forked from lijiext/lammps
163 lines
5.8 KiB
Groff
163 lines
5.8 KiB
Groff
LAMMPS (27 Nov 2018)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# 2d LJ obstacle flow
|
|
|
|
dimension 2
|
|
boundary p s p
|
|
|
|
atom_style atomic
|
|
neighbor 0.3 bin
|
|
neigh_modify delay 5
|
|
|
|
# create geometry
|
|
|
|
lattice hex 0.7
|
|
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
|
|
region box block 0 40 0 10 -0.25 0.25
|
|
create_box 3 box
|
|
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
|
|
1 by 1 by 1 MPI processor grid
|
|
create_atoms 1 box
|
|
Created 840 atoms
|
|
Time spent = 0.0004704 secs
|
|
|
|
mass 1 1.0
|
|
mass 2 1.0
|
|
mass 3 1.0
|
|
|
|
# LJ potentials
|
|
|
|
pair_style lj/cut 1.12246
|
|
pair_coeff * * 1.0 1.0 1.12246
|
|
|
|
# define groups
|
|
|
|
region 1 block INF INF INF 1.25 INF INF
|
|
group lower region 1
|
|
120 atoms in group lower
|
|
region 2 block INF INF 8.75 INF INF INF
|
|
group upper region 2
|
|
120 atoms in group upper
|
|
group boundary union lower upper
|
|
240 atoms in group boundary
|
|
group flow subtract all boundary
|
|
600 atoms in group flow
|
|
|
|
set group lower type 2
|
|
120 settings made for type
|
|
set group upper type 3
|
|
120 settings made for type
|
|
|
|
# initial velocities
|
|
|
|
compute mobile flow temp
|
|
velocity flow create 1.0 482748 temp mobile
|
|
fix 1 all nve
|
|
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
|
fix_modify 2 temp mobile
|
|
|
|
# Poiselle flow
|
|
|
|
velocity boundary set 0.0 0.0 0.0
|
|
fix 3 lower setforce 0.0 0.0 0.0
|
|
fix 4 upper setforce 0.0 NULL 0.0
|
|
fix 5 upper aveforce 0.0 -0.5 0.0
|
|
fix 6 flow addforce 1.0 0.0 0.0
|
|
|
|
# 2 obstacles
|
|
|
|
region void1 sphere 10 4 0 3
|
|
delete_atoms region void1
|
|
Deleted 36 atoms, new total = 804
|
|
region void2 sphere 20 7 0 3
|
|
delete_atoms region void2
|
|
Deleted 35 atoms, new total = 769
|
|
|
|
fix 7 flow indent 100 sphere 10 4 0 4
|
|
fix 8 flow indent 100 sphere 20 7 0 4
|
|
fix 9 all enforce2d
|
|
|
|
# Run
|
|
|
|
timestep 0.003
|
|
thermo 1000
|
|
thermo_modify temp mobile
|
|
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
|
|
|
|
#dump 1 all atom 100 dump.obstacle
|
|
|
|
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
|
|
#dump_modify 2 pad 5
|
|
|
|
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
|
|
#dump_modify 3 pad 5
|
|
|
|
run 25000
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 5 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 1.42246
|
|
ghost atom cutoff = 1.42246
|
|
binsize = 0.71123, bins = 73 32 1
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/2d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 3.055 | 3.055 | 3.055 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press Volume
|
|
0 1.0027471 0 0 0.68849216 0.46317653 1143.0857
|
|
1000 1 -0.33689286 0 0.34971312 1.2905426 1286.7728
|
|
2000 1 -0.36746164 0 0.31914434 1.1668828 1313.44
|
|
3000 1 -0.52004759 0 0.16655839 1.417774 1324.489
|
|
4000 1 -0.5052153 0 0.18139068 1.4877209 1370.8743
|
|
5000 1 -0.49501138 0 0.1915946 1.2415582 1408.4993
|
|
6000 1 -0.45834057 0 0.22826542 1.2577643 1433.2191
|
|
7000 1 -0.44788351 0 0.23872247 1.1057853 1452.7011
|
|
8000 1 -0.42511924 0 0.26148674 1.1445522 1453.2588
|
|
9000 1 -0.35807547 0 0.32853051 1.0527564 1449.2608
|
|
10000 1 -0.38692228 0 0.2996837 1.0338935 1447.9561
|
|
11000 1 -0.38893457 0 0.29767141 1.0095645 1451.1231
|
|
12000 1 -0.35706485 0 0.32954114 1.0796623 1453.0879
|
|
13000 1 -0.39551125 0 0.29109474 1.0390286 1453.2992
|
|
14000 1 -0.38153043 0 0.30507555 0.98105926 1452.5639
|
|
15000 1 -0.38762689 0 0.29897909 1.1442417 1452.0174
|
|
16000 1 -0.3685331 0 0.31807289 1.0032132 1458.431
|
|
17000 1 -0.36299809 0 0.32360789 0.93727845 1460.2986
|
|
18000 1 -0.35752931 0 0.32907667 0.98337283 1458.583
|
|
19000 1 -0.38350344 0 0.30310254 1.0148373 1458.9749
|
|
20000 1 -0.35659703 0 0.33000895 1.0264431 1460.0031
|
|
21000 1 -0.36878002 0 0.31782596 1.0877739 1455.1053
|
|
22000 1 -0.37986917 0 0.30673681 1.129754 1455.0258
|
|
23000 1 -0.39249509 0 0.29411089 0.97187435 1459.6771
|
|
24000 1 -0.33410442 0 0.35250156 0.93960021 1463.5903
|
|
25000 1 -0.37437615 0 0.31222983 0.9644765 1464.9391
|
|
Loop time of 1.98053 on 1 procs for 25000 steps with 769 atoms
|
|
|
|
Performance: 3271856.949 tau/day, 12622.905 timesteps/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 | 0.46219 | 0.46219 | 0.46219 | 0.0 | 23.34
|
|
Neigh | 0.17 | 0.17 | 0.17 | 0.0 | 8.58
|
|
Comm | 0.029093 | 0.029093 | 0.029093 | 0.0 | 1.47
|
|
Output | 0.00041389 | 0.00041389 | 0.00041389 | 0.0 | 0.02
|
|
Modify | 1.22 | 1.22 | 1.22 | 0.0 | 61.60
|
|
Other | | 0.09888 | | | 4.99
|
|
|
|
Nlocal: 769 ave 769 max 769 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 45 ave 45 max 45 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 1618 ave 1618 max 1618 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 1618
|
|
Ave neighs/atom = 2.10403
|
|
Neighbor list builds = 1622
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:01
|