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update log files for bench/POTENTIALS

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This commit is contained in:
Axel Kohlmeyer
2020-10-14 11:04:51 -04:00
parent 1e2c8ce2e6
commit 60ff1380d7
48 changed files with 1535 additions and 1453 deletions
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38
bench/POTENTIALS/log.16Mar18.adp.1 → bench/POTENTIALS/log.09Oct20.adp.1
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@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in ADP
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00184107 secs
create_atoms CPU = 0.002 seconds
pair_style adp
pair_coeff * * Ni.adp Ni
Reading adp potential file Ni.adp with DATE: 2011-06-20
velocity all create 1600.0 376847 loop geom
@ -41,35 +41,35 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 27.56 | 27.56 | 27.56 Mbytes
Per MPI rank memory allocation (min/avg/max) = 27.57 | 27.57 | 27.57 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.105
100 793.05485 -139023.13 0 -135742.9 32175.694
Loop time of 11.9854 on 1 procs for 100 steps with 32000 atoms
Loop time of 11.0841 on 1 procs for 100 steps with 32000 atoms
Performance: 3.604 ns/day, 6.659 hours/ns, 8.344 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 3.897 ns/day, 6.158 hours/ns, 9.022 timesteps/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 | 11.447 | 11.447 | 11.447 | 0.0 | 95.51
Neigh | 0.48465 | 0.48465 | 0.48465 | 0.0 | 4.04
Comm | 0.019317 | 0.019317 | 0.019317 | 0.0 | 0.16
Output | 0.00011063 | 0.00011063 | 0.00011063 | 0.0 | 0.00
Modify | 0.025319 | 0.025319 | 0.025319 | 0.0 | 0.21
Other | | 0.009125 | | | 0.08
Pair | 10.597 | 10.597 | 10.597 | 0.0 | 95.60
Neigh | 0.43765 | 0.43765 | 0.43765 | 0.0 | 3.95
Comm | 0.018561 | 0.018561 | 0.018561 | 0.0 | 0.17
Output | 0.0001123 | 0.0001123 | 0.0001123 | 0.0 | 0.00
Modify | 0.023261 | 0.023261 | 0.023261 | 0.0 | 0.21
Other | | 0.00792 | | | 0.07
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Nghost: 19911.0 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.33704e+06 ave 1.33704e+06 max 1.33704e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1337035
Ave neighs/atom = 41.7823
Ave neighs/atom = 41.782344
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:12
Total wall time: 0:00:11

36
bench/POTENTIALS/log.16Mar18.adp.4 → bench/POTENTIALS/log.09Oct20.adp.4
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@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in ADP
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000586033 secs
create_atoms CPU = 0.001 seconds
pair_style adp
pair_coeff * * Ni.adp Ni
Reading adp potential file Ni.adp with DATE: 2011-06-20
velocity all create 1600.0 376847 loop geom
@ -45,30 +45,30 @@ Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.105
100 793.05485 -139023.13 0 -135742.9 32175.694
Loop time of 3.49752 on 4 procs for 100 steps with 32000 atoms
Loop time of 3.54402 on 4 procs for 100 steps with 32000 atoms
Performance: 12.352 ns/day, 1.943 hours/ns, 28.592 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 12.190 ns/day, 1.969 hours/ns, 28.217 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3203 | 3.3261 | 3.3317 | 0.3 | 95.10
Neigh | 0.12544 | 0.12594 | 0.12634 | 0.1 | 3.60
Comm | 0.024059 | 0.03001 | 0.035574 | 2.9 | 0.86
Output | 4.8161e-05 | 6.8128e-05 | 0.00011802 | 0.0 | 0.00
Modify | 0.010666 | 0.010841 | 0.011109 | 0.2 | 0.31
Other | | 0.00457 | | | 0.13
Pair | 3.2768 | 3.3041 | 3.339 | 1.2 | 93.23
Neigh | 0.11542 | 0.11601 | 0.11661 | 0.1 | 3.27
Comm | 0.068218 | 0.10201 | 0.13103 | 7.0 | 2.88
Output | 4.4823e-05 | 8.0943e-05 | 0.000175 | 0.0 | 0.00
Modify | 0.010904 | 0.011064 | 0.011172 | 0.1 | 0.31
Other | | 0.01075 | | | 0.30
Nlocal: 8000 ave 8044 max 7960 min
Nlocal: 8000.00 ave 8044 max 7960 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 9131 ave 9171 max 9087 min
Nghost: 9131.00 ave 9171 max 9087 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 334259 ave 336108 max 332347 min
Neighs: 334259.0 ave 336108 max 332347 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 1337035
Ave neighs/atom = 41.7823
Ave neighs/atom = 41.782344
Neighbor list builds = 13
Dangerous builds = 0

