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provide working examples for all four peridynamics models and reference outputs

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This commit is contained in:
Axel Kohlmeyer
2017-07-14 13:44:12 -04:00
parent 3b1134c164
commit 14f1d646ad
13 changed files with 943 additions and 51 deletions
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examples/peri/in.peri → examples/peri/in.peri-pmb
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examples/peri/in.peri.eps Normal file
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# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
create_atoms 1 region target
pair_style peri/eps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8
set group all density 2200
set group all volume 1.25e-10
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type &
# axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type &
# axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000

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examples/peri/in.peri.lps Normal file
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# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
create_atoms 1 region target
pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
set group all density 2200
set group all volume 1.25e-10
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type &
# axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type &
# axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000

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examples/peri/in.peri.pmb Normal file
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# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
create_atoms 1 region target
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
set group all density 2200
set group all volume 1.25e-10
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type &
# axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type &
# axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000

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examples/peri/in.peri.ves Normal file
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# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
create_atoms 1 region target
pair_style peri/ves
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
set group all density 2200
set group all volume 1.25e-10
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type &
# axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type &
# axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000

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examples/peri/log.6Jul17.peri.eps.g++.1 Normal file
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LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
1 by 1 by 1 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/eps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.0025001
ghost atom cutoff = 0.0025001
binsize = 0.00125005, bins = 9 5 9
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair peri/eps, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix PERI_NEIGH, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Per MPI rank memory allocation (min/avg/max) = 50.29 | 50.29 | 50.29 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 8.3466308e+24 247103.03 0 849681.45 8.0295601e+11 5.0030006e-07
200 1.1784921e+27 1098605.6 0 86178912 1.0246967e+14 5.5353162e-07
300 2.6263212e+27 4118581.6 0 1.9372377e+08 1.662415e+14 7.6036043e-07
400 3.3085888e+27 9397203.3 0 2.4825816e+08 1.561692e+14 1.0196674e-06
500 3.9151799e+27 18408722 0 3.0106204e+08 1.5298661e+14 1.2317127e-06
600 6.2936721e+27 11346143 0 4.6571282e+08 1.9645007e+14 1.5419242e-06
700 1.2721597e+28 3830223.2 0 9.2225588e+08 3.0235577e+14 2.0250441e-06
800 1.3190107e+28 2831668.7 0 9.5508099e+08 2.4853932e+14 2.5542553e-06
900 1.3166045e+28 1911868.6 0 9.524241e+08 1.9729649e+14 3.2117896e-06
1000 1.3159578e+28 1995827.6 0 9.5204114e+08 1.6722163e+14 3.7875695e-06
Loop time of 72.5574 on 1 procs for 1000 steps with 3487 atoms
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 | 71.779 | 71.779 | 71.779 | 0.0 | 98.93
Neigh | 0.5596 | 0.5596 | 0.5596 | 0.0 | 0.77
Comm | 0.0040631 | 0.0040631 | 0.0040631 | 0.0 | 0.01
Output | 0.00056624 | 0.00056624 | 0.00056624 | 0.0 | 0.00
Modify | 0.18403 | 0.18403 | 0.18403 | 0.0 | 0.25
Other | | 0.03016 | | | 0.04
Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 569177 ave 569177 max 569177 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 40
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:12

