|
||||||
|
4850 16738.443 0 0 5269.51 12.035463
|
||||||
|
4900 16738.444 0 0 5269.5101 12.035456
|
||||||
|
4950 16738.444 0 0 5269.5102 12.035447
|
||||||
|
5000 16738.445 0 0 5269.5104 12.03544
|
||||||
|
5050 16738.445 0 0 5269.5105 12.035442
|
||||||
|
5100 16738.446 0 0 5269.5107 12.035455
|
||||||
|
5150 16738.446 0 0 5269.5108 12.03547
|
||||||
|
5200 16738.446 0 0 5269.5109 12.035479
|
||||||
|
5250 16738.447 0 0 5269.511 12.035479
|
||||||
|
5300 16738.447 0 0 5269.5111 12.03547
|
||||||
|
5350 16738.447 0 0 5269.5112 12.035454
|
||||||
|
5400 16738.448 0 0 5269.5113 12.035434
|
||||||
|
5450 16738.448 0 0 5269.5115 12.03542
|
||||||
|
5500 16738.449 0 0 5269.5117 12.035422
|
||||||
|
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||||
|
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||||
|
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||||
|
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||||
|
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||||
|
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||||
|
5850 16738.451 0 0 5269.5123 12.011709
|
||||||
|
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||||
|
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||||
|
6000 16738.452 0 0 5269.5128 12.011688
|
||||||
|
6050 16738.453 0 0 5269.513 12.011702
|
||||||
|
6100 16738.453 0 0 5269.5131 12.011716
|
||||||
|
6150 16738.454 0 0 5269.5132 12.011725
|
||||||
|
6200 16738.454 0 0 5269.5133 12.011728
|
||||||
|
6250 16738.454 0 0 5269.5134 12.011723
|
||||||
|
6300 16738.455 0 0 5269.5135 12.011712
|
||||||
|
6350 16738.455 0 0 5269.5137 12.0117
|
||||||
|
6400 16738.456 0 0 5269.5138 12.011697
|
||||||
|
6450 16738.456 0 0 5269.514 12.011704
|
||||||
|
6500 16738.456 0 0 5269.5141 12.011714
|
||||||
|
6550 16738.457 0 0 5269.5142 12.011719
|
||||||
|
6600 16738.457 0 0 5269.5143 12.011718
|
||||||
|
6650 16738.458 0 0 5269.5144 12.011713
|
||||||
|
6700 16738.458 0 0 5269.5146 12.011705
|
||||||
|
6750 16738.459 0 0 5269.5147 12.011696
|
||||||
|
6800 16738.459 0 0 5269.5149 12.01169
|
||||||
|
6850 16738.46 0 0 5269.515 12.011695
|
||||||
|
6900 16738.46 0 0 5269.5152 12.01171
|
||||||
|
6950 16738.46 0 0 5269.5153 12.011726
|
||||||
|
7000 16738.461 0 0 5269.5154 12.011736
|
||||||
|
7050 16738.461 0 0 5269.5155 12.011737
|
||||||
|
7100 16738.461 0 0 5269.5155 12.011728
|
||||||
|
7150 16738.461 0 0 5269.5156 12.011712
|
||||||
|
7200 16738.462 0 0 5269.5158 12.011691
|
||||||
|
7250 16738.463 0 0 5269.516 12.011676
|
||||||
|
7300 16738.463 0 0 5269.5162 12.011677
|
||||||
|
7350 16738.464 0 0 5269.5164 12.011693
|
||||||
|
7400 16738.464 0 0 5269.5165 12.011713
|
||||||
|
7450 16738.465 0 0 5269.5166 12.011729
|
||||||
|
7500 16738.465 0 0 5269.5167 12.011736
|
||||||
|
7550 16738.465 0 0 5269.5168 12.011734
|
||||||
|
7600 16738.465 0 0 5269.5168 12.011722
|
||||||
|
7650 16738.466 0 0 5269.517 12.011704
|
||||||
|
7700 16738.466 0 0 5269.5171 12.011687
|
||||||
|
7750 16738.467 0 0 5269.5173 12.011681
|
||||||
|
7800 16738.467 0 0 5269.5175 12.011687
|
||||||
|
7850 16738.468 0 0 5269.5176 12.0117
|
||||||
|
7900 16738.468 0 0 5269.5178 12.011712
|
||||||
|
7950 16738.469 0 0 5269.5179 12.011721
|
||||||
|
8000 16738.469 0 0 5269.518 12.011724
|
||||||
|
8050 16738.469 0 0 5269.5181 12.01172
|
||||||
|
8100 16738.47 0 0 5269.5182 12.011709
|
||||||
|
8150 16738.47 0 0 5269.5183 12.0117
|
||||||
|
8200 16738.47 0 0 5269.5185 12.0117
|
||||||
|
8250 16738.471 0 0 5269.5186 12.011709
|
||||||
|
8300 16738.471 0 0 5269.5187 12.011719
|
||||||
|
8350 16738.472 0 0 5269.5189 12.011723
|
||||||
|
8400 16738.472 0 0 5269.519 12.01172
|
||||||
|
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||||
|
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||||
|
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||||
|
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||||||
|
8650 16738.474 0 0 5269.5197 12.011699
|
||||||
|
8700 16738.475 0 0 5269.5199 12.011715
|
||||||
|
8750 16738.475 0 0 5269.52 12.011732
|
||||||
|
8800 16738.475 0 0 5269.52 12.011743
|
||||||
|
8850 16738.476 0 0 5269.5201 12.011744
|
||||||
|
8900 16738.476 0 0 5269.5202 12.011735
|
||||||
|
8950 16738.476 0 0 5269.5203 12.011719
|
||||||
|
9000 16738.477 0 0 5269.5205 12.011698
|
||||||
|
9050 16738.477 0 0 5269.5206 12.011683
|
||||||
|
9100 16738.478 0 0 5269.5208 12.011684
|
||||||
|
9150 16738.479 0 0 5269.521 12.011701
|
||||||
|
9200 16738.479 0 0 5269.5212 12.011722
|
||||||
|
9250 16738.479 0 0 5269.5213 12.011738
|
||||||
|
9300 16738.48 0 0 5269.5214 12.011746
|
||||||
|
9350 16738.48 0 0 5269.5214 12.011744
|
||||||
|
9400 16738.48 0 0 5269.5215 12.011732
|
||||||
|
9450 16738.48 0 0 5269.5216 12.011715
|
||||||
|
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
|
||||||
|
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
|
||||||
|
9600 16738.549 -0.026814369 0 5269.5163 12.011415
|
||||||
|
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||||
|
9700 16735.041 1.0589887 0 5269.4979 12.062708
|
||||||
|
9750 16738.013 0.135501 0 5269.5101 11.407245
|
||||||
|
9800 16738.512 -0.011620329 0 5269.5201 11.394973
|
||||||
|
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
|
||||||
|
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
|
||||||
|
9950 16738.49 0 0 5269.5245 11.395076
|
||||||
|
10000 16738.49 0 0 5269.5246 11.395075
|
||||||
|
Loop time of 0.21818 on 4 procs for 10000 steps with 81 atoms
|
||||||
|
|
||||||
|
Performance: 396003.948 tau/day, 45833.790 timesteps/s
|
||||||
|
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0023963 | 0.0039355 | 0.0049276 | 1.5 | 1.80
|
||||||
|
Neigh | 0.011369 | 0.011972 | 0.012855 | 0.5 | 5.49
|
||||||
|
Comm | 0.097981 | 0.10044 | 0.10334 | 0.6 | 46.04
|
||||||
|
Output | 0.0046875 | 0.004998 | 0.0058138 | 0.7 | 2.29
|
||||||
|
Modify | 0.084133 | 0.08661 | 0.089015 | 0.6 | 39.70
|
||||||
|
Other | | 0.01022 | | | 4.69
|
||||||
|
|
||||||
|
Nlocal: 20.25 ave 38 max 3 min
|
||||||
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
|
Nghost: 27.25 ave 48 max 13 min
|
||||||
|
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 998
|
||||||
|
Dangerous builds = 997
|
||||||
|
Total wall time: 0:00:00
|
||||||
@ -1,4 +1,5 @@
|
|||||||
LAMMPS (5 Oct 2016)
|
LAMMPS (20 Apr 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Simple rigid body system
|
# Simple rigid body system
|
||||||
|
|
||||||
units lj
|
units lj
|
||||||
@ -8,7 +9,7 @@ pair_style lj/cut 2.5
|
|||||||
|
|
||||||
read_data data.rigid
|
read_data data.rigid
|
||||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||||
1 by 2 by 2 MPI processor grid
|
1 by 1 by 1 MPI processor grid
|
||||||
reading atoms ...
|
reading atoms ...