90
bench/POTENTIALS/log.09Oct20.airebo.1 Normal file
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LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
Reading data file ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000 seconds
replicate 17 16 2
Replicating atoms ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
1 by 1 by 1 MPI processor grid
32640 atoms
replicate CPU = 0.002 seconds
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
Reading airebo potential file CH.airebo with DATE: 2011-10-25
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, 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) = 106.4 | 106.4 | 106.4 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139300.72 0 -138035.04 7988.6646
10 161.34683 -138712.9 0 -138032.19 33228.921
20 208.59504 -138912.79 0 -138032.74 -3211.8806
30 139.7513 -138618.85 0 -138029.25 10878.143
40 142.14562 -138629.02 0 -138029.32 14601.302
50 114.23401 -138510.95 0 -138029 24691.124
60 164.92002 -138726 0 -138030.21 35125.541
70 162.15256 -138715.9 0 -138031.79 5658.7946
80 157.16184 -138695.77 0 -138032.72 19824.698
90 196.15907 -138860.65 0 -138033.07 -7950.8463
100 178.31875 -138784.89 0 -138032.57 30997.671
Loop time of 58.0757 on 1 procs for 100 steps with 32640 atoms
Performance: 0.074 ns/day, 322.643 hours/ns, 1.722 timesteps/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 | 53.513 | 53.513 | 53.513 | 0.0 | 92.14
Neigh | 4.5013 | 4.5013 | 4.5013 | 0.0 | 7.75
Comm | 0.026609 | 0.026609 | 0.026609 | 0.0 | 0.05
Output | 0.0010192 | 0.0010192 | 0.0010192 | 0.0 | 0.00
Modify | 0.02275 | 0.02275 | 0.02275 | 0.0 | 0.04
Other | | 0.01074 | | | 0.02
Nlocal: 32640.0 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48190.0 ave 48190 max 48190 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2.22178e+07 ave 2.22178e+07 max 2.22178e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22217840
Ave neighs/atom = 680.69363
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:59

90
bench/POTENTIALS/log.09Oct20.airebo.4 Normal file
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@ -0,0 +1,90 @@
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
Reading data file ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000 seconds
replicate 17 16 2
Replicating atoms ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
2 by 2 by 1 MPI processor grid
32640 atoms
replicate CPU = 0.001 seconds
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
Reading airebo potential file CH.airebo with DATE: 2011-10-25
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, 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) = 29.43 | 29.81 | 30.19 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139300.72 0 -138035.04 7988.6646
10 161.34683 -138712.9 0 -138032.19 33228.921
20 208.59504 -138912.79 0 -138032.74 -3211.8806
30 139.7513 -138618.85 0 -138029.25 10878.143
40 142.14562 -138629.02 0 -138029.32 14601.302
50 114.23401 -138510.95 0 -138029 24691.124
60 164.92002 -138726 0 -138030.21 35125.541
70 162.15256 -138715.9 0 -138031.79 5658.7946
80 157.16184 -138695.77 0 -138032.72 19824.698
90 196.15907 -138860.65 0 -138033.07 -7950.8463
100 178.31875 -138784.89 0 -138032.57 30997.671
Loop time of 17.206 on 4 procs for 100 steps with 32640 atoms
Performance: 0.251 ns/day, 95.589 hours/ns, 5.812 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.655 | 14.727 | 14.848 | 1.9 | 85.59
Neigh | 1.5571 | 1.6135 | 1.6871 | 3.7 | 9.38
Comm | 0.7741 | 0.83422 | 0.90385 | 5.8 | 4.85
Output | 0.00047541 | 0.0027475 | 0.009517 | 7.5 | 0.02
Modify | 0.0091925 | 0.009367 | 0.0096078 | 0.2 | 0.05
Other | | 0.01908 | | | 0.11
Nlocal: 8160.00 ave 8174 max 8146 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 22614.5 ave 22629 max 22601 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5.55446e+06 ave 5.56556e+06 max 5.54192e+06 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 22217840
Ave neighs/atom = 680.69363
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:17

