269 lines
13 KiB
Groff
269 lines
13 KiB
Groff
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
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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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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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processors * 1 1
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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region box block 0 10 0 10 0 10
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create_box 3 box
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Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
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2 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
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create_atoms CPU = 0.001 seconds
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mass * 1.0
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region long block 3 6 0 10 0 10
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set region long type 2
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Setting atom values ...
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1400 settings made for type
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velocity all create 1.0 87287
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_coeff * 2 1.0 1.0 5.0
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neighbor 0.3 bin
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neigh_modify every 2 delay 4 check yes
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fix p all property/atom d_WEIGHT
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compute p all property/atom d_WEIGHT
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group fast type 1
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2600 atoms in group fast
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group slow type 2
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1400 atoms in group slow
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balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
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Balancing ...
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 2 steps, delay = 4 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.3
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ghost atom cutoff = 5.3
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binsize = 2.65, bins = 7 7 7
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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
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bin: standard
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rebalancing time: 0.001 seconds
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iteration count = 10
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group weights: fast=0.8 slow=2.5
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storing weight in atom property d_WEIGHT
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initial/final maximal load/proc = 2960 3120
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initial/final imbalance factor = 1.0609319 1.1182796
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x cuts: 0 0.44970703 1
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y cuts: 0 1
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z cuts: 0 1
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variable lastweight atom c_p
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fix 0 all balance 50 1.0 shift x 10 1.0 weight var lastweight weight time 0.5 weight store WEIGHT
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variable maximb equal f_0[1]
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variable iter equal f_0[2]
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variable prev equal f_0[3]
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variable final equal f_0
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#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
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fix 1 all nve
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#dump id all atom 50 dump.melt
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#dump id all custom 50 dump.lammpstrj id type x y z c_p
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#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 3
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#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3
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thermo 50
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run 500
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 4.709 | 4.878 | 5.046 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
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50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
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100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
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150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
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200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
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250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
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300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137
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350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137
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400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
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450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
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500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
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Loop time of 2.63649 on 2 procs for 500 steps with 4000 atoms
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Performance: 81926.988 tau/day, 189.646 timesteps/s, 758.583 katom-step/s
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99.0% CPU use with 2 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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Pair | 0.71463 | 1.3382 | 1.9618 | 53.9 | 50.76
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Neigh | 0.37719 | 0.49388 | 0.61056 | 16.6 | 18.73
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Comm | 0.047367 | 0.78842 | 1.5295 | 83.5 | 29.90
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Output | 0.00033203 | 0.00036767 | 0.0004033 | 0.0 | 0.01
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Modify | 0.0083865 | 0.0094362 | 0.010486 | 1.1 | 0.36
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Other | | 0.006199 | | | 0.24
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Nlocal: 2000 ave 2603 max 1397 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10434 ave 11430 max 9438 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 298070 ave 500187 max 95952 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 596139
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Ave neighs/atom = 149.03475
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Neighbor list builds = 51
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Dangerous builds = 0
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run 500
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 5.094 | 5.463 | 5.832 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
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550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137
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600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137
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650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137
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700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137
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750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137
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800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137
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850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137
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900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137
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950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137
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1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
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Loop time of 3.17842 on 2 procs for 500 steps with 4000 atoms
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Performance: 67958.372 tau/day, 157.311 timesteps/s, 629.244 katom-step/s
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98.1% CPU use with 2 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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Pair | 0.37522 | 1.3792 | 2.3831 | 85.5 | 43.39
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Neigh | 0.27684 | 0.50251 | 0.72818 | 31.8 | 15.81
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Comm | 0.046802 | 1.2782 | 2.5097 | 108.9 | 40.22
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Output | 0.00037247 | 0.00037744 | 0.00038242 | 0.0 | 0.01
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Modify | 0.0074902 | 0.010381 | 0.013273 | 2.8 | 0.33
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Other | | 0.007739 | | | 0.24
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Nlocal: 2000 ave 2773 max 1227 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10234 ave 11398 max 9070 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 300836 ave 527715 max 73956 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 601671
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Ave neighs/atom = 150.41775
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Neighbor list builds = 51
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Dangerous builds = 0
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balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT
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Balancing ...