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examples/peri/log.6Jul17.peri.eps.g++.4 Normal file
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LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
2 by 1 by 2 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/eps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.0025001
ghost atom cutoff = 0.0025001
binsize = 0.00125005, bins = 9 5 9
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair peri/eps, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix PERI_NEIGH, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Per MPI rank memory allocation (min/avg/max) = 44.77 | 45.04 | 45.14 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 8.3466308e+24 247103.03 0 849681.45 8.0295601e+11 5.0030006e-07
200 1.1784921e+27 1098605.6 0 86178912 1.0246967e+14 5.5353162e-07
300 2.6263212e+27 4118581.6 0 1.9372377e+08 1.662415e+14 7.6036043e-07
400 3.3085888e+27 9397203.3 0 2.4825816e+08 1.561692e+14 1.0196674e-06
500 3.9151799e+27 18408722 0 3.0106204e+08 1.5298661e+14 1.2317127e-06
600 6.2936721e+27 11346143 0 4.6571282e+08 1.9645007e+14 1.5419242e-06
700 1.2721597e+28 3830223.2 0 9.2225588e+08 3.0235577e+14 2.0250441e-06
800 1.3190107e+28 2831668.7 0 9.5508099e+08 2.4853932e+14 2.5542553e-06
900 1.3166045e+28 1911869.3 0 9.524241e+08 1.9729649e+14 3.2117896e-06
1000 1.3159578e+28 1995833.9 0 9.5204114e+08 1.6722163e+14 3.7875695e-06
Loop time of 29.6266 on 4 procs for 1000 steps with 3487 atoms
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 25.905 | 26.18 | 26.326 | 3.2 | 88.37
Neigh | 0.15352 | 0.1872 | 0.22394 | 7.6 | 0.63
Comm | 3.0374 | 3.1471 | 3.3731 | 7.5 | 10.62
Output | 0.00047588 | 0.00062978 | 0.00097752 | 0.0 | 0.00
Modify | 0.073521 | 0.081854 | 0.093222 | 2.7 | 0.28
Other | | 0.02989 | | | 0.10
Nlocal: 871.75 ave 908 max 838 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 1368.25 ave 1402 max 1332 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 142294 ave 159233 max 124729 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 40
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:29

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examples/peri/log.6Jul17.peri.lps.g++.1 Normal file
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LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
1 by 1 by 1 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.0025001
ghost atom cutoff = 0.0025001
binsize = 0.00125005, bins = 9 5 9
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair peri/lps, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix PERI_NEIGH, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Per MPI rank memory allocation (min/avg/max) = 34.91 | 34.91 | 34.91 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 1.684629e+24 133446.65 0 255067.11 1.6206343e+11 5.0030006e-07
200 1.1380148e+27 684478.05 0 82842557 9.9178307e+13 5.5225839e-07
300 2.5659218e+27 5944645.9 0 1.9118934e+08 1.6231114e+14 7.6086254e-07
400 2.9916164e+27 13677434 0 2.2965481e+08 1.4081705e+14 1.0224963e-06
500 3.3570343e+27 11130894 0 2.5348933e+08 1.2577633e+14 1.2846002e-06
600 3.9506165e+27 6986672.5 0 2.9219831e+08 1.2659956e+14 1.5019096e-06
700 7.8366157e+27 11716082 0 5.7747436e+08 1.9480124e+14 1.9361899e-06
800 8.2483231e+27 4671647.2 0 6.0015282e+08 1.7040064e+14 2.3297298e-06
900 8.2720965e+27 1249680.9 0 5.9844715e+08 1.4117116e+14 2.8202052e-06
1000 8.2441462e+27 2278265.6 0 5.9745788e+08 1.234652e+14 3.213751e-06
Loop time of 62.3833 on 1 procs for 1000 steps with 3487 atoms
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 61.608 | 61.608 | 61.608 | 0.0 | 98.76
Neigh | 0.57177 | 0.57177 | 0.57177 | 0.0 | 0.92
Comm | 0.0030825 | 0.0030825 | 0.0030825 | 0.0 | 0.00
Output | 0.00051951 | 0.00051951 | 0.00051951 | 0.0 | 0.00
Modify | 0.17278 | 0.17278 | 0.17278 | 0.0 | 0.28
Other | | 0.02745 | | | 0.04
Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 576568 ave 576568 max 576568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 37
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:02

