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update log files for body examples

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This commit is contained in:
Axel Kohlmeyer
2018-11-28 14:46:47 -05:00
parent c428088554
commit 2ed90c1669
18 changed files with 1108 additions and 1080 deletions
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0
examples/body/data.squares Executable file → Normal file
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examples/body/in.squares Executable file → Normal file
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examples/body/in.wall2d Executable file → Normal file
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36
examples/body/log.5Oct16.body.g++.1 → examples/body/log.27Nov18.body.g++.1
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d polygon nparticle bodies
units lj
@ -14,7 +15,7 @@ read_data data.body
velocity all create 1.44 87287 loop geom
pair_style body 5.0
pair_style body/nparticle 5.0
pair_coeff * * 1.0 1.0
neighbor 0.5 bin
@ -33,13 +34,18 @@ fix 2 all enforce2d
thermo 100
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.5
ghost atom cutoff = 5.5
binsize = 2.75 -> bins = 12 12 1
Memory usage per processor = 4.44944 Mbytes
binsize = 2.75, bins = 12 12 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair body/nparticle, 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) = 4.772 | 4.772 | 4.772 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.63799525 0 0.78760475 -0.15028724
100 1.642337 -1.0003869 0 0.62552682 0.16140818
@ -142,20 +148,20 @@ Step Temp E_pair E_mol TotEng Press
9800 1.6713187 -1.6842507 0 -0.029645137 0.17982115
9900 1.7707351 -1.6638268 0 0.089200949 0.2983883
10000 1.6466807 -1.592436 0 0.037777866 0.12761693
Loop time of 2.33651 on 1 procs for 10000 steps with 100 atoms
Loop time of 1.76365 on 1 procs for 10000 steps with 100 atoms
Performance: 1848909.758 tau/day, 4279.884 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 2449465.017 tau/day, 5670.058 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1308 | 2.1308 | 2.1308 | 0.0 | 91.20
Neigh | 0.011168 | 0.011168 | 0.011168 | 0.0 | 0.48
Comm | 0.02469 | 0.02469 | 0.02469 | 0.0 | 1.06
Output | 0.00063729 | 0.00063729 | 0.00063729 | 0.0 | 0.03
Modify | 0.15896 | 0.15896 | 0.15896 | 0.0 | 6.80
Other | | 0.01025 | | | 0.44
Pair | 1.5533 | 1.5533 | 1.5533 | 0.0 | 88.08
Neigh | 0.01155 | 0.01155 | 0.01155 | 0.0 | 0.65
Comm | 0.042146 | 0.042146 | 0.042146 | 0.0 | 2.39
Output | 0.00089574 | 0.00089574 | 0.00089574 | 0.0 | 0.05
Modify | 0.14124 | 0.14124 | 0.14124 | 0.0 | 8.01
Other | | 0.01448 | | | 0.82
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -168,4 +174,4 @@ Total # of neighbors = 467
Ave neighs/atom = 4.67
Neighbor list builds = 468
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:01

34
examples/body/log.5Oct16.body.g++.4 → examples/body/log.27Nov18.body.g++.4
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@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d polygon nparticle bodies
units lj
@ -14,7 +15,7 @@ read_data data.body
velocity all create 1.44 87287 loop geom
pair_style body 5.0
pair_style body/nparticle 5.0
pair_coeff * * 1.0 1.0
neighbor 0.5 bin
@ -33,13 +34,18 @@ fix 2 all enforce2d
thermo 100
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.5
ghost atom cutoff = 5.5
binsize = 2.75 -> bins = 12 12 1
Memory usage per processor = 4.43864 Mbytes
binsize = 2.75, bins = 12 12 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair body/nparticle, 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) = 4.759 | 4.759 | 4.759 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.63799525 0 0.78760475 -0.15028724
100 1.642337 -1.0003869 0 0.62552682 0.16140818
@ -142,20 +148,20 @@ Step Temp E_pair E_mol TotEng Press
9800 1.7799071 -1.7889616 0 -0.026853542 0.3169291
9900 1.5838158 -1.718909 0 -0.15093133 0.46050618
10000 1.6100625 -1.7018091 0 -0.10784725 0.10312591
Loop time of 0.849795 on 4 procs for 10000 steps with 100 atoms
Loop time of 0.715445 on 4 procs for 10000 steps with 100 atoms
Performance: 5083579.790 tau/day, 11767.546 timesteps/s
99.0% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 6038199.147 tau/day, 13977.313 timesteps/s
95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.47067 | 0.53757 | 0.61119 | 7.9 | 63.26
Neigh | 0.0030298 | 0.0032511 | 0.0035295 | 0.3 | 0.38
Comm | 0.1592 | 0.23416 | 0.30247 | 12.4 | 27.56
Output | 0.0015244 | 0.0016521 | 0.0018895 | 0.4 | 0.19
Modify | 0.039954 | 0.0415 | 0.044199 | 0.8 | 4.88
Other | | 0.03166 | | | 3.73
Pair | 0.35395 | 0.40307 | 0.45588 | 5.9 | 56.34
Neigh | 0.0033705 | 0.0036112 | 0.0039394 | 0.4 | 0.50
Comm | 0.17564 | 0.22399 | 0.26912 | 7.8 | 31.31
Output | 0.0014601 | 0.0024824 | 0.0054784 | 3.5 | 0.35
Modify | 0.038037 | 0.039219 | 0.04163 | 0.7 | 5.48
Other | | 0.04308 | | | 6.02
Nlocal: 25 ave 28 max 23 min
Histogram: 1 0 1 0 1 0 0 0 0 1

27
examples/body/log.9Jul18.body.cubes.g++.1 → examples/body/log.27Nov18.cubes.g++.1
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@ -1,4 +1,5 @@
LAMMPS (29 Jun 2018)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d rounded cubes
variable r index 3
@ -23,7 +24,7 @@ replicate 3 3 3
orthogonal box = (0 0 0) to (18 18 18)
1 by 1 by 1 MPI processor grid
54 atoms
Time spent = 0.000217915 secs
Time spent = 0.000426769 secs
velocity all create 1.2 187287 dist gaussian mom yes rot yes
@ -82,7 +83,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.953 | 4.953 | 4.953 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
@ -95,20 +96,20 @@ Step KinEng PotEng TotEng c_p2 c_1_temp
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 38.5686 on 1 procs for 10000 steps with 54 atoms
Loop time of 51.5779 on 1 procs for 10000 steps with 54 atoms
Performance: 22401.653 tau/day, 259.278 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 16751.376 tau/day, 193.882 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 | 38.426 | 38.426 | 38.426 | 0.0 | 99.63
Neigh | 0.0043154 | 0.0043154 | 0.0043154 | 0.0 | 0.01
Comm | 0.047616 | 0.047616 | 0.047616 | 0.0 | 0.12
Output | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.00
Modify | 0.082948 | 0.082948 | 0.082948 | 0.0 | 0.22
Other | | 0.007761 | | | 0.02
Pair | 51.377 | 51.377 | 51.377 | 0.0 | 99.61
Neigh | 0.0063686 | 0.0063686 | 0.0063686 | 0.0 | 0.01
Comm | 0.072127 | 0.072127 | 0.072127 | 0.0 | 0.14
Output | 0.0002768 | 0.0002768 | 0.0002768 | 0.0 | 0.00
Modify | 0.10849 | 0.10849 | 0.10849 | 0.0 | 0.21
Other | | 0.01404 | | | 0.03
Nlocal: 54 ave 54 max 54 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -122,4 +123,4 @@ Ave neighs/atom = 1.85185
Neighbor list builds = 268
Dangerous builds = 0
Total wall time: 0:00:38
Total wall time: 0:00:51

25
examples/body/log.9Jul18.body.cubes.g++.4 → examples/body/log.27Nov18.cubes.g++.4
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@ -1,4 +1,5 @@
LAMMPS (29 Jun 2018)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d rounded cubes
variable r index 3
@ -23,7 +24,7 @@ replicate 3 3 3
orthogonal box = (0 0 0) to (18 18 18)
1 by 2 by 2 MPI processor grid
54 atoms
Time spent = 0.00103807 secs
Time spent = 0.000776052 secs
velocity all create 1.2 187287 dist gaussian mom yes rot yes
@ -95,20 +96,20 @@ Step KinEng PotEng TotEng c_p2 c_1_temp
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 20.5306 on 4 procs for 10000 steps with 54 atoms
Loop time of 25.5798 on 4 procs for 10000 steps with 54 atoms
Performance: 42083.509 tau/day, 487.078 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 33776.718 tau/day, 390.934 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.5288 | 10.878 | 19.952 | 159.0 | 52.98
Neigh | 0.0014424 | 0.0016552 | 0.0021195 | 0.7 | 0.01
Comm | 0.50623 | 9.5805 | 12.93 | 169.4 | 46.66
Output | 0.00011921 | 0.00014341 | 0.00021386 | 0.0 | 0.00
Modify | 0.044663 | 0.047684 | 0.05382 | 1.6 | 0.23
Other | | 0.023 | | | 0.11
Pair | 9.256 | 13.423 | 24.653 | 177.1 | 52.47
Neigh | 0.0021949 | 0.0024942 | 0.0031152 | 0.7 | 0.01
Comm | 0.73678 | 11.948 | 16.096 | 187.4 | 46.71
Output | 0.00023246 | 0.00041932 | 0.0009768 | 0.0 | 0.00
Modify | 0.12505 | 0.15661 | 0.18165 | 6.0 | 0.61
Other | | 0.04968 | | | 0.19
Nlocal: 13.5 ave 17 max 9 min
Histogram: 1 0 0 1 0 0 0 0 1 1
@ -122,4 +123,4 @@ Ave neighs/atom = 1.85185
Neighbor list builds = 268
Dangerous builds = 0
Total wall time: 0:00:20
Total wall time: 0:00:25

74
examples/body/log.27Nov18.pour3d.g++.1 Normal file
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@ -0,0 +1,74 @@
LAMMPS (27 Nov 2018)
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 object:
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 object:
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 object:
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 object:
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
ERROR: Unknown fix style pour (src/modify.cpp:898)