42
bench/POTENTIALS/log.16Mar18.bop.1 → bench/POTENTIALS/log.09Oct20.bop.1
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@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk CdTe via BOP
@ -7,19 +6,18 @@ units metal
atom_style atomic
lattice custom 6.82884 basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
Lattice spacing in x,y,z = 6.8288400 6.8288400 6.8288400
region box block 0 20 0 20 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (136.57680 136.57680 68.288400)
1 by 1 by 1 MPI processor grid
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
Created 32000 atoms
Time spent = 0.00191426 secs
create_atoms CPU = 0.002 seconds
pair_style bop
pair_coeff * * CdTe.bop.table Cd Te
Reading potential file CdTe.bop.table with DATE: 2012-06-25
Reading potential file CdTe.bop.table with DATE: 2012-06-25
Reading bop potential file CdTe.bop.table with DATE: 2012-06-25
mass 1 112.4
mass 2 127.6
@ -51,32 +49,32 @@ Per MPI rank memory allocation (min/avg/max) = 19.39 | 19.39 | 19.39 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -69539.487 0 -65403.292 3473.2595
100 572.16481 -67769.936 0 -65403.35 1838.6993
Loop time of 24.1696 on 1 procs for 100 steps with 32000 atoms
Loop time of 36.0284 on 1 procs for 100 steps with 32000 atoms
Performance: 0.357 ns/day, 67.138 hours/ns, 4.137 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.240 ns/day, 100.079 hours/ns, 2.776 timesteps/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 | 23.355 | 23.355 | 23.355 | 0.0 | 96.63
Neigh | 0.7545 | 0.7545 | 0.7545 | 0.0 | 3.12
Comm | 0.026978 | 0.026978 | 0.026978 | 0.0 | 0.11
Output | 0.0001111 | 0.0001111 | 0.0001111 | 0.0 | 0.00
Modify | 0.024145 | 0.024145 | 0.024145 | 0.0 | 0.10
Other | | 0.009326 | | | 0.04
Pair | 35.306 | 35.306 | 35.306 | 0.0 | 97.99
Neigh | 0.66375 | 0.66375 | 0.66375 | 0.0 | 1.84
Comm | 0.027954 | 0.027954 | 0.027954 | 0.0 | 0.08
Output | 9.9182e-05 | 9.9182e-05 | 9.9182e-05 | 0.0 | 0.00
Modify | 0.022574 | 0.022574 | 0.022574 | 0.0 | 0.06
Other | | 0.008374 | | | 0.02
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 35071 ave 35071 max 35071 min
Nghost: 35071.0 ave 35071 max 35071 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 141288 ave 141288 max 141288 min
FullNghs: 141288.0 ave 141288 max 141288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 141288
Ave neighs/atom = 4.41525
Ave neighs/atom = 4.4152500
Neighbor list builds = 14
Dangerous builds = 0
Total wall time: 0:00:24
Total wall time: 0:00:36

44
bench/POTENTIALS/log.16Mar18.bop.4 → bench/POTENTIALS/log.09Oct20.bop.4
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@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk CdTe via BOP
@ -7,19 +6,18 @@ units metal
atom_style atomic
lattice custom 6.82884 basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
Lattice spacing in x,y,z = 6.8288400 6.8288400 6.8288400
region box block 0 20 0 20 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (136.57680 136.57680 68.288400)
2 by 2 by 1 MPI processor grid
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
Created 32000 atoms
Time spent = 0.000597477 secs
create_atoms CPU = 0.001 seconds
pair_style bop
pair_coeff * * CdTe.bop.table Cd Te
Reading potential file CdTe.bop.table with DATE: 2012-06-25
Reading potential file CdTe.bop.table with DATE: 2012-06-25
Reading bop potential file CdTe.bop.table with DATE: 2012-06-25
mass 1 112.4
mass 2 127.6
@ -47,36 +45,36 @@ Neighbor list info ...
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.497 | 8.497 | 8.497 Mbytes
Per MPI rank memory allocation (min/avg/max) = 8.495 | 8.495 | 8.495 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -69539.487 0 -65403.292 3473.2595
100 572.16481 -67769.936 0 -65403.35 1838.6993
Loop time of 6.50033 on 4 procs for 100 steps with 32000 atoms
Loop time of 10.2579 on 4 procs for 100 steps with 32000 atoms
Performance: 1.329 ns/day, 18.056 hours/ns, 15.384 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.842 ns/day, 28.494 hours/ns, 9.749 timesteps/s
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.7879 | 5.975 | 6.1607 | 5.4 | 91.92
Neigh | 0.27603 | 0.27621 | 0.27647 | 0.0 | 4.25
Comm | 0.049869 | 0.23531 | 0.42241 | 27.2 | 3.62
Output | 4.9829e-05 | 5.9724e-05 | 8.5592e-05 | 0.0 | 0.00
Modify | 0.0089927 | 0.0090921 | 0.0092406 | 0.1 | 0.14
Other | | 0.004665 | | | 0.07
Pair | 9.0899 | 9.3839 | 9.6808 | 6.9 | 91.48
Neigh | 0.24734 | 0.2533 | 0.25828 | 0.8 | 2.47
Comm | 0.30495 | 0.60685 | 0.89832 | 27.5 | 5.92
Output | 4.673e-05 | 7.695e-05 | 0.00016189 | 0.0 | 0.00
Modify | 0.0092409 | 0.00937 | 0.0094445 | 0.1 | 0.09
Other | | 0.004455 | | | 0.04
Nlocal: 8000 ave 8006 max 7994 min
Nlocal: 8000.00 ave 8006 max 7994 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 15171 ave 15177 max 15165 min
Nghost: 15171.0 ave 15177 max 15165 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 35322 ave 35412 max 35267 min
FullNghs: 35322.0 ave 35412 max 35267 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 141288
Ave neighs/atom = 4.41525
Ave neighs/atom = 4.4152500
Neighbor list builds = 14
Dangerous builds = 0
Total wall time: 0:00:06
Total wall time: 0:00:10

