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Updating examples

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This commit is contained in:
Joel Clemmer
2021-02-05 16:43:52 -07:00
parent 56841ba912
commit c94a740b4e
16 changed files with 20681 additions and 256 deletions
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2
doc/src/Examples.rst
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@ -108,6 +108,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| msst | MSST shock dynamics |
+-------------+------------------------------------------------------------------+
| multi | multi neighboring for systems with large interaction disparities |
+-------------+------------------------------------------------------------------+
| nb3b | use of non-bonded 3-body harmonic pair style |
+-------------+------------------------------------------------------------------+
| neb | nudged elastic band (NEB) calculation for barrier finding |

20015
examples/multi/data.powerlaw Executable file
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File diff suppressed because it is too large Load Diff

2
examples/multi/in.colloid
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@ -31,7 +31,7 @@ velocity all create 1.44 87287 loop geom
neighbor 1 multi #multi/old
neigh_modify delay 0 collection/type 2 1*4 5
comm_modify mode multi reduce/multi
comm_modify mode multi reduce/multi #multi/old
# colloid potential

16
examples/multi/in.granular
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@ -1,4 +1,4 @@
# Bidisperse set of grains
# Big colloid particles and small LJ particles
units lj
atom_style sphere
@ -28,10 +28,10 @@ velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #multi/old
neigh_modify delay 0
comm_modify mode multi vel yes reduce/multi
neigh_modify delay 0 collection/interval 2 1 20
comm_modify mode multi vel yes reduce/multi #multi/old
# colloid potential
# granular potential
pair_style granular
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
@ -42,14 +42,6 @@ fix 3 all deform 1 xy erate 1e-3
#dump 1 all custom 1000 dump.granular id x y z radius
#dump 2 all image 1000 image.*.jpg type type &
# zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type &
# zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000

33
examples/multi/in.powerlaw Executable file
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@ -0,0 +1,33 @@
# Shear power-law distributed granular particles
units lj
atom_style sphere
dimension 2
read_data data.powerlaw
change_box all triclinic
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200
comm_modify mode multi vel yes reduce/multi
# granular potential
pair_style granular
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
# fixes
fix 1 all nve/sphere
fix 2 all enforce2d
fix 3 all deform 1 xy erate 2e-4
# dump 1 all custom 2000 dump.granular id x y z radius
thermo_style custom step temp epair etotal press vol pxy
thermo 1000
timestep 0.005
run 100000

32
examples/multi/log.30Nov20.colloid.intel.1
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@ -1,5 +1,5 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #/old
neigh_modify delay 0 multi/custom 2 1*4 5
comm_modify mode multi multi/reduce
neighbor 1 multi #multi/old
neigh_modify delay 0 collection/type 2 1*4 5
comm_modify mode multi reduce/multi #multi/old
# colloid potential
@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 1000 dump.colloid
#dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
@ -98,7 +98,7 @@ Neighbor list info ...
pair build: half/multi/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 5.538 | 5.538 | 5.538 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.385 | 4.385 | 4.385 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395241 0.121 36000
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume
48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246
49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093
50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715
Loop time of 20.4651 on 1 procs for 50000 steps with 3026 atoms
Loop time of 19.7532 on 1 procs for 50000 steps with 3026 atoms
Performance: 1055453.279 tau/day, 2443.179 timesteps/s
Performance: 1093493.133 tau/day, 2531.234 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.099 | 11.099 | 11.099 | 0.0 | 54.23
Neigh | 2.7536 | 2.7536 | 2.7536 | 0.0 | 13.46
Comm | 0.53353 | 0.53353 | 0.53353 | 0.0 | 2.61
Output | 0.11209 | 0.11209 | 0.11209 | 0.0 | 0.55
Modify | 5.1627 | 5.1627 | 5.1627 | 0.0 | 25.23
Other | | 0.8046 | | | 3.93
Pair | 10.789 | 10.789 | 10.789 | 0.0 | 54.62
Neigh | 2.6848 | 2.6848 | 2.6848 | 0.0 | 13.59
Comm | 0.53244 | 0.53244 | 0.53244 | 0.0 | 2.70
Output | 0.0010482 | 0.0010482 | 0.0010482 | 0.0 | 0.01
Modify | 4.9599 | 4.9599 | 4.9599 | 0.0 | 25.11
Other | | 0.7856 | | | 3.98
Nlocal: 3026.00 ave 3026 max 3026 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -180,4 +180,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:20
Total wall time: 0:00:19

30
examples/multi/log.30Nov20.colloid.intel.4
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@ -1,5 +1,5 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #/old
neigh_modify delay 0 multi/custom 2 1*4 5
comm_modify mode multi multi/reduce
neighbor 1 multi #multi/old
neigh_modify delay 0 collection/type 2 1*4 5
comm_modify mode multi reduce/multi #multi/old
# colloid potential
@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 1000 dump.colloid
#dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
@ -98,7 +98,7 @@ Neighbor list info ...
pair build: half/multi/newton
stencil: half/multi/2d
bin: multi
Per MPI rank memory allocation (min/avg/max) = 5.379 | 5.382 | 5.384 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.327 | 4.329 | 4.330 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395241 0.121 36000
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume
48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453
49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918
50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268
Loop time of 7.28248 on 4 procs for 50000 steps with 3026 atoms
Loop time of 6.98615 on 4 procs for 50000 steps with 3026 atoms
Performance: 2966022.789 tau/day, 6865.793 timesteps/s
Performance: 3091831.080 tau/day, 7157.016 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1624 | 2.5918 | 2.9227 | 17.4 | 35.59
Neigh | 0.62508 | 0.7436 | 0.83321 | 9.2 | 10.21
Comm | 1.1035 | 1.5265 | 2.0746 | 29.3 | 20.96
Output | 0.050094 | 0.050233 | 0.05062 | 0.1 | 0.69
Modify | 1.8164 | 1.8966 | 1.9583 | 4.2 | 26.04
Other | | 0.4737 | | | 6.50
Pair | 2.2795 | 2.5856 | 2.9414 | 17.4 | 37.01
Neigh | 0.62273 | 0.70156 | 0.76736 | 7.4 | 10.04
Comm | 1.0765 | 1.4945 | 1.8884 | 28.6 | 21.39
Output | 0.00076496 | 0.0008953 | 0.0012832 | 0.0 | 0.01
Modify | 1.718 | 1.7755 | 1.827 | 3.7 | 25.41
Other | | 0.4281 | | | 6.13
Nlocal: 756.500 ave 839 max 673 min
Histogram: 1 0 1 0 0 0 0 1 0 1