Last command: 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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examples/body/log.27Nov18.pour3d.g++.4 Normal file
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@ -0,0 +1,74 @@
LAMMPS (27 Nov 2018)
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 2 by 2 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 object:
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 object:
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 object:
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 object:
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
ERROR: Unknown fix style pour (src/modify.cpp:898)
Last command: fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25

222
examples/body/log.27Nov18.squares.g++.1 Normal file
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@ -0,0 +1,222 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies
variable r index 4
variable steps index 100000
variable T index 0.5
variable P index 0.1
variable seed index 980411
units lj
dimension 2
atom_style body rounded/polygon 1 6
atom_modify map array
read_data data.squares
orthogonal box = (0 0 -0.5) to (12 12 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
2 atoms
2 bodies
replicate $r $r 1
replicate 4 $r 1
replicate 4 4 1
orthogonal box = (0 0 -0.5) to (48 48 0.5)
1 by 1 by 1 MPI processor grid
32 atoms
Time spent = 0.000279665 secs
velocity all create $T ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 980411 dist gaussian mom yes rot yes
variable cut_inner equal 0.5
variable k_n equal 100
variable k_na equal 2
variable c_n equal 1
variable c_t equal 1
variable mu equal 0.1
variable delta_ua equal 0.5
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2
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 $T $T 1.0
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
fix 2 all enforce2d
#compute 1 all body/local id 1 2 3
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
thermo_style custom step ke pe etotal press
thermo 1000
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
#dump_modify 2 pad 6
run ${steps}
run 100000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.15685
ghost atom cutoff = 6.15685
binsize = 3.07843, bins = 16 16 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair body/rounded/polygon, 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) = 4.781 | 4.781 | 4.781 Mbytes
Step KinEng PotEng TotEng Press
0 0.484375 0.25 0.734375 0.0067274306
1000 0.38428256 0.0014168922 0.38569945 0.0020468171
2000 0.41372193 0.015263236 0.42898517 0.0029343462
3000 0.54844547 0.014870378 0.56331585 0.001978353
4000 0.73816048 0.031668204 0.76982869 0.0025939718
5000 0.84536165 0.011504649 0.8568663 0.0037990517
6000 0.73776478 0.14445932 0.8822241 0.0086538113
7000 0.52022565 0.069507637 0.58973329 0.0072098694
8000 0.72653213 0.12783368 0.85436581 0.023907183
9000 0.87685727 0.1239819 1.0008392 0.0064590959
10000 0.7250918 0.097243508 0.82233531 0.0012448267
11000 0.62302234 0.05597557 0.67899791 0.00080239872
12000 0.57159363 0.18199602 0.75358965 0.01033626
13000 0.7505295 0.071545266 0.82207477 0.011480236
14000 0.84703598 0.15914379 1.0061798 0.032814039
15000 0.41905013 0.090552572 0.5096027 0.015717153
16000 0.41805189 0.042916881 0.46096877 0.020702707
17000 0.59966233 0.05285043 0.65251275 0.016526024
18000 0.54282285 0.20835047 0.75117332 0.036414059
19000 0.777922 0.034754101 0.8126761 0.036467537
20000 0.54703924 0.14633506 0.6933743 0.012917248
21000 0.49337931 0.1858754 0.67925471 0.037890735
22000 0.64916623 0.19281344 0.84197967 0.011996773
23000 0.66958738 0.20459682 0.8741842 0.023639466
24000 0.63729755 0.1111959 0.74849345 0.025049919
25000 0.60094316 0.13375799 0.73470115 0.035286376
26000 0.35419589 0.22049451 0.5746904 0.0024215291
27000 0.33789786 0.18494942 0.52284728 0.0066457643
28000 0.32376056 0.13151726 0.45527782 0.010773856
29000 0.36198203 0.11044834 0.47243037 0.063012638
30000 0.22624436 0.19690087 0.42314523 0.037422734
31000 0.32284312 0.059623656 0.38246677 0.0287682
32000 0.4457193 0.042396136 0.48811544 0.022025252
33000 0.61078662 0.059447221 0.67023384 0.030335089
34000 0.63157762 0.062056279 0.6936339 0.044624352
35000 0.69577644 0.086216204 0.78199264 0.0319995
36000 0.76814336 0.062105963 0.83024933 0.044316891
37000 0.58641664 0.095034548 0.68145119 0.03234133
38000 0.48772813 0.12911854 0.61684667 0.038732146
39000 0.74957742 0.09823432 0.84781174 0.053181162
40000 0.57881374 0.2932491 0.87206284 0.065740126
41000 0.4415176 0.22899179 0.67050939 0.026159841
42000 0.5260339 0.2048105 0.7308444 0.046294432
43000 0.33493572 0.32500572 0.65994144 -0.01250241
44000 0.46467243 0.07907132 0.54374375 0.13386238
45000 0.48135518 0.2618908 0.74324598 -0.016767159
46000 0.27223209 0.24562643 0.51785852 0.052118439
47000 0.26402739 0.1838767 0.44790409 -0.0015878764
48000 0.10229166 0.25519169 0.35748335 -0.033927088
49000 0.24313495 0.16578185 0.40891679 0.12414926
50000 0.27400066 0.27688032 0.55088098 0.10421157
51000 0.43081855 0.18111733 0.61193587 0.16373371
52000 0.81969298 0.060995894 0.88068887 0.057285357
53000 0.99936159 0.029137886 1.0284995 0.19425015
54000 0.69750047 0.038079774 0.73558024 -0.089236384
55000 0.54823746 0.056369886 0.60460734 -0.021320579
56000 0.6752322 0.050322917 0.72555512 0.25303548
57000 0.90328009 0.061107142 0.96438723 -0.1962713
58000 0.81463148 0.050387847 0.86501933 0.35952157
59000 0.61636455 0.064910223 0.68127478 -0.27208497
60000 0.62573918 0.052264617 0.67800379 0.4493407
61000 0.81065726 0.071269668 0.88192693 -0.34643283
62000 0.86420318 0.052799365 0.91700254 0.48308047
63000 0.67848508 0.069087342 0.74757242 -0.31814526
64000 0.61430417 0.052109373 0.66641354 0.38336646
65000 0.75782937 0.063488206 0.82131757 -0.19113322
66000 0.88735857 0.051779306 0.93913787 0.29410996
67000 0.70684373 0.061786313 0.76863005 -0.16503578
68000 0.58571951 0.052402151 0.63812166 0.30173228
69000 0.64997491 0.064435462 0.71441037 -0.1920633
70000 0.75071821 0.053416991 0.8041352 0.3846747
71000 0.8124718 0.06877986 0.88125166 -0.26852566
72000 0.71352066 0.05358784 0.7671085 0.41321806
73000 0.55151827 0.066470642 0.61798891 -0.2211738
74000 0.65473635 0.061946814 0.71668316 0.29536873
75000 0.88704613 0.059476353 0.94652248 -0.0312656
76000 0.76899803 0.057351665 0.8263497 0.017885214
77000 0.65149455 0.05407174 0.70556629 0.25192449
78000 0.68614394 0.074251169 0.76039511 -0.19369404
79000 0.97451567 0.06262739 1.0371431 0.4217182
80000 0.88207775 0.070157004 0.95223476 -0.27318477
81000 0.69294455 0.062623957 0.75556851 0.40150141
82000 0.70748016 0.073924331 0.78140449 -0.17128794
83000 0.78180774 0.063513978 0.84532172 0.22033652
84000 0.80170993 0.065812223 0.86752216 0.083202913
85000 0.64788122 0.070348079 0.7182293 -0.066913668
86000 0.56575431 0.064865112 0.63061942 0.33905786
87000 0.78205358 0.07983702 0.8618906 -0.22844912
88000 0.87426443 0.065703482 0.93996791 0.448573
89000 0.73269893 0.079827385 0.81252632 -0.24183162
90000 0.66703106 0.065630146 0.73266121 0.35410109
91000 0.73107154 0.07402702 0.80509856 -0.085492997
92000 1.043635 0.067156523 1.1107915 0.14311135
93000 0.86063344 0.065607238 0.92624068 0.20750649
94000 0.68304235 0.075962239 0.75900459 -0.14594625
95000 0.7069191 0.067125732 0.77404483 0.39459759
96000 0.79860046 0.090957588 0.88955805 -0.24202125
97000 0.81366777 0.071387081 0.88505485 0.32217266
98000 0.61885746 0.041524228 0.66038169 0.31635364
99000 0.57007759 0.055438456 0.62551604 -0.21172902
100000 0.80462394 0.045542313 0.85016626 0.099207503
Loop time of 6.34495 on 1 procs for 100000 steps with 32 atoms
Performance: 1361713.788 tau/day, 15760.576 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0158 | 5.0158 | 5.0158 | 0.0 | 79.05
Neigh | 0.0072868 | 0.0072868 | 0.0072868 | 0.0 | 0.11
Comm | 0.18669 | 0.18669 | 0.18669 | 0.0 | 2.94
Output | 0.00098681 | 0.00098681 | 0.00098681 | 0.0 | 0.02
Modify | 1.0417 | 1.0417 | 1.0417 | 0.0 | 16.42
Other | | 0.09245 | | | 1.46
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 35 ave 35 max 35 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 61 ave 61 max 61 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 61
Ave neighs/atom = 1.90625
Neighbor list builds = 1545
Dangerous builds = 0
Total wall time: 0:00:06

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies
variable r index 4
variable steps index 100000
variable T index 0.5
variable P index 0.1
variable seed index 980411
units lj
dimension 2
atom_style body rounded/polygon 1 6
atom_modify map array
read_data data.squares
orthogonal box = (0 0 -0.5) to (12 12 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
2 atoms
2 bodies
replicate $r $r 1
replicate 4 $r 1
replicate 4 4 1
orthogonal box = (0 0 -0.5) to (48 48 0.5)
2 by 2 by 1 MPI processor grid
32 atoms
Time spent = 0.000400782 secs
velocity all create $T ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 980411 dist gaussian mom yes rot yes