35
bench/POTENTIALS/log.16Mar18.comb.1 → bench/POTENTIALS/log.09Oct20.comb.1
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@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# SiO2 for COMB potential
@ -7,10 +6,12 @@ units metal
atom_style charge
read_data data.comb
triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (74.580000 74.580000 83.064000) with tilt (0.0000000 0.0000000 0.0000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
32400 atoms
read_data CPU = 0.022 seconds
mass 1 28.0855
group type1 type 1
@ -63,32 +64,32 @@ Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
80 272.98301 -6.803583 -6.8388677 4.6404093 -11.479277 2.8932784 -1.4466392 -9896.1704 462016.62
90 305.77651 -6.8036184 -6.8431419 4.6512736 -11.494415 2.8953109 -1.4476554 -15675.983 462016.62
100 331.58255 -6.8036753 -6.8465344 4.662727 -11.509261 2.897273 -1.4486365 -21675.515 462016.62
Loop time of 517.206 on 1 procs for 100 steps with 32400 atoms
Loop time of 426.185 on 1 procs for 100 steps with 32400 atoms
Performance: 0.003 ns/day, 7183.417 hours/ns, 0.193 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.004 ns/day, 5919.239 hours/ns, 0.235 timesteps/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 | 114.18 | 114.18 | 114.18 | 0.0 | 22.08
Neigh | 0.47558 | 0.47558 | 0.47558 | 0.0 | 0.09
Comm | 0.030611 | 0.030611 | 0.030611 | 0.0 | 0.01
Output | 0.0024922 | 0.0024922 | 0.0024922 | 0.0 | 0.00
Modify | 402.51 | 402.51 | 402.51 | 0.0 | 77.82
Other | | 0.006137 | | | 0.00
Pair | 87.4 | 87.4 | 87.4 | 0.0 | 20.51
Neigh | 0.3908 | 0.3908 | 0.3908 | 0.0 | 0.09
Comm | 0.029936 | 0.029936 | 0.029936 | 0.0 | 0.01
Output | 0.0024605 | 0.0024605 | 0.0024605 | 0.0 | 0.00
Modify | 338.36 | 338.36 | 338.36 | 0.0 | 79.39
Other | | 0.005751 | | | 0.00
Nlocal: 32400 ave 32400 max 32400 min
Nlocal: 32400.0 ave 32400 max 32400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 42518 ave 42518 max 42518 min
Nghost: 42518.0 ave 42518 max 42518 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.85317e+07 ave 1.85317e+07 max 1.85317e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18531740
Ave neighs/atom = 571.967
Ave neighs/atom = 571.96728
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:09:18
Total wall time: 0:07:40

37
bench/POTENTIALS/log.16Mar18.comb.4 → bench/POTENTIALS/log.09Oct20.comb.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# SiO2 for COMB potential
@ -7,10 +6,12 @@ units metal
atom_style charge
read_data data.comb
triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (74.580000 74.580000 83.064000) with tilt (0.0000000 0.0000000 0.0000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
32400 atoms
read_data CPU = 0.031 seconds
mass 1 28.0855
group type1 type 1
@ -50,7 +51,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 32.11 | 32.11 | 32.11 Mbytes
Per MPI rank memory allocation (min/avg/max) = 32.28 | 32.28 | 32.29 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
0 300 -6.8032038 -6.8419806 4.6274455 -11.469426 2.8875895 -1.4437947 13386.415 462016.62
10 273.21913 -6.8032489 -6.8385642 4.6221303 -11.460695 2.8872353 -1.4436176 13076.442 462016.62
@ -63,32 +64,32 @@ Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
80 272.98301 -6.803583 -6.8388677 4.6404093 -11.479277 2.8932784 -1.4466392 -9896.1704 462016.62
90 305.77651 -6.8036184 -6.8431419 4.6512736 -11.494415 2.8953109 -1.4476554 -15675.983 462016.62
100 331.58255 -6.8036753 -6.8465344 4.662727 -11.509261 2.897273 -1.4486365 -21675.515 462016.62
Loop time of 131.437 on 4 procs for 100 steps with 32400 atoms
Loop time of 116.902 on 4 procs for 100 steps with 32400 atoms
Performance: 0.013 ns/day, 1825.518 hours/ns, 0.761 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.015 ns/day, 1623.637 hours/ns, 0.855 timesteps/s
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 28.847 | 28.874 | 28.913 | 0.5 | 21.97
Neigh | 0.10981 | 0.11084 | 0.11145 | 0.2 | 0.08
Comm | 0.28924 | 0.32866 | 0.3556 | 4.5 | 0.25
Output | 0.0010426 | 0.0011656 | 0.0015302 | 0.6 | 0.00
Modify | 102.12 | 102.12 | 102.12 | 0.0 | 77.69
Other | | 0.003455 | | | 0.00
Pair | 22.866 | 23.181 | 23.375 | 4.0 | 19.83
Neigh | 0.093812 | 0.094818 | 0.095301 | 0.2 | 0.08
Comm | 0.94054 | 1.1329 | 1.4505 | 18.1 | 0.97
Output | 0.0011141 | 0.001422 | 0.0023448 | 1.4 | 0.00
Modify | 92.485 | 92.488 | 92.494 | 0.0 | 79.12
Other | | 0.003673 | | | 0.00
Nlocal: 8100 ave 8110 max 8090 min
Nlocal: 8100.00 ave 8110 max 8090 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 20725.2 ave 20772 max 20694 min
Nghost: 20725.2 ave 20772 max 20694 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4.63294e+06 ave 4.63866e+06 max 4.62736e+06 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 18531740
Ave neighs/atom = 571.967
Ave neighs/atom = 571.96728
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:02:21
Total wall time: 0:02:06

