149 lines
5.1 KiB
Groff
149 lines
5.1 KiB
Groff
LAMMPS (28 Mar 2023 - Development)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# pouring 3d rounded polyhedron bodies
|
|
|
|
variable steps index 6000
|
|
|
|
units lj
|
|
boundary p p fm
|
|
comm_modify vel yes
|
|
|
|
atom_style body rounded/polyhedron 1 8
|
|
atom_modify map array
|
|
|
|
region reg block 0 50 0 50 0 50 units box
|
|
create_box 4 reg
|
|
Created orthogonal box = (0 0 0) to (50 50 50)
|
|
1 by 1 by 1 MPI processor grid
|
|
|
|
variable cut_inner equal 0.5
|
|
variable k_n equal 100
|
|
variable k_na equal 5
|
|
variable c_n equal 20
|
|
variable c_t equal 5
|
|
variable mu equal 0
|
|
variable A_ua equal 1
|
|
|
|
pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
|
|
pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
|
|
pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
|
|
pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
|
|
pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
|
|
pair_style body/rounded/polyhedron 20 5 0 1 0.5
|
|
pair_coeff * * ${k_n} ${k_na}
|
|
pair_coeff * * 100 ${k_na}
|
|
pair_coeff * * 100 5
|
|
|
|
neighbor 0.5 bin
|
|
neigh_modify every 1 delay 0 check yes
|
|
|
|
timestep 0.001
|
|
|
|
fix 1 all nve/body
|
|
fix 2 all gravity 1.0 spherical 0.0 -180.0
|
|
|
|
molecule object molecule.cube molecule.tetra toff 1 molecule.rod3d toff 2 molecule.point3d toff 3
|
|
Read molecule template object:
|
|
1 molecules
|
|
0 fragments
|
|
1 atoms with max type 1
|
|
0 bonds with max type 0
|
|
0 angles with max type 0
|
|
0 dihedrals with max type 0
|
|
0 impropers with max type 0
|
|
Read molecule template object:
|
|
1 molecules
|
|
0 fragments
|
|
1 atoms with max type 2
|
|
0 bonds with max type 0
|
|
0 angles with max type 0
|
|
0 dihedrals with max type 0
|
|
0 impropers with max type 0
|
|
Read molecule template object:
|
|
1 molecules
|
|
0 fragments
|
|
1 atoms with max type 3
|
|
0 bonds with max type 0
|
|
0 angles with max type 0
|
|
0 dihedrals with max type 0
|
|
0 impropers with max type 0
|
|
Read molecule template object:
|
|
1 molecules
|
|
0 fragments
|
|
1 atoms with max type 4
|
|
0 bonds with max type 0
|
|
0 angles with max type 0
|
|
0 dihedrals with max type 0
|
|
0 impropers with max type 0
|
|
|
|
region slab block 5 45 5 45 25 35 units box
|
|
fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25
|
|
Particle insertion: 134 every 4472 steps, 500 by step 13417
|
|
|
|
fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL
|
|
|
|
#compute 1 all body/local type 1 2 3
|
|
#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4]
|
|
#dump 10 all custom 1000 tmp.dump id type x y z radius
|
|
|
|
thermo_style custom step atoms ke pe etotal press
|
|
|
|
thermo 1000
|
|
|
|
#dump 2 all image 500 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 75 15
|
|
#dump_modify 2 pad 6
|
|
|
|
run ${steps}
|
|
run 6000
|
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 5
|
|
ghost atom cutoff = 5
|
|
binsize = 2.5, bins = 20 20 20
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair body/rounded/polyhedron, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 0.508 | 0.508 | 0.508 Mbytes
|
|
Step Atoms KinEng PotEng TotEng Press
|
|
0 0 -0 0 0 0
|
|
1000 134 -0 0.0038737172 0.0038737172 -3.395325e-06
|
|
2000 134 -0 -0.0009235483 -0.0009235483 -6.5977025e-07
|
|
3000 134 -0 0.004338364 0.004338364 -1.4565607e-05
|
|
4000 134 -0 0.0028464278 0.0028464278 -7.6723299e-06
|
|
5000 268 -0 0.017425002 0.017425002 0.000175191
|
|
6000 268 -0 0.035730061 0.035730061 0.00019697961
|
|
Loop time of 0.432886 on 1 procs for 6000 steps with 268 atoms
|
|
|
|
Performance: 1197543.331 tau/day, 13860.455 timesteps/s, 3.715 Matom-step/s
|
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.29261 | 0.29261 | 0.29261 | 0.0 | 67.59
|
|
Neigh | 0.0040123 | 0.0040123 | 0.0040123 | 0.0 | 0.93
|
|
Comm | 0.0019937 | 0.0019937 | 0.0019937 | 0.0 | 0.46
|
|
Output | 5.8179e-05 | 5.8179e-05 | 5.8179e-05 | 0.0 | 0.01
|
|
Modify | 0.12864 | 0.12864 | 0.12864 | 0.0 | 29.72
|
|
Other | | 0.005574 | | | 1.29
|
|
|
|
Nlocal: 268 ave 268 max 268 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 2 ave 2 max 2 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 95 ave 95 max 95 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 95
|
|
Ave neighs/atom = 0.35447761
|
|
Neighbor list builds = 167
|
|
Dangerous builds = 0
|
|
|
|
|
|
Total wall time: 0:00:00
|