variable cut_inner equal 0.5
variable k_n equal 100
variable k_na equal 2
variable c_n equal 1
variable c_t equal 1
variable mu equal 0.1
variable delta_ua equal 0.5
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2
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 $T $T 1.0
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
fix 2 all enforce2d
#compute 1 all body/local id 1 2 3
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
thermo_style custom step ke pe etotal press
thermo 1000
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
#dump_modify 2 pad 6
run ${steps}
run 100000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.15685
ghost atom cutoff = 6.15685
binsize = 3.07843, bins = 16 16 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair body/rounded/polygon, 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) = 4.774 | 4.774 | 4.774 Mbytes
Step KinEng PotEng TotEng Press
0 0.484375 0.25 0.734375 0.0067274306
1000 0.38428256 0.0014168922 0.38569945 0.0020468171
2000 0.41372193 0.015263236 0.42898517 0.0029343462
3000 0.54844547 0.014870378 0.56331585 0.001978353
4000 0.73816048 0.031668204 0.76982869 0.0025939718
5000 0.84536165 0.011504649 0.8568663 0.0037990517
6000 0.73776478 0.14445932 0.8822241 0.0086538113
7000 0.52022565 0.069507637 0.58973329 0.0072098694
8000 0.72653213 0.12783367 0.85436581 0.023907185
9000 0.87685728 0.12398193 1.0008392 0.0064591005
10000 0.72509641 0.097241969 0.82233837 0.0012418726
11000 0.62314955 0.056042914 0.67919247 0.0018880786
12000 0.57157436 0.18187429 0.75344865 0.0096135623
13000 0.7489742 0.08262775 0.83160195 0.009183917
14000 0.78835138 0.18761048 0.97596186 0.023684357
15000 0.40408761 0.079431327 0.48351893 0.025285348
16000 0.4071013 0.13207058 0.53917188 0.02015488
17000 0.48417067 0.16699781 0.65116848 0.059188189
18000 0.60038567 0.18317457 0.78356024 -0.046456387
19000 0.73796958 0.064271521 0.8022411 0.090257204
20000 0.62508659 0.14486336 0.76994994 0.04948543
21000 0.5596837 0.10018831 0.65987201 0.044961962
22000 0.30731517 0.1386103 0.44592547 0.015096596
23000 0.34371843 0.1486761 0.49239453 0.026100892
24000 0.33484204 0.25428479 0.58912683 0.01974393
25000 0.48714744 0.32743616 0.8145836 0.037925893
26000 0.33255994 0.29851422 0.63107417 0.049419529
27000 0.21735889 0.18816203 0.40552093 0.050622152
28000 0.31911317 0.12559898 0.44471215 -0.0036236361
29000 0.53280161 0.055185441 0.58798705 0.083856225
30000 0.52916941 0.28697284 0.81614225 0.055873213
31000 0.47861645 0.21932568 0.69794214 0.02762301
32000 0.46786314 0.041856438 0.50971958 0.029923804
33000 0.69944716 0.039356744 0.7388039 0.028174645
34000 0.39964317 0.1027175 0.50236068 0.039495865
35000 0.70199237 0.10421859 0.80621095 0.015943417
36000 0.45053533 0.078626602 0.52916193 0.0073950287
37000 0.41587918 0.056551665 0.47243084 0.034091318
38000 0.58663473 0.039228671 0.6258634 0.033093641
39000 0.72480658 0.14792564 0.87273222 0.030903741
40000 0.51163285 0.13445292 0.64608577 -0.03114559
41000 0.56273761 0.16720374 0.72994135 0.027968528
42000 0.61850184 0.10584389 0.72434573 -0.036301799
43000 0.60039772 0.11984289 0.72024062 0.080894236
44000 0.57499839 0.068211092 0.64320948 0.049726122
45000 0.69937239 0.16287141 0.8622438 0.044921114
46000 0.23303785 0.2391726 0.47221045 0.021668935
47000 0.27051781 0.10690378 0.37742159 0.11963476
48000 0.408895 0.079919688 0.48881469 0.087484004
49000 0.74363181 0.040819422 0.78445123 0.011937456
50000 0.84482316 0.10205256 0.94687572 0.064133262
51000 0.84923574 0.089882984 0.93911872 0.062696388
52000 0.66278324 0.0331554 0.69593864 0.035150337
53000 0.64737251 0.039608076 0.68698058 0.057687461
54000 0.68931435 0.042661403 0.73197576 0.069664795
55000 0.84523308 0.10293275 0.94816583 0.047343755
56000 0.80033937 0.1534797 0.95381907 0.070206074
57000 0.6214799 0.1174575 0.7389374 0.078530452
58000 0.64228495 0.088089896 0.73037485 0.060245994
59000 0.89376363 0.065171887 0.95893552 0.071658895
60000 0.90162992 0.016564761 0.91819468 0.089245946
61000 0.72439995 0.0076508835 0.73205083 0.031430213
62000 0.71590702 0.0046728326 0.72057986 0.10153514
63000 0.74491219 0.0046757926 0.74958798 0.077145851
64000 0.77173614 0.008265632 0.78000178 -0.049932265
65000 0.72789092 0.0053605745 0.73325149 0.27060389
66000 0.63001101 0.013871945 0.64388296 -0.17766692
67000 0.65887071 0.0069105692 0.66578128 0.31632918
68000 0.89042862 0.0026334652 0.89306209 -0.050495873
69000 0.83442374 0.0059232957 0.84034703 -0.21871692
70000 0.65149642 0.004885383 0.65638181 0.50428108
71000 0.66888808 0.01125057 0.68013865 -0.29575772
72000 0.74941609 0.0026616299 0.75207772 0.34800716
73000 0.7898844 0.0048982026 0.7947826 -0.096872644
74000 0.68823538 0.0021467794 0.69038216 0.12272852
75000 0.5238808 0.0046112795 0.52849208 0.25760316
76000 0.65512889 0.014567969 0.66969686 -0.24622674
77000 0.82292373 0.0092471048 0.83217083 0.4002304
78000 0.76305221 0.01101937 0.77407158 -0.10704945
79000 0.66279814 0.0090486405 0.67184678 0.037466134
80000 0.65808885 0.010000569 0.66808942 0.31742291
81000 0.91357798 0.046226814 0.95980479 -0.20945693
82000 0.87611859 -0.016794871 0.85932372 0.31759733
83000 0.66285455 -0.017921021 0.64493353 0.27065273
84000 0.67460715 -0.0076174891 0.66698966 -0.024772659
85000 0.77786135 0.0014316505 0.779293 -0.21635327
86000 0.83246393 0.087489797 0.91995372 -0.13431455
87000 0.62935573 0.045088823 0.67444455 0.037766395
88000 0.55264538 -0.024625272 0.52802011 0.18121213
89000 0.74171392 -0.012629926 0.729084 -0.27666424
90000 0.82542165 -0.02296567 0.80245598 -0.30497174
91000 0.72958657 -0.026275093 0.70331147 -0.27624518
92000 0.6319558 0.022568297 0.65452409 -0.33539318
93000 0.66685301 0.021889807 0.68874282 -0.39890762
94000 0.91243243 0.0078218509 0.92025428 -0.27213648
95000 0.81125179 -0.0096756295 0.80157616 -0.099802335
96000 0.63354907 -0.018329423 0.61521965 0.18199604
97000 0.66812347 -0.016650228 0.65147324 0.49878257
98000 0.81490013 -0.0049164866 0.80998365 -0.13473106
99000 0.82131147 0.0043198846 0.82563136 -0.3083957
100000 0.50880983 -0.010467027 0.4983428 0.060606332
Loop time of 4.3169 on 4 procs for 100000 steps with 32 atoms
Performance: 2001435.573 tau/day, 23164.764 timesteps/s
95.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2078 | 1.3972 | 1.6653 | 15.1 | 32.36
Neigh | 0.0030954 | 0.003284 | 0.0034814 | 0.3 | 0.08
Comm | 1.074 | 1.3595 | 1.6003 | 16.2 | 31.49
Output | 0.001703 | 0.0030067 | 0.0068843 | 4.1 | 0.07
Modify | 1.2071 | 1.2647 | 1.3062 | 3.6 | 29.30
Other | | 0.2893 | | | 6.70
Nlocal: 8 ave 9 max 6 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 17.75 ave 20 max 16 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 14 ave 18 max 7 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 56
Ave neighs/atom = 1.75
Neighbor list builds = 1566
Dangerous builds = 0
Total wall time: 0:00:04

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examples/body/log.27Nov18.wall2d.g++.1 Normal file
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies
variable r index 4
variable steps index 100000
variable T index 0.5
variable P index 0.1
variable seed index 980411
units lj
dimension 2
atom_style body rounded/polygon 1 6
atom_modify map array
read_data data.squares
orthogonal box = (0 0 -0.5) to (12 12 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
2 atoms
2 bodies
replicate $r $r 1
replicate 4 $r 1
replicate 4 4 1
orthogonal box = (0 0 -0.5) to (48 48 0.5)
1 by 1 by 1 MPI processor grid
32 atoms
Time spent = 0.000318766 secs
velocity all create $T ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 980411 dist gaussian mom yes rot yes
change_box all boundary p f p
variable cut_inner equal 0.5
variable k_n equal 100
variable k_na equal 2
variable c_n equal 0.1
variable c_t equal 0.1
variable mu equal 0.1
variable delta_ua equal 0.5
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2
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 $T $T 1.0
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
fix 2 all enforce2d
fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
#compute 1 all body/local id 1 2 3
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
thermo_style custom step ke pe etotal press
thermo 1000
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
#dump_modify 2 pad 6
run ${steps}
run 100000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.15685
ghost atom cutoff = 6.15685
binsize = 3.07843, bins = 16 16 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair body/rounded/polygon, 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) = 4.771 | 4.771 | 4.771 Mbytes
Step KinEng PotEng TotEng Press
0 0.484375 0.25 0.734375 0.0067274306
1000 0.51467204 0.00099202506 0.51566407 0.013452386
2000 0.55674899 0.0040762275 0.56082522 0.0034529066
3000 0.7546177 0.02259362 0.77721132 0.003650781
4000 0.72710218 0.10284108 0.82994326 0.0059629371
5000 0.5771012 0.069052145 0.64615335 0.00053937622