|
||||||
81 atoms
|
81 atoms
|
||||||
|
|
||||||
@ -91,13 +92,18 @@ timestep 0.0001
|
|||||||
thermo 50
|
thermo 50
|
||||||
run 10000
|
run 10000
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
1 neighbor list requests
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
update every 1 steps, delay 10 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
master list distance cutoff = 2.8
|
master list distance cutoff = 2.8
|
||||||
ghost atom cutoff = 2.8
|
ghost atom cutoff = 2.8
|
||||||
binsize = 1.4 -> bins = 18 18 18
|
binsize = 1.4, bins = 18 18 18
|
||||||
Memory usage per processor = 3.62803 Mbytes
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||||
50 14910.685 571.71558 0 5265.82 32.006171
|
50 14910.685 571.71558 0 5265.82 32.006171
|
||||||
@ -151,7 +157,7 @@ Step Temp E_pair E_mol TotEng Press
|
|||||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||||
2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
|
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
|
||||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||||
@ -173,7 +179,7 @@ Step Temp E_pair E_mol TotEng Press
|
|||||||
3550 16713.405 7.846062 0 5269.4737 12.389816
|
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
3700 16738.602 -0.070934367 0 5269.4889 12.025288
|
||||||
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||||
@ -269,7 +275,7 @@ Step Temp E_pair E_mol TotEng Press
|
|||||||
8350 16738.472 0 0 5269.5189 12.011723
|
8350 16738.472 0 0 5269.5189 12.011723
|
||||||
8400 16738.472 0 0 5269.519 12.01172
|
8400 16738.472 0 0 5269.519 12.01172
|
||||||
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
|
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
|
||||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
|
||||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||||
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||||
8650 16738.474 0 0 5269.5197 12.011699
|
8650 16738.474 0 0 5269.5197 12.011699
|
||||||
@ -290,37 +296,37 @@ Step Temp E_pair E_mol TotEng Press
|
|||||||
9400 16738.48 0 0 5269.5215 12.011732
|
9400 16738.48 0 0 5269.5215 12.011732
|
||||||
9450 16738.48 0 0 5269.5216 12.011715
|
9450 16738.48 0 0 5269.5216 12.011715
|
||||||
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
|
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
|
||||||
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
|
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
|
||||||
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||||
9700 16735.041 1.0589894 0 5269.4979 12.062708
|
9700 16735.041 1.0589893 0 5269.4979 12.062708
|
||||||
9750 16738.013 0.13550109 0 5269.5101 11.407246
|
9750 16738.013 0.13550102 0 5269.5101 11.407246
|
||||||
9800 16738.512 -0.011620327 0 5269.5201 11.394974
|
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||||
9850 16738.489 -0.00067270507 0 5269.5237 11.395098
|
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
|
||||||
9900 16738.489 -0.00024984555 0 5269.5242 11.395085
|
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
|
||||||
9950 16738.49 0 0 5269.5245 11.395076
|
9950 16738.49 0 0 5269.5245 11.395076
|
||||||
10000 16738.49 0 0 5269.5246 11.395075
|
10000 16738.49 0 0 5269.5246 11.395075
|
||||||
Loop time of 0.169479 on 4 procs for 10000 steps with 81 atoms
|
Loop time of 0.139615 on 1 procs for 10000 steps with 81 atoms
|
||||||
|
|
||||||
Performance: 509796.561 tau/day, 59004.232 timesteps/s
|
Performance: 618845.476 tau/day, 71625.634 timesteps/s
|
||||||
98.1% CPU use with 4 MPI tasks x no OpenMP threads
|
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 0.0024633 | 0.0031875 | 0.0039403 | 0.9 | 1.88
|
Pair | 0.010352 | 0.010352 | 0.010352 | 0.0 | 7.41
|
||||||
Neigh | 0.010975 | 0.011817 | 0.013459 | 0.9 | 6.97
|
Neigh | 0.036875 | 0.036875 | 0.036875 | 0.0 | 26.41
|
||||||
Comm | 0.072126 | 0.074024 | 0.076456 | 0.7 | 43.68
|
Comm | 0.008925 | 0.008925 | 0.008925 | 0.0 | 6.39
|
||||||
Output | 0.0034711 | 0.0036327 | 0.0040615 | 0.4 | 2.14
|
Output | 0.0024204 | 0.0024204 | 0.0024204 | 0.0 | 1.73
|
||||||
Modify | 0.069286 | 0.070574 | 0.073233 | 0.6 | 41.64
|
Modify | 0.075421 | 0.075421 | 0.075421 | 0.0 | 54.02
|
||||||
Other | | 0.006244 | | | 3.68
|
Other | | 0.005621 | | | 4.03
|
||||||
|
|
||||||
Nlocal: 20.25 ave 38 max 3 min
|
Nlocal: 81 ave 81 max 81 min
|
||||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 27.25 ave 48 max 13 min
|
Nghost: 84 ave 84 max 84 min
|
||||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 0 ave 0 max 0 min
|
Neighs: 0 ave 0 max 0 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 0
|
Total # of neighbors = 0
|
||||||
Ave neighs/atom = 0
|
Ave neighs/atom = 0
|
||||||
@ -1,4 +1,5 @@
|
|||||||
LAMMPS (5 Oct 2016)
|
LAMMPS (20 Apr 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
# Simple rigid body system
|
# Simple rigid body system
|
||||||
|
|
||||||
units lj
|
units lj
|
||||||
@ -8,7 +9,7 @@ pair_style lj/cut 2.5
|
|||||||
|
|
||||||
read_data data.rigid
|
read_data data.rigid
|
||||||
orthogonal box = (-12 -12 -12) to (12 12 12)
|
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||||
1 by 1 by 1 MPI processor grid
|
1 by 2 by 2 MPI processor grid
|
||||||
reading atoms ...
|
reading atoms ...
|
||||||
81 atoms
|
81 atoms
|
||||||
|
|
||||||
@ -91,13 +92,18 @@ timestep 0.0001
|
|||||||
thermo 50
|
thermo 50
|
||||||
run 10000
|
run 10000
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
1 neighbor list requests
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
update every 1 steps, delay 10 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
master list distance cutoff = 2.8
|
master list distance cutoff = 2.8
|
||||||
ghost atom cutoff = 2.8
|
ghost atom cutoff = 2.8
|
||||||
binsize = 1.4 -> bins = 18 18 18
|
binsize = 1.4, bins = 18 18 18
|
||||||
Memory usage per processor = 3.65531 Mbytes
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||||
50 14910.685 571.71558 0 5265.82 32.006171
|
50 14910.685 571.71558 0 5265.82 32.006171
|
||||||
@ -151,8 +157,8 @@ Step Temp E_pair E_mol TotEng Press
|
|||||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||||
2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
|
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
|
||||||
2650 16733.017 1.7051479 0 5269.5067 14.596295
|
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||||
@ -160,7 +166,7 @@ Step Temp E_pair E_mol TotEng Press
|
|||||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||||
@ -170,7 +176,7 @@ Step Temp E_pair E_mol TotEng Press
|
|||||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||||
3550 16713.405 7.8460621 0 5269.4737 12.389816
|
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||||
@ -268,8 +274,8 @@ Step Temp E_pair E_mol TotEng Press
|
|||||||
8300 16738.471 0 0 5269.5187 12.011719
|
8300 16738.471 0 0 5269.5187 12.011719
|
||||||
8350 16738.472 0 0 5269.5189 12.011723
|
8350 16738.472 0 0 5269.5189 12.011723
|
||||||
8400 16738.472 0 0 5269.519 12.01172
|
8400 16738.472 0 0 5269.519 12.01172
|
||||||
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
|
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||||
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
|
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||||
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||||||
8650 16738.474 0 0 5269.5197 12.011699
|
8650 16738.474 0 0 5269.5197 12.011699
|
||||||
@ -289,38 +295,38 @@ Step Temp E_pair E_mol TotEng Press
|
|||||||
9350 16738.48 0 0 5269.5214 12.011744
|
9350 16738.48 0 0 5269.5214 12.011744
|
||||||
9400 16738.48 0 0 5269.5215 12.011732
|
9400 16738.48 0 0 5269.5215 12.011732
|
||||||
9450 16738.48 0 0 5269.5216 12.011715
|
9450 16738.48 0 0 5269.5216 12.011715
|
||||||
9500 16738.481 -0.00037652434 0 5269.5216 12.011692
|
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
|
||||||
9550 16738.493 -0.005315616 0 5269.5203 12.011611
|
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
|
||||||
9600 16738.549 -0.026814368 0 5269.5163 12.011415
|
9600 16738.549 -0.026814369 0 5269.5163 12.011415
|
||||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||||
9700 16735.041 1.0589885 0 5269.4979 12.062708
|
9700 16735.041 1.0589887 0 5269.4979 12.062708
|
||||||
9750 16738.013 0.13550123 0 5269.5101 11.407245
|
9750 16738.013 0.135501 0 5269.5101 11.407245
|
||||||
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
9800 16738.512 -0.011620329 0 5269.5201 11.394973
|
||||||
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
|
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
|
||||||
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
|
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
|
||||||
9950 16738.49 0 0 5269.5245 11.395076
|
9950 16738.49 0 0 5269.5245 11.395076
|
||||||
10000 16738.49 0 0 5269.5246 11.395075
|
10000 16738.49 0 0 5269.5246 11.395075
|
||||||
Loop time of 0.125672 on 1 procs for 10000 steps with 81 atoms
|
Loop time of 0.2002 on 4 procs for 10000 steps with 81 atoms
|
||||||
|
|
||||||
Performance: 687503.421 tau/day, 79572.155 timesteps/s
|
Performance: 431567.743 tau/day, 49949.970 timesteps/s
|
||||||
100.2% CPU use with 1 MPI tasks x no OpenMP threads
|
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 0.0097554 | 0.0097554 | 0.0097554 | 0.0 | 7.76
|
Pair | 0.0024362 | 0.0033384 | 0.003999 | 1.0 | 1.67
|
||||||
Neigh | 0.038657 | 0.038657 | 0.038657 | 0.0 | 30.76
|
Neigh | 0.010847 | 0.011388 | 0.012662 | 0.7 | 5.69
|
||||||
Comm | 0.0074 | 0.0074 | 0.0074 | 0.0 | 5.89
|
Comm | 0.0868 | 0.089339 | 0.090493 | 0.5 | 44.62
|
||||||
Output | 0.0010791 | 0.0010791 | 0.0010791 | 0.0 | 0.86
|
Output | 0.0047204 | 0.0049811 | 0.0056612 | 0.6 | 2.49
|
||||||
Modify | 0.064604 | 0.064604 | 0.064604 | 0.0 | 51.41