30
examples/multi/log.30Nov20.colloid.old.intel.1
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@ -1,5 +1,5 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi/old
neighbor 1 multi/old #multi
neigh_modify delay 0 #multi/custom 2 1*4 5
comm_modify mode multi #multi/reduce
comm_modify mode multi/old #multi multi/reduce
# colloid potential
@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 1000 dump.colloid
#dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
@ -98,7 +98,7 @@ Neighbor list info ...
pair build: half/multi/old/newton
stencil: half/multi/old/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.611 | 5.611 | 5.611 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395241 0.121 36000
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume
48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933
49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165
50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069
Loop time of 29.8066 on 1 procs for 50000 steps with 3026 atoms
Loop time of 28.5339 on 1 procs for 50000 steps with 3026 atoms
Performance: 724671.093 tau/day, 1677.479 timesteps/s
Performance: 756994.490 tau/day, 1752.302 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.698 | 11.698 | 11.698 | 0.0 | 39.25
Neigh | 10.292 | 10.292 | 10.292 | 0.0 | 34.53
Comm | 1.405 | 1.405 | 1.405 | 0.0 | 4.71
Output | 0.11474 | 0.11474 | 0.11474 | 0.0 | 0.38
Modify | 5.3019 | 5.3019 | 5.3019 | 0.0 | 17.79
Other | | 0.9947 | | | 3.34
Pair | 10.918 | 10.918 | 10.918 | 0.0 | 38.26
Neigh | 10.375 | 10.375 | 10.375 | 0.0 | 36.36
Comm | 1.2856 | 1.2856 | 1.2856 | 0.0 | 4.51
Output | 0.0010955 | 0.0010955 | 0.0010955 | 0.0 | 0.00
Modify | 5.0132 | 5.0132 | 5.0132 | 0.0 | 17.57
Other | | 0.9412 | | | 3.30
Nlocal: 3026.00 ave 3026 max 3026 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -180,4 +180,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:29
Total wall time: 0:00:28

32
examples/multi/log.30Nov20.colloid.old.intel.4
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@ -1,5 +1,5 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
@ -53,9 +53,9 @@ velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi/old
neighbor 1 multi/old #multi
neigh_modify delay 0 #multi/custom 2 1*4 5
comm_modify mode multi #multi/reduce
comm_modify mode multi/old #multi multi/reduce
# colloid potential
@ -72,7 +72,7 @@ pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
dump 1 all atom 1000 dump.colloid
#dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
@ -98,7 +98,7 @@ Neighbor list info ...
pair build: half/multi/old/newton
stencil: half/multi/old/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.438 | 5.441 | 5.444 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.404 | 4.406 | 4.410 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395241 0.121 36000
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
@ -151,20 +151,20 @@ Step Temp E_pair TotEng Press Volume
48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543
49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823
50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277
Loop time of 11.239 on 4 procs for 50000 steps with 3026 atoms
Loop time of 10.7578 on 4 procs for 50000 steps with 3026 atoms
Performance: 1921872.705 tau/day, 4448.779 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 2007847.166 tau/day, 4647.794 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3936 | 2.7411 | 3.1078 | 16.7 | 24.39
Neigh | 2.2948 | 2.6755 | 3.1013 | 18.5 | 23.81
Comm | 2.522 | 3.3135 | 4.0361 | 31.7 | 29.48
Output | 0.040863 | 0.041031 | 0.041456 | 0.1 | 0.37
Modify | 1.844 | 1.9014 | 1.9701 | 3.4 | 16.92
Other | | 0.5666 | | | 5.04
Pair | 2.3814 | 2.6878 | 2.9507 | 15.2 | 24.98
Neigh | 2.3959 | 2.6615 | 2.9677 | 16.2 | 24.74
Comm | 2.4113 | 2.9894 | 3.5621 | 29.6 | 27.79
Output | 0.00077024 | 0.00091029 | 0.0012971 | 0.0 | 0.01
Modify | 1.7966 | 1.8497 | 1.907 | 3.8 | 17.19
Other | | 0.5686 | | | 5.29
Nlocal: 756.500 ave 838 max 693 min
Histogram: 2 0 0 0 0 0 0 1 0 1
@ -180,4 +180,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:11
Total wall time: 0:00:10