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examples/peri/log.6Jul17.peri.lps.g++.4 Normal file
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LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
2 by 1 by 2 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.0025001
ghost atom cutoff = 0.0025001
binsize = 0.00125005, bins = 9 5 9
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair peri/lps, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix PERI_NEIGH, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Per MPI rank memory allocation (min/avg/max) = 29.4 | 29.66 | 29.76 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 1.684629e+24 133446.65 0 255067.11 1.6206343e+11 5.0030006e-07
200 1.1380148e+27 684478.05 0 82842557 9.9178307e+13 5.5225839e-07
300 2.5659218e+27 5944645.9 0 1.9118934e+08 1.6231114e+14 7.6086254e-07
400 2.9916164e+27 13677434 0 2.2965481e+08 1.4081705e+14 1.0224963e-06
500 3.3570343e+27 11130894 0 2.5348933e+08 1.2577633e+14 1.2846002e-06
600 3.9506165e+27 6986672.5 0 2.9219831e+08 1.2659956e+14 1.5019096e-06
700 7.8366157e+27 11716082 0 5.7747436e+08 1.9480124e+14 1.9361899e-06
800 8.2483231e+27 4671647.2 0 6.0015282e+08 1.7040064e+14 2.3297298e-06
900 8.2720965e+27 1249680.9 0 5.9844715e+08 1.4117116e+14 2.8202052e-06
1000 8.2441489e+27 2277476.2 0 5.9745729e+08 1.2346524e+14 3.213751e-06
Loop time of 23.2656 on 4 procs for 1000 steps with 3487 atoms
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 20.801 | 21.119 | 21.525 | 6.3 | 90.78
Neigh | 0.13851 | 0.18557 | 0.22747 | 8.5 | 0.80
Comm | 1.5175 | 1.8689 | 2.1386 | 18.0 | 8.03
Output | 0.00049806 | 0.00059026 | 0.00071931 | 0.0 | 0.00
Modify | 0.063441 | 0.066235 | 0.069135 | 0.9 | 0.28
Other | | 0.02496 | | | 0.11
Nlocal: 871.75 ave 939 max 805 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 1343.25 ave 1410 max 1276 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 144142 ave 176488 max 113797 min
Histogram: 1 0 1 0 0 0 1 0 0 1
FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 37
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:23

57
examples/peri/log.5Oct16.peri.g++.1 → examples/peri/log.6Jul17.peri.pmb.g++.1
View File

@ -1,10 +1,11 @@
LAMMPS (5 Oct 2016)
LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile
units si
units si
boundary s s s
atom_style peri
atom_modify map array
atom_modify map array
neighbor 0.0010 bin
# small target
@ -41,24 +42,34 @@ thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.0025001
ghost atom cutoff = 0.0025001
binsize = 0.00125005 -> bins = 9 5 9
binsize = 0.00125005, bins = 9 5 9
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair peri/pmb, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix PERI_NEIGH, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Memory usage per processor = 26.6858 Mbytes
Per MPI rank memory allocation (min/avg/max) = 34.79 | 34.79 | 34.79 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 1.7890585e+24 552721.8 0 681881.47 1.7210968e+11 5.0030006e-07
@ -68,28 +79,28 @@ Step Temp E_pair E_mol TotEng Press Volume
500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
800 1.2424839e+28 2407361.6 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358395e+28 4532520.6 0 8.9673706e+08 1.9097312e+14 3.1145903e-06
1000 1.2341057e+28 3219939.5 0 8.9417279e+08 1.5968597e+14 3.7196039e-06
Loop time of 20.3026 on 1 procs for 1000 steps with 3487 atoms
800 1.2424839e+28 2407365.1 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358397e+28 4532424.3 0 8.9673716e+08 1.9097316e+14 3.1145903e-06
1000 1.2341048e+28 3219355.8 0 8.9417154e+08 1.5968585e+14 3.7196039e-06
Loop time of 28.565 on 1 procs for 1000 steps with 3487 atoms
99.9% CPU use with 1 MPI tasks x no OpenMP threads
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 19.625 | 19.625 | 19.625 | 0.0 | 96.66
Neigh | 0.57013 | 0.57013 | 0.57013 | 0.0 | 2.81
Comm | 0.0014448 | 0.0014448 | 0.0014448 | 0.0 | 0.01
Output | 0.00024772 | 0.00024772 | 0.00024772 | 0.0 | 0.00
Modify | 0.092173 | 0.092173 | 0.092173 | 0.0 | 0.45
Other | | 0.01359 | | | 0.07
Pair | 27.721 | 27.721 | 27.721 | 0.0 | 97.04
Neigh | 0.66353 | 0.66353 | 0.66353 | 0.0 | 2.32
Comm | 0.0027969 | 0.0027969 | 0.0027969 | 0.0 | 0.01
Output | 0.00042295 | 0.00042295 | 0.00042295 | 0.0 | 0.00
Modify | 0.1566 | 0.1566 | 0.1566 | 0.0 | 0.55
Other | | 0.02086 | | | 0.07
Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 567140 ave 567140 max 567140 min
Neighs: 567132 ave 567132 max 567132 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -101,4 +112,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:20
Total wall time: 0:00:28