6000 0.53848154 0.041891239 0.58037277 0.0018693312
7000 0.61777556 0.033379829 0.65115538 0.0027584418
8000 0.47427227 0.059558934 0.5338312 0.017087187
9000 0.46822364 0.064382578 0.53260622 0.023258465
10000 0.46511051 0.027799371 0.49290988 0.015319493
11000 0.58686703 0.088016891 0.67488392 0.0088428936
12000 0.49962603 0.09879099 0.59841702 0.00074311497
13000 0.53160049 0.069625775 0.60122626 0.017019775
14000 0.49574902 0.041214164 0.53696318 0.0060355978
15000 0.56620415 0.13621516 0.70241931 0.045583297
16000 0.40942564 0.11469877 0.52412441 0.029905784
17000 0.608066 0.096938921 0.70500493 0.018509814
18000 0.45622168 0.057018077 0.51323975 0.0034035281
19000 0.48763322 0.057832224 0.54546545 0.0022972169
20000 0.41577025 0.14480819 0.56057844 0.023882542
21000 0.58565738 0.1601676 0.74582498 0.01702799
22000 0.60430354 0.16740706 0.7717106 -0.0047632836
23000 0.45659601 0.13740896 0.59400497 0.0191143
24000 0.42741367 0.25490516 0.68231884 0.051459175
25000 0.40851048 0.077823072 0.48633355 0.024392284
26000 0.53392894 0.14504323 0.67897217 0.028964572
27000 0.39775205 0.13101153 0.52876358 0.0080564916
28000 0.63138106 0.17706612 0.80844718 0.017594524
29000 0.57897788 0.26855503 0.84753292 0.019310624
30000 0.37401002 0.2274666 0.60147663 0.0044804008
31000 0.60924323 0.23142663 0.84066986 0.088271242
32000 0.60310397 0.35719837 0.96030234 0.0096762289
33000 0.47468105 0.17727177 0.65195282 0.0078486602
34000 0.42270829 0.20131235 0.62402064 0.090216203
35000 0.49578606 0.1697981 0.66558416 0.079099134
36000 0.50744538 0.29600416 0.80344954 0.018819487
37000 0.66728184 0.28166655 0.94894838 -0.01679437
38000 0.38972905 0.25798163 0.64771068 0.040442456
39000 0.38292839 0.21774389 0.60067228 0.016754932
40000 0.61770336 0.34202184 0.9597252 0.10986262
41000 0.42252651 0.13424708 0.5567736 0.040987711
42000 0.67513868 0.29515562 0.9702943 0.0013757417
43000 0.36768915 0.20349753 0.57118668 0.031443504
44000 0.49371025 0.095615653 0.5893259 0.032289477
45000 0.42144079 0.28894639 0.71038718 0.040302569
46000 0.36360136 0.33117431 0.69477567 0.010881881
47000 0.4206309 0.19557595 0.61620685 0.051137535
48000 0.4131465 0.37027912 0.78342561 0.11903042
49000 0.544703 0.38013565 0.92483865 0.054939742
50000 0.47394272 0.32384493 0.79778764 0.088363602
51000 0.55377533 0.38103395 0.93480927 0.097981664
52000 0.60648433 0.30877364 0.91525797 0.088877781
53000 0.62933509 0.33187159 0.96120668 0.10275954
54000 0.55077522 0.39050008 0.94127529 0.066721412
55000 0.41646397 0.34545572 0.76191969 0.011056796
56000 0.44244954 0.39274744 0.83519698 0.039963853
57000 0.41963092 0.33483982 0.75447073 0.032555938
58000 0.37941475 0.36905323 0.74846798 0.043952263
59000 0.53008564 0.32843795 0.85852359 0.080787301
60000 0.43408908 0.19840268 0.63249176 0.06421165
61000 0.56287814 0.31500577 0.87788391 0.12031895
62000 0.5185192 0.18275672 0.70127592 -0.0086212356
63000 0.57275413 0.45147395 1.0242281 0.054617465
64000 0.28322907 0.33687722 0.62010629 0.07268947
65000 0.40230876 0.37989067 0.78219943 -0.029604066
66000 0.58601209 0.52721274 1.1132248 -0.00037054404
67000 0.52669356 0.44276199 0.96945554 0.18969356
68000 0.41566831 0.47320489 0.8888732 0.040635264
69000 0.52140574 0.4261935 0.94759923 0.016566201
70000 0.42034133 0.55867009 0.97901142 0.047465899
71000 0.48720036 0.43749264 0.924693 0.15984789
72000 0.5244238 0.55854139 1.0829652 0.10155994
73000 0.69990219 0.57313852 1.2730407 0.11108648
74000 0.38274347 0.23359664 0.61634011 0.027968087
75000 0.47493369 0.49472607 0.96965976 0.10961568
76000 0.57064727 0.37996383 0.9506111 0.034746271
77000 0.50401727 0.34437588 0.84839315 0.015116686
78000 0.59504118 0.44154772 1.0365889 0.059341875
79000 0.4920801 0.58935767 1.0814378 0.12139906
80000 0.56992818 0.38916606 0.95909424 0.073618074
81000 0.38446945 0.77314417 1.1576136 0.12173381
82000 0.48734531 0.56198203 1.0493273 0.1080115
83000 0.5516933 0.56743096 1.1191243 0.13936805
84000 0.53336893 0.62914863 1.1625176 0.0084970895
85000 0.46456977 0.77446084 1.2390306 0.18024688
86000 0.58067599 0.53109608 1.1117721 0.012492021
87000 0.55096446 0.61715622 1.1681207 0.13264723
88000 0.56548774 0.74463701 1.3101247 0.14491188
89000 0.52492634 0.58482194 1.1097483 0.21155245
90000 0.64973565 0.85514474 1.5048804 0.036911953
91000 0.55367722 0.74046971 1.2941469 0.23918851
92000 0.44863249 0.56773761 1.0163701 0.00042860088
93000 0.64728356 0.66594086 1.3132244 0.0022850006
94000 0.65255497 0.82136644 1.4739214 0.10037643
95000 0.62266654 0.82642147 1.449088 0.11964602
96000 0.50656004 0.83312844 1.3396885 0.078491084
97000 0.47126712 0.70469684 1.175964 0.12956056
98000 0.48661103 1.0121726 1.4987837 0.043537851
99000 0.48379797 0.9520931 1.4358911 0.082047522
100000 0.54266361 1.0959698 1.6386334 -0.13092175
Loop time of 3.8532 on 1 procs for 100000 steps with 32 atoms
Performance: 2242290.202 tau/day, 25952.433 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3917 | 2.3917 | 2.3917 | 0.0 | 62.07
Neigh | 0.012386 | 0.012386 | 0.012386 | 0.0 | 0.32
Comm | 0.11307 | 0.11307 | 0.11307 | 0.0 | 2.93
Output | 0.0010369 | 0.0010369 | 0.0010369 | 0.0 | 0.03
Modify | 1.246 | 1.246 | 1.246 | 0.0 | 32.34
Other | | 0.08895 | | | 2.31
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 55 ave 55 max 55 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 55
Ave neighs/atom = 1.71875
Neighbor list builds = 2886
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies
variable r index 4
variable steps index 100000
variable T index 0.5
variable P index 0.1
variable seed index 980411
units lj
dimension 2
atom_style body rounded/polygon 1 6
atom_modify map array
read_data data.squares
orthogonal box = (0 0 -0.5) to (12 12 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
2 atoms
2 bodies
replicate $r $r 1
replicate 4 $r 1
replicate 4 4 1
orthogonal box = (0 0 -0.5) to (48 48 0.5)
2 by 2 by 1 MPI processor grid
32 atoms
Time spent = 0.000329733 secs
velocity all create $T ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 980411 dist gaussian mom yes rot yes
change_box all boundary p f p
variable cut_inner equal 0.5
variable k_n equal 100
variable k_na equal 2
variable c_n equal 0.1
variable c_t equal 0.1
variable mu equal 0.1
variable delta_ua equal 0.5
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2
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 $T $T 1.0
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
fix 2 all enforce2d
fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
#compute 1 all body/local id 1 2 3
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
thermo_style custom step ke pe etotal press
thermo 1000
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
#dump_modify 2 pad 6
run ${steps}
run 100000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.15685
ghost atom cutoff = 6.15685
binsize = 3.07843, bins = 16 16 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair body/rounded/polygon, 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) = 4.773 | 4.773 | 4.773 Mbytes
Step KinEng PotEng TotEng Press
0 0.484375 0.25 0.734375 0.0067274306
1000 0.51467204 0.00099202506 0.51566407 0.013452386
2000 0.55674899 0.0040762275 0.56082522 0.0034529066
3000 0.7546177 0.02259362 0.77721132 0.003650781
4000 0.72710218 0.10284108 0.82994326 0.0059629371
5000 0.57710119 0.069052154 0.64615335 0.00053937664
6000 0.53848104 0.041891152 0.58037219 0.0018693259
7000 0.61777485 0.033380825 0.65115568 0.0027584782
8000 0.47427732 0.059553658 0.53383098 0.017087698
9000 0.46820943 0.064379697 0.53258913 0.02325702
10000 0.46605511 0.02332689 0.489382 0.013699209
11000 0.57547516 0.090133398 0.66560855 0.0083913962
12000 0.465348 0.084853345 0.55020135 0.006231552
13000 0.55340889 0.07116165 0.62457054 0.030622563
14000 0.58866362 0.052281859 0.64094548 0.0079106838
15000 0.51757672 0.12255618 0.6401329 0.014005369
16000 0.42696011 0.086987541 0.51394765 -0.0017128649
17000 0.37612579 0.13054778 0.50667357 0.0046284992
18000 0.47659682 0.14670523 0.62330205 0.02206928
19000 0.47897909 0.15540332 0.63438241 0.02544138
20000 0.59377323 0.15357757 0.7473508 0.030262926
21000 0.52781204 0.22074491 0.74855695 -0.0022170167
22000 0.44843285 0.12779345 0.5762263 0.0097268482
23000 0.60400735 0.18098124 0.78498858 0.05778325
24000 0.58254338 0.1570243 0.73956769 0.022530491
25000 0.60524318 0.23660272 0.8418459 0.062530421
26000 0.45892702 0.34294121 0.80186823 0.038657393
27000 0.58418023 0.19551937 0.7796996 -0.0055396645
28000 0.45655369 0.26718934 0.72374303 0.006593108
29000 0.50277299 0.1747088 0.67748179 0.016059369
30000 0.38640717 0.1631573 0.54956447 0.036055723
31000 0.46944541 0.22076826 0.69021367 0.014334038
32000 0.53862858 0.26867594 0.80730452 0.057406282
33000 0.45666352 0.21796554 0.67462906 0.056555205
34000 0.51644038 0.21866786 0.73510824 0.015713
35000 0.50489584 0.1596236 0.66451945 0.040400644
36000 0.41723489 0.16227853 0.57951342 0.02863261
37000 0.481638 0.28830624 0.76994424 0.038381986