142
examples/multi/log.30Nov20.granular.intel.1
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@ -1,5 +1,5 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
@ -51,9 +51,9 @@ velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #/old
neigh_modify delay 0
comm_modify mode multi vel yes
neighbor 1 multi #multi/old
neigh_modify delay 0 collection/interval 2 1 20
comm_modify mode multi vel yes reduce/multi #multi/old
# colloid potential
@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix 2 all enforce2d
fix 3 all deform 1 xy erate 1e-3
dump 1 all custom 1000 dump.granular id x y z radius
#dump 1 all custom 1000 dump.granular id x y z radius
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
@ -90,86 +90,86 @@ Neighbor list info ...
pair build: half/size/multi/newton/tri
stencil: half/multi/2d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes
Per MPI rank memory allocation (min/avg/max) = 10.29 | 10.29 | 10.29 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395623 0.66837658 7200
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
6000 0.025856 0 0.025848141 0.021241317 7603.5534
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
9000 0.016370159 0 0.016365184 0.020261904 6515.3445
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
11000 0.014156551 0 0.014152248 0.021324815 5815.4665
12000 0.013725406 0 0.013721235 0.021159958 5483.6304
13000 0.013215746 0 0.013211729 0.021685712 5165.4758
14000 0.012398153 0 0.012394384 0.024155434 4862.8657
15000 0.011842796 0 0.011839196 0.028503991 4577.9008
16000 0.011433182 0 0.011429706 0.033564839 4309.8792
17000 0.011166574 0 0.01116318 0.040592677 4058.9964
18000 0.01100067 0 0.010997326 0.04899206 3825.155
19000 0.010224474 0 0.010221366 0.063670337 3607.6577
20000 0.0091360559 0 0.0091332789 0.088230111 3408.5658
21000 0.007733647 0 0.0077312964 0.11769368 3227.7002
22000 0.0060202358 0 0.0060184059 0.15272491 3064.3986
23000 0.004670574 0 0.0046691543 0.19450724 2918.0014
24000 0.0040248313 0 0.004023608 0.24161742 2788.4113
25000 0.0032075275 0 0.0032065526 0.2897693 2674.5604
26000 0.0021358024 0 0.0021351532 0.33635617 2574.9564
27000 0.0016902752 0 0.0016897614 0.37624266 2487.2379
28000 0.0014038218 0 0.0014033951 0.41492104 2409.2461
29000 0.00090262506 0 0.0009023507 0.45392905 2340.0308
30000 0.00049466342 0 0.00049451306 0.49295072 2279.2316
31000 0.00056998139 0 0.00056980815 0.53299515 2226.5683
32000 0.00057326945 0 0.0005730952 0.56856537 2181.7092
33000 0.00044845112 0 0.00044831481 0.59623471 2142.7573
34000 0.00059840183 0 0.00059821994 0.61758983 2107.1253
35000 0.00075310993 0 0.00075288103 0.63756827 2072.7217
36000 0.00053774066 0 0.00053757721 0.66026064 2039.1655
37000 0.00030440106 0 0.00030430853 0.69059102 2007.7903
38000 0.00034436264 0 0.00034425797 0.72166344 1980.7137
39000 0.00039693498 0 0.00039681433 0.74680327 1957.9531
40000 0.00035425567 0 0.000354148 0.76604186 1937.3834
41000 0.0003094733 0 0.00030937924 0.78323163 1916.7027
42000 0.00027259246 0 0.0002725096 0.80315535 1895.0714
43000 0.00020659817 0 0.00020653538 0.8274603 1873.5407
44000 0.00016023333 0 0.00016018463 0.85418969 1853.8674
45000 0.00016111931 0 0.00016107034 0.87913944 1837.1141
46000 0.00016130888 0 0.00016125985 0.89921705 1822.7354
47000 0.00015755049 0 0.0001575026 0.91653538 1809.0285
48000 0.00017794781 0 0.00017789372 0.93582908 1794.7041
49000 0.00018878437 0 0.00018872699 0.95775203 1780.032
50000 0.0001778042 0 0.00017775016 0.97893714 1765.9439
Loop time of 77.4487 on 1 procs for 50000 steps with 3290 atoms
1000 0.32604952 0 0.32595042 0.17341597 7862.5013
2000 0.12631038 0 0.12627198 0.069126477 8216.6956
3000 0.069351715 0 0.069330635 0.040799593 8344.1931
4000 0.045023755 0 0.04501007 0.029184795 8239.1832
5000 0.032735149 0 0.0327252 0.025640841 7943.5691
6000 0.026205227 0 0.026197262 0.021206924 7617.6672
7000 0.02165475 0 0.021648168 0.018789365 7255.2897
8000 0.018299317 0 0.018293755 0.019272158 6887.3386
9000 0.016283763 0 0.016278813 0.020434892 6524.0274
10000 0.015148918 0 0.015144313 0.021650465 6168.4941
11000 0.014180465 0 0.014176155 0.022320009 5823.98
12000 0.013505744 0 0.013501639 0.023978674 5492.4853
13000 0.013009585 0 0.01300563 0.024391329 5175.7455
14000 0.012494373 0 0.012490576 0.027331543 4874.3212
15000 0.012057669 0 0.012054004 0.030561239 4589.518
16000 0.011510988 0 0.01150749 0.034613772 4321.1694
17000 0.011198594 0 0.01119519 0.042263536 4070.0115
18000 0.010978603 0 0.010975266 0.053637275 3836.0304
19000 0.010768789 0 0.010765516 0.069472547 3619.75
20000 0.0102256 0 0.010222492 0.085332898 3420.2738
21000 0.0089630315 0 0.0089603072 0.11199196 3236.9821
22000 0.006565581 0 0.0065635854 0.14807426 3071.3012
23000 0.0050916998 0 0.0050901522 0.1903446 2923.4162
24000 0.0040345997 0 0.0040333734 0.237983 2792.2658
25000 0.0032995328 0 0.0032985299 0.29120001 2677.7475
26000 0.0024157863 0 0.002415052 0.33851944 2578.4972
27000 0.0020664445 0 0.0020658164 0.37561848 2491.0264
28000 0.0017843883 0 0.0017838459 0.41119961 2412.3871
29000 0.0011813262 0 0.0011809672 0.44749341 2341.7208
30000 0.00063084711 0 0.00063065536 0.4879202 2279.0452
31000 0.00056027405 0 0.00056010376 0.52932126 2224.9456
32000 0.00053304715 0 0.00053288513 0.56822504 2179.1224
33000 0.00052245707 0 0.00052229826 0.60025509 2140.5345
34000 0.00073726189 0 0.0007370378 0.62001489 2106.3045
35000 0.00075804791 0 0.0007578175 0.6359631 2072.525
36000 0.00052579203 0 0.00052563222 0.65678516 2038.1907
37000 0.00036977909 0 0.0003696667 0.68784389 2005.5831
38000 0.00036252798 0 0.00036241779 0.72116044 1977.7441
39000 0.00036254566 0 0.00036243547 0.74720837 1954.9127
40000 0.00036237175 0 0.00036226161 0.76605408 1934.6006
41000 0.00032453104 0 0.00032443239 0.78424188 1914.1939
42000 0.00025394755 0 0.00025387036 0.80529272 1893.064
43000 0.00021067821 0 0.00021061418 0.82962095 1872.365
44000 0.00017927684 0 0.00017922235 0.85522899 1853.531
45000 0.0001464225 0 0.000146378 0.87925998 1837.2423
46000 0.00012922979 0 0.00012919051 0.8986549 1822.9227
47000 0.0001643557 0 0.00016430575 0.91743602 1809.0605
48000 0.00020154753 0 0.00020148627 0.93686779 1794.9227
49000 0.00017742528 0 0.00017737135 0.94988773 1780.3811
50000 0.00015150521 0 0.00015145916 0.97929588 1764.7507
Loop time of 54.9135 on 1 procs for 50000 steps with 3290 atoms
Performance: 278894.354 tau/day, 645.589 timesteps/s
Performance: 393345.914 tau/day, 910.523 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 60.017 | 60.017 | 60.017 | 0.0 | 77.49
Neigh | 0.47 | 0.47 | 0.47 | 0.0 | 0.61
Comm | 6.6765 | 6.6765 | 6.6765 | 0.0 | 8.62
Output | 0.24799 | 0.24799 | 0.24799 | 0.0 | 0.32
Modify | 8.8677 | 8.8677 | 8.8677 | 0.0 | 11.45
Other | | 1.17 | | | 1.51
Pair | 44.691 | 44.691 | 44.691 | 0.0 | 81.38
Neigh | 0.21653 | 0.21653 | 0.21653 | 0.0 | 0.39
Comm | 0.75388 | 0.75388 | 0.75388 | 0.0 | 1.37
Output | 0.0011999 | 0.0011999 | 0.0011999 | 0.0 | 0.00
Modify | 8.4718 | 8.4718 | 8.4718 | 0.0 | 15.43
Other | | 0.7794 | | | 1.42
Nlocal: 3290.00 ave 3290 max 3290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6295.00 ave 6295 max 6295 min
Nghost: 525.000 ave 525 max 525 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 53729.0 ave 53729 max 53729 min
Neighs: 26732.0 ave 26732 max 26732 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 53729
Ave neighs/atom = 16.331003
Neighbor list builds = 348
Total # of neighbors = 26732
Ave neighs/atom = 8.1252280
Neighbor list builds = 342
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:17
Total wall time: 0:00:54