67
examples/peri/log.5Oct16.peri.g++.4 → examples/peri/log.6Jul17.peri.pmb.g++.4
View File

@ -1,10 +1,11 @@
LAMMPS (5 Oct 2016)
LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile
units si
units si
boundary s s s
atom_style peri
atom_modify map array
atom_modify map array
neighbor 0.0010 bin
# small target
@ -41,24 +42,34 @@ thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.0025001
ghost atom cutoff = 0.0025001
binsize = 0.00125005 -> bins = 9 5 9
binsize = 0.00125005, bins = 9 5 9
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair peri/pmb, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix PERI_NEIGH, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Memory usage per processor = 26.9049 Mbytes
Per MPI rank memory allocation (min/avg/max) = 29.27 | 29.54 | 29.64 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 1.7890585e+24 552721.8 0 681881.47 1.7210968e+11 5.0030006e-07
@ -68,29 +79,29 @@ Step Temp E_pair E_mol TotEng Press Volume
500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
800 1.2424839e+28 2407361.5 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358395e+28 4532520.1 0 8.9673706e+08 1.9097312e+14 3.1145903e-06
1000 1.2341057e+28 3219974.3 0 8.9417286e+08 1.5968598e+14 3.7196039e-06
Loop time of 5.91321 on 4 procs for 1000 steps with 3487 atoms
800 1.2424839e+28 2407365.2 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358397e+28 4532423 0 8.9673716e+08 1.9097316e+14 3.1145903e-06
1000 1.2341048e+28 3219408.7 0 8.9417158e+08 1.5968585e+14 3.7196039e-06
Loop time of 9.59889 on 4 procs for 1000 steps with 3487 atoms
99.6% CPU use with 4 MPI tasks x no OpenMP threads
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.5763 | 5.0164 | 5.502 | 15.8 | 84.83
Neigh | 0.11212 | 0.14636 | 0.1811 | 7.8 | 2.48
Comm | 0.18545 | 0.70922 | 1.1869 | 45.6 | 11.99
Output | 0.00026011 | 0.00030977 | 0.00038433 | 0.3 | 0.01
Modify | 0.028668 | 0.029356 | 0.030043 | 0.4 | 0.50
Other | | 0.01158 | | | 0.20
Pair | 7.9131 | 8.1341 | 8.3286 | 6.7 | 84.74
Neigh | 0.19736 | 0.22539 | 0.25643 | 5.6 | 2.35
Comm | 0.92843 | 1.1536 | 1.402 | 18.4 | 12.02
Output | 0.00053358 | 0.00059688 | 0.00070548 | 0.0 | 0.01
Modify | 0.060774 | 0.06358 | 0.068375 | 1.2 | 0.66
Other | | 0.02165 | | | 0.23
Nlocal: 871.75 ave 920 max 824 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 1343.25 ave 1391 max 1295 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 141785 ave 170754 max 115891 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nlocal: 871.75 ave 920 max 829 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 1343.25 ave 1386 max 1295 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 141783 ave 157099 max 127518 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1
@ -101,4 +112,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:05
Total wall time: 0:00:09