38000 0.6036094 0.33479287 0.93840227 0.0032059452
39000 0.47822122 0.18876355 0.66698476 0.029252649
40000 0.54949607 0.35011086 0.89960693 0.093909148
41000 0.54876522 0.27501735 0.82378257 -0.0084167014
42000 0.67801592 0.18102522 0.85904114 -0.0058395209
43000 0.54342066 0.34322081 0.88664146 0.12263806
44000 0.46672513 0.29749157 0.76421671 0.051073701
45000 0.4679867 0.25820875 0.72619545 0.069790993
46000 0.59598501 0.22285276 0.81883777 0.050578807
47000 0.48858341 0.29811577 0.78669917 0.080971431
48000 0.41238073 0.29362937 0.7060101 0.031893588
49000 0.61516435 0.33082609 0.94599044 -0.010710982
50000 0.57576635 0.37137185 0.94713819 0.062160249
51000 0.54614001 0.36960628 0.91574629 -0.0083424769
52000 0.42232354 0.25214442 0.67446796 0.028666126
53000 0.43025129 0.24479385 0.67504514 0.030342054
54000 0.54614922 0.29602426 0.84217348 0.083070642
55000 0.60719748 0.3577285 0.96492598 0.053799744
56000 0.47073149 0.31070429 0.78143579 0.083895368
57000 0.56861582 0.33249784 0.90111366 0.032324233
58000 0.75061035 0.33313728 1.0837476 0.031039937
59000 0.59473893 0.48870773 1.0834467 0.039503585
60000 0.55252481 0.38350562 0.93603043 0.0027643882
61000 0.45010855 0.43945065 0.8895592 0.028168222
62000 0.63942467 0.53372899 1.1731537 0.13790959
63000 0.69407873 0.37980402 1.0738828 0.035919608
64000 0.54898275 0.39910419 0.94808693 0.0015016851
65000 0.58229838 0.42300361 1.005302 0.089787193
66000 0.53443537 0.5597136 1.094149 -0.015781756
67000 0.59212426 0.56172146 1.1538457 0.030464683
68000 0.68164926 0.48724393 1.1688932 0.071465948
69000 0.59721737 0.49476309 1.0919805 0.07575647
70000 0.52314551 0.31950477 0.84265028 0.11206672
71000 0.53230509 0.53846575 1.0707708 0.0047204701
72000 0.71341933 0.4924749 1.2058942 0.116568
73000 0.70498496 0.54121008 1.246195 0.11210249
74000 0.54188682 0.61729607 1.1591829 0.044083048
75000 0.44073609 0.42072284 0.86145893 -0.041508511
76000 0.51225567 0.36848317 0.88073884 -0.028636748
77000 0.6517329 0.5503086 1.2020415 0.049605026
78000 0.60053898 0.52760266 1.1281416 0.094361256
79000 0.51560788 0.46563043 0.98123832 -0.03336136
80000 0.53357884 0.60743981 1.1410186 0.027259883
81000 0.6256228 0.40412923 1.029752 0.083274981
82000 0.6903519 0.69599412 1.386346 0.168747
83000 0.62621394 0.50082841 1.1270424 0.12294403
84000 0.5682146 0.73827702 1.3064916 0.085884707
85000 0.48179077 0.73669563 1.2184864 0.065002035
86000 0.61101399 0.80673836 1.4177523 0.037555163
87000 0.52278725 0.71608722 1.2388745 0.020943688
88000 0.53318823 0.50916748 1.0423557 -0.01946691
89000 0.56428713 0.56042234 1.1247095 0.040998134
90000 0.58720508 0.66023073 1.2474358 0.040313529
91000 0.61509407 0.86254343 1.4776375 0.15215034
92000 0.5640475 0.57694543 1.1409929 0.10238679
93000 0.60586378 0.67978456 1.2856483 -0.043948113
94000 0.75406595 0.74795347 1.5020194 0.015341415
95000 0.4974314 0.60192267 1.0993541 -0.018173218
96000 0.50048302 0.82845218 1.3289352 0.045394283
97000 0.65335222 0.6470855 1.3004377 0.011624967
98000 0.65693072 0.45222133 1.109152 0.13763684
99000 0.60573344 0.50284289 1.1085763 0.12853674
100000 0.50677068 0.58143063 1.0882013 0.11351254
Loop time of 3.24642 on 4 procs for 100000 steps with 32 atoms
Performance: 2661396.711 tau/day, 30803.203 timesteps/s
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.64148 | 0.70244 | 0.76391 | 6.5 | 21.64
Neigh | 0.0049012 | 0.0050417 | 0.0052478 | 0.2 | 0.16
Comm | 0.79447 | 0.88412 | 0.97443 | 8.1 | 27.23
Output | 0.001776 | 0.0031438 | 0.0072262 | 4.2 | 0.10
Modify | 1.325 | 1.3684 | 1.4049 | 2.4 | 42.15
Other | | 0.2833 | | | 8.73
Nlocal: 8 ave 9 max 7 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 14 ave 15 max 13 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 13.25 ave 16 max 11 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 53
Ave neighs/atom = 1.65625
Neighbor list builds = 2654
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (29 Jun 2018)
# 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 object:
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 object:
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 object:
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 object:
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
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/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 0.5065 | 0.5065 | 0.5065 Mbytes
Step Atoms KinEng PotEng TotEng Press
0 0 -0 0 0 0
1000 134 -0 0.00083010524 0.00083010524 -2.1515152e-06
2000 134 -0 -0.00069962476 -0.00069962476 -1.4170663e-08
3000 134 -0 -0.00069962687 -0.00069962687 -4.1478181e-11
4000 134 -0 -0.00069962687 -0.00069962687 -1.2141026e-13
5000 268 -0 0.014969705 0.014969705 3.0797164e-05
6000 268 -0 0.042467887 0.042467887 0.00056148005
Loop time of 0.634737 on 1 procs for 6000 steps with 268 atoms
Performance: 816716.196 tau/day, 9452.734 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.41391 | 0.41391 | 0.41391 | 0.0 | 65.21
Neigh | 0.010547 | 0.010547 | 0.010547 | 0.0 | 1.66
Comm | 0.0030921 | 0.0030921 | 0.0030921 | 0.0 | 0.49
Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.02
Modify | 0.19736 | 0.19736 | 0.19736 | 0.0 | 31.09
Other | | 0.009719 | | | 1.53
Nlocal: 268 ave 268 max 268 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 68 ave 68 max 68 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 68
Ave neighs/atom = 0.253731
Neighbor list builds = 168
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (29 Jun 2018)
# 2d rounded polygon bodies
variable r index 4
variable steps index 100000
variable T index 0.5
variable P index 0.1
variable seed index 980411
units lj
dimension 2
atom_style body rounded/polygon 1 6
atom_modify map array
read_data data.squares
orthogonal box = (0 0 -0.5) to (12 12 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
2 atoms
2 bodies
replicate $r $r 1
replicate 4 $r 1
replicate 4 4 1
orthogonal box = (0 0 -0.5) to (48 48 0.5)
1 by 1 by 1 MPI processor grid
32 atoms
Time spent = 0.00020504 secs
velocity all create $T ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 980411 dist gaussian mom yes rot yes
variable cut_inner equal 0.5
variable k_n equal 100
variable k_na equal 2
variable c_n equal 1
variable c_t equal 1
variable mu equal 0.1
variable delta_ua equal 0.5
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2
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 $T $T 1.0
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
fix 2 all enforce2d
#compute 1 all body/local id 1 2 3
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
thermo_style custom step ke pe etotal press
thermo 1000
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
#dump_modify 2 pad 6
run ${steps}
run 100000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.15685
ghost atom cutoff = 6.15685
binsize = 3.07843, bins = 16 16 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair body/rounded/polygon, 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) = 4.781 | 4.781 | 4.781 Mbytes
Step KinEng PotEng TotEng Press
0 0.484375 0.25 0.734375 0.0067274306
1000 0.39423376 0.0017918048 0.39602557 0.0021941612
2000 0.42284177 0.01346585 0.43630762 0.0029377883
3000 0.58154405 0.011321689 0.59286574 0.003667871
4000 0.73518304 0.034603175 0.76978621 0.0018689207
5000 0.84367476 0.025292163 0.86896692 0.0089161373
6000 0.70803236 0.0085631016 0.71659546 0.0045552895
7000 0.56206452 0.10453031 0.66659483 0.010255161
8000 0.64538994 0.088817673 0.73420761 0.0037633655
9000 0.90540819 0.063696004 0.96910419 0.0077673359
10000 0.68632042 0.093265016 0.77958544 0.0057864838
11000 0.59118074 0.025654748 0.61683549 0.012518759
12000 0.67522767 0.038176401 0.71340407 0.01741153
13000 0.7644843 0.10429844 0.86878274 0.013161339
14000 0.56152694 0.067836655 0.62936359 0.016852121
15000 0.41895506 0.019513348 0.43846841 0.015225695
16000 0.55799421 0.1564559 0.71445011 0.011703561
17000 0.59391964 0.034450221 0.62836986 0.026215002
18000 0.75911858 0.030885726 0.7900043 0.018396366
19000 0.64417995 0.12110912 0.76528907 0.010247952
20000 0.57751435 0.16965651 0.74717086 0.023392323
21000 0.7613368 0.13405354 0.89539034 0.021498982
22000 0.57676692 0.18011879 0.75688571 0.024469161
23000 0.54043723 0.11842026 0.65885749 0.019799067
24000 0.62276061 0.038967924 0.66172853 0.019080086
25000 0.53157536 0.11651937 0.64809473 0.017019298
26000 0.72213293 0.039012448 0.76114538 0.015434904
27000 0.62157832 0.13697494 0.75855326 0.028711011
28000 0.41323738 0.16301101 0.57624839 0.041792632
29000 0.45774328 0.17569066 0.63343394 0.019975231
30000 0.78901796 0.099791386 0.88880934 0.024116947
31000 0.85205397 0.11977547 0.97182945 0.026667489
32000 0.37137095 0.1232622 0.49463315 0.00087637364
33000 0.26860871 0.26056381 0.52917252 0.036110517
34000 0.3018636 0.21336905 0.51523265 0.040315549
35000 0.39915129 0.28245957 0.68161085 0.034876856
36000 0.25761236 0.2352705 0.49288286 0.022772767