150
examples/multi/log.30Nov20.granular.intel.4
View File

@ -1,5 +1,5 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
@ -52,8 +52,8 @@ velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi #multi/old
neigh_modify delay 0
comm_modify mode multi vel yes multi/reduce
neigh_modify delay 0 collection/interval 2 1 20
comm_modify mode multi vel yes reduce/multi #multi/old
# colloid potential
@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix 2 all enforce2d
fix 3 all deform 1 xy erate 1e-3
dump 1 all custom 1000 dump.granular id x y z radius
#dump 1 all custom 1000 dump.granular id x y z radius
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
@ -90,86 +90,86 @@ Neighbor list info ...
pair build: half/size/multi/newton/tri
stencil: half/multi/2d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 11.33 | 11.33 | 11.33 Mbytes
Per MPI rank memory allocation (min/avg/max) = 10.09 | 10.10 | 10.10 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395623 0.66837658 7200
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
6000 0.025856 0 0.025848141 0.021241317 7603.5534
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
9000 0.01637016 0 0.016365184 0.020261904 6515.3445
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
11000 0.014156553 0 0.01415225 0.021324818 5815.4665
12000 0.013725412 0 0.01372124 0.021159958 5483.6304
13000 0.013215733 0 0.013211716 0.021685624 5165.4758
14000 0.012398179 0 0.012394411 0.024155572 4862.8657
15000 0.01184269 0 0.01183909 0.028504106 4577.901
16000 0.01143291 0 0.011429435 0.033564204 4309.88
17000 0.011166204 0 0.01116281 0.040588854 4058.9972
18000 0.011000875 0 0.010997532 0.048998904 3825.1569
19000 0.010225905 0 0.010222797 0.063669586 3607.6622
20000 0.0091390249 0 0.0091362471 0.088165396 3408.567
21000 0.0077382016 0 0.0077358496 0.11770473 3227.6936
22000 0.0060173113 0 0.0060154823 0.15261992 3064.3873
23000 0.0046667554 0 0.004665337 0.19453813 2917.9782
24000 0.0040425764 0 0.0040413476 0.24145834 2788.3897
25000 0.0031933187 0 0.0031923481 0.28989732 2674.5164
26000 0.0021139018 0 0.0021132592 0.33598721 2574.9313
27000 0.0017005052 0 0.0016999884 0.37665029 2487.1628
28000 0.001443434 0 0.0014429952 0.41572112 2409.3271
29000 0.00089885805 0 0.00089858484 0.45343123 2340.2314
30000 0.00048558336 0 0.00048543577 0.49175966 2279.2156
31000 0.00058132898 0 0.00058115228 0.53236819 2226.2347
32000 0.00057751441 0 0.00057733887 0.56915062 2181.2736
33000 0.00044720497 0 0.00044706904 0.59696122 2142.5709
34000 0.00060927898 0 0.00060909379 0.61734988 2107.128
35000 0.00077422577 0 0.00077399045 0.63696024 2072.6004
36000 0.00055753008 0 0.00055736062 0.65981839 2038.8237
37000 0.0003140158 0 0.00031392035 0.69018918 2007.323
38000 0.00034970199 0 0.0003495957 0.72155094 1980.1702
39000 0.00041435514 0 0.00041422919 0.7468053 1957.3837
40000 0.00037229543 0 0.00037218227 0.76581519 1936.8032
41000 0.00031027679 0 0.00031018248 0.78321128 1916.1103
42000 0.00026621832 0 0.00026613741 0.80267694 1894.4646
43000 0.00020544063 0 0.00020537818 0.82714181 1872.768
44000 0.00015635243 0 0.00015630491 0.85496512 1853.0303
45000 0.00014985611 0 0.00014981056 0.87924561 1836.4779
46000 0.00015645346 0 0.00015640591 0.89896131 1822.2004
47000 0.00016007816 0 0.00016002951 0.91662026 1808.4601
48000 0.00017439363 0 0.00017434063 0.93565314 1794.1244
49000 0.00018647711 0 0.00018642043 0.95733125 1779.401
50000 0.00018463414 0 0.00018457802 0.96449755 1765.1506
Loop time of 22.3987 on 4 procs for 50000 steps with 3290 atoms
1000 0.32605303 0 0.32595393 0.17341558 7862.5037
2000 0.12631567 0 0.12627728 0.069188881 8216.7174
3000 0.069373812 0 0.069352726 0.040740832 8344.2982
4000 0.045084633 0 0.045070929 0.029328609 8239.3656
5000 0.032681746 0 0.032671813 0.025416741 7943.7831
6000 0.026301239 0 0.026293245 0.021418793 7617.8426
7000 0.021666723 0 0.021660138 0.018961011 7255.9338
8000 0.018141337 0 0.018135823 0.019306113 6887.4963
9000 0.015922309 0 0.015917469 0.020033398 6524.016
10000 0.014744547 0 0.014740066 0.020959503 6168.1945
11000 0.013872852 0 0.013868636 0.021708943 5823.3153
12000 0.013321594 0 0.013317545 0.02332141 5491.4979
13000 0.01269964 0 0.012695779 0.024796428 5174.6263
14000 0.01227055 0 0.012266821 0.027785072 4873.4516
15000 0.012120508 0 0.012116824 0.029656636 4588.8603
16000 0.011612027 0 0.011608498 0.034695109 4320.4674
17000 0.011216697 0 0.011213288 0.042746966 4069.4275
18000 0.010950166 0 0.010946838 0.053528994 3835.5439
19000 0.010887635 0 0.010884325 0.069684492 3619.562
20000 0.010563449 0 0.010560238 0.08654561 3420.2636
21000 0.0092336323 0 0.0092308257 0.11286068 3237.1408
22000 0.006929086 0 0.0069269799 0.15018917 3072.0438
23000 0.0052239156 0 0.0052223277 0.19067193 2924.441
24000 0.0044210081 0 0.0044196644 0.23908686 2793.2426
25000 0.0034916086 0 0.0034905473 0.29112824 2678.7912
26000 0.002549072 0 0.0025482972 0.33567824 2579.3738
27000 0.0020890726 0 0.0020884377 0.37328514 2491.0502
28000 0.001772982 0 0.0017724431 0.41079958 2411.9111
29000 0.001127719 0 0.0011273762 0.44752241 2341.1888
30000 0.00053266563 0 0.00053250373 0.48791815 2278.5611
31000 0.00050278646 0 0.00050263364 0.52896525 2224.5328
32000 0.00051880956 0 0.00051865187 0.56884574 2178.6674
33000 0.00054908167 0 0.00054891477 0.6016387 2140.3696
34000 0.00075213884 0 0.00075191023 0.62070188 2106.6504
35000 0.00081295162 0 0.00081270452 0.63492031 2073.0077
36000 0.00056699821 0 0.00056682587 0.65608409 2038.3251
37000 0.0003540723 0 0.00035396468 0.68803919 2005.497
38000 0.00031139738 0 0.00031130273 0.72103717 1977.7345
39000 0.00034087822 0 0.00034077461 0.74697975 1954.8979
40000 0.00035452426 0 0.0003544165 0.76682035 1934.5695
41000 0.00030882258 0 0.00030872871 0.78390763 1914.3326
42000 0.00025492799 0 0.00025485051 0.80439795 1893.1474
43000 0.00021545017 0 0.00021538468 0.82803644 1872.073
44000 0.00017293257 0 0.00017288 0.85436769 1852.6548
45000 0.00014097725 0 0.0001409344 0.8796181 1836.0087
46000 0.0001139199 0 0.00011388527 0.90006173 1821.7977
47000 0.00012678598 0 0.00012674745 0.90876359 1808.4913
48000 0.00013796773 0 0.00013792579 0.93661523 1793.8082
49000 0.00014723144 0 0.00014718669 0.95869417 1779.1875
50000 0.00013610653 0 0.00013606516 0.97777198 1765.3247
Loop time of 17.7405 on 4 procs for 50000 steps with 3290 atoms
Performance: 964340.770 tau/day, 2232.270 timesteps/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 1217551.996 tau/day, 2818.407 timesteps/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.5158 | 12.318 | 15.836 | 92.1 | 54.99
Neigh | 0.092527 | 0.11392 | 0.13595 | 5.6 | 0.51
Comm | 2.7127 | 6.2337 | 10.096 | 131.0 | 27.83
Output | 0.088027 | 0.088284 | 0.088812 | 0.1 | 0.39
Modify | 2.8544 | 3.0435 | 3.2034 | 9.2 | 13.59
Other | | 0.6017 | | | 2.69
Pair | 6.6629 | 9.6168 | 12.444 | 76.6 | 54.21
Neigh | 0.049771 | 0.055182 | 0.06133 | 2.0 | 0.31
Comm | 1.7883 | 4.6306 | 7.6179 | 111.5 | 26.10
Output | 0.00085342 | 0.0010606 | 0.0015425 | 0.9 | 0.01
Modify | 2.7244 | 2.895 | 3.0436 | 8.2 | 16.32
Other | | 0.5419 | | | 3.05
Nlocal: 822.500 ave 859 max 785 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 395.750 ave 424 max 368 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 13439.5 ave 14346 max 12017 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nlocal: 822.500 ave 897 max 779 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 190.500 ave 211 max 179 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 6665.75 ave 7329 max 6104 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 53758
Ave neighs/atom = 16.339818
Neighbor list builds = 348
Total # of neighbors = 26663
Ave neighs/atom = 8.1042553
Neighbor list builds = 342
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:22
Total wall time: 0:00:17