|
Modify | 0.078237 | 0.082033 | 0.085066 | 0.9 | 40.98
|
||||||
Other | | 0.004176 | | | 3.32
|
Other | | 0.009121 | | | 4.56
|
||||||
|
|
||||||
Nlocal: 81 ave 81 max 81 min
|
Nlocal: 20.25 ave 38 max 3 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
Nghost: 84 ave 84 max 84 min
|
Nghost: 27.25 ave 48 max 13 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||||
Neighs: 0 ave 0 max 0 min
|
Neighs: 0 ave 0 max 0 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 0
|
Total # of neighbors = 0
|
||||||
Ave neighs/atom = 0
|
Ave neighs/atom = 0
|
||||||
335
examples/rigid/log.20Apr18.rigid.nve.g++.1
Normal file
335
examples/rigid/log.20Apr18.rigid.nve.g++.1
Normal file
@ -0,0 +1,335 @@
|
|||||||
|
LAMMPS (20 Apr 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Simple rigid body system
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
|
||||||
|
read_data data.rigid
|
||||||
|
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
81 atoms
|
||||||
|
|
||||||
|
velocity all create 100.0 4928459
|
||||||
|
|
||||||
|
# unconnected bodies
|
||||||
|
|
||||||
|
group clump1 id <> 1 9
|
||||||
|
9 atoms in group clump1
|
||||||
|
group clump2 id <> 10 18
|
||||||
|
9 atoms in group clump2
|
||||||
|
group clump3 id <> 19 27
|
||||||
|
9 atoms in group clump3
|
||||||
|
group clump4 id <> 28 36
|
||||||
|
9 atoms in group clump4
|
||||||
|
group clump5 id <> 37 45
|
||||||
|
9 atoms in group clump5
|
||||||
|
group clump6 id <> 46 54
|
||||||
|
9 atoms in group clump6
|
||||||
|
group clump7 id <> 55 63
|
||||||
|
9 atoms in group clump7
|
||||||
|
group clump8 id <> 64 72
|
||||||
|
9 atoms in group clump8
|
||||||
|
group clump9 id <> 73 81
|
||||||
|
9 atoms in group clump9
|
||||||
|
|
||||||
|
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||||
|
9 rigid bodies with 81 atoms
|
||||||
|
|
||||||
|
# 1 chain of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 36 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
# 2 chains of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 37 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||||
|
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
neigh_modify exclude group clump1 clump1
|
||||||
|
neigh_modify exclude group clump2 clump2
|
||||||
|
neigh_modify exclude group clump3 clump3
|
||||||
|
neigh_modify exclude group clump4 clump4
|
||||||
|
neigh_modify exclude group clump5 clump5
|
||||||
|
neigh_modify exclude group clump6 clump6
|
||||||
|
neigh_modify exclude group clump7 clump7
|
||||||
|
neigh_modify exclude group clump8 clump8
|
||||||
|
neigh_modify exclude group clump9 clump9
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.rigid
|
||||||
|
|
||||||
|
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
thermo 50
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 18 18 18
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||||
|
50 14910.69 571.70921 0 5265.8153 32.005816
|
||||||
|
100 16298.128 136.75661 0 5267.6488 16.449029
|
||||||
|
150 16682.532 17.504156 0 5269.4124 14.901186
|
||||||
|
200 16733.906 1.3755079 0 5269.4571 14.571305
|
||||||
|
250 16738.861 -0.15272039 0 5269.4886 14.498342
|
||||||
|
300 16738.608 -0.055216883 0 5269.5066 14.498
|
||||||
|
350 16738.5 -0.017457072 0 5269.5104 14.498392
|
||||||
|
400 16738.451 -0.0060161309 0 5269.5063 14.49851
|
||||||
|
450 16738.435 -0.001271965 0 5269.5059 14.498571
|
||||||
|
500 16738.443 -0.00081074175 0 5269.509 14.498598
|
||||||
|
550 16738.452 -0.00083208965 0 5269.5118 14.498618
|
||||||
|
600 16738.45 -0.00058358431 0 5269.5116 14.498617
|
||||||
|
650 16738.443 -0.00047228525 0 5269.5093 14.4986
|
||||||
|
700 16738.444 0 0 5269.5102 14.498612
|
||||||
|
750 16738.461 0 0 5269.5157 14.498654
|
||||||
|
800 16738.479 0 0 5269.521 14.498697
|
||||||
|
850 16738.473 0 0 5269.5192 14.498683
|
||||||
|
900 16738.449 0 0 5269.5116 14.498624
|
||||||
|
950 16738.438 -0.0035324203 0 5269.5046 14.498537
|
||||||
|
1000 16738.562 -0.051134242 0 5269.4963 14.498093
|
||||||
|
1050 16737.343 0.32970192 0 5269.4934 14.527634
|
||||||
|
1100 16737.878 0.16213235 0 5269.4941 14.533864
|
||||||
|
1150 16738.682 -0.089236256 0 5269.4959 14.511765
|
||||||
|
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
|
||||||
|
1250 16738.45 0 0 5269.5119 14.512611
|
||||||
|
1300 16738.475 0 0 5269.5199 14.512673
|
||||||
|
1350 16738.484 0 0 5269.5228 14.512696
|
||||||
|
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
|
||||||
|
1450 16738.45 -0.0010933363 0 5269.511 14.512595
|
||||||
|
1500 16738.445 -0.00057484239 0 5269.51 14.512591
|
||||||
|
1550 16738.451 0 0 5269.5123 14.512615
|
||||||
|
1600 16738.452 0 0 5269.5127 14.512618
|
||||||
|
1650 16738.443 0 0 5269.5099 14.512596
|
||||||
|
1700 16738.433 0 0 5269.5068 14.512572
|
||||||
|
1750 16738.438 0 0 5269.5084 14.512584
|
||||||
|
1800 16738.459 0 0 5269.5149 14.512635
|
||||||
|
1850 16738.473 0 0 5269.5193 14.51267
|
||||||
|
1900 16738.462 0 0 5269.5159 14.512644
|
||||||
|
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
|
||||||
|
2000 16738.463 -0.013425408 0 5269.5027 14.512382
|
||||||
|
2050 16738.535 -0.036964311 0 5269.5017 14.512152
|
||||||
|
2100 16738.621 -0.063490509 0 5269.5023 14.512108
|
||||||
|
2150 16738.594 -0.056143934 0 5269.5012 14.512117
|
||||||
|
2200 16738.536 -0.038486645 0 5269.5007 14.512277
|
||||||
|
2250 16738.496 -0.023712406 0 5269.503 14.51242
|
||||||
|
2300 16738.488 -0.013209094 0 5269.5109 14.51255
|
||||||
|
2350 16738.486 -0.0045244524 0 5269.519 14.512693
|
||||||
|
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
|
||||||
|
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
|
||||||
|
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
|
||||||
|
2550 16738.552 -0.04420046 0 5269.4998 14.512177
|
||||||
|
2600 16738.42 -0.004347531 0 5269.4982 14.512783
|
||||||
|
2650 16734.241 1.3131302 0 5269.5 14.577195
|
||||||
|
2700 16738.737 -0.10612056 0 5269.4961 14.503874
|
||||||
|
2750 16732.705 1.7939719 0 5269.4974 14.629294
|
||||||
|
2800 16738.558 -0.042867033 0 5269.5032 14.519893
|
||||||
|
2850 16738.499 -0.01271227 0 5269.5146 14.518524
|
||||||
|
2900 16738.486 -0.0032778045 0 5269.52 14.518712
|
||||||
|
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
|
||||||
|
3000 16738.647 -0.070862542 0 5269.5031 14.51803
|
||||||
|
3050 16678.313 18.829038 0 5269.409 15.533426
|
||||||
|
3100 16632.312 33.399217 0 5269.4975 14.588597
|
||||||
|
3150 16739.318 -0.31388148 0 5269.4715 13.520782
|
||||||
|
3200 16727.951 3.26736 0 5269.4741 12.288358
|
||||||
|
3250 16686.364 16.353793 0 5269.4682 14.152517
|
||||||
|
3300 16738.532 -0.031574462 0 5269.5064 13.310615
|
||||||
|
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
|
||||||
|
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
|
||||||
|
3450 16738.489 -0.021623738 0 5269.5026 13.308001
|
||||||
|
3500 16737.78 0.19719043 0 5269.4983 13.325999
|
||||||
|
3550 16658.578 25.116206 0 5269.4834 13.778249
|
||||||
|
3600 16738.51 -0.032864725 0 5269.4981 12.392389
|
||||||
|
3650 16738.899 -0.15952703 0 5269.4938 12.383503
|
||||||
|
3700 16738.879 -0.16025994 0 5269.487 12.382575
|
||||||
|
3750 16738.878 -0.16608251 0 5269.4806 12.382765
|
||||||
|
3800 16738.591 -0.078679341 0 5269.4776 12.383227
|
||||||
|
3850 16738.429 -0.024729409 0 5269.4807 12.382942
|
||||||
|
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
|
||||||
|
3950 16738.428 -0.002521266 0 5269.5027 12.383324
|
||||||
|
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
|
||||||
|
4050 16738.488 0 0 5269.5241 12.383531
|
||||||
|
4100 16738.468 0 0 5269.5178 12.383482
|
||||||
|
4150 16738.422 0 0 5269.5033 12.383369
|
||||||
|
4200 16738.387 0 0 5269.4921 12.383281
|
||||||
|
4250 16738.383 0 0 5269.4908 12.38327
|
||||||
|
4300 16738.4 0 0 5269.4964 12.383314
|
||||||
|
4350 16738.423 0 0 5269.5036 12.38337
|
||||||
|
4400 16738.441 0 0 5269.5092 12.383414
|
||||||
|
4450 16738.45 0 0 5269.5121 12.383437
|
||||||
|
4500 16738.45 0 0 5269.5122 12.383438
|
||||||
|
4550 16738.442 0 0 5269.5095 12.383417
|
||||||
|
4600 16738.425 0 0 5269.5042 12.383376
|
||||||
|
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
|
||||||
|
4700 16738.444 -0.024020551 0 5269.4862 12.382975
|
||||||
|
4750 16738.49 -0.048521421 0 5269.4761 12.385777
|
||||||
|
4800 16735.057 1.0347219 0 5269.4786 12.43543
|
||||||
|
4850 16735.441 0.92650928 0 5269.4913 12.418653
|
||||||
|
4900 16723.839 4.5908971 0 5269.5033 13.410103
|
||||||
|
4950 16738.531 -0.021537669 0 5269.5159 13.089982
|
||||||
|
5000 16738.45 -0.0042589693 0 5269.5077 13.090062
|
||||||
|
5050 16738.409 -0.00024692474 0 5269.4987 13.090038
|
||||||
|
5100 16738.404 0 0 5269.4976 13.090032
|
||||||
|
5150 16738.421 0 0 5269.5029 13.090073
|
||||||
|
5200 16738.44 0 0 5269.5087 13.090119
|
||||||
|
5250 16738.448 -0.0012793921 0 5269.5102 13.090114
|
||||||
|
5300 16738.456 -0.0064376397 0 5269.5075 13.090026
|
||||||
|
5350 16738.479 -0.020383842 0 5269.5007 13.089898
|
||||||
|
5400 16735.845 0.79889481 0 5269.4909 13.136244
|
||||||
|
5450 16735.558 0.87619898 0 5269.4778 12.324482
|
||||||
|
5500 16711.494 8.47243 0 5269.4984 12.65658
|
||||||
|
5550 16454.525 89.074845 0 5269.2031 16.996503
|
||||||
|
5600 16713.084 7.9801091 0 5269.5065 13.774971
|
||||||
|
5650 16738.676 -0.079987812 0 5269.5033 13.168292
|
||||||
|
5700 16446.281 91.866085 0 5269.399 23.764658
|
||||||
|
5750 16738.549 -0.039869082 0 5269.5034 13.378117
|
||||||
|
5800 16738.487 -0.014994464 0 5269.5086 13.378394
|
||||||
|
5850 16738.466 -0.0051267378 0 5269.512 13.378555
|
||||||
|
5900 16738.462 -0.0043689966 0 5269.5113 13.378568
|
||||||
|
5950 16738.528 -0.032727396 0 5269.5039 13.378192
|
||||||
|