115
examples/peri/log.6Jul17.peri.ves.g++.1 Normal file
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@ -0,0 +1,115 @@
LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
1 by 1 by 1 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/ves
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.0025001
ghost atom cutoff = 0.0025001
binsize = 0.00125005, bins = 9 5 9
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair peri/ves, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix PERI_NEIGH, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Per MPI rank memory allocation (min/avg/max) = 65.41 | 65.41 | 65.41 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 8.3392177e+24 247040.57 0 849083.8 8.0224286e+11 5.0030006e-07
200 1.1849022e+27 1158030.5 0 86701105 1.0301578e+14 5.5359205e-07
300 2.6287222e+27 4389155.1 0 1.9416767e+08 1.6636212e+14 7.6050375e-07
400 3.2718778e+27 7458219 0 2.4366885e+08 1.5439709e+14 1.0199269e-06
500 3.8413187e+27 6151611.4 0 2.8347258e+08 1.5008974e+14 1.2318007e-06
600 6.1409926e+27 18424316 0 4.6176842e+08 1.9507512e+14 1.5151227e-06
700 1.0046131e+28 11478344 0 7.3675086e+08 2.4228512e+14 1.9956447e-06
800 1.0402132e+28 4421233.6 0 7.5539495e+08 2.0512303e+14 2.4407262e-06
900 1.0419515e+28 7223261.3 0 7.594519e+08 1.6647307e+14 3.0124137e-06
1000 1.0503737e+28 2621490.6 0 7.6093049e+08 1.4315634e+14 3.5313793e-06
Loop time of 77.2175 on 1 procs for 1000 steps with 3487 atoms
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 76.421 | 76.421 | 76.421 | 0.0 | 98.97
Neigh | 0.56616 | 0.56616 | 0.56616 | 0.0 | 0.73
Comm | 0.0038247 | 0.0038247 | 0.0038247 | 0.0 | 0.00
Output | 0.00051951 | 0.00051951 | 0.00051951 | 0.0 | 0.00
Modify | 0.19434 | 0.19434 | 0.19434 | 0.0 | 0.25
Other | | 0.03197 | | | 0.04
Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 561942 ave 561942 max 561942 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 37
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:17

115
examples/peri/log.6Jul17.peri.ves.g++.4 Normal file
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@ -0,0 +1,115 @@
LAMMPS (6 Jul 2017)
using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
2 by 1 by 2 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/ves
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.0025001
ghost atom cutoff = 0.0025001
binsize = 0.00125005, bins = 9 5 9
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair peri/ves, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix PERI_NEIGH, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Per MPI rank memory allocation (min/avg/max) = 59.9 | 60.16 | 60.26 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 8.3392177e+24 247040.57 0 849083.8 8.0224286e+11 5.0030006e-07
200 1.1849022e+27 1158030.5 0 86701105 1.0301578e+14 5.5359205e-07
300 2.6287222e+27 4389155.1 0 1.9416767e+08 1.6636212e+14 7.6050375e-07
400 3.2718778e+27 7458219 0 2.4366885e+08 1.5439709e+14 1.0199269e-06
500 3.8413187e+27 6151611.4 0 2.8347258e+08 1.5008974e+14 1.2318007e-06
600 6.1409926e+27 18424316 0 4.6176842e+08 1.9507512e+14 1.5151227e-06
700 1.0046131e+28 11478344 0 7.3675086e+08 2.4228512e+14 1.9956447e-06
800 1.0402132e+28 4421233.6 0 7.5539495e+08 2.0512303e+14 2.4407262e-06
900 1.0419515e+28 7223258.7 0 7.594519e+08 1.6647307e+14 3.0124137e-06
1000 1.0503738e+28 2621480.4 0 7.6093057e+08 1.4315636e+14 3.5313793e-06
Loop time of 25.9768 on 4 procs for 1000 steps with 3487 atoms
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.455 | 23.348 | 24.175 | 14.1 | 89.88
Neigh | 0.14472 | 0.18294 | 0.2299 | 8.6 | 0.70
Comm | 1.4715 | 2.3485 | 3.2075 | 44.8 | 9.04
Output | 0.000489 | 0.00059682 | 0.0007987 | 0.0 | 0.00
Modify | 0.063634 | 0.071411 | 0.076907 | 1.9 | 0.27
Other | | 0.02506 | | | 0.10
Nlocal: 871.75 ave 896 max 852 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1293.25 ave 1313 max 1269 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 140486 ave 167239 max 121255 min
Histogram: 2 0 0 0 0 0 1 0 0 1
FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 37
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:26