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update log files. make Si example (much) smaller

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This commit is contained in:
Axel Kohlmeyer
2021-06-13 17:40:00 -04:00
parent 66cf2319a1
commit 84d04752d3
6 changed files with 102 additions and 96 deletions
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2
examples/mliap/in.mliap.so3.Ni_Mo
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@ -17,7 +17,7 @@ variable N equal count(all)
thermo_style custom pe pxx pyy pzz pxy pxz pyz thermo_style custom pe pxx pyy pzz pxy pxz pyz
thermo 1 thermo 1
dump 1 all custom 1 dump.myforce.* id type fx fy fz # dump 1 all custom 1 dump.myforce.* id type fx fy fz
velocity all create 300.0 4928459 loop geom velocity all create 300.0 4928459 loop geom
fix 1 all nve fix 1 all nve

2
examples/mliap/in.mliap.so3.nn.Si
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@ -12,7 +12,7 @@ atom_modify sort 0 0.0
#read_data Si.data #read_data Si.data
lattice diamond 5.43 lattice diamond 5.43
region box block 0 10 0 10 0 10 region box block 0 2 0 2 0 2
create_box 1 box create_box 1 box
create_atoms 1 box create_atoms 1 box
mass 1 29.0 mass 1 29.0

24
examples/mliap/log.09Jun21.mliap.so3.Ni_Mo.g++.1
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@ -1,6 +1,8 @@
LAMMPS (8 Apr 2021) LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# ---------- Initialize Simulation --------------------- # ---------- Initialize Simulation ---------------------
clear clear
using 1 OpenMP thread(s) per MPI task
units metal units metal
dimension 3 dimension 3
boundary p p p boundary p p p
@ -33,7 +35,7 @@ variable N equal count(all)
thermo_style custom pe pxx pyy pzz pxy pxz pyz thermo_style custom pe pxx pyy pzz pxy pxz pyz
thermo 1 thermo 1
dump 1 all custom 1 dump.myforce.* id type fx fy fz # dump 1 all custom 1 dump.myforce.* id type fx fy fz
velocity all create 300.0 4928459 loop geom velocity all create 300.0 4928459 loop geom
fix 1 all nve fix 1 all nve
@ -51,26 +53,26 @@ Neighbor list info ...
pair build: full/bin/atomonly pair build: full/bin/atomonly
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 18.47 | 18.47 | 18.47 Mbytes Per MPI rank memory allocation (min/avg/max) = 17.22 | 17.22 | 17.22 Mbytes
PotEng Pxx Pyy Pzz Pxy Pxz Pyz PotEng Pxx Pyy Pzz Pxy Pxz Pyz
-60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498 -60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498
-60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829 -60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829
-60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456 -60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456
-60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916 -60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916
Loop time of 0.00652385 on 1 procs for 3 steps with 10 atoms Loop time of 0.0093536 on 1 procs for 3 steps with 10 atoms
Performance: 39.731 ns/day, 0.604 hours/ns, 459.851 timesteps/s Performance: 27.711 ns/day, 0.866 hours/ns, 320.732 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.0063381 | 0.0063381 | 0.0063381 | 0.0 | 97.15 Pair | 0.0092137 | 0.0092137 | 0.0092137 | 0.0 | 98.50
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 8.5831e-06 | 8.5831e-06 | 8.5831e-06 | 0.0 | 0.13 Comm | 1.5188e-05 | 1.5188e-05 | 1.5188e-05 | 0.0 | 0.16
Output | 0.00017047 | 0.00017047 | 0.00017047 | 0.0 | 2.61 Output | 0.00010311 | 0.00010311 | 0.00010311 | 0.0 | 1.10
Modify | 2.3842e-06 | 2.3842e-06 | 2.3842e-06 | 0.0 | 0.04 Modify | 5.4e-06 | 5.4e-06 | 5.4e-06 | 0.0 | 0.06
Other | | 4.292e-06 | | | 0.07 Other | | 1.621e-05 | | | 0.17
Nlocal: 10.0000 ave 10 max 10 min Nlocal: 10.0000 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

24
examples/mliap/log.09Jun21.mliap.so3.Ni_Mo.g++.4
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@ -1,6 +1,8 @@
LAMMPS (8 Apr 2021) LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# ---------- Initialize Simulation --------------------- # ---------- Initialize Simulation ---------------------
clear clear
using 1 OpenMP thread(s) per MPI task
units metal units metal
dimension 3 dimension 3
boundary p p p boundary p p p
@ -33,7 +35,7 @@ variable N equal count(all)
thermo_style custom pe pxx pyy pzz pxy pxz pyz thermo_style custom pe pxx pyy pzz pxy pxz pyz
thermo 1 thermo 1
dump 1 all custom 1 dump.myforce.* id type fx fy fz # dump 1 all custom 1 dump.myforce.* id type fx fy fz
velocity all create 300.0 4928459 loop geom velocity all create 300.0 4928459 loop geom
fix 1 all nve fix 1 all nve
@ -51,26 +53,26 @@ Neighbor list info ...
