133 lines
5.6 KiB
Groff
133 lines
5.6 KiB
Groff
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-700-g901ed98d31)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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### LAMMPS input file
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units metal
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dimension 3
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boundary p p p
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atom_style charge
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read_data data.NaPO3
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Reading data file ...
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orthogonal box = (0 0 0) to (34.33782 34.33782 34.33782)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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3000 atoms
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reading velocities ...
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3000 velocities
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read_data CPU = 0.011 seconds
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pair_style hybrid/overlay coul/dsf 0.2 12.0 table spline 20000 buck 7.0 nb3b/screened
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pair_coeff * * coul/dsf
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pair_coeff 1 3 table Table_NP.dat Pair_P-O 7.0
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WARNING: 1 of 4995 force values in table Pair_P-O are inconsistent with -dE/dr.
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WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
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pair_coeff 2 3 table Table_NP.dat Pair_Na-O 7.0
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WARNING: 2 of 4995 force values in table Pair_Na-O are inconsistent with -dE/dr.
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WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
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pair_coeff 3 3 table Table_NP.dat Pair_O-O 7.0
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# pair Buckingham
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pair_coeff 1 1 buck 5.093669 0.905598 0.0
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# shrm
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pair_coeff * * nb3b/screened PSiO.nb3b.screened P NULL O
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Reading nb3b/screened potential file PSiO.nb3b.screened with DATE: 2023-10-30
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neighbor 1.0 bin
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neigh_modify every 10 delay 10 check no
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timestep 0.002
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thermo 100
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thermo_style custom step density lx press pe evdwl ecoul temp
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#dump 2 all custom 10000 NaPO3-melt.lammpstrj id type element x y z
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#dump_modify 2 element P Na O
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variable temp equal 2500
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fix 1 all npt temp ${temp} ${temp} $(100*dt) iso 1 1 $(1000*dt)
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fix 1 all npt temp 2500 ${temp} $(100*dt) iso 1 1 $(1000*dt)
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fix 1 all npt temp 2500 2500 $(100*dt) iso 1 1 $(1000*dt)
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fix 1 all npt temp 2500 2500 0.2000000000000000111 iso 1 1 $(1000*dt)
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fix 1 all npt temp 2500 2500 0.2000000000000000111 iso 1 1 2
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run 1000
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Neighbor list info ...
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update: every = 10 steps, delay = 10 steps, check = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 13
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ghost atom cutoff = 13
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binsize = 6.5, bins = 6 6 6
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6 neighbor lists, perpetual/occasional/extra = 6 0 0
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(1) pair coul/dsf, 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
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bin: standard
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(2) pair table, perpetual, skip from (5)
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attributes: half, newton on, cut 8
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pair build: skip
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stencil: none
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bin: none
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(3) pair buck, perpetual, skip from (5)
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attributes: half, newton on, cut 8
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pair build: skip
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stencil: none
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bin: none
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(4) pair nb3b/screened, perpetual, skip from (6)
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attributes: full, newton on, cut 4.3
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pair build: skip
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stencil: none
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bin: none
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(5) neighbor class addition, perpetual, trim from (1)
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attributes: half, newton on, cut 8
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pair build: trim
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stencil: none
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bin: none
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(6) neighbor class addition, perpetual
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attributes: full, newton on, cut 4.3
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 7.188 | 7.188 | 7.189 Mbytes
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Step Density Lx Press PotEng E_vdwl E_coul Temp
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0 2.509108 34.33782 46464.417 -50581.248 2292.3853 -52873.634 2500
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100 2.4533672 34.595928 33156.229 -50182.221 2373.5614 -52555.782 1666.1883
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200 2.3649528 35.021791 29182.391 -50158.578 2367.6353 -52526.213 1885.4424
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300 2.2932707 35.382952 14450.387 -50100.892 2239.9823 -52340.875 2045.1557
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400 2.2282371 35.723887 16680.683 -50048.753 2281.6385 -52330.392 2257.1768
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500 2.1753698 36.010969 15871.062 -49981.163 2285.6757 -52266.839 2396.7925
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600 2.1285968 36.272824 15066.532 -49934.767 2282.4577 -52217.225 2540.7515
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700 2.0841139 36.529076 7572.3446 -49895.929 2222.7474 -52118.677 2577.5774
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800 2.0485057 36.739517 6642.7277 -49870.601 2230.3802 -52100.981 2556.7856
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900 2.0180051 36.923689 8318.7257 -49890.301 2255.153 -52145.454 2538.1115
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1000 1.990678 37.091879 7730.4071 -49928.905 2250.9166 -52179.822 2492.4197
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Loop time of 9.72954 on 4 procs for 1000 steps with 3000 atoms
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Performance: 17.760 ns/day, 1.351 hours/ns, 102.780 timesteps/s, 308.339 katom-step/s
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99.3% CPU use with 4 MPI tasks x 1 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 | 7.1441 | 8.0123 | 8.622 | 19.6 | 82.35
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Neigh | 0.7458 | 0.78431 | 0.80001 | 2.5 | 8.06
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Comm | 0.26061 | 0.88607 | 1.7928 | 61.3 | 9.11
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Output | 0.00024827 | 0.00027521 | 0.00035196 | 0.0 | 0.00
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Modify | 0.03802 | 0.038395 | 0.038805 | 0.1 | 0.39
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Other | | 0.008186 | | | 0.08
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Nlocal: 750 ave 765 max 731 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Nghost: 6607.5 ave 6671 max 6552 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Neighs: 202867 ave 217674 max 182729 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Total # of neighbors = 811469
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Ave neighs/atom = 270.48967
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Neighbor list builds = 100
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Dangerous builds not checked
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Total wall time: 0:00:09
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