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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rebalancing time: 0.000 seconds
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iteration count = 10
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group weights: fast=0.8 slow=2.5
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storing weight in atom property d_WEIGHT
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initial/final maximal load/proc = 4598.4 2803.1
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initial/final imbalance factor = 1.648172 1.0046953
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x cuts: 0 0.45499213 1
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y cuts: 0 1
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z cuts: 0 1
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fix 0 all balance 50 1.0 shift x 5 1.0 weight var lastweight weight neigh 0.5 weight store WEIGHT
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run 500
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 5.483 | 5.66 | 5.837 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
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1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137
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1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137
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1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137
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1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137
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1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418134 4738.2137
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1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137
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1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137
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1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137
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1450 0.54218439 -6.2574683 0 -5.444395 -1.7901189 4738.2137
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1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
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Loop time of 3.02969 on 2 procs for 500 steps with 4000 atoms
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Performance: 71294.507 tau/day, 165.034 timesteps/s, 660.134 katom-step/s
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98.7% CPU use with 2 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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Pair | 0.5714 | 1.3936 | 2.2158 | 69.6 | 46.00
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Neigh | 0.2744 | 0.51127 | 0.74814 | 33.1 | 16.88
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Comm | 0.046434 | 1.1076 | 2.1688 | 100.8 | 36.56
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Output | 0.00031672 | 0.00037175 | 0.00042678 | 0.0 | 0.01
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Modify | 0.0066955 | 0.0094869 | 0.012278 | 2.9 | 0.31
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Other | | 0.007313 | | | 0.24
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Nlocal: 2000 ave 3014 max 986 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10343 ave 12125 max 8561 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 302958 ave 519610 max 86307 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 605917
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Ave neighs/atom = 151.47925
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Neighbor list builds = 51
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Dangerous builds = 0
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run 500
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Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 5.864 | 5.882 | 5.899 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137
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1550 0.5371361 -6.2504031 0 -5.4449003 -1.7647032 4738.2137
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1600 0.54679571 -6.2646443 0 -5.4446558 -1.8115722 4738.2137
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1650 0.53806589 -6.2519009 0 -5.4450038 -1.740915 4738.2137
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1700 0.53479448 -6.2469033 0 -5.4449122 -1.7162445 4738.2137
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1750 0.53714069 -6.2506511 0 -5.4451415 -1.734019 4738.2137
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1800 0.52750498 -6.2358815 0 -5.4448219 -1.6875349 4738.2137
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1850 0.54585338 -6.2629367 0 -5.4443613 -1.7758582 4738.2137
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1900 0.53011122 -6.2387673 0 -5.4437993 -1.6382079 4738.2137
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1950 0.5428773 -6.2583146 0 -5.4442022 -1.7367714 4738.2137
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2000 0.52771538 -6.2349676 0 -5.4435924 -1.5594006 4738.2137
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Loop time of 3.18739 on 2 procs for 500 steps with 4000 atoms
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Performance: 67767.083 tau/day, 156.868 timesteps/s, 627.473 katom-step/s
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98.5% CPU use with 2 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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Pair | 0.39584 | 1.3793 | 2.3628 | 83.7 | 43.27
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Neigh | 0.21951 | 0.48818 | 0.75684 | 38.5 | 15.32
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Comm | 0.047346 | 1.3021 | 2.5568 | 110.0 | 40.85
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Output | 0.00031641 | 0.00037624 | 0.00043608 | 0.0 | 0.01
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Modify | 0.0061382 | 0.0096203 | 0.013102 | 3.6 | 0.30
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Other | | 0.007838 | | | 0.25
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Nlocal: 2000 ave 3033 max 967 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10266 ave 12244 max 8288 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 303996 ave 525260 max 82733 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 607993
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Ave neighs/atom = 151.99825
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Neighbor list builds = 51
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Dangerous builds = 0
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Total wall time: 0:00:12
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