pair build: full/bin/atomonly pair build: full/bin/atomonly
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 18.48 | 18.48 | 18.48 Mbytes Per MPI rank memory allocation (min/avg/max) = 17.23 | 17.23 | 17.23 Mbytes
PotEng Pxx Pyy Pzz Pxy Pxz Pyz PotEng Pxx Pyy Pzz Pxy Pxz Pyz
-60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498 -60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498
-60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829 -60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829
-60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456 -60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456
-60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916 -60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916
Loop time of 0.00700521 on 4 procs for 3 steps with 10 atoms Loop time of 0.00731116 on 4 procs for 3 steps with 10 atoms
Performance: 37.001 ns/day, 0.649 hours/ns, 428.252 timesteps/s Performance: 35.453 ns/day, 0.677 hours/ns, 410.331 timesteps/s
83.7% CPU use with 4 MPI tasks x no OpenMP threads 84.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.0029368 | 0.0044926 | 0.0064001 | 1.8 | 64.13 Pair | 0.0027137 | 0.0039915 | 0.0065214 | 2.5 | 54.60
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00015497 | 0.0020633 | 0.0036275 | 2.7 | 29.45 Comm | 0.00021023 | 0.002945 | 0.0044067 | 3.0 | 40.28
Output | 0.00042009 | 0.00043052 | 0.00044107 | 0.0 | 6.15 Output | 9.7476e-05 | 0.00030125 | 0.00043822 | 0.0 | 4.12
Modify | 2.861e-06 | 4.2915e-06 | 5.0068e-06 | 0.0 | 0.06 Modify | 4.574e-06 | 5.1632e-06 | 6.299e-06 | 0.0 | 0.07
Other | | 1.448e-05 | | | 0.21 Other | | 6.82e-05 | | | 0.93
Nlocal: 2.50000 ave 3 max 2 min Nlocal: 2.50000 ave 3 max 2 min
Histogram: 2 0 0 0 0 0 0 0 0 2 Histogram: 2 0 0 0 0 0 0 0 0 2

61
examples/mliap/log.09Jun21.mliap.so3.nn.Si.g++.1
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@ -1,4 +1,5 @@
LAMMPS (8 Apr 2021) LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# Run NPT MD simulation for Si at 500 K. # Run NPT MD simulation for Si at 500 K.
variable nsteps index 100 #0 variable nsteps index 100 #0
@ -14,12 +15,12 @@ atom_modify sort 0 0.0
#read_data Si.data #read_data Si.data
lattice diamond 5.43 lattice diamond 5.43
Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000 Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000
region box block 0 10 0 10 0 10 region box block 0 2 0 2 0 2
create_box 1 box create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (54.300000 54.300000 54.300000) Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 8000 atoms Created 64 atoms
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.001 seconds
mass 1 29.0 mass 1 29.0
@ -73,52 +74,52 @@ Neighbor list info ...