6000 16702.774 10.969422 0 5269.2502 13.788847
|
||||||
|
6050 16682.271 17.483217 0 5269.3092 13.353098
|
||||||
|
6100 16738.508 -0.028838289 0 5269.5016 12.521077
|
||||||
|
6150 16738.425 -0.0067595568 0 5269.4974 12.521216
|
||||||
|
6200 16738.401 -0.0011499904 0 5269.4955 12.521247
|
||||||
|
6250 16738.455 0 0 5269.5136 12.521403
|
||||||
|
6300 16738.523 0 0 5269.5352 12.521573
|
||||||
|
6350 16738.503 0 0 5269.5287 12.521525
|
||||||
|
6400 16738.427 0 0 5269.5047 12.521337
|
||||||
|
6450 16738.399 0 0 5269.496 12.521268
|
||||||
|
6500 16738.425 0 0 5269.5042 12.521331
|
||||||
|
6550 16738.441 0 0 5269.5093 12.521372
|
||||||
|
6600 16738.42 0 0 5269.5025 12.521319
|
||||||
|
6650 16738.398 0 0 5269.4957 12.521266
|
||||||
|
6700 16738.435 0 0 5269.5074 12.521355
|
||||||
|
6750 16738.505 0 0 5269.5293 12.521527
|
||||||
|
6800 16738.508 0 0 5269.5303 12.521536
|
||||||
|
6850 16738.446 0 0 5269.5108 12.521384
|
||||||
|
6900 16738.414 0 0 5269.5009 12.521306
|
||||||
|
6950 16738.432 0 0 5269.5063 12.521348
|
||||||
|
7000 16738.444 0 0 5269.5102 12.521378
|
||||||
|
7050 16738.421 0 0 5269.5029 12.521322
|
||||||
|
7100 16738.393 0 0 5269.4941 12.521253
|
||||||
|
7150 16738.419 0 0 5269.5022 12.521315
|
||||||
|
7200 16738.489 0 0 5269.5244 12.521489
|
||||||
|
7250 16738.505 0 0 5269.5293 12.521528
|
||||||
|
7300 16738.443 0 0 5269.5098 12.521376
|
||||||
|
7350 16738.404 0 0 5269.4976 12.521281
|
||||||
|
7400 16738.43 0 0 5269.5058 12.521343
|
||||||
|
7450 16738.461 0 0 5269.5156 12.521421
|
||||||
|
7500 16738.447 0 0 5269.5109 12.521385
|
||||||
|
7550 16738.407 0 0 5269.4986 12.521288
|
||||||
|
7600 16738.412 0 0 5269.5002 12.5213
|
||||||
|
7650 16738.478 0 0 5269.5208 12.52146
|
||||||
|
7700 16738.51 0 0 5269.5309 12.521541
|
||||||
|
7750 16738.454 0 0 5269.5135 12.521405
|
||||||
|
7800 16738.398 0 0 5269.4958 12.521267
|
||||||
|
7850 16738.407 -0.0002118068 0 5269.4982 12.521283
|
||||||
|
7900 16738.441 -0.00021679441 0 5269.509 12.521366
|
||||||
|
7950 16738.446 -0.00023847865 0 5269.5107 12.52138
|
||||||
|
8000 16738.423 0 0 5269.5035 12.521326
|
||||||
|
8050 16738.423 0 0 5269.5034 12.521325
|
||||||
|
8100 16738.478 -0.00069624411 0 5269.52 12.521447
|
||||||
|
8150 16738.523 -0.0040058094 0 5269.531 12.521494
|
||||||
|
8200 16738.486 -0.0092298399 0 5269.5142 12.521327
|
||||||
|
8250 16738.458 -0.023189572 0 5269.4914 12.521008
|
||||||
|
8300 16738.513 -0.045847775 0 5269.4861 12.520773
|
||||||
|
8350 16723.734 4.5722877 0 5269.4516 12.849562
|
||||||
|
8400 16738.466 -0.020202622 0 5269.497 12.835807
|
||||||
|
8450 16738.437 -0.012822209 0 5269.4952 12.829975
|
||||||
|
8500 16738.408 -0.001683355 0 5269.4972 12.8301
|
||||||
|
8550 16738.464 -0.00097382251 0 5269.5155 12.830254
|
||||||
|
8600 16738.669 -0.050581166 0 5269.5304 12.829973
|
||||||
|
8650 15918.256 250.07455 0 5261.3774 24.539208
|
||||||
|
8700 16738.446 0.00084613367 0 5269.5116 10.591358
|
||||||
|
8750 16738.472 -0.010145611 0 5269.5089 10.590277
|
||||||
|
8800 16738.468 0 0 5269.5176 10.590497
|
||||||
|
8850 16738.508 0 0 5269.5303 10.590596
|
||||||
|
8900 16738.509 0 0 5269.5306 10.590599
|
||||||
|
8950 16738.496 0 0 5269.5266 10.590568
|
||||||
|
9000 16738.477 0 0 5269.5204 10.59052
|
||||||
|
9050 16738.455 0 0 5269.5135 10.590465
|
||||||
|
9100 16738.477 0 0 5269.5205 10.590519
|
||||||
|
9150 16738.512 0 0 5269.5315 10.590606
|
||||||
|
9200 16738.502 0 0 5269.5285 10.590583
|
||||||
|
9250 16738.493 0 0 5269.5254 10.590559
|
||||||
|
9300 16738.482 0 0 5269.522 10.590532
|
||||||
|
9350 16738.46 0 0 5269.5151 10.590478
|
||||||
|
9400 16738.48 0 0 5269.5216 10.590528
|
||||||
|
9450 16738.509 0 0 5269.5306 10.590599
|
||||||
|
9500 16738.49 0 0 5269.5247 10.590554
|
||||||
|
9550 16738.484 0 0 5269.5226 10.590536
|
||||||
|
9600 16738.483 0 0 5269.5223 10.590534
|
||||||
|
9650 16738.464 0 0 5269.5165 10.590489
|
||||||
|
9700 16738.484 0 0 5269.5228 10.590537
|
||||||
|
9750 16738.507 0 0 5269.53 10.590595
|
||||||
|
9800 16738.482 0 0 5269.522 10.590532
|
||||||
|
9850 16738.478 0 0 5269.5207 10.590521
|
||||||
|
9900 16738.487 -0.00030979882 0 5269.5233 10.590538
|
||||||
|
9950 16738.476 -0.00095967357 0 5269.5193 10.590496
|
||||||
|
10000 16738.494 -0.00062714625 0 5269.5253 10.590548
|
||||||
|
Loop time of 0.164107 on 1 procs for 10000 steps with 81 atoms
|
||||||
|
|
||||||
|
Performance: 526485.498 tau/day, 60935.822 timesteps/s
|
||||||
|
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.011662 | 0.011662 | 0.011662 | 0.0 | 7.11
|
||||||
|
Neigh | 0.038184 | 0.038184 | 0.038184 | 0.0 | 23.27
|
||||||
|
Comm | 0.0085709 | 0.0085709 | 0.0085709 | 0.0 | 5.22
|
||||||
|
Output | 0.0024281 | 0.0024281 | 0.0024281 | 0.0 | 1.48
|
||||||
|
Modify | 0.097581 | 0.097581 | 0.097581 | 0.0 | 59.46
|
||||||
|
Other | | 0.005681 | | | 3.46
|
||||||
|
|
||||||
|
Nlocal: 81 ave 81 max 81 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 49 ave 49 max 49 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 3 ave 3 max 3 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 3
|
||||||
|
Ave neighs/atom = 0.037037
|
||||||
|
Neighbor list builds = 998
|
||||||
|
Dangerous builds = 997
|
||||||
|
Total wall time: 0:00:00
|
||||||
335
examples/rigid/log.20Apr18.rigid.nve.g++.4
Normal file
335
examples/rigid/log.20Apr18.rigid.nve.g++.4
Normal file
@ -0,0 +1,335 @@
|
|||||||
|
LAMMPS (20 Apr 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Simple rigid body system
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
|
||||||
|
read_data data.rigid
|
||||||
|
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
81 atoms
|
||||||
|
|
||||||
|
velocity all create 100.0 4928459
|
||||||
|
|
||||||
|
# unconnected bodies
|
||||||
|
|
||||||
|
group clump1 id <> 1 9
|
||||||
|
9 atoms in group clump1
|
||||||
|
group clump2 id <> 10 18
|
||||||
|
9 atoms in group clump2
|
||||||
|
group clump3 id <> 19 27
|
||||||
|
9 atoms in group clump3
|
||||||
|
group clump4 id <> 28 36
|
||||||
|
9 atoms in group clump4
|
||||||
|
group clump5 id <> 37 45
|
||||||
|
9 atoms in group clump5
|
||||||
|
group clump6 id <> 46 54
|
||||||
|
9 atoms in group clump6
|
||||||
|
group clump7 id <> 55 63
|
||||||
|
9 atoms in group clump7
|
||||||
|
group clump8 id <> 64 72
|
||||||
|
9 atoms in group clump8
|
||||||
|
group clump9 id <> 73 81
|
||||||
|
9 atoms in group clump9
|
||||||
|
|
||||||
|
fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||||
|
9 rigid bodies with 81 atoms
|
||||||
|
|
||||||
|
# 1 chain of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 36 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
# 2 chains of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 37 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||||
|
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
neigh_modify exclude group clump1 clump1
|
||||||
|
neigh_modify exclude group clump2 clump2
|
||||||
|
neigh_modify exclude group clump3 clump3
|
||||||
|
neigh_modify exclude group clump4 clump4
|
||||||
|
neigh_modify exclude group clump5 clump5
|
||||||
|
neigh_modify exclude group clump6 clump6
|
||||||
|
neigh_modify exclude group clump7 clump7
|
||||||
|
neigh_modify exclude group clump8 clump8
|
||||||
|
neigh_modify exclude group clump9 clump9
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.rigid
|
||||||
|
|
||||||
|
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
thermo 50
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 18 18 18
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||||
|
50 14910.69 571.70921 0 5265.8153 32.005816
|
||||||
|
100 16298.128 136.75661 0 5267.6488 16.449029
|
||||||
|
150 16682.532 17.504156 0 5269.4124 14.901186
|
||||||
|
200 16733.906 1.3755079 0 5269.4571 14.571305
|
||||||
|
250 16738.861 -0.15272039 0 5269.4886 14.498342
|
||||||
|
300 16738.608 -0.055216883 0 5269.5066 14.498
|
||||||
|
350 16738.5 -0.017457072 0 5269.5104 14.498392
|
||||||
|
400 16738.451 -0.0060161309 0 5269.5063 14.49851
|
||||||
|
450 16738.435 -0.001271965 0 5269.5059 14.498571
|
||||||
|
500 16738.443 -0.00081074175 0 5269.509 14.498598
|
||||||
|
550 16738.452 -0.00083208965 0 5269.5118 14.498618
|
||||||
|
600 16738.45 -0.00058358431 0 5269.5116 14.498617
|
||||||
|
650 16738.443 -0.00047228525 0 5269.5093 14.4986
|
||||||
|
700 16738.444 0 0 5269.5102 14.498612
|
||||||
|
750 16738.461 0 0 5269.5157 14.498654
|
||||||
|
800 16738.479 0 0 5269.521 14.498697
|
||||||
|
850 16738.473 0 0 5269.5192 14.498683
|
||||||
|
900 16738.449 0 0 5269.5116 14.498624
|
||||||
|
950 16738.438 -0.0035324203 0 5269.5046 14.498537
|
||||||
|
1000 16738.562 -0.051134242 0 5269.4963 14.498093
|
||||||
|
1050 16737.343 0.32970192 0 5269.4934 14.527634
|
||||||
|
1100 16737.878 0.16213235 0 5269.4941 14.533864
|
||||||
|
1150 16738.682 -0.089236256 0 5269.4959 14.511765
|
||||||
|
1200 16738.444 -0.0075446558 0 5269.5025 14.512479
|
||||||
|
1250 16738.45 0 0 5269.5119 14.512611
|
||||||
|
1300 16738.475 0 0 5269.5199 14.512673
|
||||||
|
1350 16738.484 0 0 5269.5228 14.512696
|
||||||
|
1400 16738.469 -0.00044683992 0 5269.5175 14.512651
|
||||||
|
1450 16738.45 -0.0010933363 0 5269.511 14.512595
|
||||||
|
1500 16738.445 -0.00057484239 0 5269.51 14.512591
|
||||||
|
1550 16738.451 0 0 5269.5123 14.512615
|
||||||
|
1600 16738.452 0 0 5269.5127 14.512618
|
||||||
|
1650 16738.443 0 0 5269.5099 14.512596
|
||||||
|
1700 16738.433 0 0 5269.5068 14.512572
|
||||||
|
1750 16738.438 0 0 5269.5084 14.512584
|
||||||
|
1800 16738.459 0 0 5269.5149 14.512635
|
||||||
|
1850 16738.473 0 0 5269.5193 14.51267
|
||||||
|
1900 16738.462 0 0 5269.5159 14.512644
|
||||||
|
1950 16738.446 -0.0032069962 0 5269.5076 14.512539
|
||||||
|
2000 16738.463 -0.013425408 0 5269.5027 14.512382
