131 lines
4.7 KiB
Groff
131 lines
4.7 KiB
Groff
LAMMPS (28 Mar 2023 - Development)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# 3d rounded cubes
|
|
|
|
variable r index 3
|
|
variable steps index 10000
|
|
|
|
units lj
|
|
dimension 3
|
|
|
|
atom_style body rounded/polyhedron 1 10
|
|
|
|
read_data data.cubes
|
|
Reading data file ...
|
|
orthogonal box = (0 0 0) to (6 6 6)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
2 atoms
|
|
2 bodies
|
|
read_data CPU = 0.001 seconds
|
|
|
|
replicate $r $r $r
|
|
replicate 3 $r $r
|
|
replicate 3 3 $r
|
|
replicate 3 3 3
|
|
Replication is creating a 3x3x3 = 27 times larger system...
|
|
orthogonal box = (0 0 0) to (18 18 18)
|
|
1 by 1 by 1 MPI processor grid
|
|
54 atoms
|
|
replicate CPU = 0.001 seconds
|
|
|
|
velocity all create 1.2 187287 dist gaussian mom yes rot yes
|
|
|
|
variable cut_inner equal 0.5
|
|
variable k_n equal 100
|
|
variable k_na equal 1
|
|
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 1
|
|
|
|
comm_modify vel yes
|
|
|
|
neighbor 0.5 bin
|
|
neigh_modify every 1 delay 0 check yes
|
|
|
|
timestep 0.001
|
|
|
|
#fix 1 all nve/body
|
|
fix 1 all nvt/body temp 1.2 1.2 0.1
|
|
#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0
|
|
|
|
compute p2 all pressure 1_temp
|
|
|
|
#compute 1 all body/local id 1 2 3
|
|
#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
|
|
|
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15
|
|
#dump_modify 2 pad 6
|
|
|
|
thermo_style custom step ke pe etotal c_p2 c_1_temp
|
|
|
|
thermo 1000
|
|
|
|
run ${steps}
|
|
run 10000
|
|
Generated 0 of 0 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 = 3.9641016
|
|
ghost atom cutoff = 3.9641016
|
|
binsize = 1.9820508, bins = 10 10 10
|
|
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) = 5.973 | 5.973 | 5.973 Mbytes
|
|
Step KinEng PotEng TotEng c_p2 c_1_temp
|
|
0 1.7666667 0 1.7666667 0.01090535 0.59439252
|
|
1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694
|
|
2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624
|
|
3000 3.090491 0.16511199 3.255603 0.018691142 1.23672
|
|
4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839
|
|
5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154
|
|
6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839
|
|
7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326
|
|
8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056
|
|
9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914
|
|
10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679
|
|
Loop time of 33.0201 on 1 procs for 10000 steps with 54 atoms
|
|
|
|
Performance: 26165.890 tau/day, 302.846 timesteps/s, 16.354 katom-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 | 32.897 | 32.897 | 32.897 | 0.0 | 99.63
|
|
Neigh | 0.0028124 | 0.0028124 | 0.0028124 | 0.0 | 0.01
|
|
Comm | 0.034404 | 0.034404 | 0.034404 | 0.0 | 0.10
|
|
Output | 0.00017643 | 0.00017643 | 0.00017643 | 0.0 | 0.00
|
|
Modify | 0.078202 | 0.078202 | 0.078202 | 0.0 | 0.24
|
|
Other | | 0.00767 | | | 0.02
|
|
|
|
Nlocal: 54 ave 54 max 54 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 96 ave 96 max 96 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 100 ave 100 max 100 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 100
|
|
Ave neighs/atom = 1.8518519
|
|
Neighbor list builds = 268
|
|
Dangerous builds = 0
|
|
|
|
Total wall time: 0:00:33
|