32
examples/multi/log.30Nov20.granular.old.intel.1
View File

@ -1,5 +1,5 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
@ -51,9 +51,9 @@ velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi/old
neigh_modify delay 0
comm_modify mode multi vel yes
neighbor 1 multi/old #multi
neigh_modify delay 0 #collection/interval 2 1 20
comm_modify mode multi/old vel yes #reduce/multi
# colloid potential
@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix 2 all enforce2d
fix 3 all deform 1 xy erate 1e-3
dump 1 all custom 1000 dump.granular id x y z radius
#dump 1 all custom 1000 dump.granular id x y z radius
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
@ -90,7 +90,7 @@ Neighbor list info ...
pair build: half/size/multi/old/newton/tri
stencil: half/multi/old/2d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.75 | 11.75 Mbytes
Per MPI rank memory allocation (min/avg/max) = 10.38 | 10.38 | 10.38 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395623 0.66837658 7200
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
@ -143,20 +143,20 @@ Step Temp E_pair TotEng Press Volume
48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043
49000 0.00018879338 0 0.000188736 0.95775166 1780.0323
50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442
Loop time of 80.8597 on 1 procs for 50000 steps with 3290 atoms
Loop time of 74.6636 on 1 procs for 50000 steps with 3290 atoms
Performance: 267129.375 tau/day, 618.355 timesteps/s
Performance: 289297.713 tau/day, 669.671 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 61.524 | 61.524 | 61.524 | 0.0 | 76.09
Neigh | 2.2021 | 2.2021 | 2.2021 | 0.0 | 2.72
Comm | 6.748 | 6.748 | 6.748 | 0.0 | 8.35
Output | 0.25904 | 0.25904 | 0.25904 | 0.0 | 0.32
Modify | 8.9408 | 8.9408 | 8.9408 | 0.0 | 11.06
Other | | 1.186 | | | 1.47
Pair | 56.696 | 56.696 | 56.696 | 0.0 | 75.93
Neigh | 2.2232 | 2.2232 | 2.2232 | 0.0 | 2.98
Comm | 6.1867 | 6.1867 | 6.1867 | 0.0 | 8.29
Output | 0.0012016 | 0.0012016 | 0.0012016 | 0.0 | 0.00
Modify | 8.432 | 8.432 | 8.432 | 0.0 | 11.29
Other | | 1.125 | | | 1.51
Nlocal: 3290.00 ave 3290 max 3290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -172,4 +172,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:20
Total wall time: 0:01:14

34
examples/multi/log.30Nov20.granular.old.intel.4
View File

@ -1,5 +1,5 @@
LAMMPS (30 Nov 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95)
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
@ -15,7 +15,7 @@ Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.8528
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 3600 atoms
create_atoms CPU = 0.001 seconds
create_atoms CPU = 0.063 seconds
change_box all triclinic
Changing box ...
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
@ -51,9 +51,9 @@ velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi/old
neigh_modify delay 0
comm_modify mode multi vel yes #multi/reduce
neighbor 1 multi/old #multi
neigh_modify delay 0 #collection/interval 2 1 20
comm_modify mode multi/old vel yes #reduce/multi
# colloid potential
@ -64,7 +64,7 @@ fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix 2 all enforce2d
fix 3 all deform 1 xy erate 1e-3
dump 1 all custom 1000 dump.granular id x y z radius
#dump 1 all custom 1000 dump.granular id x y z radius
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
@ -90,7 +90,7 @@ Neighbor list info ...
pair build: half/size/multi/old/newton/tri
stencil: half/multi/old/2d/tri
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.48 | 11.48 | 11.49 Mbytes
Per MPI rank memory allocation (min/avg/max) = 10.20 | 10.20 | 10.20 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 0 1.4395623 0.66837658 7200
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
@ -143,20 +143,20 @@ Step Temp E_pair TotEng Press Volume
48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258
49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032
50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534
Loop time of 30.9351 on 4 procs for 50000 steps with 3290 atoms
Loop time of 30.1448 on 4 procs for 50000 steps with 3290 atoms
Performance: 698235.574 tau/day, 1616.286 timesteps/s
89.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 716540.413 tau/day, 1658.658 timesteps/s
90.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.3702 | 12.796 | 16.045 | 84.3 | 41.36
Neigh | 0.43499 | 0.55158 | 0.64861 | 12.8 | 1.78
Comm | 10.183 | 13.476 | 16.961 | 83.7 | 43.56
Output | 0.088474 | 0.088715 | 0.089272 | 0.1 | 0.29
Modify | 3.0446 | 3.1809 | 3.3227 | 7.4 | 10.28
Other | | 0.8418 | | | 2.72
Pair | 8.7565 | 12.704 | 16.036 | 89.8 | 42.14
Neigh | 0.4494 | 0.56436 | 0.66263 | 11.8 | 1.87
Comm | 9.5962 | 12.989 | 17.006 | 90.8 | 43.09
Output | 0.00088467 | 0.0011022 | 0.0015811 | 0.9 | 0.00
Modify | 2.9732 | 3.0944 | 3.2463 | 7.0 | 10.27
Other | | 0.7918 | | | 2.63
Nlocal: 822.500 ave 859 max 785 min
Histogram: 1 0 1 0 0 0 0 0 1 1