|
||||||
|
2050 16738.535 -0.036964311 0 5269.5017 14.512152
|
||||||
|
2100 16738.621 -0.063490509 0 5269.5023 14.512108
|
||||||
|
2150 16738.594 -0.056143934 0 5269.5012 14.512117
|
||||||
|
2200 16738.536 -0.038486645 0 5269.5007 14.512277
|
||||||
|
2250 16738.496 -0.023712406 0 5269.503 14.51242
|
||||||
|
2300 16738.488 -0.013209094 0 5269.5109 14.51255
|
||||||
|
2350 16738.486 -0.0045244524 0 5269.519 14.512693
|
||||||
|
2400 16738.475 -0.00051678325 0 5269.5194 14.512743
|
||||||
|
2450 16738.456 -0.0023209272 0 5269.5115 14.512659
|
||||||
|
2500 16738.442 -0.0052101787 0 5269.5042 14.512594
|
||||||
|
2550 16738.552 -0.04420046 0 5269.4998 14.512177
|
||||||
|
2600 16738.42 -0.004347531 0 5269.4982 14.512783
|
||||||
|
2650 16734.241 1.3131302 0 5269.5 14.577195
|
||||||
|
2700 16738.737 -0.10612056 0 5269.4961 14.503874
|
||||||
|
2750 16732.705 1.7939719 0 5269.4974 14.629294
|
||||||
|
2800 16738.558 -0.042867033 0 5269.5032 14.519893
|
||||||
|
2850 16738.499 -0.01271227 0 5269.5146 14.518524
|
||||||
|
2900 16738.486 -0.0032778045 0 5269.52 14.518712
|
||||||
|
2950 16738.482 -0.0089544631 0 5269.5133 14.518629
|
||||||
|
3000 16738.647 -0.070862542 0 5269.5031 14.51803
|
||||||
|
3050 16678.313 18.829038 0 5269.409 15.533426
|
||||||
|
3100 16632.312 33.399217 0 5269.4975 14.588597
|
||||||
|
3150 16739.318 -0.31388148 0 5269.4715 13.520782
|
||||||
|
3200 16727.951 3.26736 0 5269.4741 12.288358
|
||||||
|
3250 16686.364 16.353793 0 5269.4682 14.152517
|
||||||
|
3300 16738.532 -0.031574462 0 5269.5064 13.310615
|
||||||
|
3350 16738.454 -0.0062292918 0 5269.5071 13.308187
|
||||||
|
3400 16738.445 -0.0049349125 0 5269.5055 13.308178
|
||||||
|
3450 16738.489 -0.021623738 0 5269.5026 13.308001
|
||||||
|
3500 16737.78 0.19719043 0 5269.4983 13.325999
|
||||||
|
3550 16658.578 25.116206 0 5269.4834 13.778249
|
||||||
|
3600 16738.51 -0.032864725 0 5269.4981 12.392389
|
||||||
|
3650 16738.899 -0.15952703 0 5269.4938 12.383503
|
||||||
|
3700 16738.879 -0.16025994 0 5269.487 12.382575
|
||||||
|
3750 16738.878 -0.16608251 0 5269.4806 12.382765
|
||||||
|
3800 16738.591 -0.078679341 0 5269.4776 12.383227
|
||||||
|
3850 16738.429 -0.024729409 0 5269.4807 12.382942
|
||||||
|
3900 16738.399 -0.0062729967 0 5269.4897 12.383192
|
||||||
|
3950 16738.428 -0.002521266 0 5269.5027 12.383324
|
||||||
|
4000 16738.467 -0.0002068506 0 5269.5173 12.383474
|
||||||
|
4050 16738.488 0 0 5269.5241 12.383531
|
||||||
|
4100 16738.468 0 0 5269.5178 12.383482
|
||||||
|
4150 16738.422 0 0 5269.5033 12.383369
|
||||||
|
4200 16738.387 0 0 5269.4921 12.383281
|
||||||
|
4250 16738.383 0 0 5269.4908 12.38327
|
||||||
|
4300 16738.4 0 0 5269.4964 12.383314
|
||||||
|
4350 16738.423 0 0 5269.5036 12.38337
|
||||||
|
4400 16738.441 0 0 5269.5092 12.383414
|
||||||
|
4450 16738.45 0 0 5269.5121 12.383437
|
||||||
|
4500 16738.45 0 0 5269.5122 12.383438
|
||||||
|
4550 16738.442 0 0 5269.5095 12.383417
|
||||||
|
4600 16738.425 0 0 5269.5042 12.383376
|
||||||
|
4650 16738.404 -0.0014438316 0 5269.4961 12.383299
|
||||||
|
4700 16738.444 -0.024020551 0 5269.4862 12.382975
|
||||||
|
4750 16738.49 -0.048521424 0 5269.4761 12.385777
|
||||||
|
4800 16735.057 1.0347218 0 5269.4786 12.43543
|
||||||
|
4850 16735.441 0.92650925 0 5269.4913 12.418653
|
||||||
|
4900 16723.839 4.5908973 0 5269.5033 13.410103
|
||||||
|
4950 16738.531 -0.021537669 0 5269.5159 13.089982
|
||||||
|
5000 16738.45 -0.0042589693 0 5269.5077 13.090062
|
||||||
|
5050 16738.409 -0.00024692474 0 5269.4987 13.090038
|
||||||
|
5100 16738.404 0 0 5269.4976 13.090032
|
||||||
|
5150 16738.421 0 0 5269.5029 13.090073
|
||||||
|
5200 16738.44 0 0 5269.5087 13.090119
|
||||||
|
5250 16738.448 -0.0012793921 0 5269.5102 13.090114
|
||||||
|
5300 16738.456 -0.0064376396 0 5269.5075 13.090026
|
||||||
|
5350 16738.479 -0.020383843 0 5269.5007 13.089898
|
||||||
|
5400 16735.845 0.79889489 0 5269.4909 13.136244
|
||||||
|
5450 16735.558 0.87619907 0 5269.4778 12.324482
|
||||||
|
5500 16711.494 8.4724273 0 5269.4984 12.656579
|
||||||
|
5550 16454.525 89.074821 0 5269.2031 16.996502
|
||||||
|
5600 16713.084 7.9801107 0 5269.5065 13.774972
|
||||||
|
5650 16738.676 -0.079987805 0 5269.5033 13.168292
|
||||||
|
5700 16446.281 91.866085 0 5269.399 23.764659
|
||||||
|
5750 16738.549 -0.039869082 0 5269.5034 13.378118
|
||||||
|
5800 16738.487 -0.014994465 0 5269.5086 13.378394
|
||||||
|
5850 16738.466 -0.0051267396 0 5269.512 13.378555
|
||||||
|
5900 16738.462 -0.004368998 0 5269.5113 13.378568
|
||||||
|
5950 16738.528 -0.032727397 0 5269.5039 13.378192
|
||||||
|
6000 16702.774 10.969422 0 5269.2502 13.788847
|
||||||
|
6050 16682.271 17.483223 0 5269.3092 13.353098
|
||||||
|
6100 16738.508 -0.028838294 0 5269.5016 12.521077
|
||||||
|
6150 16738.425 -0.0067595586 0 5269.4974 12.521216
|
||||||
|
6200 16738.401 -0.0011499906 0 5269.4955 12.521248
|
||||||
|
6250 16738.455 0 0 5269.5136 12.521404
|
||||||
|
6300 16738.523 0 0 5269.5352 12.521573
|
||||||
|
6350 16738.503 0 0 5269.5287 12.521525
|
||||||
|
6400 16738.427 0 0 5269.5047 12.521337
|
||||||
|
6450 16738.399 0 0 5269.496 12.521268
|
||||||
|
6500 16738.425 0 0 5269.5042 12.521331
|
||||||
|
6550 16738.441 0 0 5269.5093 12.521372
|
||||||
|
6600 16738.42 0 0 5269.5025 12.521319
|
||||||
|
6650 16738.398 0 0 5269.4957 12.521266
|
||||||
|
6700 16738.435 0 0 5269.5074 12.521355
|
||||||
|
6750 16738.505 0 0 5269.5293 12.521527
|
||||||
|
6800 16738.508 0 0 5269.5303 12.521536
|
||||||
|
6850 16738.446 0 0 5269.5108 12.521384
|
||||||
|
6900 16738.414 0 0 5269.5009 12.521306
|
||||||
|
6950 16738.432 0 0 5269.5063 12.521348
|
||||||
|
7000 16738.444 0 0 5269.5102 12.521379
|
||||||
|
7050 16738.421 0 0 5269.5029 12.521322
|
||||||
|
7100 16738.393 0 0 5269.4941 12.521253
|
||||||
|
7150 16738.419 0 0 5269.5022 12.521315
|
||||||
|
7200 16738.489 0 0 5269.5244 12.521489
|
||||||
|
7250 16738.505 0 0 5269.5293 12.521528
|
||||||
|
7300 16738.443 0 0 5269.5098 12.521377
|
||||||
|
7350 16738.404 0 0 5269.4976 12.521281
|
||||||
|
7400 16738.43 0 0 5269.5058 12.521344
|
||||||
|
7450 16738.461 0 0 5269.5156 12.521421
|
||||||
|
7500 16738.447 0 0 5269.5109 12.521385
|
||||||
|
7550 16738.407 0 0 5269.4986 12.521288
|
||||||
|
7600 16738.412 0 0 5269.5002 12.5213
|
||||||
|
7650 16738.478 0 0 5269.5208 12.521461
|
||||||
|
7700 16738.51 0 0 5269.5309 12.521541
|
||||||
|
7750 16738.454 0 0 5269.5135 12.521406
|
||||||
|
7800 16738.398 0 0 5269.4958 12.521267
|
||||||
|
7850 16738.407 -0.00021180715 0 5269.4982 12.521283
|
||||||
|
7900 16738.441 -0.0002167946 0 5269.509 12.521367
|
||||||
|
7950 16738.446 -0.0002384787 0 5269.5107 12.52138
|
||||||
|
8000 16738.423 0 0 5269.5035 12.521327
|
||||||
|
8050 16738.423 0 0 5269.5034 12.521325
|
||||||
|
8100 16738.478 -0.00069624484 0 5269.52 12.521448
|
||||||
|
8150 16738.523 -0.0040058183 0 5269.531 12.521494
|
||||||
|
8200 16738.486 -0.0092298512 0 5269.5142 12.521328
|
||||||
|
8250 16738.458 -0.023189661 0 5269.4914 12.521008
|
||||||
|
8300 16738.513 -0.045847765 0 5269.4861 12.520773
|
||||||
|
8350 16723.735 4.5720344 0 5269.4516 12.849543
|
||||||
|
8400 16738.466 -0.02019859 0 5269.497 12.835812
|
||||||
|
8450 16738.437 -0.012822198 0 5269.4952 12.829979
|
||||||
|
8500 16738.408 -0.0016833646 0 5269.4972 12.830104
|
||||||
|
8550 16738.464 -0.00097382606 0 5269.5155 12.830258
|
||||||
|
8600 16738.669 -0.050581176 0 5269.5304 12.829977
|
||||||
|
8650 15918.073 250.131 0 5261.3761 24.542327
|
||||||
|
8700 16738.446 0.00085039409 0 5269.5116 10.59114
|
||||||
|
8750 16738.472 -0.010146632 0 5269.5089 10.590059
|
||||||
|
8800 16738.468 0 0 5269.5176 10.590278
|
||||||
|
8850 16738.508 0 0 5269.5303 10.590378
|
||||||
|
8900 16738.509 0 0 5269.5306 10.590381
|
||||||
|
8950 16738.496 0 0 5269.5266 10.590349
|
||||||
|
9000 16738.477 0 0 5269.5204 10.590302
|
||||||
|
9050 16738.455 0 0 5269.5135 10.590247
|
||||||
|
9100 16738.477 0 0 5269.5205 10.590301
|
||||||
|
9150 16738.512 0 0 5269.5315 10.590388
|
||||||
|
9200 16738.502 0 0 5269.5285 10.590364
|
||||||
|
9250 16738.493 0 0 5269.5254 10.59034
|
||||||
|
9300 16738.482 0 0 5269.522 10.590314
|
||||||
|
9350 16738.46 0 0 5269.5151 10.59026
|
||||||
|
9400 16738.48 0 0 5269.5216 10.59031
|
||||||
|
9450 16738.509 0 0 5269.5306 10.590381
|
||||||
|
9500 16738.49 0 0 5269.5247 10.590335
|
||||||
|
9550 16738.484 0 0 5269.5226 10.590318
|
||||||
|
9600 16738.483 0 0 5269.5223 10.590316
|
||||||
|
9650 16738.464 0 0 5269.5165 10.590271
|
||||||
|
9700 16738.484 0 0 5269.5228 10.590319
|
||||||
|
9750 16738.507 0 0 5269.53 10.590376
|
||||||
|
9800 16738.482 0 0 5269.522 10.590314
|
||||||
|
9850 16738.478 0 0 5269.5207 10.590303
|
||||||
|
9900 16738.487 -0.00030979874 0 5269.5233 10.59032
|
||||||
|
9950 16738.476 -0.00095967134 0 5269.5192 10.590278
|
||||||
|
10000 16738.494 -0.00062714318 0 5269.5253 10.590329
|
||||||
|
Loop time of 0.229326 on 4 procs for 10000 steps with 81 atoms
|
||||||
|
|
||||||
|
Performance: 376756.903 tau/day, 43606.123 timesteps/s
|
||||||
|
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.003273 | 0.0043935 | 0.0052235 | 1.1 | 1.92
|
||||||
|
Neigh | 0.011258 | 0.012805 | 0.015637 | 1.5 | 5.58
|
||||||
|
Comm | 0.086959 | 0.091051 | 0.099018 | 1.6 | 39.70
|
||||||
|
Output | 0.0044641 | 0.0048054 | 0.0055933 | 0.7 | 2.10
|
||||||
|
Modify | 0.10085 | 0.10594 | 0.11123 | 1.4 | 46.19
|
||||||
|
Other | | 0.01034 | | | 4.51
|
||||||
|
|
||||||
|
Nlocal: 20.25 ave 34 max 9 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 38.5 ave 43 max 26 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||||
|
Neighs: 0.75 ave 2 max 0 min
|
||||||
|
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 3
|
||||||
|