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6 master list distance cutoff = 6
ghost atom cutoff = 6 ghost atom cutoff = 6
binsize = 3, bins = 19 19 19 binsize = 3, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual (1) pair mliap, perpetual
attributes: full, newton on attributes: full, newton on
pair build: full/bin/atomonly pair build: full/bin/atomonly
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 308.6 | 308.6 | 308.6 Mbytes Per MPI rank memory allocation (min/avg/max) = 298.3 | 298.3 | 298.3 Mbytes
Step Temp E_pair c_energy TotEng Press v_press Step Temp E_pair c_energy TotEng Press v_press
0 500 -3.8376374 -3.8376374 -3.7730154 -7241.7798 7241.7798 0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456
10 490.38075 -3.8363493 -3.8363493 -3.7729705 -6905.607 6905.607 10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624
20 461.60083 -3.8325872 -3.8325872 -3.7729281 -5943.433 5943.433 20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165
30 416.53292 -3.8267188 -3.8267188 -3.7728845 -4484.7771 4484.7771 30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641
40 361.07069 -3.8195026 -3.8195026 -3.7728364 -2752.1553 2752.1553 40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177
50 304.26606 -3.812108 -3.812108 -3.7727834 -1038.0742 1038.0742 50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008
60 256.18955 -3.8058374 -3.8058374 -3.7727265 364.81585 -364.81585 60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639
70 223.86195 -3.8015965 -3.8015965 -3.7726637 1258.7414 -1258.7414 70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391
80 208.28902 -3.799511 -3.799511 -3.7725909 1602.5954 -1602.5954 80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675
90 205.19655 -3.7990256 -3.7990256 -3.7725051 1498.693 -1498.693 90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78
100 208.38945 -3.7993407 -3.7993407 -3.7724076 1121.1675 -1121.1675 100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458
Loop time of 310.377 on 1 procs for 100 steps with 8000 atoms Loop time of 5.83795 on 1 procs for 100 steps with 64 atoms
Performance: 0.014 ns/day, 1724.319 hours/ns, 0.322 timesteps/s Performance: 0.740 ns/day, 32.433 hours/ns, 17.129 timesteps/s
86.6% CPU use with 1 MPI tasks x no OpenMP threads 91.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 310.34 | 310.34 | 310.34 | 0.0 | 99.99 Pair | 5.8338 | 5.8338 | 5.8338 | 0.0 | 99.93
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0033481 | 0.0033481 | 0.0033481 | 0.0 | 0.00 Comm | 0.00053236 | 0.00053236 | 0.00053236 | 0.0 | 0.01
Output | 0.00336 | 0.00336 | 0.00336 | 0.0 | 0.00 Output | 0.0006904 | 0.0006904 | 0.0006904 | 0.0 | 0.01
Modify | 0.024909 | 0.024909 | 0.024909 | 0.0 | 0.01 Modify | 0.0025477 | 0.0025477 | 0.0025477 | 0.0 | 0.04
Other | | 0.00329 | | | 0.00 Other | | 0.0003419 | | | 0.01
Nlocal: 8000.00 ave 8000 max 8000 min Nlocal: 64.0000 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6725.00 ave 6725 max 6725 min Nghost: 557.000 ave 557 max 557 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 368000.0 ave 368000 max 368000 min FullNghs: 2944.00 ave 2944 max 2944 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 368000 Total # of neighbors = 2944
Ave neighs/atom = 46.000000 Ave neighs/atom = 46.000000
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:05:15 Total wall time: 0:00:05

61
examples/mliap/log.09Jun21.mliap.so3.nn.Si.g++.4
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@ -1,4 +1,5 @@
LAMMPS (8 Apr 2021) LAMMPS (27 May 2021)
using 1 OpenMP thread(s) per MPI task
# Run NPT MD simulation for Si at 500 K. # Run NPT MD simulation for Si at 500 K.
variable nsteps index 100 #0 variable nsteps index 100 #0
@ -14,12 +15,12 @@ atom_modify sort 0 0.0
#read_data Si.data #read_data Si.data
lattice diamond 5.43 lattice diamond 5.43
Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000 Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000
region box block 0 10 0 10 0 10 region box block 0 2 0 2 0 2
create_box 1 box create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (54.300000 54.300000 54.300000) Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000)
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 8000 atoms Created 64 atoms
create_atoms CPU = 0.000 seconds create_atoms CPU = 0.000 seconds
mass 1 29.0 mass 1 29.0
@ -73,52 +74,52 @@ Neighbor list info ...