37
bench/POTENTIALS/log.16Mar18.dpd.1 → bench/POTENTIALS/log.09Oct20.dpd.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# DPD benchmark
@ -8,14 +7,14 @@ atom_style atomic
comm_modify mode single vel yes
lattice fcc 3.0
Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (22.012848 22.012848 22.012848)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.0018332 secs
create_atoms CPU = 0.002 seconds
mass 1 1.0
velocity all create 1.0 87287 loop geom
@ -46,30 +45,30 @@ Per MPI rank memory allocation (min/avg/max) = 11.32 | 11.32 | 11.32 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 3.6872574 0 5.1872105 28.880274
100 1.0246036 4.5727353 0 6.1095927 23.859969
Loop time of 3.09286 on 1 procs for 100 steps with 32000 atoms
Loop time of 2.63541 on 1 procs for 100 steps with 32000 atoms
Performance: 111741.340 tau/day, 32.333 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 131137.146 tau/day, 37.945 timesteps/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 | 1.5326 | 1.5326 | 1.5326 | 0.0 | 49.55
Neigh | 1.4771 | 1.4771 | 1.4771 | 0.0 | 47.76
Comm | 0.044292 | 0.044292 | 0.044292 | 0.0 | 1.43
Output | 0.00011039 | 0.00011039 | 0.00011039 | 0.0 | 0.00
Modify | 0.022322 | 0.022322 | 0.022322 | 0.0 | 0.72
Other | | 0.01648 | | | 0.53
Pair | 1.1841 | 1.1841 | 1.1841 | 0.0 | 44.93
Neigh | 1.3737 | 1.3737 | 1.3737 | 0.0 | 52.12
Comm | 0.04266 | 0.04266 | 0.04266 | 0.0 | 1.62
Output | 9.5844e-05 | 9.5844e-05 | 9.5844e-05 | 0.0 | 0.00
Modify | 0.020128 | 0.020128 | 0.020128 | 0.0 | 0.76
Other | | 0.01468 | | | 0.56
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14981 ave 14981 max 14981 min
Nghost: 14981.0 ave 14981 max 14981 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 660587 ave 660587 max 660587 min
Neighs: 660587.0 ave 660587 max 660587 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 660587
Ave neighs/atom = 20.6433
Ave neighs/atom = 20.643344
Neighbor list builds = 50
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:02

37
bench/POTENTIALS/log.16Mar18.dpd.4 → bench/POTENTIALS/log.09Oct20.dpd.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# DPD benchmark
@ -8,14 +7,14 @@ atom_style atomic
comm_modify mode single vel yes
lattice fcc 3.0
Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
Lattice spacing in x,y,z = 1.1006424 1.1006424 1.1006424
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (22.012848 22.012848 22.012848)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000589132 secs
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.0 87287 loop geom
@ -42,34 +41,34 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.874 | 3.874 | 3.874 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.875 | 3.875 | 3.875 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 3.6872574 0 5.1872105 28.911346
100 1.0219182 4.5817845 0 6.1146139 23.803115
Loop time of 0.83904 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.882096 on 4 procs for 100 steps with 32000 atoms
Performance: 411899.440 tau/day, 119.184 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 391793.935 tau/day, 113.366 timesteps/s
93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.39605 | 0.40101 | 0.40702 | 0.6 | 47.79
Neigh | 0.38186 | 0.38494 | 0.38738 | 0.4 | 45.88
Comm | 0.032073 | 0.039688 | 0.045953 | 2.9 | 4.73
Output | 4.4823e-05 | 5.4002e-05 | 7.844e-05 | 0.0 | 0.01
Modify | 0.0056572 | 0.0056887 | 0.0057547 | 0.1 | 0.68
Other | | 0.007655 | | | 0.91
Pair | 0.31428 | 0.33654 | 0.37754 | 4.4 | 38.15
Neigh | 0.36308 | 0.3849 | 0.41542 | 3.1 | 43.63
Comm | 0.07276 | 0.14322 | 0.1842 | 11.3 | 16.24
Output | 4.22e-05 | 5.2989e-05 | 8.2493e-05 | 0.0 | 0.01
Modify | 0.0057678 | 0.0060433 | 0.0065472 | 0.4 | 0.69
Other | | 0.01134 | | | 1.29
Nlocal: 8000 ave 8014 max 7986 min
Nlocal: 8000.00 ave 8014 max 7986 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 6744 ave 6764 max 6726 min
Nghost: 6744.00 ave 6764 max 6726 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 165107 ave 166433 max 163419 min
Neighs: 165107.0 ave 166433 max 163419 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 660428
Ave neighs/atom = 20.6384
Ave neighs/atom = 20.638375
Neighbor list builds = 50
Dangerous builds = 0
Total wall time: 0:00:00