Ave neighs/atom = 0.037037
|
||||||
|
Neighbor list builds = 998
|
||||||
|
Dangerous builds = 997
|
||||||
|
Total wall time: 0:00:00
|
||||||
340
examples/rigid/log.20Apr18.rigid.property.g++.1
Normal file
340
examples/rigid/log.20Apr18.rigid.property.g++.1
Normal file
@ -0,0 +1,340 @@
|
|||||||
|
LAMMPS (20 Apr 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Simple rigid body system
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
atom_modify map array
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
|
||||||
|
fix 0 all property/atom i_bodies
|
||||||
|
|
||||||
|
read_data data.rigid-property fix 0 NULL Bodies
|
||||||
|
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
81 atoms
|
||||||
|
|
||||||
|
velocity all create 100.0 4928459
|
||||||
|
|
||||||
|
|
||||||
|
# unconnected bodies
|
||||||
|
|
||||||
|
group clump1 id <> 1 9
|
||||||
|
9 atoms in group clump1
|
||||||
|
group clump2 id <> 10 18
|
||||||
|
9 atoms in group clump2
|
||||||
|
group clump3 id <> 19 27
|
||||||
|
9 atoms in group clump3
|
||||||
|
group clump4 id <> 28 36
|
||||||
|
9 atoms in group clump4
|
||||||
|
group clump5 id <> 37 45
|
||||||
|
9 atoms in group clump5
|
||||||
|
group clump6 id <> 46 54
|
||||||
|
9 atoms in group clump6
|
||||||
|
group clump7 id <> 55 63
|
||||||
|
9 atoms in group clump7
|
||||||
|
group clump8 id <> 64 72
|
||||||
|
9 atoms in group clump8
|
||||||
|
group clump9 id <> 73 81
|
||||||
|
9 atoms in group clump9
|
||||||
|
|
||||||
|
# assemble bodies from per-atom custom integer property bodies
|
||||||
|
fix 1 all rigid custom i_bodies
|
||||||
|
9 rigid bodies with 81 atoms
|
||||||
|
|
||||||
|
# 1 chain of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 36 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
# 2 chains of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 37 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||||
|
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
neigh_modify exclude group clump1 clump1
|
||||||
|
neigh_modify exclude group clump2 clump2
|
||||||
|
neigh_modify exclude group clump3 clump3
|
||||||
|
neigh_modify exclude group clump4 clump4
|
||||||
|
neigh_modify exclude group clump5 clump5
|
||||||
|
neigh_modify exclude group clump6 clump6
|
||||||
|
neigh_modify exclude group clump7 clump7
|
||||||
|
neigh_modify exclude group clump8 clump8
|
||||||
|
neigh_modify exclude group clump9 clump9
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.rigid
|
||||||
|
|
||||||
|
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
thermo 50
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 18 18 18
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.046 | 4.046 | 4.046 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||||
|
50 14910.685 571.71558 0 5265.82 32.006171
|
||||||
|
100 16298.442 136.66184 0 5267.653 16.444229
|
||||||
|
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||||
|
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||||
|
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||||
|
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||||
|
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||||
|
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||||
|
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||||
|
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||||
|
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||||
|
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||||
|
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||||
|
700 16738.455 0 0 5269.5136 14.496713
|
||||||
|
750 16738.455 0 0 5269.5136 14.49671
|
||||||
|
800 16738.455 0 0 5269.5137 14.496709
|
||||||
|
850 16738.455 0 0 5269.5137 14.49671
|
||||||
|
900 16738.456 0 0 5269.5138 14.496713
|
||||||
|
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||||
|
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||||
|
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||||
|
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||||
|
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||||
|
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||||
|
1250 16738.456 0 0 5269.514 14.510704
|
||||||
|
1300 16738.457 0 0 5269.5141 14.510701
|
||||||
|
1350 16738.457 0 0 5269.5141 14.510699
|
||||||
|
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||||
|
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||||
|
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||||
|
1550 16738.457 0 0 5269.5143 14.51071
|
||||||
|
1600 16738.457 0 0 5269.5144 14.510712
|
||||||
|
1650 16738.457 0 0 5269.5144 14.510712
|
||||||
|
1700 16738.458 0 0 5269.5144 14.51071
|
||||||
|
1750 16738.458 0 0 5269.5145 14.510708
|
||||||
|
1800 16738.458 0 0 5269.5145 14.510706
|
||||||
|
1850 16738.458 0 0 5269.5146 14.510705
|
||||||
|
1900 16738.458 0 0 5269.5146 14.510706
|
||||||
|
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||||
|
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||||
|
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||||
|
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||||
|
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||||
|
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||||
|
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||||
|
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||||
|
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||||
|
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||||
|
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||||
|
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||||
|
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||||
|
2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
|
||||||
|
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||||
|
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||||
|
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||||
|
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||||
|
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||||
|
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||||
|
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||||
|
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||||
|
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||||
|
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||||
|
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||||
|
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||||
|
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||||
|
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||||
|
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||||
|
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||||
|
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||||
|
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||||
|
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||||
|
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||||
|
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||||
|
3700 16738.602 -0.070934367 0 5269.4889 12.025288
|
||||||
|
3750 16737.731 0.20706557 0 5269.4927 12.061948
|
||||||
|
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||||
|
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||||
|
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||||
|
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||||
|
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||||
|
4050 16738.437 0 0 5269.5078 12.035454
|
||||||
|
4100 16738.437 0 0 5269.508 12.035435
|
||||||
|
4150 16738.438 0 0 5269.5081 12.035426
|
||||||
|
4200 16738.438 0 0 5269.5083 12.035432
|
||||||
|
4250 16738.439 0 0 5269.5085 12.035447
|
||||||
|
4300 16738.439 0 0 5269.5086 12.035463
|
||||||
|
4350 16738.44 0 0 5269.5087 12.035474
|
||||||
|
4400 16738.44 0 0 5269.5088 12.035478
|
||||||
|
4450 16738.44 0 0 5269.5089 12.035474
|
||||||
|
4500 16738.44 0 0 5269.509 12.035462
|
||||||
|
4550 16738.441 0 0 5269.5092 12.035449
|
||||||
|
4600 16738.441 0 0 5269.5093 12.035445
|
||||||
|
4650 16738.442 0 0 5269.5095 12.035451
|
||||||
|
4700 16738.442 0 0 5269.5096 12.03546
|
||||||
|
4750 16738.443 0 0 5269.5097 12.035465
|
||||||
|
4800 16738.443 0 0 5269.5098 12.035466
|
||||||
|
4850 16738.443 0 0 5269.51 12.035463
|
||||||
|
4900 16738.444 0 0 5269.5101 12.035456
|
||||||
|
4950 16738.444 0 0 5269.5102 12.035447
|
||||||
|
5000 16738.445 0 0 5269.5104 12.03544
|
||||||
|
5050 16738.445 0 0 5269.5105 12.035442
|
||||||
|
5100 16738.446 0 0 5269.5107 12.035455
|
||||||
|
5150 16738.446 0 0 5269.5108 12.03547
|
||||||
|
5200 16738.446 0 0 5269.5109 12.035479
|
||||||
|
5250 16738.447 0 0 5269.511 12.035479
|
||||||
|
5300 16738.447 0 0 5269.5111 12.03547
|
||||||
|
5350 16738.447 0 0 5269.5112 12.035454
|
||||||
|
5400 16738.448 0 0 5269.5113 12.035434
|
||||||
|
5450 16738.448 0 0 5269.5115 12.03542
|
||||||
|
5500 16738.449 0 0 5269.5117 12.035422
|
||||||
|
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||||
|
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||||
|
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||||
|
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||||
|
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||||
|
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||||
|
5850 16738.451 0 0 5269.5123 12.011709
|
||||||
|
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
|
||||||
|
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||||
|
6000 16738.452 0 0 5269.5128 12.011688
|
||||||
|
6050 16738.453 0 0 5269.513 12.011702
|
||||||
|
6100 16738.453 0 0 5269.5131 12.011716
|
||||||
|
6150 16738.454 0 0 5269.5132 12.011725
|
||||||
|
6200 16738.454 0 0 5269.5133 12.011728
|
||||||
|
6250 16738.454 0 0 5269.5134 12.011723
|
||||||
|
6300 16738.455 0 0 5269.5135 12.011712
|
||||||
|
