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update example logs for change in cutoff setting

This commit is contained in:
Axel Kohlmeyer 2024-02-22 13:37:59 -05:00
parent 36fa601fe0
commit 22d0b202c4
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GPG Key ID: D9B44E93BF0C375A
4 changed files with 71 additions and 75 deletions
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35
examples/threebody/log.22Feb24.mos2-bulk.g++.1
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@ -1,5 +1,4 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-70-ge51a65696d-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
using 1 OpenMP thread(s) per MPI task
units metal
@ -40,46 +39,46 @@ run 20
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 20.1
ghost atom cutoff = 20.1
binsize = 10.05, bins = 3 3 2
master list distance cutoff = 13.4
ghost atom cutoff = 13.4
binsize = 6.7, bins = 5 4 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebomos, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.759 | 6.759 | 6.759 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.996 | 4.996 | 4.996 Mbytes
Step Temp Press PotEng KinEng CellGamma Volume
0 0 28799.53 -2061.6112 0 113.40187 5922.4926
10 80.776057 13540.088 -2064.6132 2.9966028 113.40187 5922.4926
20 146.17503 -20669.371 -2067.0428 5.4227518 113.40187 5922.4926
Loop time of 0.173901 on 1 procs for 20 steps with 288 atoms
Loop time of 0.058071 on 1 procs for 20 steps with 288 atoms
Performance: 9.937 ns/day, 2.415 hours/ns, 115.008 timesteps/s, 33.122 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 29.757 ns/day, 0.807 hours/ns, 344.406 timesteps/s, 99.189 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17213 | 0.17213 | 0.17213 | 0.0 | 98.98
Pair | 0.057666 | 0.057666 | 0.057666 | 0.0 | 99.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013913 | 0.0013913 | 0.0013913 | 0.0 | 0.80
Output | 5.0377e-05 | 5.0377e-05 | 5.0377e-05 | 0.0 | 0.03
Modify | 6.9212e-05 | 6.9212e-05 | 6.9212e-05 | 0.0 | 0.04
Other | | 0.000264 | | | 0.15
Comm | 0.00024654 | 0.00024654 | 0.00024654 | 0.0 | 0.42
Output | 2.3975e-05 | 2.3975e-05 | 2.3975e-05 | 0.0 | 0.04
Modify | 3.8394e-05 | 3.8394e-05 | 3.8394e-05 | 0.0 | 0.07
Other | | 9.596e-05 | | | 0.17
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10002 ave 10002 max 10002 min
Nghost: 4285 ave 4285 max 4285 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 477120 ave 477120 max 477120 min
FullNghs: 142848 ave 142848 max 142848 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 477120
Ave neighs/atom = 1656.6667
Total # of neighbors = 142848
Ave neighs/atom = 496
Neighbor list builds = 0
Dangerous builds = 0

37
examples/threebody/log.22Feb24.mos2-bulk.g++.4
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@ -1,5 +1,4 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-70-ge51a65696d-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
using 1 OpenMP thread(s) per MPI task
units metal
@ -23,7 +22,7 @@ Created triclinic box = (0 0 0) to (19.147099 22.121185 13.982768) with tilt (-9
create_atoms 2 box basis 1 1 basis 2 1 basis 3 2 basis 4 2 basis 5 2 basis 6 2
Created 288 atoms
using lattice units in triclinic box = (0 0 0) to (19.147099 22.121185 13.982768) with tilt (-9.5735495 0 0)
create_atoms CPU = 0.001 seconds
create_atoms CPU = 0.000 seconds
mass 1 95.95 #Mo
mass 2 32.065 #S
@ -40,46 +39,46 @@ run 20
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 20.1
ghost atom cutoff = 20.1
binsize = 10.05, bins = 3 3 2
master list distance cutoff = 13.4
ghost atom cutoff = 13.4