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6 master list distance cutoff = 6
ghost atom cutoff = 6 ghost atom cutoff = 6
binsize = 3, bins = 19 19 19 binsize = 3, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual (1) pair mliap, perpetual
attributes: full, newton on attributes: full, newton on
pair build: full/bin/atomonly pair build: full/bin/atomonly
stencil: full/bin/3d stencil: full/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 300.6 | 300.6 | 300.6 Mbytes Per MPI rank memory allocation (min/avg/max) = 298.2 | 298.2 | 298.2 Mbytes
Step Temp E_pair c_energy TotEng Press v_press Step Temp E_pair c_energy TotEng Press v_press
0 500 -3.8376374 -3.8376374 -3.7730154 -7241.7798 7241.7798 0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456
10 490.38075 -3.8363493 -3.8363493 -3.7729705 -6905.607 6905.607 10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624
20 461.60083 -3.8325872 -3.8325872 -3.7729281 -5943.433 5943.433 20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165
30 416.53292 -3.8267188 -3.8267188 -3.7728845 -4484.7771 4484.7771 30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641
40 361.07069 -3.8195026 -3.8195026 -3.7728364 -2752.1553 2752.1553 40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177
50 304.26606 -3.812108 -3.812108 -3.7727834 -1038.0742 1038.0742 50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008
60 256.18955 -3.8058374 -3.8058374 -3.7727265 364.81585 -364.81585 60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639
70 223.86195 -3.8015965 -3.8015965 -3.7726637 1258.7414 -1258.7414 70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391
80 208.28902 -3.799511 -3.799511 -3.7725909 1602.5954 -1602.5954 80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675
90 205.19655 -3.7990256 -3.7990256 -3.7725051 1498.693 -1498.693 90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78
100 208.38945 -3.7993407 -3.7993407 -3.7724076 1121.1675 -1121.1675 100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458
Loop time of 82.8939 on 4 procs for 100 steps with 8000 atoms Loop time of 2.61422 on 4 procs for 100 steps with 64 atoms
Performance: 0.052 ns/day, 460.522 hours/ns, 1.206 timesteps/s Performance: 1.653 ns/day, 14.523 hours/ns, 38.252 timesteps/s
86.0% CPU use with 4 MPI tasks x no OpenMP threads 91.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 82.395 | 82.572 | 82.813 | 1.7 | 99.61 Pair | 2.4136 | 2.4671 | 2.569 | 3.9 | 94.37
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.070041 | 0.31023 | 0.48768 | 28.0 | 0.37 Comm | 0.037437 | 0.13954 | 0.19315 | 16.2 | 5.34
Output | 0.0018134 | 0.0018318 | 0.001883 | 0.1 | 0.00 Output | 0.00088435 | 0.0013739 | 0.0028352 | 2.3 | 0.05
Modify | 0.0079656 | 0.0080939 | 0.0082271 | 0.1 | 0.01 Modify | 0.004319 | 0.0054199 | 0.0059273 | 0.9 | 0.21
Other | | 0.00147 | | | 0.00 Other | | 0.0007924 | | | 0.03
Nlocal: 2000.00 ave 2000 max 2000 min Nlocal: 16.0000 ave 16 max 16 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3165.00 ave 3165 max 3165 min Nghost: 349.000 ave 349 max 349 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 92000.0 ave 92000 max 92000 min FullNghs: 736.000 ave 736 max 736 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 368000 Total # of neighbors = 2944
Ave neighs/atom = 46.000000 Ave neighs/atom = 46.000000
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:01:24 Total wall time: 0:00:02