34
bench/POTENTIALS/log.16Mar18.eam.1 → bench/POTENTIALS/log.09Oct20.eam.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Cu in EAM
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
Lattice spacing in x,y,z = 3.6150000 3.6150000 3.6150000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (72.300000 72.300000 72.300000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00185037 secs
create_atoms CPU = 0.002 seconds
pair_style eam
pair_coeff 1 1 Cu_u3.eam
Reading eam potential file Cu_u3.eam with DATE: 2007-06-11
velocity all create 1600.0 376847 loop geom
@ -45,30 +45,30 @@ Per MPI rank memory allocation (min/avg/max) = 16.83 | 16.83 | 16.83 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 3.92295 on 1 procs for 100 steps with 32000 atoms
Loop time of 3.70399 on 1 procs for 100 steps with 32000 atoms
Performance: 11.012 ns/day, 2.179 hours/ns, 25.491 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 11.663 ns/day, 2.058 hours/ns, 26.998 timesteps/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 | 3.3913 | 3.3913 | 3.3913 | 0.0 | 86.45
Neigh | 0.48107 | 0.48107 | 0.48107 | 0.0 | 12.26
Comm | 0.01729 | 0.01729 | 0.01729 | 0.0 | 0.44
Output | 0.00011253 | 0.00011253 | 0.00011253 | 0.0 | 0.00
Modify | 0.024349 | 0.024349 | 0.024349 | 0.0 | 0.62
Other | | 0.008847 | | | 0.23
Pair | 3.2216 | 3.2216 | 3.2216 | 0.0 | 86.98
Neigh | 0.43766 | 0.43766 | 0.43766 | 0.0 | 11.82
Comm | 0.015404 | 0.015404 | 0.015404 | 0.0 | 0.42
Output | 0.000103 | 0.000103 | 0.000103 | 0.0 | 0.00
Modify | 0.021604 | 0.021604 | 0.021604 | 0.0 | 0.58
Other | | 0.007627 | | | 0.21
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19909 ave 19909 max 19909 min
Nghost: 19909.0 ave 19909 max 19909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Ave neighs/atom = 37.743250
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:03

38
bench/POTENTIALS/log.16Mar18.eam.4 → bench/POTENTIALS/log.09Oct20.eam.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Cu in EAM
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
Lattice spacing in x,y,z = 3.6150000 3.6150000 3.6150000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (72.300000 72.300000 72.300000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000595331 secs
create_atoms CPU = 0.001 seconds
pair_style eam
pair_coeff 1 1 Cu_u3.eam
Reading eam potential file Cu_u3.eam with DATE: 2007-06-11
velocity all create 1600.0 376847 loop geom
@ -41,34 +41,34 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.381 | 7.381 | 7.381 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.382 | 7.382 | 7.382 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 1.04497 on 4 procs for 100 steps with 32000 atoms
Loop time of 1.01466 on 4 procs for 100 steps with 32000 atoms
Performance: 41.341 ns/day, 0.581 hours/ns, 95.697 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 42.576 ns/day, 0.564 hours/ns, 98.555 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.88513 | 0.88724 | 0.89191 | 0.3 | 84.91
Neigh | 0.12418 | 0.12458 | 0.12511 | 0.1 | 11.92
Comm | 0.015654 | 0.020543 | 0.022984 | 2.0 | 1.97
Output | 4.8637e-05 | 5.8711e-05 | 8.6546e-05 | 0.0 | 0.01
Modify | 0.0085199 | 0.0085896 | 0.0086446 | 0.1 | 0.82
Other | | 0.003959 | | | 0.38
Pair | 0.86683 | 0.86797 | 0.86877 | 0.1 | 85.54
Neigh | 0.11567 | 0.11681 | 0.11992 | 0.5 | 11.51
Comm | 0.015399 | 0.017346 | 0.018526 | 0.9 | 1.71
Output | 4.6253e-05 | 8.1241e-05 | 0.00017262 | 0.0 | 0.01
Modify | 0.0085337 | 0.0085824 | 0.0086181 | 0.0 | 0.85
Other | | 0.003876 | | | 0.38
Nlocal: 8000 ave 8008 max 7993 min
Nlocal: 8000.00 ave 8008 max 7993 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 9130.25 ave 9138 max 9122 min
Nghost: 9130.25 ave 9138 max 9122 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 301946 ave 302392 max 301360 min
Neighs: 301946.0 ave 302392 max 301360 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Ave neighs/atom = 37.743250
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:01