191
examples/multi/log.30Nov20.powerlaw.intel.1 Normal file
View File

@ -0,0 +1,191 @@
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
read_data data
Reading data file ...
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
10000 atoms
reading velocities ...
10000 velocities
read_data CPU = 0.027 seconds
change_box all triclinic
Changing box ...
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200
comm_modify mode multi vel yes reduce/multi
# granular potential
pair_style granular
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
# fixes
fix 1 all nve/sphere
fix 2 all enforce2d
fix 3 all deform 1 xy erate 2e-4
# dump 1 all custom 2000 dump.granular id x y z radius
thermo_style custom step temp epair etotal press vol pxy
thermo 1000
timestep 0.005
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 = 164.7888
ghost atom cutoff = 164.7888
binsize = 82.3944, bins = 4 4 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/newton/tri
stencil: half/multi/2d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 14.76 | 14.76 | 14.76 Mbytes
Step Temp E_pair TotEng Press Volume Pxy
0 0.00014649953 0 0.00014648488 0.027643657 103595.49 -0.0014952693
1000 0.00014726802 0 0.00014725329 0.029388139 103595.49 -0.00172238
2000 0.00014880425 0 0.00014878937 0.029608995 103595.49 -0.0023614491
3000 0.00015154766 0 0.0001515325 0.029668747 103595.49 -0.0029243775
4000 0.00015547813 0 0.00015546258 0.029662951 103595.49 -0.0034433688
5000 0.00015919808 0 0.00015918216 0.02988062 103595.49 -0.0037443111
6000 0.00016272902 0 0.00016271275 0.029776943 103595.49 -0.0042445445
7000 0.00016666322 0 0.00016664655 0.029919286 103595.49 -0.0045231987
8000 0.00017137531 0 0.00017135817 0.029849078 103595.49 -0.0049023441
9000 0.00017774522 0 0.00017772744 0.029925275 103595.49 -0.0051437804
10000 0.00018294048 0 0.00018292219 0.030166956 103595.49 -0.0052769381
11000 0.00019030719 0 0.00019028816 0.02988594 103595.49 -0.0058095975
12000 0.00019806568 0 0.00019804587 0.029852302 103595.49 -0.0060925449
13000 0.00020800749 0 0.00020798669 0.029927995 103595.49 -0.0062667347
14000 0.00021854888 0 0.00021852703 0.029984135 103595.49 -0.0064949797
15000 0.00022975749 0 0.00022973451 0.030063358 103595.49 -0.0065788835
16000 0.00024074076 0 0.00024071668 0.03006058 103595.49 -0.006757928
17000 0.00025363768 0 0.00025361232 0.030138053 103595.49 -0.0068153904
18000 0.00026618156 0 0.00026615494 0.030621109 103595.49 -0.0067026865
19000 0.00028000661 0 0.00027997861 0.030520699 103595.49 -0.0067126187
20000 0.00029472369 0 0.00029469422 0.030182866 103595.49 -0.0071232374
21000 0.00031065822 0 0.00031062716 0.030417926 103595.49 -0.0070815254
22000 0.00032789694 0 0.00032786415 0.030434044 103595.49 -0.007044194
23000 0.00034491703 0 0.00034488253 0.031195478 103595.49 -0.006895101
24000 0.00036262497 0 0.00036258871 0.030348688 103595.49 -0.0073503964
25000 0.00038232332 0 0.00038228509 0.030429549 103595.49 -0.0073043833
26000 0.00040292952 0 0.00040288922 0.030277517 103595.49 -0.0074475354
27000 0.00042260162 0 0.00042255936 0.030270875 103595.49 -0.0074037511
28000 0.00044296255 0 0.00044291826 0.030568983 103595.49 -0.0070827585
29000 0.00046164594 0 0.00046159978 0.030392129 103595.49 -0.0070495682
30000 0.00048018966 0 0.00048014164 0.03027035 103595.49 -0.0071339757
31000 0.00049904958 0 0.00049899968 0.030278024 103595.49 -0.0070690708
32000 0.00051586592 0 0.00051581433 0.030105498 103595.49 -0.007134143
33000 0.000533257 0 0.00053320367 0.029788452 103595.49 -0.0072245811
34000 0.00054849405 0 0.0005484392 0.029873916 103595.49 -0.0069597013
35000 0.00056356221 0 0.00056350586 0.029706011 103595.49 -0.00704387
36000 0.00057701153 0 0.00057695383 0.029584377 103595.49 -0.006959137
37000 0.00058975804 0 0.00058969906 0.029510998 103595.49 -0.0069205813
38000 0.00060106815 0 0.00060100804 0.029866588 103595.49 -0.006493655
39000 0.00061178223 0 0.00061172105 0.0294686 103595.49 -0.0066809721
40000 0.00062087616 0 0.00062081407 0.029305512 103595.49 -0.0067040127
41000 0.00062938061 0 0.00062931767 0.029313523 103595.49 -0.0065943738
42000 0.0006366437 0 0.00063658004 0.029294719 103595.49 -0.0065039414
43000 0.00064403805 0 0.00064397364 0.029169615 103595.49 -0.0065453715
44000 0.00064990286 0 0.00064983787 0.029173689 103595.49 -0.0064757302
45000 0.00065485285 0 0.00065478736 0.02911295 103595.49 -0.0065336599
46000 0.00065918851 0 0.00065912259 0.029664657 103595.49 -0.0060618092
47000 0.00066143867 0 0.00066137253 0.029672077 103595.49 -0.0061605571
48000 0.00066260774 0 0.00066254148 0.029356515 103595.49 -0.0063944326
49000 0.0006641111 0 0.00066404469 0.029771162 103595.49 -0.0061440485
50000 0.00066562386 0 0.0006655573 0.02944773 103595.49 -0.0063912951
51000 0.00066744319 0 0.00066737645 0.029507067 103595.49 -0.00636767
52000 0.00066927675 0 0.00066920982 0.029773443 103595.49 -0.0062192673
53000 0.00066999455 0 0.00066992755 0.029626747 103595.49 -0.0062819185
54000 0.00067204697 0 0.00067197976 0.029608834 103595.49 -0.0063047897
55000 0.00067089926 0 0.00067083217 0.029778336 103595.49 -0.006198876
56000 0.00067044673 0 0.00067037969 0.029707087 103595.49 -0.0062920606
57000 0.00066987451 0 0.00066980752 0.029751879 103595.49 -0.0062887511
58000 0.00066781462 0 0.00066774784 0.029673932 103595.49 -0.0063301658
59000 0.00065347402 0 0.00065340867 0.029540521 103595.49 -0.0064527808
60000 0.00065304518 0 0.00065297988 0.029801357 103595.49 -0.0062633754
61000 0.00065183192 0 0.00065176673 0.029786145 103595.49 -0.0063152956
62000 0.00065242331 0 0.00065235807 0.030461931 103595.49 -0.0060591261
63000 0.00065491938 0 0.00065485389 0.029715839 103595.49 -0.0065344894
64000 0.00065769719 0 0.00065763142 0.02977148 103595.49 -0.0065105553
65000 0.00066125407 0 0.00066118795 0.029534462 103595.49 -0.0066901883
66000 0.00066433913 0 0.0006642727 0.029949304 103595.49 -0.0064367129
67000 0.00066819344 0 0.00066812662 0.029629692 103595.49 -0.0067136218
68000 0.00067300953 0 0.00067294223 0.029793673 103595.49 -0.0065898421
69000 0.00067875538 0 0.0006786875 0.029651968 103595.49 -0.0067198512
70000 0.00068416104 0 0.00068409262 0.030125821 103595.49 -0.0063225262
71000 0.00068728347 0 0.00068721475 0.02958142 103595.49 -0.0066417995
72000 0.00068926082 0 0.00068919189 0.02976018 103595.49 -0.0063898599
73000 0.00068953168 0 0.00068946272 0.029574927 103595.49 -0.0065193167
74000 0.00069104787 0 0.00069097876 0.030209247 103595.49 -0.0060666707
75000 0.00069606779 0 0.00069599818 0.029636657 103595.49 -0.006387635
76000 0.00070399158 0 0.00070392118 0.029585803 103595.49 -0.0063291939
77000 0.00070284473 0 0.00070277445 0.029936591 103595.49 -0.0060359763
78000 0.00070619015 0 0.00070611953 0.029554333 103595.49 -0.0062453302
79000 0.00070892936 0 0.00070885847 0.029853506 103595.49 -0.0060833753
80000 0.00071125368 0 0.00071118255 0.029625268 103595.49 -0.0062046031
81000 0.00070944317 0 0.00070937223 0.029629542 103595.49 -0.0062343125
82000 0.00070892851 0 0.00070885762 0.029664456 103595.49 -0.006250692
83000 0.00070946812 0 0.00070939718 0.029964177 103595.49 -0.006159583
84000 0.00071198659 0 0.00071191539 0.029813631 103595.49 -0.0062607732
85000 0.00071266579 0 0.00071259453 0.029645729 103595.49 -0.0064004319
86000 0.00071461592 0 0.00071454446 0.029700002 103595.49 -0.0063398759
87000 0.00071781454 0 0.00071774276 0.029748726 103595.49 -0.0063600357
88000 0.00072016268 0 0.00072009067 0.029772487 103595.49 -0.0063655529
89000 0.00072272254 0 0.00072265027 0.030006837 103595.49 -0.0063122612
90000 0.00072122914 0 0.00072115701 0.029982109 103595.49 -0.006439831
91000 0.00072443479 0 0.00072436235 0.029830121 103595.49 -0.0065202831
92000 0.00072738733 0 0.00072731459 0.030194727 103595.49 -0.0062808688
93000 0.00072899838 0 0.00072892548 0.030175295 103595.49 -0.0062914883
94000 0.00072984304 0 0.00072977006 0.029844017 103595.49 -0.0064737335
95000 0.00073206475 0 0.00073199154 0.029798899 103595.49 -0.0064644006
96000 0.00073374806 0 0.00073367468 0.030226823 103595.49 -0.0061626549
97000 0.00073388886 0 0.00073381547 0.029993629 103595.49 -0.0063710254
98000 0.00073534207 0 0.00073526854 0.030245848 103595.49 -0.0063407392
99000 0.00073805531 0 0.0007379815 0.030287955 103595.49 -0.0063646707
100000 0.0007385798 0 0.00073850594 0.030172948 103595.49 -0.0064654963
Loop time of 233.709 on 1 procs for 100000 steps with 10000 atoms
Performance: 184845.371 tau/day, 427.883 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 193.18 | 193.18 | 193.18 | 0.0 | 82.66
Neigh | 1.1138 | 1.1138 | 1.1138 | 0.0 | 0.48
Comm | 2.3652 | 2.3652 | 2.3652 | 0.0 | 1.01
Output | 0.0092981 | 0.0092981 | 0.0092981 | 0.0 | 0.00
Modify | 32.407 | 32.407 | 32.407 | 0.0 | 13.87
Other | | 4.628 | | | 1.98
Nlocal: 10000.0 ave 10000 max 10000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 446.000 ave 446 max 446 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 34464.0 ave 34464 max 34464 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 34464
Ave neighs/atom = 3.4464000
Neighbor list builds = 153
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:03:53

