re-enable perpertual neighborlist for compute entropy/atom if avg flag is used only
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,4 @@
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LAMMPS (4 Jan 2019)
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LAMMPS (18 Feb 2020)
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units metal
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atom_style full
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@ -6,7 +6,7 @@ atom_style full
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read_data data.interface
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Reading data file ...
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triclinic box = (0 0 0) to (138.4 34.57 34.57) with tilt (0 0 0)
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4 by 1 by 1 MPI processor grid
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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4096 atoms
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reading velocities ...
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@ -18,6 +18,8 @@ Finding 1-2 1-3 1-4 neighbors ...
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.00048995 secs
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read_data CPU = 0.0104239 secs
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mass 1 22.98977
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neigh_modify delay 10 every 1
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@ -45,28 +47,28 @@ fix 1 all nph x 1. 1. 10.
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fix 2 all temp/csvr 350. 350. 0.1 64582
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run 1000
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WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
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WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
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WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
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WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
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WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
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WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
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WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
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WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
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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 = 13.2
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ghost atom cutoff = 13.2
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binsize = 6.6, bins = 21 6 6
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5 neighbor lists, perpetual/occasional/extra = 5 0 0
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(1) pair eam/fs, perpetual, half/full from (2)
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5 neighbor lists, perpetual/occasional/extra = 3 2 0
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(1) pair eam/fs, perpetual
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attributes: half, newton on
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pair build: halffull/newton
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pair build: half/bin/newton/tri
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stencil: half/bin/3d/newton/tri
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bin: standard
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(2) compute entropy/atom, occasional, copy from (4)
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attributes: full, newton on
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pair build: copy
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stencil: none
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bin: none
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(2) compute entropy/atom, perpetual
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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(3) compute entropy/atom, perpetual, copy from (2)
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(3) compute entropy/atom, occasional, copy from (4)
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attributes: full, newton on
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pair build: copy
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stencil: none
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@ -85,35 +87,35 @@ Setting up Verlet run ...
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Unit style : metal
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Current step : 0
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Time step : 0.002
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Per MPI rank memory allocation (min/avg/max) = 19.6 | 19.6 | 19.6 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 58.81 | 58.81 | 58.81 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75
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500 359.33769 -4285.2472 0 -4095.0424 472.02043 165847.09
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1000 348.99683 -4276.2282 0 -4091.4971 149.38771 166965.86
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Loop time of 4.4394 on 4 procs for 1000 steps with 4096 atoms
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Loop time of 20.309 on 1 procs for 1000 steps with 4096 atoms
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Performance: 38.924 ns/day, 0.617 hours/ns, 225.256 timesteps/s
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99.5% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 8.509 ns/day, 2.821 hours/ns, 49.239 timesteps/s
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99.4% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 3.5298 | 3.5931 | 3.6669 | 2.6 | 80.94
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Bond | 8.2099e-05 | 0.00011444 | 0.00014673 | 0.0 | 0.00
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Neigh | 0.43384 | 0.4445 | 0.45558 | 1.4 | 10.01
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Comm | 0.048904 | 0.11122 | 0.16728 | 12.7 | 2.51
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Output | 0.22595 | 0.22595 | 0.22596 | 0.0 | 5.09
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Modify | 0.053103 | 0.053795 | 0.054549 | 0.3 | 1.21
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Other | | 0.01068 | | | 0.24
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Pair | 17.851 | 17.851 | 17.851 | 0.0 | 87.89
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Bond | 0.00029588 | 0.00029588 | 0.00029588 | 0.0 | 0.00
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Neigh | 1.5377 | 1.5377 | 1.5377 | 0.0 | 7.57
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Comm | 0.083142 | 0.083142 | 0.083142 | 0.0 | 0.41
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Output | 0.59598 | 0.59598 | 0.59598 | 0.0 | 2.93
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Modify | 0.20727 | 0.20727 | 0.20727 | 0.0 | 1.02
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Other | | 0.03411 | | | 0.17
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Nlocal: 1024 ave 1040 max 1001 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Nghost: 4614.25 ave 4700 max 4540 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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Neighs: 121747 ave 126398 max 116930 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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FullNghs: 243494 ave 252523 max 233841 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Nlocal: 4096 ave 4096 max 4096 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11116 ave 11116 max 11116 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 486987 ave 486987 max 486987 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 973974 ave 973974 max 973974 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 973974
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Ave neighs/atom = 237.787
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@ -121,4 +123,4 @@ Ave special neighs/atom = 0
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Neighbor list builds = 13
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Dangerous builds = 0
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Total wall time: 0:00:04
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Total wall time: 0:00:20
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