binsize = 6.7, bins = 5 4 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebomos, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.977 | 4.978 | 4.978 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.15 | 4.151 | 4.151 Mbytes
Step Temp Press PotEng KinEng CellGamma Volume
0 0 28799.53 -2061.6112 0 113.40187 5922.4926
10 80.776057 13540.088 -2064.6132 2.9966028 113.40187 5922.4926
20 146.17503 -20669.371 -2067.0428 5.4227518 113.40187 5922.4926
Loop time of 0.0644788 on 4 procs for 20 steps with 288 atoms
Loop time of 0.0219485 on 4 procs for 20 steps with 288 atoms
Performance: 26.799 ns/day, 0.896 hours/ns, 310.179 timesteps/s, 89.332 katom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 78.730 ns/day, 0.305 hours/ns, 911.225 timesteps/s, 262.433 katom-step/s
96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.057739 | 0.059918 | 0.06231 | 0.7 | 92.93
Pair | 0.018118 | 0.019372 | 0.020087 | 0.5 | 88.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0018848 | 0.0042821 | 0.0064683 | 2.6 | 6.64
Output | 3.7548e-05 | 4.1425e-05 | 5.1594e-05 | 0.0 | 0.06
Modify | 3.4882e-05 | 3.5821e-05 | 3.6589e-05 | 0.0 | 0.06
Other | | 0.0002014 | | | 0.31
Comm | 0.0015635 | 0.0023195 | 0.0035967 | 1.6 | 10.57
Output | 2.5017e-05 | 4.6834e-05 | 0.00010543 | 0.0 | 0.21
Modify | 1.3954e-05 | 1.423e-05 | 1.4594e-05 | 0.0 | 0.06
Other | | 0.0001957 | | | 0.89
Nlocal: 72 ave 72 max 72 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 7113.5 ave 7114 max 7113 min
Nghost: 2771.5 ave 2775 max 2768 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 119280 ave 119280 max 119280 min
FullNghs: 35712 ave 35712 max 35712 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 477120
Ave neighs/atom = 1656.6667
Total # of neighbors = 142848
Ave neighs/atom = 496
Neighbor list builds = 0
Dangerous builds = 0

37
examples/threebody/log.22Feb24.mos2.rebomos.g++.1
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@ -1,5 +1,4 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-70-ge51a65696d-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
using 1 OpenMP thread(s) per MPI task
# monolayer MoS2
units metal
@ -15,7 +14,7 @@ WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain
1 by 1 by 1 MPI processor grid
reading atoms ...
768 atoms
read_data CPU = 0.003 seconds
read_data CPU = 0.002 seconds
mass * 32.065 # mass of sulphur atom , uint: a.u.=1.66X10^(-27)kg
mass 1 95.94 # mass of molebdenum atom , uint: a.u.=1.66X10^(-27)kg
@ -43,16 +42,16 @@ run 5000
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 20.1
ghost atom cutoff = 20.1
binsize = 10.05, bins = 8 5 20
master list distance cutoff = 13.4
ghost atom cutoff = 13.4
binsize = 6.7, bins = 12 7 30
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebomos, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.273 | 5.273 | 5.273 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.473 | 4.473 | 4.473 Mbytes
Step TotEng PotEng KinEng Temp
0 -5466.9785 -5496.7212 29.742759 300
500 -5466.964 -5482.6985 15.734505 158.7059
@ -65,32 +64,32 @@ Per MPI rank memory allocation (min/avg/max) = 5.273 | 5.273 | 5.273 Mbytes
4000 -5466.9628 -5481.848 14.885236 150.13977
4500 -5466.9648 -5483.5045 16.539775 166.82825
5000 -5466.9649 -5483.4932 16.528298 166.71249
Loop time of 36.2406 on 1 procs for 5000 steps with 768 atoms
Loop time of 19.1009 on 1 procs for 5000 steps with 768 atoms
Performance: 11.920 ns/day, 2.013 hours/ns, 137.967 timesteps/s, 105.959 katom-step/s