191
examples/multi/log.30Nov20.powerlaw.intel.4 Normal file
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@ -0,0 +1,191 @@
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
read_data data
Reading data file ...
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
2 by 2 by 1 MPI processor grid
reading atoms ...
10000 atoms
reading velocities ...
10000 velocities
read_data CPU = 0.024 seconds
change_box all triclinic
Changing box ...
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200
comm_modify mode multi vel yes reduce/multi
# granular potential
pair_style granular
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
# fixes
fix 1 all nve/sphere
fix 2 all enforce2d
fix 3 all deform 1 xy erate 2e-4
# dump 1 all custom 2000 dump.granular id x y z radius
thermo_style custom step temp epair etotal press vol pxy
thermo 1000
timestep 0.005
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 = 164.7888
ghost atom cutoff = 164.7888
binsize = 82.3944, bins = 4 4 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair granular, perpetual
attributes: half, newton on, size, history
pair build: half/size/multi/newton/tri
stencil: half/multi/2d/tri
bin: multi
Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.67 | 12.68 Mbytes
Step Temp E_pair TotEng Press Volume Pxy
0 0.00014649953 0 0.00014648488 0.027643657 103595.49 -0.0014952693
1000 0.00014726802 0 0.00014725329 0.029388139 103595.49 -0.00172238
2000 0.00014880425 0 0.00014878937 0.029608995 103595.49 -0.0023614491
3000 0.00015154766 0 0.0001515325 0.029668747 103595.49 -0.0029243775
4000 0.00015547813 0 0.00015546258 0.029662951 103595.49 -0.0034433688
5000 0.00015919808 0 0.00015918216 0.02988062 103595.49 -0.0037443111
6000 0.00016272902 0 0.00016271275 0.029776943 103595.49 -0.0042445445
7000 0.00016666322 0 0.00016664655 0.029919286 103595.49 -0.0045231987
8000 0.00017137531 0 0.00017135817 0.029849078 103595.49 -0.0049023441
9000 0.00017774522 0 0.00017772744 0.029925275 103595.49 -0.0051437804
10000 0.00018294048 0 0.00018292219 0.030166956 103595.49 -0.0052769381
11000 0.00019030719 0 0.00019028816 0.02988594 103595.49 -0.0058095975
12000 0.00019806568 0 0.00019804587 0.029852302 103595.49 -0.0060925449
13000 0.00020800749 0 0.00020798669 0.029927995 103595.49 -0.0062667347
14000 0.00021854888 0 0.00021852703 0.029984135 103595.49 -0.0064949797
15000 0.00022975749 0 0.00022973451 0.030063358 103595.49 -0.0065788835
16000 0.00024074076 0 0.00024071668 0.03006058 103595.49 -0.006757928
17000 0.00025363768 0 0.00025361232 0.030138053 103595.49 -0.0068153904
18000 0.00026618156 0 0.00026615494 0.030621109 103595.49 -0.0067026865
19000 0.00028000661 0 0.00027997861 0.030520699 103595.49 -0.0067126187
20000 0.00029472369 0 0.00029469422 0.030182866 103595.49 -0.0071232374
21000 0.00031065822 0 0.00031062716 0.030417926 103595.49 -0.0070815254
22000 0.00032789694 0 0.00032786415 0.030434044 103595.49 -0.007044194
23000 0.00034491703 0 0.00034488253 0.031195478 103595.49 -0.006895101
24000 0.00036262497 0 0.00036258871 0.030348688 103595.49 -0.0073503964
25000 0.00038232332 0 0.00038228509 0.030429549 103595.49 -0.0073043833
26000 0.00040292952 0 0.00040288922 0.030277517 103595.49 -0.0074475354
27000 0.00042260162 0 0.00042255936 0.030270875 103595.49 -0.0074037511
28000 0.00044296255 0 0.00044291826 0.030568983 103595.49 -0.0070827585
29000 0.00046164594 0 0.00046159978 0.030392129 103595.49 -0.0070495682
30000 0.00048018966 0 0.00048014164 0.03027035 103595.49 -0.0071339757
31000 0.00049904958 0 0.00049899968 0.030278024 103595.49 -0.0070690709
32000 0.00051586592 0 0.00051581433 0.030105498 103595.49 -0.007134143
33000 0.000533257 0 0.00053320367 0.029788452 103595.49 -0.0072245811
34000 0.00054849405 0 0.0005484392 0.029873916 103595.49 -0.0069597013
35000 0.00056356221 0 0.00056350586 0.029706011 103595.49 -0.00704387
36000 0.00057701153 0 0.00057695383 0.029584377 103595.49 -0.006959137
37000 0.00058975804 0 0.00058969906 0.029510998 103595.49 -0.0069205813
38000 0.00060106815 0 0.00060100804 0.029866588 103595.49 -0.006493655
39000 0.0006117822 0 0.00061172102 0.029468049 103595.49 -0.0066810094
40000 0.00062087615 0 0.00062081406 0.02930398 103595.49 -0.0067044715
41000 0.00062938044 0 0.0006293175 0.029314381 103595.49 -0.0065941361
42000 0.00063664289 0 0.00063657923 0.029294787 103595.49 -0.0065039202
43000 0.00064404027 0 0.00064397587 0.029224232 103595.49 -0.0065035306
44000 0.00064990723 0 0.00064984224 0.029142324 103595.49 -0.0065034116
45000 0.00065485343 0 0.00065478795 0.029121173 103595.49 -0.0065214973
46000 0.00065918796 0 0.00065912204 0.029651005 103595.49 -0.0060509446
47000 0.00066144517 0 0.00066137903 0.029234729 103595.49 -0.0064672274
48000 0.00066261185 0 0.00066254559 0.029229845 103595.49 -0.0065053596
49000 0.00066414215 0 0.00066407574 0.029562705 103595.49 -0.0062441985
50000 0.0006656453 0 0.00066557874 0.029728174 103595.49 -0.0062147051
51000 0.00066738973 0 0.00066732299 0.029928822 103595.49 -0.0060118516
