149 lines
5.1 KiB
Groff
149 lines
5.1 KiB
Groff
LAMMPS (28 Mar 2023 - Development)
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using 1 OpenMP thread(s) per MPI task
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# pouring 3d rounded polyhedron bodies
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variable steps index 6000
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units lj
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boundary p p fm
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comm_modify vel yes
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atom_style body rounded/polyhedron 1 8
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atom_modify map array
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region reg block 0 50 0 50 0 50 units box
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create_box 4 reg
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Created orthogonal box = (0 0 0) to (50 50 50)
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1 by 2 by 2 MPI processor grid
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variable cut_inner equal 0.5
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variable k_n equal 100
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variable k_na equal 5
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variable c_n equal 20
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variable c_t equal 5
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variable mu equal 0
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variable A_ua equal 1
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pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
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pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
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pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
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pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
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pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
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pair_style body/rounded/polyhedron 20 5 0 1 0.5
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pair_coeff * * ${k_n} ${k_na}
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pair_coeff * * 100 ${k_na}
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pair_coeff * * 100 5
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neighbor 0.5 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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fix 1 all nve/body
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fix 2 all gravity 1.0 spherical 0.0 -180.0
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molecule object molecule.cube molecule.tetra toff 1 molecule.rod3d toff 2 molecule.point3d toff 3
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Read molecule template object:
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1 molecules
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0 fragments
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1 atoms with max type 1
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0 bonds with max type 0
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0 angles with max type 0
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0 dihedrals with max type 0
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0 impropers with max type 0
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Read molecule template object:
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1 molecules
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0 fragments
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1 atoms with max type 2
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0 bonds with max type 0
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0 angles with max type 0
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0 dihedrals with max type 0
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0 impropers with max type 0
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Read molecule template object:
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1 molecules
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0 fragments
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1 atoms with max type 3
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0 bonds with max type 0
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0 angles with max type 0
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0 dihedrals with max type 0
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0 impropers with max type 0
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Read molecule template object:
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1 molecules
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0 fragments
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1 atoms with max type 4
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0 bonds with max type 0
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0 angles with max type 0
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0 dihedrals with max type 0
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0 impropers with max type 0
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region slab block 5 45 5 45 25 35 units box
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fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25
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Particle insertion: 134 every 4472 steps, 500 by step 13417
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fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL
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#compute 1 all body/local type 1 2 3
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#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4]
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#dump 10 all custom 1000 tmp.dump id type x y z radius
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thermo_style custom step atoms ke pe etotal press
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thermo 1000
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#dump 2 all image 500 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 75 15
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#dump_modify 2 pad 6
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run ${steps}
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run 6000
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5
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ghost atom cutoff = 5
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binsize = 2.5, bins = 20 20 20
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair body/rounded/polyhedron, 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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Per MPI rank memory allocation (min/avg/max) = 0.4666 | 0.4666 | 0.4666 Mbytes
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Step Atoms KinEng PotEng TotEng Press
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0 0 -0 0 0 0
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1000 134 -0 0.0038737172 0.0038737172 -3.395325e-06
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2000 134 -0 -0.0009235483 -0.0009235483 -6.5977025e-07
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3000 134 -0 0.004338364 0.004338364 -1.4565607e-05
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4000 134 -0 0.0028464278 0.0028464278 -7.6723299e-06
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5000 268 -0 0.017425002 0.017425002 0.000175191
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6000 268 -0 0.035730061 0.035730061 0.00019697961
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Loop time of 0.266391 on 4 procs for 6000 steps with 268 atoms
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Performance: 1946012.521 tau/day, 22523.293 timesteps/s, 6.036 Matom-step/s
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92.6% 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 | 0.024599 | 0.072944 | 0.14627 | 18.6 | 27.38
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Neigh | 0.0011942 | 0.0013474 | 0.0014323 | 0.3 | 0.51
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Comm | 0.047438 | 0.11992 | 0.17106 | 14.8 | 45.02
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Output | 7.6297e-05 | 0.00017637 | 0.00044875 | 0.0 | 0.07
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Modify | 0.029377 | 0.035972 | 0.040396 | 2.4 | 13.50
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Other | | 0.03603 | | | 13.52
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Nlocal: 67 ave 89 max 43 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Nghost: 38 ave 53 max 25 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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Neighs: 23.75 ave 42 max 7 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Total # of neighbors = 95
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Ave neighs/atom = 0.35447761
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Neighbor list builds = 167
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Dangerous builds = 0
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Total wall time: 0:00:00
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