37000 0.1071233 0.31692858 0.42405188 0.017994666
38000 0.083729577 0.28473145 0.36846103 -0.0045370431
39000 0.070355565 0.26682083 0.33717639 0.017921556
40000 0.075894079 0.20077896 0.27667304 0.014873186
41000 0.05891028 0.15989064 0.21880092 0.025547873
42000 0.1225107 0.16583605 0.28834675 0.038842785
43000 0.17049189 0.14323991 0.3137318 0.029550161
44000 0.26823939 0.15208257 0.42032196 0.028113612
45000 0.10172203 0.1729706 0.27469264 -0.013769913
46000 0.14841355 0.19085074 0.33926429 -0.00073741985
47000 0.27654927 0.19097937 0.46752864 0.04021431
48000 0.53432331 0.080769923 0.61509323 0.029932845
49000 0.69111634 0.13064951 0.82176585 0.028985406
50000 0.24520806 0.18317453 0.42838258 0.05179746
51000 0.23541368 0.14281364 0.37822732 0.071884238
52000 0.25464996 0.095730242 0.3503802 0.034488204
53000 0.53677633 0.1058745 0.64265084 0.059932498
54000 0.32970921 0.27979128 0.60950049 0.062869716
55000 0.49094054 0.096735015 0.58767556 0.04728005
56000 0.54398249 0.2216472 0.76562969 0.056712022
57000 0.60869068 0.2338422 0.84253288 0.077143302
58000 0.72175509 0.18687368 0.90862877 0.019357656
59000 0.79442757 0.092502981 0.88693055 0.066882632
60000 0.6810555 0.077699385 0.75875488 0.095975173
61000 0.63178834 0.05071143 0.68249977 0.043586668
62000 0.76589344 0.044615704 0.81050914 0.085718411
63000 0.84815889 0.030527848 0.87868674 0.053072795
64000 0.7309043 0.051938637 0.78284294 0.058887766
65000 0.62498816 0.034474465 0.65946262 0.068446407
66000 0.69817494 0.068546004 0.76672094 0.062634433
67000 0.86444275 0.010184259 0.87462701 0.073635055
68000 0.77820319 0.0079319524 0.78613515 0.090330925
69000 0.56938919 0.0092629332 0.57865213 0.061838729
70000 0.61870712 0.010047381 0.6287545 0.066501338
71000 0.71651803 0.0088366199 0.72535465 0.079136316
72000 0.76278925 0.008828151 0.77161741 0.063672771
73000 0.75447428 0.0083985526 0.76287283 0.078256913
74000 0.66185251 0.0091910052 0.67104351 0.069840511
75000 0.58458829 0.0097671568 0.59435544 0.076123422
76000 0.7487564 0.0100022 0.7587586 0.076171741
77000 0.89505465 0.009250681 0.90430533 0.074921699
78000 0.73738164 0.0092029279 0.74658457 0.078835344
79000 0.65735281 0.010099528 0.66745233 0.077940627
80000 0.70247542 0.010306464 0.71278189 0.079560093
81000 0.74839505 0.010199092 0.75859415 0.080835104
82000 0.75193767 0.010274058 0.76221173 0.081086684
83000 0.71392598 0.010495573 0.72442156 0.082746145
84000 0.58498928 0.011027388 0.59601667 0.08356465
85000 0.59022869 0.011729474 0.60195817 0.084519397
86000 0.81753578 0.011208964 0.82874475 0.085490261
87000 0.83480682 0.010542579 0.8453494 0.086268527
88000 0.67322538 0.011170734 0.68439611 0.08751623
89000 0.62637389 0.012033316 0.6384072 0.088548094
90000 0.92828557 0.011750388 0.94003596 0.089199823
91000 0.96072564 0.010324509 0.97105015 0.090204803
92000 0.72105071 0.011484152 0.73253486 0.09140819
93000 0.65762527 0.012558219 0.67018349 0.092453474
94000 0.73991591 0.01261909 0.752535 0.093373477
95000 0.91791653 0.011980455 0.92989699 0.094182136
96000 0.76562561 0.011807085 0.7774327 0.095323684
97000 0.57292104 0.013610205 0.58653124 0.096505977
98000 0.68141076 0.013863204 0.69527396 0.097380069
99000 0.82390969 0.013002341 0.83691203 0.098235926
100000 0.77639728 0.012989342 0.78938662 0.099274147
Loop time of 3.88899 on 1 procs for 100000 steps with 32 atoms
Performance: 2221655.884 tau/day, 25713.610 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.056 | 3.056 | 3.056 | 0.0 | 78.58
Neigh | 0.0051048 | 0.0051048 | 0.0051048 | 0.0 | 0.13
Comm | 0.091444 | 0.091444 | 0.091444 | 0.0 | 2.35
Output | 0.0011995 | 0.0011995 | 0.0011995 | 0.0 | 0.03
Modify | 0.69909 | 0.69909 | 0.69909 | 0.0 | 17.98
Other | | 0.03616 | | | 0.93
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 57 ave 57 max 57 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 57
Ave neighs/atom = 1.78125
Neighbor list builds = 1445
Dangerous builds = 0
Total wall time: 0:00:03

221
examples/body/log.9Jul18.body.squares.g++.4
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@ -1,221 +0,0 @@
LAMMPS (29 Jun 2018)
# 2d rounded polygon bodies
variable r index 4
variable steps index 100000
variable T index 0.5
variable P index 0.1
variable seed index 980411
units lj
dimension 2
atom_style body rounded/polygon 1 6
atom_modify map array
read_data data.squares
orthogonal box = (0 0 -0.5) to (12 12 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
2 atoms
2 bodies
replicate $r $r 1
replicate 4 $r 1
replicate 4 4 1
orthogonal box = (0 0 -0.5) to (48 48 0.5)
2 by 2 by 1 MPI processor grid
32 atoms
Time spent = 0.000324011 secs
velocity all create $T ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 980411 dist gaussian mom yes rot yes
variable cut_inner equal 0.5
variable k_n equal 100
variable k_na equal 2
variable c_n equal 1
variable c_t equal 1
variable mu equal 0.1
variable delta_ua equal 0.5
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2
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 $T $T 1.0
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
fix 2 all enforce2d
#compute 1 all body/local id 1 2 3
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
thermo_style custom step ke pe etotal press
thermo 1000
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
#dump_modify 2 pad 6
run ${steps}
run 100000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.15685
ghost atom cutoff = 6.15685
binsize = 3.07843, bins = 16 16 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair body/rounded/polygon, 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) = 4.774 | 4.774 | 4.774 Mbytes
Step KinEng PotEng TotEng Press
0 0.484375 0.25 0.734375 0.0067274306
1000 0.39423376 0.0017918048 0.39602557 0.0021941612
2000 0.42284177 0.01346585 0.43630762 0.0029377883
3000 0.58154405 0.011321689 0.59286574 0.003667871
4000 0.73518304 0.034603175 0.76978621 0.0018689207
5000 0.84367476 0.025292163 0.86896692 0.0089161373
6000 0.70803236 0.0085631016 0.71659546 0.0045552895
7000 0.56206452 0.10453031 0.66659483 0.010255161
8000 0.64538994 0.088817673 0.73420761 0.0037633655
9000 0.90540819 0.063696004 0.96910419 0.0077673359
10000 0.68632042 0.093265016 0.77958544 0.0057864837
11000 0.59118074 0.025654748 0.61683549 0.012518759
12000 0.67522767 0.038176401 0.71340407 0.01741153
13000 0.7644843 0.10429844 0.86878274 0.013161339
14000 0.56152694 0.067836656 0.6293636 0.016852113
15000 0.41895505 0.019513353 0.43846841 0.015225696
16000 0.55799443 0.15645637 0.7144508 0.011703646
17000 0.59385248 0.03451986 0.62837234 0.025482966
18000 0.75902169 0.031103586 0.79012527 0.018263354
19000 0.64266826 0.12535314 0.76802141 0.014884119
20000 0.57836261 0.16581188 0.74417449 0.024667165
21000 0.78281936 0.11877527 0.90159464 -0.0090089213
22000 0.5312006 0.13300874 0.66420934 0.025797278
23000 0.56458861 0.084369128 0.64895774 0.024630917
24000 0.65126875 0.06122992 0.71249867 0.034377198
25000 0.55173441 0.15694886 0.70868327 0.021634086
26000 0.59121615 0.17071182 0.76192797 0.024758366
27000 0.6394843 0.17442949 0.81391378 0.034919937
28000 0.31144221 0.41243036 0.72387256 0.074115225
29000 0.13516917 0.3075419 0.44271107 0.023861298
30000 0.14094934 0.24407203 0.38502137 0.037030438
31000 0.26313749 0.087395422 0.35053291 0.042347005
32000 0.51602457 0.063012079 0.57903664 0.018550299
33000 0.55628829 0.200213 0.75650129 0.026507686
34000 0.97399408 0.082504517 1.0564986 0.037889878
35000 0.64710533 0.17662002 0.82372535 0.058295508
36000 0.45769083 0.08241194 0.54010277 0.014957415
37000 0.72850105 0.053874061 0.78237512 0.037194593
38000 0.44177995 0.28939498 0.73117493 0.045194029
39000 0.46828451 0.077630686 0.54591519 0.089849009
40000 0.46786451 0.092828423 0.56069294 0.028042052
41000 0.71861856 0.097085715 0.81570427 0.036473296
42000 0.74121021 0.10553127 0.84674148 0.054058843
43000 0.62945489 0.12770673 0.75716161 0.047267994
44000 0.49900638 0.085150056 0.58415644 0.054798793
45000 0.70199572 0.063415877 0.7654116 0.038363546
46000 0.49513142 0.10649384 0.60162526 0.059392561
47000 0.3858898 0.079458749 0.46534855 0.051825764
48000 0.62585854 0.028585902 0.65444444 0.054074424
49000 0.65934482 0.51865062 1.1779954 -0.035272836
50000 0.5420438 0.082056756 0.62410056 0.031187494
51000 0.36685223 0.14224019 0.50909241 0.073790397
52000 0.19044627 0.15368389 0.34413016 0.059034266
53000 0.26847678 0.075693324 0.3441701 0.032276915
54000 0.3593711 0.19034549 0.54971659 0.070827883
55000 0.21659198 0.1929074 0.40949939 0.035916364
56000 0.28242715 0.12313241 0.40555956 0.062083926
57000 0.34067475 0.14711992 0.48779467 0.059321458
58000 0.4842796 0.16143425 0.64571385 0.059048247
59000 0.84438871 0.076546849 0.92093556 0.048046901
60000 0.92794849 0.054331626 0.98228012 0.058392272
61000 0.6916736 0.076168342 0.76784194 0.058654987
62000 0.63317965 0.094506389 0.72768604 0.061044719
63000 0.63317266 0.038785593 0.67195825 0.097236147
64000 0.81696668 0.121811 0.93877769 0.064935373