Performance: 22.617 ns/day, 1.061 hours/ns, 261.768 timesteps/s, 201.038 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 36.14 | 36.14 | 36.14 | 0.0 | 99.72
Pair | 19.042 | 19.042 | 19.042 | 0.0 | 99.69
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.043166 | 0.043166 | 0.043166 | 0.0 | 0.12
Output | 0.00021785 | 0.00021785 | 0.00021785 | 0.0 | 0.00
Modify | 0.034547 | 0.034547 | 0.034547 | 0.0 | 0.10
Other | | 0.02219 | | | 0.06
Comm | 0.018451 | 0.018451 | 0.018451 | 0.0 | 0.10
Output | 0.00015575 | 0.00015575 | 0.00015575 | 0.0 | 0.00
Modify | 0.023931 | 0.023931 | 0.023931 | 0.0 | 0.13
Other | | 0.01658 | | | 0.09
Nlocal: 768 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2054 ave 2054 max 2054 min
Nghost: 1158 ave 1158 max 1158 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 330752 ave 330752 max 330752 min
FullNghs: 141824 ave 141824 max 141824 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 330752
Ave neighs/atom = 430.66667
Total # of neighbors = 141824
Ave neighs/atom = 184.66667
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:36
Total wall time: 0:00:19

37
examples/threebody/log.22Feb24.mos2.rebomos.g++.4
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@ -1,5 +1,4 @@
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-70-ge51a65696d-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-73-g36fa601fe0)
using 1 OpenMP thread(s) per MPI task
# monolayer MoS2
units metal
@ -43,16 +42,16 @@ run 5000
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 20.1
ghost atom cutoff = 20.1
binsize = 10.05, bins = 8 5 20
master list distance cutoff = 13.4
ghost atom cutoff = 13.4
binsize = 6.7, bins = 12 7 30
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebomos, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.464 | 4.464 | 4.464 Mbytes
Per MPI rank memory allocation (min/avg/max) = 4.045 | 4.045 | 4.045 Mbytes
Step TotEng PotEng KinEng Temp
0 -5466.9785 -5496.7212 29.742759 300
500 -5466.964 -5482.6985 15.734505 158.7059
@ -65,32 +64,32 @@ Per MPI rank memory allocation (min/avg/max) = 4.464 | 4.464 | 4.464 Mbytes
4000 -5466.9628 -5481.848 14.885236 150.13977
4500 -5466.9648 -5483.5045 16.539775 166.82825
5000 -5466.9649 -5483.4932 16.528298 166.71249
Loop time of 10.2878 on 4 procs for 5000 steps with 768 atoms
Loop time of 5.69326 on 4 procs for 5000 steps with 768 atoms
Performance: 41.992 ns/day, 0.572 hours/ns, 486.014 timesteps/s, 373.259 katom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 75.879 ns/day, 0.316 hours/ns, 878.231 timesteps/s, 674.482 katom-step/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.7925 | 9.9286 | 10.096 | 3.6 | 96.51
Pair | 5.2611 | 5.3666 | 5.4358 | 3.0 | 94.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.16754 | 0.33518 | 0.47096 | 19.5 | 3.26
Output | 0.00016889 | 0.00018727 | 0.00023915 | 0.0 | 0.00
Modify | 0.010131 | 0.010502 | 0.011106 | 0.4 | 0.10
Other | | 0.01333 | | | 0.13
Comm | 0.23476 | 0.30106 | 0.40642 | 12.8 | 5.29
Output | 0.00014996 | 0.0004478 | 0.0013353 | 0.0 | 0.01
Modify | 0.0068861 | 0.0069917 | 0.0072247 | 0.2 | 0.12
Other | | 0.01814 | | | 0.32
Nlocal: 192 ave 194 max 190 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 1350 ave 1352 max 1348 min
Nghost: 710 ave 712 max 708 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 82688 ave 83548 max 81828 min
FullNghs: 35456 ave 35824 max 35088 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 330752
Ave neighs/atom = 430.66667
Total # of neighbors = 141824
Ave neighs/atom = 184.66667
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:10
Total wall time: 0:00:05