52000 0.00066929756 0 0.00066923063 0.029886551 103595.49 -0.0061374389
53000 0.00067003172 0 0.00066996472 0.029567015 103595.49 -0.0063482821
54000 0.00067198511 0 0.00067191791 0.029833698 103595.49 -0.0061879264
55000 0.00067091193 0 0.00067084484 0.029711467 103595.49 -0.006233379
56000 0.00067046578 0 0.00067039873 0.030035238 103595.49 -0.0060959401
57000 0.00066988234 0 0.00066981535 0.030055225 103595.49 -0.0060935858
58000 0.00066786916 0 0.00066780238 0.029282172 103595.49 -0.0066021495
59000 0.00065350543 0 0.00065344008 0.029343567 103595.49 -0.0065364678
60000 0.0006530936 0 0.0006530283 0.02940862 103595.49 -0.0065558353
61000 0.00065187483 0 0.00065180964 0.02929946 103595.49 -0.0066840857
62000 0.00065245428 0 0.00065238904 0.030084765 103595.49 -0.0063065368
63000 0.0006549311 0 0.00065486561 0.029725525 103595.49 -0.0065305296
64000 0.00065774123 0 0.00065767546 0.029562667 103595.49 -0.0066194535
65000 0.00066126698 0 0.00066120085 0.029524987 103595.49 -0.0067008104
66000 0.0006643846 0 0.00066431816 0.029589813 103595.49 -0.0066689844
67000 0.00066823073 0 0.00066816391 0.029613668 103595.49 -0.0067372273
68000 0.00067301835 0 0.00067295104 0.029568568 103595.49 -0.0067808311
69000 0.00067876831 0 0.00067870043 0.029948152 103595.49 -0.0065107568
70000 0.00068419902 0 0.0006841306 0.029572996 103595.49 -0.0067066975
71000 0.00068730343 0 0.0006872347 0.029970497 103595.49 -0.0063646358
72000 0.00068930016 0 0.00068923123 0.029602044 103595.49 -0.0064953597
73000 0.00068953092 0 0.00068946197 0.029671751 103595.49 -0.0064422021
74000 0.00069106659 0 0.00069099748 0.029918321 103595.49 -0.0062634576
75000 0.00069609345 0 0.00069602384 0.029666179 103595.49 -0.0063552778
76000 0.00070399534 0 0.00070392494 0.029599912 103595.49 -0.0063251165
77000 0.00070284669 0 0.00070277641 0.029658992 103595.49 -0.0061988379
78000 0.00070619715 0 0.00070612653 0.029578035 103595.49 -0.0062153063
79000 0.00070895477 0 0.00070888388 0.029617734 103595.49 -0.0062090554
80000 0.00071127424 0 0.00071120311 0.029539347 103595.49 -0.0062883775
81000 0.00070945256 0 0.00070938162 0.029515493 103595.49 -0.0063350852
82000 0.00070895167 0 0.00070888078 0.029537389 103595.49 -0.0063819074
83000 0.00070948858 0 0.00070941763 0.02998589 103595.49 -0.0061284544
84000 0.00071197606 0 0.00071190486 0.030005566 103595.49 -0.0061829926
85000 0.00071266684 0 0.00071259557 0.029675137 103595.49 -0.0063804963
86000 0.00071465352 0 0.00071458205 0.029762675 103595.49 -0.0062924985
87000 0.00071779428 0 0.0007177225 0.029712831 103595.49 -0.0063812951
88000 0.00072016431 0 0.0007200923 0.029932619 103595.49 -0.0063145709
89000 0.00072271727 0 0.000722645 0.029818327 103595.49 -0.0064025621
90000 0.00072122834 0 0.00072115622 0.029829495 103595.49 -0.0065870713
91000 0.00072441206 0 0.00072433962 0.029939415 103595.49 -0.0064224045
92000 0.00072735846 0 0.00072728572 0.02991447 103595.49 -0.0064256019
93000 0.00072898882 0 0.00072891592 0.030230938 103595.49 -0.0061929729
94000 0.00072985209 0 0.00072977911 0.030145973 103595.49 -0.0062797016
95000 0.0007320685 0 0.0007319953 0.030113809 103595.49 -0.0062765142
96000 0.0007337917 0 0.00073371832 0.029919191 103595.49 -0.0063350801
97000 0.00073385417 0 0.00073378078 0.030184207 103595.49 -0.0062855982
98000 0.00073531629 0 0.00073524276 0.029974905 103595.49 -0.0064826333
99000 0.0007380024 0 0.0007379286 0.030678507 103595.49 -0.0060867823
100000 0.00073858055 0 0.00073850669 0.030048209 103595.49 -0.0065772058
Loop time of 77.8133 on 4 procs for 100000 steps with 10000 atoms
Performance: 555175.163 tau/day, 1285.128 timesteps/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 28.939 | 48.992 | 61.808 | 189.4 | 62.96
Neigh | 0.22765 | 0.31872 | 0.38751 | 10.9 | 0.41
Comm | 3.53 | 16.362 | 36.515 | 328.8 | 21.03
Output | 0.0046275 | 0.0064601 | 0.008626 | 1.8 | 0.01
Modify | 5.0862 | 8.3128 | 10.255 | 74.1 | 10.68
Other | | 3.821 | | | 4.91
Nlocal: 2500.00 ave 3016 max 1605 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 221.500 ave 273 max 176 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 8616.00 ave 10377 max 5447 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 34464
Ave neighs/atom = 3.4464000
Neighbor list builds = 153
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:17

5
src/nbin_multi.cpp
View File

@ -232,8 +232,9 @@ void NBinMulti::setup_bins(int /*style*/)
bininvz_multi[n] = 1.0 / binsizez_multi[n];
if (binsize_optimal*bininvx_multi[n] > CUT2BIN_RATIO ||
binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO ||
binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO)
binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO)
error->all(FLERR,"Cannot use neighbor bins - box size << cutoff");
if(dimension == 3 and binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO)
error->all(FLERR,"Cannot use neighbor bins - box size << cutoff");
// mbinlo/hi = lowest and highest global bins my ghost atoms could be in