65000 0.82644758 0.25188344 1.078331 0.093352359
66000 0.64975019 0.17930857 0.82905876 0.058805254
67000 0.63487678 0.16877059 0.80364737 0.070254696
68000 0.79140717 0.11631004 0.9077172 0.064646394
69000 0.85687272 0.057835331 0.91470805 0.071057291
70000 0.67785976 0.040686768 0.71854653 0.074687222
71000 0.60594577 0.032193155 0.63813893 0.069349268
72000 0.77586745 0.024068533 0.79993598 0.083394193
73000 0.88877625 0.025746326 0.91452258 0.081511105
74000 0.73507888 0.036574786 0.77165367 0.075360233
75000 0.68787782 0.042098622 0.72997644 0.068651098
76000 0.72515745 0.04360868 0.76876613 0.069594624
77000 0.77580944 0.041826702 0.81763614 0.071937144
78000 0.76640394 0.039285046 0.80568899 0.074274921
79000 0.62504309 0.039593585 0.66463667 0.076443295
80000 0.60001642 0.043468215 0.64348464 0.094547719
81000 0.82175037 0.045608873 0.86735924 0.080186295
82000 0.85783276 0.042692576 0.90052534 0.081576548
83000 0.71367707 0.042172193 0.75584926 0.08256625
84000 0.68532406 0.044724759 0.73004882 0.083672013
85000 0.72576789 0.046982462 0.77275035 0.084789331
86000 0.75597701 0.04765086 0.80362787 0.085758056
87000 0.74190598 0.047629096 0.78953507 0.086679976
88000 0.60967704 0.049906172 0.65958321 0.085526191
89000 0.54490288 0.054768238 0.59967112 0.090604027
90000 0.75398341 0.057153453 0.81113686 0.091900858
91000 0.84577472 0.052753512 0.89852823 0.091913909
92000 0.7176235 0.050677427 0.76830093 0.092032507
93000 0.61699446 0.054097013 0.67109147 0.092071275
94000 0.76330752 0.057398618 0.82070614 0.092435043
95000 0.98754458 0.053801311 1.0413459 0.093526707
96000 0.7405897 0.052135628 0.79272533 0.095011929
97000 0.65587599 0.057011962 0.71288795 0.096692123
98000 0.72345634 0.060700171 0.78415651 0.097510345
99000 0.88283624 0.061795247 0.94463149 0.09799633
100000 0.86303812 0.058912988 0.92195111 0.09892993
Loop time of 2.80074 on 4 procs for 100000 steps with 32 atoms
Performance: 3084895.573 tau/day, 35704.810 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.81169 | 0.89466 | 0.97669 | 8.4 | 31.94
Neigh | 0.0017524 | 0.0018129 | 0.0018773 | 0.1 | 0.06
Comm | 0.91307 | 0.99193 | 1.0691 | 7.3 | 35.42
Output | 0.00076914 | 0.00093722 | 0.0013936 | 0.0 | 0.03
Modify | 0.75335 | 0.75779 | 0.76346 | 0.4 | 27.06
Other | | 0.1536 | | | 5.48
Nlocal: 8 ave 10 max 4 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 17.25 ave 19 max 15 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 13.5 ave 21 max 5 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 54
Ave neighs/atom = 1.6875
Neighbor list builds = 1443
Dangerous builds = 0
Total wall time: 0:00:02

223
examples/body/log.9Jul18.body.wall2d.g++.1
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@ -1,223 +0,0 @@
LAMMPS (29 Jun 2018)
# 2d rounded polygon bodies
variable r index 4
variable steps index 100000
variable T index 0.5
variable P index 0.1
variable seed index 980411
units lj
dimension 2
atom_style body rounded/polygon 1 6
atom_modify map array
read_data data.squares
orthogonal box = (0 0 -0.5) to (12 12 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
2 atoms
2 bodies
replicate $r $r 1
replicate 4 $r 1
replicate 4 4 1
orthogonal box = (0 0 -0.5) to (48 48 0.5)
1 by 1 by 1 MPI processor grid
32 atoms
Time spent = 0.00029707 secs
velocity all create $T ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 980411 dist gaussian mom yes rot yes
change_box all boundary p f p
variable cut_inner equal 0.5
variable k_n equal 100
variable k_na equal 2
variable c_n equal 0.1
variable c_t equal 0.1
variable mu equal 0.1
variable delta_ua equal 0.5
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2
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 $T $T 1.0
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
fix 2 all enforce2d
fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
#compute 1 all body/local id 1 2 3
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
thermo_style custom step ke pe etotal press
thermo 1000
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
#dump_modify 2 pad 6
run ${steps}
run 100000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.15685
ghost atom cutoff = 6.15685
binsize = 3.07843, bins = 16 16 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair body/rounded/polygon, 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) = 4.771 | 4.771 | 4.771 Mbytes
Step KinEng PotEng TotEng Press
0 0.484375 0.25 0.734375 0.0067274306
1000 0.49241101 0.0031318767 0.49554289 0.017768281
2000 0.56118632 0.0026068888 0.56379321 0.003410416
3000 0.75565115 0.025578366 0.78122951 0.0071862988
4000 0.72298647 0.093150646 0.81613712 0.003190158
5000 0.51684166 0.049164868 0.56600653 0.0096960168
6000 0.56627905 0.048132853 0.6144119 0.020733586
7000 0.58122129 0.018223718 0.59944501 0.0038160759
8000 0.64297977 0.025934821 0.66891459 0.0041091784
9000 0.41748404 0.0077890042 0.42527305 0.0039270065
10000 0.35738377 0.078487805 0.43587158 3.9079782e-05
11000 0.41529308 0.13619284 0.55148592 -0.0067482285
12000 0.43274718 0.071315497 0.50406268 0.007006378
13000 0.4748331 0.069904647 0.54473775 0.0010384372
14000 0.6287791 0.12721033 0.75598943 0.0047792448
15000 0.4692413 0.12344005 0.59268136 0.018033616
16000 0.43157074 0.14306789 0.57463862 0.042356676
17000 0.53085999 0.22126296 0.75212294 0.027509646
18000 0.52688968 0.13225282 0.6591425 0.0021558013
19000 0.55032328 0.12513047 0.67545375 0.025036251
20000 0.48465097 0.1431055 0.62775647 0.017193781
21000 0.53166734 0.21928574 0.75095307 0.011564317
22000 0.62177353 0.09296159 0.71473512 0.017660922
23000 0.6972939 0.12434123 0.82163514 0.024432327
24000 0.42767372 0.22152311 0.64919684 -0.013712449
25000 0.4816037 0.19272865 0.67433236 0.052386055
26000 0.72642579 0.19697046 0.92339625 0.020407694
27000 0.39649144 0.15058326 0.5470747 0.023705766
28000 0.44896324 0.18500106 0.6339643 -0.0089410286
29000 0.5565759 0.11085772 0.66743362 0.048437166
30000 0.58173584 0.21773281 0.79946865 0.0057357773
31000 0.49199415 0.23601982 0.72801397 0.046744152
32000 0.55665496 0.20542161 0.76207658 -0.0038756805
33000 0.62730739 0.24460524 0.87191263 0.045330682
34000 0.58107044 0.16395278 0.74502322 -0.0049496051
35000 0.56838849 0.21842922 0.78681771 0.0062086036
36000 0.45910273 0.28464172 0.74374445 -0.011700747
37000 0.37092037 0.27646862 0.647389 0.022305679
38000 0.7278047 0.30674438 1.0345491 0.07698342
39000 0.5132923 0.27395066 0.78724295 0.026898634
40000 0.62348649 0.24424644 0.86773293 0.039403899
41000 0.3658401 0.15512326 0.52096337 0.022559003
42000 0.4912253 0.35712978 0.84835508 -0.010336341
43000 0.70225957 0.36314638 1.0654059 0.004148866
44000 0.56958157 0.25488927 0.82447084 0.067537066
45000 0.45854352 0.30149439 0.76003791 -0.017002401
46000 0.62787247 0.34567995 0.97355242 0.11894801
47000 0.61348914 0.29378625 0.90727539 0.067873976
48000 0.71301829 0.34135284 1.0543711 0.021077736
49000 0.53520804 0.30593196 0.84113999 0.0059257647
50000 0.44966403 0.35370793 0.80337195 0.0020395669
51000 0.5236113 0.32296924 0.84658054 -0.051011506
52000 0.53905573 0.351771 0.89082672 0.013720106
53000 0.55978158 0.41293947 0.97272106 0.068558589
54000 0.52170459 0.2718066 0.7935112 0.0093138985
55000 0.61078876 0.43353897 1.0443277 0.045377392
56000 0.51300655 0.33182278 0.84482933 -0.018418487
57000 0.54882822 0.38380093 0.93262915 0.10249946
58000 0.72106212 0.45361279 1.1746749 0.030313481
59000 0.55871447 0.63823029 1.1969448 0.019079703
60000 0.49395192 0.58283102 1.0767829 0.0179349
61000 0.45991079 0.62540573 1.0853165 0.074398804
62000 0.4655788 0.60862262 1.0742014 0.11472976
63000 0.55634524 0.63069255 1.1870378 -0.0025676135
64000 0.57688903 0.45435264 1.0312417 0.0083813852
65000 0.57168922 0.42217005 0.99385927 0.044931269
66000 0.6206044 0.46727538 1.0878798 0.019686229
67000 0.61037155 0.41840109 1.0287726 0.0195109
68000 0.63848598 0.41305347 1.0515395 0.072940144
69000 0.49244916 0.3834095 0.87585866 0.07963677
70000 0.41847062 0.51907975 0.93755037 0.18447904
71000 0.45198986 0.52973709 0.98172695 0.078419371
72000 0.47064262 0.37808165 0.84872427 -0.00046308054
73000 0.6690143 0.37549359 1.0445079 0.061208432
74000 0.60444955 0.33779636 0.94224592 -0.068840321
75000 0.61762382 0.3916421 1.0092659 0.16253292
76000 0.63657961 0.50277989 1.1393595 0.013857508
77000 0.52524028 0.43597896 0.96121924 -0.03296482
78000 0.43803533 0.33172284 0.76975817 0.078763029
79000 0.67156089 0.55272177 1.2242827 0.080822223
80000 0.68678238 0.46061627 1.1473987 0.0027036992
81000 0.64956678 0.44959229 1.0991591 0.11201483
82000 0.51060477 0.43508342 0.9456882 0.028000608
83000 0.59550548 0.69026083 1.2857663 -0.0015809004
84000 0.64222145 0.38768816 1.0299096 0.014153173
85000 0.7661229 0.43445261 1.2005755 0.048034534
86000 0.60025257 0.53027929 1.1305319 0.0056865157
87000 0.46220939 0.47470035 0.93690974 0.075311946
88000 0.54123847 0.62899839 1.1702369 0.13260162
89000 0.61212272 0.6114241 1.2235468 0.033284822