6350 16738.455 0 0 5269.5137 12.0117
|
||||||
|
6400 16738.456 0 0 5269.5138 12.011697
|
||||||
|
6450 16738.456 0 0 5269.514 12.011704
|
||||||
|
6500 16738.456 0 0 5269.5141 12.011714
|
||||||
|
6550 16738.457 0 0 5269.5142 12.011719
|
||||||
|
6600 16738.457 0 0 5269.5143 12.011718
|
||||||
|
6650 16738.458 0 0 5269.5144 12.011713
|
||||||
|
6700 16738.458 0 0 5269.5146 12.011705
|
||||||
|
6750 16738.459 0 0 5269.5147 12.011696
|
||||||
|
6800 16738.459 0 0 5269.5149 12.01169
|
||||||
|
6850 16738.46 0 0 5269.515 12.011695
|
||||||
|
6900 16738.46 0 0 5269.5152 12.01171
|
||||||
|
6950 16738.46 0 0 5269.5153 12.011726
|
||||||
|
7000 16738.461 0 0 5269.5154 12.011736
|
||||||
|
7050 16738.461 0 0 5269.5155 12.011737
|
||||||
|
7100 16738.461 0 0 5269.5155 12.011728
|
||||||
|
7150 16738.461 0 0 5269.5156 12.011712
|
||||||
|
7200 16738.462 0 0 5269.5158 12.011691
|
||||||
|
7250 16738.463 0 0 5269.516 12.011676
|
||||||
|
7300 16738.463 0 0 5269.5162 12.011677
|
||||||
|
7350 16738.464 0 0 5269.5164 12.011693
|
||||||
|
7400 16738.464 0 0 5269.5165 12.011713
|
||||||
|
7450 16738.465 0 0 5269.5166 12.011729
|
||||||
|
7500 16738.465 0 0 5269.5167 12.011736
|
||||||
|
7550 16738.465 0 0 5269.5168 12.011734
|
||||||
|
7600 16738.465 0 0 5269.5168 12.011722
|
||||||
|
7650 16738.466 0 0 5269.517 12.011704
|
||||||
|
7700 16738.466 0 0 5269.5171 12.011687
|
||||||
|
7750 16738.467 0 0 5269.5173 12.011681
|
||||||
|
7800 16738.467 0 0 5269.5175 12.011687
|
||||||
|
7850 16738.468 0 0 5269.5176 12.0117
|
||||||
|
7900 16738.468 0 0 5269.5178 12.011712
|
||||||
|
7950 16738.469 0 0 5269.5179 12.011721
|
||||||
|
8000 16738.469 0 0 5269.518 12.011724
|
||||||
|
8050 16738.469 0 0 5269.5181 12.01172
|
||||||
|
8100 16738.47 0 0 5269.5182 12.011709
|
||||||
|
8150 16738.47 0 0 5269.5183 12.0117
|
||||||
|
8200 16738.47 0 0 5269.5185 12.0117
|
||||||
|
8250 16738.471 0 0 5269.5186 12.011709
|
||||||
|
8300 16738.471 0 0 5269.5187 12.011719
|
||||||
|
8350 16738.472 0 0 5269.5189 12.011723
|
||||||
|
8400 16738.472 0 0 5269.519 12.01172
|
||||||
|
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
|
||||||
|
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
|
||||||
|
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||||
|
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
|
||||||
|
8650 16738.474 0 0 5269.5197 12.011699
|
||||||
|
8700 16738.475 0 0 5269.5199 12.011715
|
||||||
|
8750 16738.475 0 0 5269.52 12.011732
|
||||||
|
8800 16738.475 0 0 5269.52 12.011743
|
||||||
|
8850 16738.476 0 0 5269.5201 12.011744
|
||||||
|
8900 16738.476 0 0 5269.5202 12.011735
|
||||||
|
8950 16738.476 0 0 5269.5203 12.011719
|
||||||
|
9000 16738.477 0 0 5269.5205 12.011698
|
||||||
|
9050 16738.477 0 0 5269.5206 12.011683
|
||||||
|
9100 16738.478 0 0 5269.5208 12.011684
|
||||||
|
9150 16738.479 0 0 5269.521 12.011701
|
||||||
|
9200 16738.479 0 0 5269.5212 12.011722
|
||||||
|
9250 16738.479 0 0 5269.5213 12.011738
|
||||||
|
9300 16738.48 0 0 5269.5214 12.011746
|
||||||
|
9350 16738.48 0 0 5269.5214 12.011744
|
||||||
|
9400 16738.48 0 0 5269.5215 12.011732
|
||||||
|
9450 16738.48 0 0 5269.5216 12.011715
|
||||||
|
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
|
||||||
|
9550 16738.493 -0.0053156162 0 5269.5203 12.011611
|
||||||
|
9600 16738.549 -0.026814371 0 5269.5163 12.011415
|
||||||
|
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||||
|
9700 16735.041 1.0589893 0 5269.4979 12.062708
|
||||||
|
9750 16738.013 0.13550102 0 5269.5101 11.407246
|
||||||
|
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||||
|
9850 16738.489 -0.00067270521 0 5269.5237 11.395098
|
||||||
|
9900 16738.489 -0.00024984561 0 5269.5242 11.395085
|
||||||
|
9950 16738.49 0 0 5269.5245 11.395076
|
||||||
|
10000 16738.49 0 0 5269.5246 11.395075
|
||||||
|
Loop time of 0.147063 on 1 procs for 10000 steps with 81 atoms
|
||||||
|
|
||||||
|
Performance: 587503.247 tau/day, 67998.061 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 | 0.011234 | 0.011234 | 0.011234 | 0.0 | 7.64
|
||||||
|
Neigh | 0.038835 | 0.038835 | 0.038835 | 0.0 | 26.41
|
||||||
|
Comm | 0.0099175 | 0.0099175 | 0.0099175 | 0.0 | 6.74
|
||||||
|
Output | 0.002502 | 0.002502 | 0.002502 | 0.0 | 1.70
|
||||||
|
Modify | 0.078281 | 0.078281 | 0.078281 | 0.0 | 53.23
|
||||||
|
Other | | 0.006294 | | | 4.28
|
||||||
|
|
||||||
|
Nlocal: 81 ave 81 max 81 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 84 ave 84 max 84 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
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 998
|
||||||
|
Dangerous builds = 997
|
||||||
|
Total wall time: 0:00:00
|
||||||
340
examples/rigid/log.20Apr18.rigid.property.g++.4
Normal file
340
examples/rigid/log.20Apr18.rigid.property.g++.4
Normal file
@ -0,0 +1,340 @@
|
|||||||
|
LAMMPS (20 Apr 2018)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Simple rigid body system
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
atom_modify map array
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
|
||||||
|
fix 0 all property/atom i_bodies
|
||||||
|
|
||||||
|
read_data data.rigid-property fix 0 NULL Bodies
|
||||||
|
orthogonal box = (-12 -12 -12) to (12 12 12)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
81 atoms
|
||||||
|
|
||||||
|
velocity all create 100.0 4928459
|
||||||
|
|
||||||
|
|
||||||
|
# unconnected bodies
|
||||||
|
|
||||||
|
group clump1 id <> 1 9
|
||||||
|
9 atoms in group clump1
|
||||||
|
group clump2 id <> 10 18
|
||||||
|
9 atoms in group clump2
|
||||||
|
group clump3 id <> 19 27
|
||||||
|
9 atoms in group clump3
|
||||||
|
group clump4 id <> 28 36
|
||||||
|
9 atoms in group clump4
|
||||||
|
group clump5 id <> 37 45
|
||||||
|
9 atoms in group clump5
|
||||||
|
group clump6 id <> 46 54
|
||||||
|
9 atoms in group clump6
|
||||||
|
group clump7 id <> 55 63
|
||||||
|
9 atoms in group clump7
|
||||||
|
group clump8 id <> 64 72
|
||||||
|
9 atoms in group clump8
|
||||||
|
group clump9 id <> 73 81
|
||||||
|
9 atoms in group clump9
|
||||||
|
|
||||||
|
# assemble bodies from per-atom custom integer property bodies
|
||||||
|
fix 1 all rigid custom i_bodies
|
||||||
|
9 rigid bodies with 81 atoms
|
||||||
|
|
||||||
|
# 1 chain of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 36 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
# 2 chains of connected bodies
|
||||||
|
|
||||||
|
#group clump1 id <> 1 9
|
||||||
|
#group clump2 id <> 9 18
|
||||||
|
#group clump3 id <> 18 27
|
||||||
|
#group clump4 id <> 27 36
|
||||||
|
#group clump5 id <> 37 45
|
||||||
|
#group clump6 id <> 45 54
|
||||||
|
#group clump7 id <> 54 63
|
||||||
|
#group clump8 id <> 63 72
|
||||||
|
#group clump9 id <> 72 81
|
||||||
|
|
||||||
|
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||||
|
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||||
|
|
||||||
|
neigh_modify exclude group clump1 clump1
|
||||||
|
neigh_modify exclude group clump2 clump2
|
||||||
|
neigh_modify exclude group clump3 clump3
|
||||||
|
neigh_modify exclude group clump4 clump4
|
||||||
|
neigh_modify exclude group clump5 clump5
|
||||||
|
neigh_modify exclude group clump6 clump6
|
||||||
|
neigh_modify exclude group clump7 clump7
|
||||||
|
neigh_modify exclude group clump8 clump8
|
||||||
|
neigh_modify exclude group clump9 clump9
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
#dump 1 all atom 50 dump.rigid
|
||||||
|
|
||||||
|
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 2 pad 5
|
||||||
|
|
||||||
|
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 3 pad 5
|
||||||
|
|
||||||
|
timestep 0.0001
|
||||||
|
thermo 50
|
||||||
|
run 10000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 18 18 18
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.017 | 4.111 | 4.392 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||||
|
50 14910.685 571.71558 0 5265.82 32.006171
|
||||||
|
100 16298.442 136.66184 0 5267.653 16.444229
|
||||||
|
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||||
|
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||||
|
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||||
|
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||||
|
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||||
|
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||||
|
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||||
|
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||||
|
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||||
|
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||||
|
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||||
|
700 16738.455 0 0 5269.5136 14.496713
|
||||||
|
750 16738.455 0 0 5269.5136 14.49671
|
||||||
|
800 16738.455 0 0 5269.5137 14.496709
|
||||||
|
850 16738.455 0 0 5269.5137 14.49671
|
||||||
|
900 16738.456 0 0 5269.5138 14.496713
|
||||||
|
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||||
|
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||||
|
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||||
|
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||||
|
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||||
|
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||||
|
1250 16738.456 0 0 5269.514 14.510704
|
||||||
|
1300 16738.457 0 0 5269.5141 14.510701
|
||||||
|
1350 16738.457 0 0 5269.5141 14.510699
|
||||||
|
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||||
|
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||||
|
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||||
|
1550 16738.457 0 0 5269.5143 14.51071
|
||||||
|
1600 16738.457 0 0 5269.5144 14.510712
|
||||||
|
1650 16738.457 0 0 5269.5144 14.510712
|
||||||
|
1700 16738.458 0 0 5269.5144 14.51071
|
||||||
|