33
bench/POTENTIALS/log.16Mar18.eff.1 → bench/POTENTIALS/log.09Oct20.eff.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# eFF benchmark of H plasma
@ -7,12 +6,14 @@ units electron
atom_style electron
read_data data.eff
orthogonal box = (0 0 0) to (41.9118 41.9118 41.9118)
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (41.911791 41.911791 41.911791)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.040 seconds
pair_style eff/cut 12
pair_coeff * *
@ -42,7 +43,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 370.9 | 370.9 | 370.9 Mbytes
Per MPI rank memory allocation (min/avg/max) = 371.5 | 371.5 | 371.5 Mbytes
Step TotEng PotEng KinEng Temp Press
0 4046.5854 796.63785 3249.9475 42763.133 4.4764483e+12
5 4046.5854 796.95799 3249.6274 42758.92 4.4728546e+12
@ -65,33 +66,33 @@ Step TotEng PotEng KinEng Temp Press
90 4046.5857 864.14162 3182.4441 41874.916 4.3868277e+12
95 4046.5857 871.30234 3175.2834 41780.695 4.3805068e+12
100 4046.5858 878.76023 3167.8255 41682.563 4.3740731e+12
Loop time of 323.031 on 1 procs for 100 steps with 32000 atoms
Loop time of 344.943 on 1 procs for 100 steps with 32000 atoms
Performance: 26.747 fs/day, 0.897 hours/fs, 0.310 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 25.048 fs/day, 0.958 hours/fs, 0.290 timesteps/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 | 322.78 | 322.78 | 322.78 | 0.0 | 99.92
Pair | 344.71 | 344.71 | 344.71 | 0.0 | 99.93
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.1876 | 0.1876 | 0.1876 | 0.0 | 0.06
Output | 0.0027025 | 0.0027025 | 0.0027025 | 0.0 | 0.00
Modify | 0.032475 | 0.032475 | 0.032475 | 0.0 | 0.01
Other | | 0.02538 | | | 0.01
Comm | 0.1763 | 0.1763 | 0.1763 | 0.0 | 0.05
Output | 0.0024362 | 0.0024362 | 0.0024362 | 0.0 | 0.00
Modify | 0.030869 | 0.030869 | 0.030869 | 0.0 | 0.01
Other | | 0.02272 | | | 0.01
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 114349 ave 114349 max 114349 min
Nghost: 114349.0 ave 114349 max 114349 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 8.10572e+07 ave 8.10572e+07 max 8.10572e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 81057159
Ave neighs/atom = 2533.04
Ave neighs/atom = 2533.0362
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:05:27
Total wall time: 0:05:49

33
bench/POTENTIALS/log.16Mar18.eff.4 → bench/POTENTIALS/log.09Oct20.eff.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# eFF benchmark of H plasma
@ -7,12 +6,14 @@ units electron
atom_style electron
read_data data.eff
orthogonal box = (0 0 0) to (41.9118 41.9118 41.9118)
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (41.911791 41.911791 41.911791)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.064 seconds
pair_style eff/cut 12
pair_coeff * *
@ -42,7 +43,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 101.4 | 104.8 | 108.3 Mbytes
Per MPI rank memory allocation (min/avg/max) = 102.1 | 105.5 | 109.0 Mbytes
Step TotEng PotEng KinEng Temp Press
0 4046.5854 796.63785 3249.9475 42763.133 4.4764483e+12
5 4046.5854 796.95799 3249.6274 42758.92 4.4728546e+12
@ -65,33 +66,33 @@ Step TotEng PotEng KinEng Temp Press
90 4046.5857 864.14162 3182.4441 41874.916 4.3868277e+12
95 4046.5857 871.30234 3175.2834 41780.695 4.3805068e+12
100 4046.5858 878.76023 3167.8255 41682.563 4.3740731e+12
Loop time of 90.1636 on 4 procs for 100 steps with 32000 atoms
Loop time of 100.431 on 4 procs for 100 steps with 32000 atoms
Performance: 95.826 fs/day, 0.250 hours/fs, 1.109 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 86.029 fs/day, 0.279 hours/fs, 0.996 timesteps/s
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 83.772 | 86.516 | 89.593 | 29.5 | 95.95
Pair | 89.149 | 93.787 | 97.971 | 41.9 | 93.38
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.51677 | 3.5934 | 6.3368 | 144.6 | 3.99
Output | 0.0012872 | 0.0018208 | 0.0024981 | 1.0 | 0.00
Modify | 0.017231 | 0.018405 | 0.01983 | 0.8 | 0.02
Other | | 0.03431 | | | 0.04
Comm | 2.4073 | 6.5821 | 11.21 | 157.8 | 6.55
Output | 0.0014203 | 0.0094504 | 0.019111 | 8.3 | 0.01
Modify | 0.016678 | 0.016999 | 0.017425 | 0.2 | 0.02
Other | | 0.03524 | | | 0.04
Nlocal: 8000 ave 8112 max 7875 min
Nlocal: 8000.00 ave 8112 max 7875 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 65589 ave 66004 max 65177 min
Nghost: 65589.0 ave 66004 max 65177 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 2.02643e+07 ave 2.11126e+07 max 1.94058e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 81057159
Ave neighs/atom = 2533.04
Ave neighs/atom = 2533.0362
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:31
Total wall time: 0:01:42