90000 0.63924773 0.6916249 1.3308726 0.045088296
91000 0.49316865 0.51037033 1.003539 0.023203598
92000 0.57572123 0.43496319 1.0106844 0.297092
93000 0.65187559 0.56815972 1.2200353 0.1538215
94000 0.64107331 0.58948521 1.2305585 0.031117778
95000 0.64584158 0.6364688 1.2823104 0.096154676
96000 0.60509093 0.601487 1.2065779 0.03457172
97000 0.68837218 0.77974186 1.468114 0.17801164
98000 0.62725266 0.64137144 1.2686241 0.17449001
99000 0.46861221 0.67000291 1.1386151 0.2429588
100000 0.5879119 0.7140612 1.3019731 0.064634257
Loop time of 2.50594 on 1 procs for 100000 steps with 32 atoms
Performance: 3447804.126 tau/day, 39905.140 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5639 | 1.5639 | 1.5639 | 0.0 | 62.41
Neigh | 0.0086911 | 0.0086911 | 0.0086911 | 0.0 | 0.35
Comm | 0.058926 | 0.058926 | 0.058926 | 0.0 | 2.35
Output | 0.0012379 | 0.0012379 | 0.0012379 | 0.0 | 0.05
Modify | 0.83537 | 0.83537 | 0.83537 | 0.0 | 33.34
Other | | 0.03781 | | | 1.51
Nlocal: 32 ave 32 max 32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 20 ave 20 max 20 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 57 ave 57 max 57 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 57
Ave neighs/atom = 1.78125
Neighbor list builds = 2705
Dangerous builds = 0
Total wall time: 0:00:02

223
examples/body/log.9Jul18.body.wall2d.g++.4
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@ -1,223 +0,0 @@
LAMMPS (29 Jun 2018)
# 2d rounded polygon bodies
variable r index 4
variable steps index 100000
variable T index 0.5
variable P index 0.1
variable seed index 980411
units lj
dimension 2
atom_style body rounded/polygon 1 6
atom_modify map array
read_data data.squares
orthogonal box = (0 0 -0.5) to (12 12 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
2 atoms
2 bodies
replicate $r $r 1
replicate 4 $r 1
replicate 4 4 1
orthogonal box = (0 0 -0.5) to (48 48 0.5)
2 by 2 by 1 MPI processor grid
32 atoms
Time spent = 0.000386 secs
velocity all create $T ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity all create 0.5 980411 dist gaussian mom yes rot yes
change_box all boundary p f p
variable cut_inner equal 0.5
variable k_n equal 100
variable k_na equal 2
variable c_n equal 0.1
variable c_t equal 0.1
variable mu equal 0.1
variable delta_ua equal 0.5
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2
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 $T $T 1.0
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
fix 2 all enforce2d
fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
#compute 1 all body/local id 1 2 3
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
thermo_style custom step ke pe etotal press
thermo 1000
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
#dump_modify 2 pad 6
run ${steps}
run 100000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.15685
ghost atom cutoff = 6.15685
binsize = 3.07843, bins = 16 16 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair body/rounded/polygon, 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) = 4.773 | 4.773 | 4.773 Mbytes
Step KinEng PotEng TotEng Press
0 0.484375 0.25 0.734375 0.0067274306
1000 0.49241101 0.0031318767 0.49554289 0.017768281
2000 0.56118632 0.0026068888 0.56379321 0.003410416
3000 0.75565115 0.025578366 0.78122951 0.0071862988
4000 0.72298647 0.093150646 0.81613712 0.003190158
5000 0.51684166 0.049164868 0.56600653 0.0096960168
6000 0.56627905 0.048132853 0.6144119 0.020733586
7000 0.58122129 0.018223718 0.59944501 0.0038160759
8000 0.64297977 0.025934821 0.66891459 0.0041091784
9000 0.41748404 0.0077890042 0.42527305 0.0039270065
10000 0.35738377 0.078487805 0.43587158 3.9079865e-05
11000 0.41529307 0.13619284 0.55148591 -0.0067482285
12000 0.43274718 0.071315527 0.50406271 0.007006369
13000 0.4748324 0.069905666 0.54473807 0.0010385254
14000 0.62603727 0.098905625 0.7249429 0.0048876764
15000 0.44512086 0.10415235 0.54927321 0.01902062
16000 0.47460177 0.18053316 0.65513493 0.045013976
17000 0.52742676 0.10110706 0.62853382 0.013615471
18000 0.46111734 0.096118795 0.55723613 0.0073676834
19000 0.59668439 0.13652292 0.73320731 0.029403553
20000 0.46840192 0.11611719 0.58451911 -0.00034412499
21000 0.53550533 0.096457461 0.6319628 0.0019785732
22000 0.46599715 0.13206373 0.59806087 0.031970672
23000 0.49280776 0.20404726 0.69685501 0.03657433
24000 0.60901688 0.18255214 0.79156902 0.044955017
25000 0.47345185 0.13671357 0.61016542 0.020313539
26000 0.47653832 0.12448225 0.60102057 0.01878099
27000 0.50008212 0.24740634 0.74748845 0.021862639
28000 0.41627204 0.2519463 0.66821834 0.054683701
29000 0.55608273 0.23100212 0.78708485 -0.0043318497
30000 0.53884537 0.3001584 0.83900377 -0.012838186
31000 0.53036238 0.2300328 0.76039518 -0.0061688449
32000 0.42666792 0.20536256 0.63203048 0.045305282
33000 0.62908185 0.1652033 0.79428515 0.0072777588
34000 0.47028154 0.388736 0.85901754 0.04332288
35000 0.54602322 0.2775624 0.82358562 0.02898206
36000 0.59860544 0.21824655 0.81685199 0.0025936194
37000 0.62467827 0.11983499 0.74451326 0.050052743
38000 0.72594229 0.36584781 1.0917901 0.04280621
39000 0.51129656 0.23859043 0.74988699 0.050817447
40000 0.53263836 0.24212889 0.77476725 0.036245922
41000 0.50288088 0.36668283 0.86956371 0.018381415
42000 0.46653688 0.21974887 0.68628574 0.012661062
43000 0.61738785 0.32131037 0.93869821 0.012709433
44000 0.56603903 0.26515554 0.83119457 0.03315102
45000 0.56231638 0.32111693 0.88343331 0.06079756
46000 0.7096208 0.2570131 0.96663391 0.048770468
47000 0.588755 0.1880748 0.7768298 0.035962604
48000 0.56296339 0.25783519 0.82079858 0.053019928
49000 0.419885 0.42328618 0.84317118 0.038105269
50000 0.63073351 0.41426285 1.0449964 0.0015271048
51000 0.59357935 0.184222 0.77780136 0.015996218
52000 0.60608471 0.36247533 0.96856003 0.10984665
53000 0.5227842 0.27686739 0.79965159 0.02761699
54000 0.39435923 0.34197355 0.73633278 0.061183263
55000 0.46748455 0.34230903 0.80979358 0.077441382
56000 0.59819827 0.29212061 0.89031889 0.043772353
57000 0.61682559 0.32788566 0.94471124 0.03992069
58000 0.52702478 0.24891506 0.77593984 0.058480883
59000 0.66925719 0.4109031 1.0801603 0.072434423
60000 0.66807714 0.39233068 1.0604078 0.082370324
61000 0.5724275 0.43308567 1.0055132 0.0072945426
62000 0.49433556 0.38453743 0.87887299 0.0036097443
63000 0.57575143 0.54067119 1.1164226 0.073339638
64000 0.68045383 0.38246533 1.0629192 0.025314593
65000 0.59843527 0.42928622 1.0277215 -0.030096445
66000 0.60274797 0.50186417 1.1046121 0.069797184
67000 0.47450407 0.52689807 1.0014021 0.008758012
68000 0.5514135 0.64113187 1.1925454 0.093863314
69000 0.52008074 0.45749565 0.97757639 -0.066061381
70000 0.69042662 0.50416006 1.1945867 0.014128617
71000 0.63925854 0.35153425 0.9907928 -0.01134957
72000 0.52088835 0.47626986 0.99715821 0.10198133
73000 0.46333852 0.5515537 1.0148922 0.00060582772
74000 0.53481418 0.50409531 1.0389095 0.00919451
75000 0.67182749 0.50380162 1.1756291 0.043301985
76000 0.70492289 0.4112122 1.1161351 0.14880484
77000 0.59781817 0.50197661 1.0997948 -0.057111711
78000 0.51677429 0.4348232 0.95159749 -0.0074619446
79000 0.50663297 0.55000424 1.0566372 0.0052071216
80000 0.59392006 0.48394003 1.0778601 -0.018990234
81000 0.66323593 0.40358336 1.0668193 -0.02961345
82000 0.61596979 0.49177944 1.1077492 0.1314853
83000 0.63917554 0.61656584 1.2557414 0.11908351
84000 0.49305291 0.46161646 0.95466937 0.033558488
85000 0.52552044 0.54250555 1.068026 0.13015174
86000 0.55140914 0.38924725 0.94065638 0.047412499
87000 0.60952504 0.52603688 1.1355619 0.039230066
88000 0.50119735 0.547539 1.0487364 0.019659933
89000 0.40331401 0.50331134 0.90662535 -0.056906034
90000 0.47067839 0.51306911 0.9837475 0.11918166
91000 0.45564995 0.38693455 0.8425845 0.12040045
92000 0.64163032 0.34232532 0.98395564 0.0057051641
93000 0.70375593 0.53646186 1.2402178 0.16044241
94000 0.53378112 0.51971406 1.0534952 0.11389004
95000 0.47055342 0.50396004 0.97451346 0.079424215
96000 0.59543473 0.40204536 0.99748009 0.096813093
97000 0.64821917 0.50051728 1.1487365 0.054071312
98000 0.55723937 0.4945909 1.0518303 0.047316424
99000 0.56044424 0.50773312 1.0681774 0.0149959
100000 0.68254229 0.32704484 1.0095871 0.0069212661
Loop time of 2.20043 on 4 procs for 100000 steps with 32 atoms
Performance: 3926501.701 tau/day, 45445.622 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.41008 | 0.41366 | 0.41719 | 0.4 | 18.80
Neigh | 0.0027823 | 0.0030481 | 0.0034747 | 0.5 | 0.14
Comm | 0.74581 | 0.7675 | 0.78684 | 2.0 | 34.88
Output | 0.00082111 | 0.0010884 | 0.0016899 | 1.1 | 0.05
Modify | 0.83828 | 0.85329 | 0.86656 | 1.4 | 38.78
Other | | 0.1618 | | | 7.36
Nlocal: 8 ave 9 max 7 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 12.75 ave 14 max 12 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 11 ave 19 max 5 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 44
Ave neighs/atom = 1.375
Neighbor list builds = 2663
Dangerous builds = 0
Total wall time: 0:00:02