1750 16738.458 0 0 5269.5145 14.510708
|
||||||
|
1800 16738.458 0 0 5269.5145 14.510706
|
||||||
|
1850 16738.458 0 0 5269.5146 14.510705
|
||||||
|
1900 16738.458 0 0 5269.5146 14.510706
|
||||||
|
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||||
|
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||||
|
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||||
|
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||||
|
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||||
|
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||||
|
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||||
|
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||||
|
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||||
|
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||||
|
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||||
|
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||||
|
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||||
|
2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
|
||||||
|
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||||
|
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||||
|
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||||
|
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||||
|
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||||
|
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||||
|
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||||
|
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||||
|
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||||
|
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||||
|
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||||
|
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||||
|
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||||
|
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||||
|
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||||
|
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||||
|
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||||
|
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||||
|
3550 16713.405 7.846062 0 5269.4737 12.389816
|
||||||
|
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||||
|
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||||
|
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||||
|
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||||
|
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||||
|
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||||
|
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||||
|
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||||
|
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||||
|
4050 16738.437 0 0 5269.5078 12.035454
|
||||||
|
4100 16738.437 0 0 5269.508 12.035435
|
||||||
|
4150 16738.438 0 0 5269.5081 12.035426
|
||||||
|
4200 16738.438 0 0 5269.5083 12.035432
|
||||||
|
4250 16738.439 0 0 5269.5085 12.035447
|
||||||
|
4300 16738.439 0 0 5269.5086 12.035463
|
||||||
|
4350 16738.44 0 0 5269.5087 12.035474
|
||||||
|
4400 16738.44 0 0 5269.5088 12.035478
|
||||||
|
4450 16738.44 0 0 5269.5089 12.035474
|
||||||
|
4500 16738.44 0 0 5269.509 12.035462
|
||||||
|
4550 16738.441 0 0 5269.5092 12.035449
|
||||||
|
4600 16738.441 0 0 5269.5093 12.035445
|
||||||
|
4650 16738.442 0 0 5269.5095 12.035451
|
||||||
|
4700 16738.442 0 0 5269.5096 12.03546
|
||||||
|
4750 16738.443 0 0 5269.5097 12.035465
|
||||||
|
4800 16738.443 0 0 5269.5098 12.035466
|
||||||
|
4850 16738.443 0 0 5269.51 12.035463
|
||||||
|
4900 16738.444 0 0 5269.5101 12.035456
|
||||||
|
4950 16738.444 0 0 5269.5102 12.035447
|
||||||
|
5000 16738.445 0 0 5269.5104 12.03544
|
||||||
|
5050 16738.445 0 0 5269.5105 12.035442
|
||||||
|
5100 16738.446 0 0 5269.5107 12.035455
|
||||||
|
5150 16738.446 0 0 5269.5108 12.03547
|
||||||
|
5200 16738.446 0 0 5269.5109 12.035479
|
||||||
|
5250 16738.447 0 0 5269.511 12.035479
|
||||||
|
5300 16738.447 0 0 5269.5111 12.03547
|
||||||
|
5350 16738.447 0 0 5269.5112 12.035454
|
||||||
|
5400 16738.448 0 0 5269.5113 12.035434
|
||||||
|
5450 16738.448 0 0 5269.5115 12.03542
|
||||||
|
5500 16738.449 0 0 5269.5117 12.035422
|
||||||
|
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||||
|
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||||
|
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||||
|
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||||
|
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||||
|
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||||
|
5850 16738.451 0 0 5269.5123 12.011709
|
||||||
|
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||||
|
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||||
|
6000 16738.452 0 0 5269.5128 12.011688
|
||||||
|
6050 16738.453 0 0 5269.513 12.011702
|
||||||
|
6100 16738.453 0 0 5269.5131 12.011716
|
||||||
|
6150 16738.454 0 0 5269.5132 12.011725
|
||||||
|
6200 16738.454 0 0 5269.5133 12.011728
|
||||||
|
6250 16738.454 0 0 5269.5134 12.011723
|
||||||
|
6300 16738.455 0 0 5269.5135 12.011712
|
||||||
|
6350 16738.455 0 0 5269.5137 12.0117
|
||||||
|
6400 16738.456 0 0 5269.5138 12.011697
|
||||||
|
6450 16738.456 0 0 5269.514 12.011704
|
||||||
|
6500 16738.456 0 0 5269.5141 12.011714
|
||||||
|
6550 16738.457 0 0 5269.5142 12.011719
|
||||||
|
6600 16738.457 0 0 5269.5143 12.011718
|
||||||
|
6650 16738.458 0 0 5269.5144 12.011713
|
||||||
|
6700 16738.458 0 0 5269.5146 12.011705
|
||||||
|
6750 16738.459 0 0 5269.5147 12.011696
|
||||||
|
6800 16738.459 0 0 5269.5149 12.01169
|
||||||
|
6850 16738.46 0 0 5269.515 12.011695
|
||||||
|
6900 16738.46 0 0 5269.5152 12.01171
|
||||||
|
6950 16738.46 0 0 5269.5153 12.011726
|
||||||
|
7000 16738.461 0 0 5269.5154 12.011736
|
||||||
|
7050 16738.461 0 0 5269.5155 12.011737
|
||||||
|
7100 16738.461 0 0 5269.5155 12.011728
|
||||||
|
7150 16738.461 0 0 5269.5156 12.011712
|
||||||
|
7200 16738.462 0 0 5269.5158 12.011691
|
||||||
|
7250 16738.463 0 0 5269.516 12.011676
|
||||||
|
7300 16738.463 0 0 5269.5162 12.011677
|
||||||
|
7350 16738.464 0 0 5269.5164 12.011693
|
||||||
|
7400 16738.464 0 0 5269.5165 12.011713
|
||||||
|
7450 16738.465 0 0 5269.5166 12.011729
|
||||||
|
7500 16738.465 0 0 5269.5167 12.011736
|
||||||
|
7550 16738.465 0 0 5269.5168 12.011734
|
||||||
|
7600 16738.465 0 0 5269.5168 12.011722
|
||||||
|
7650 16738.466 0 0 5269.517 12.011704
|
||||||
|
7700 16738.466 0 0 5269.5171 12.011687
|
||||||
|
7750 16738.467 0 0 5269.5173 12.011681
|
||||||
|
7800 16738.467 0 0 5269.5175 12.011687
|
||||||
|
7850 16738.468 0 0 5269.5176 12.0117
|
||||||
|
7900 16738.468 0 0 5269.5178 12.011712
|
||||||
|
7950 16738.469 0 0 5269.5179 12.011721
|
||||||
|
8000 16738.469 0 0 5269.518 12.011724
|
||||||
|
8050 16738.469 0 0 5269.5181 12.01172
|
||||||
|
8100 16738.47 0 0 5269.5182 12.011709
|
||||||
|
8150 16738.47 0 0 5269.5183 12.0117
|
||||||
|
8200 16738.47 0 0 5269.5185 12.0117
|
||||||
|
8250 16738.471 0 0 5269.5186 12.011709
|
||||||
|
8300 16738.471 0 0 5269.5187 12.011719
|
||||||
|
8350 16738.472 0 0 5269.5189 12.011723
|
||||||
|
8400 16738.472 0 0 5269.519 12.01172
|
||||||
|
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||||
|
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||||
|
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||||
|
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||||||
|
8650 16738.474 0 0 5269.5197 12.011699
|
||||||
|
8700 16738.475 0 0 5269.5199 12.011715
|
||||||
|
8750 16738.475 0 0 5269.52 12.011732
|
||||||
|
8800 16738.475 0 0 5269.52 12.011743
|
||||||
|
8850 16738.476 0 0 5269.5201 12.011744
|
||||||
|
8900 16738.476 0 0 5269.5202 12.011735
|
||||||
|
8950 16738.476 0 0 5269.5203 12.011719
|
||||||
|
9000 16738.477 0 0 5269.5205 12.011698
|
||||||
|
9050 16738.477 0 0 5269.5206 12.011683
|
||||||
|
9100 16738.478 0 0 5269.5208 12.011684
|
||||||
|
9150 16738.479 0 0 5269.521 12.011701
|
||||||
|
9200 16738.479 0 0 5269.5212 12.011722
|
||||||
|
9250 16738.479 0 0 5269.5213 12.011738
|
||||||
|
9300 16738.48 0 0 5269.5214 12.011746
|
||||||
|
9350 16738.48 0 0 5269.5214 12.011744
|
||||||
|
9400 16738.48 0 0 5269.5215 12.011732
|
||||||
|
9450 16738.48 0 0 5269.5216 12.011715
|
||||||
|
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
|
||||||
|
9550 16738.493 -0.0053156159 0 5269.5203 12.011611
|
||||||
|
9600 16738.549 -0.026814369 0 5269.5163 12.011415
|
||||||
|
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||||
|
9700 16735.041 1.0589887 0 5269.4979 12.062708
|
||||||
|
9750 16738.013 0.135501 0 5269.5101 11.407245
|
||||||
|
9800 16738.512 -0.011620329 0 5269.5201 11.394973
|
||||||
|
9850 16738.489 -0.00067270548 0 5269.5237 11.395098
|
||||||
|
9900 16738.489 -0.00024984569 0 5269.5242 11.395084
|
||||||
|
9950 16738.49 0 0 5269.5245 11.395076
|
||||||
|
10000 16738.49 0 0 5269.5246 11.395075
|
||||||
|
Loop time of 0.198144 on 4 procs for 10000 steps with 81 atoms
|
||||||
|
|
||||||
|
Performance: 436047.258 tau/day, 50468.433 timesteps/s
|
||||||
|
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0023599 | 0.0036138 | 0.004488 | 1.3 | 1.82
|
||||||
|
Neigh | 0.011142 | 0.01173 | 0.01336 | 0.9 | 5.92
|
||||||
|
Comm | 0.085794 | 0.087198 | 0.089059 | 0.4 | 44.01
|
||||||
|
Output | 0.0044518 | 0.0047111 | 0.0054488 | 0.6 | 2.38
|
||||||
|
Modify | 0.078396 | 0.08157 | 0.083827 | 0.8 | 41.17
|
||||||
|
Other | | 0.009321 | | | 4.70
|
||||||
|
|
||||||
|
Nlocal: 20.25 ave 38 max 3 min
|
||||||
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
|
Nghost: 27.25 ave 48 max 13 min
|
||||||
|
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 998
|
||||||
|
Dangerous builds = 997
|
||||||
|
Total wall time: 0:00:00
|
||||||
Reference in New Issue
Block a user