41
bench/POTENTIALS/log.16Mar18.eim.1 → bench/POTENTIALS/log.09Oct20.eim.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# EIM benchmark
# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
@ -9,12 +8,14 @@ units metal
atom_style atomic
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
Reading data file ...
orthogonal box = (-0.5 -0.5 -0.5) to (71.580002 143.66000 71.580002)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.024 seconds
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
@ -44,34 +45,34 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.72 | 17.72 | 17.72 Mbytes
Per MPI rank memory allocation (min/avg/max) = 17.74 | 17.74 | 17.74 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -90567.58 -117883.6 -118039.81 -117894.07 1400
100 -91997.012 -4104.7052 -4138.276 -4145.8936 944.10136
Loop time of 11.4536 on 1 procs for 100 steps with 32000 atoms
100 -91997.39 -4127.237 -4160.9799 -4169.0581 944.09785
Loop time of 10.3731 on 1 procs for 100 steps with 32000 atoms
Performance: 0.377 ns/day, 63.631 hours/ns, 8.731 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.416 ns/day, 57.628 hours/ns, 9.640 timesteps/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 | 9.8277 | 9.8277 | 9.8277 | 0.0 | 85.80
Neigh | 1.484 | 1.484 | 1.484 | 0.0 | 12.96
Comm | 0.028584 | 0.028584 | 0.028584 | 0.0 | 0.25
Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00
Modify | 0.09791 | 0.09791 | 0.09791 | 0.0 | 0.85
Other | | 0.0152 | | | 0.13
Pair | 8.8937 | 8.8937 | 8.8937 | 0.0 | 85.74
Neigh | 1.344 | 1.344 | 1.344 | 0.0 | 12.96
Comm | 0.028207 | 0.028207 | 0.028207 | 0.0 | 0.27
Output | 0.00020099 | 0.00020099 | 0.00020099 | 0.0 | 0.00
Modify | 0.093584 | 0.093584 | 0.093584 | 0.0 | 0.90
Other | | 0.0134 | | | 0.13
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21505 ave 21505 max 21505 min
Nghost: 21505.0 ave 21505 max 21505 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.5839e+06 ave 1.5839e+06 max 1.5839e+06 min
Neighs: 1.58387e+06 ave 1.58387e+06 max 1.58387e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1583901
Ave neighs/atom = 49.4969
Total # of neighbors = 1583871
Ave neighs/atom = 49.495969
Neighbor list builds = 37
Dangerous builds = 12
Total wall time: 0:00:11
Total wall time: 0:00:10

39
bench/POTENTIALS/log.16Mar18.eim.4 → bench/POTENTIALS/log.09Oct20.eim.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# EIM benchmark
# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
@ -9,12 +8,14 @@ units metal
atom_style atomic
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
Reading data file ...
orthogonal box = (-0.5 -0.5 -0.5) to (71.580002 143.66000 71.580002)
1 by 4 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.023 seconds
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
@ -44,34 +45,34 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.285 | 7.285 | 7.285 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.460 | 7.460 | 7.460 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -90567.58 -117883.6 -118039.81 -117894.07 1400
100 -91997.012 -4104.7052 -4138.276 -4145.8936 944.10136
Loop time of 3.12061 on 4 procs for 100 steps with 32000 atoms
100 -91997.39 -4127.237 -4160.9799 -4169.0581 944.09785
Loop time of 3.14457 on 4 procs for 100 steps with 32000 atoms
Performance: 1.384 ns/day, 17.337 hours/ns, 32.045 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 1.374 ns/day, 17.470 hours/ns, 31.801 timesteps/s
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6504 | 2.6583 | 2.6685 | 0.5 | 85.18
Neigh | 0.36996 | 0.37847 | 0.39396 | 1.5 | 12.13
Comm | 0.037041 | 0.040586 | 0.04504 | 1.4 | 1.30
Output | 7.081e-05 | 8.75e-05 | 0.00012994 | 0.0 | 0.00
Modify | 0.029286 | 0.035978 | 0.047942 | 3.9 | 1.15
Other | | 0.007206 | | | 0.23
Pair | 2.6017 | 2.6264 | 2.6758 | 1.8 | 83.52
Neigh | 0.34384 | 0.35308 | 0.36784 | 1.6 | 11.23
Comm | 0.039635 | 0.099661 | 0.15326 | 15.0 | 3.17
Output | 6.485e-05 | 9.656e-05 | 0.0001905 | 0.0 | 0.00
Modify | 0.035666 | 0.055446 | 0.098401 | 10.6 | 1.76
Other | | 0.009939 | | | 0.32
Nlocal: 8000 ave 8000 max 8000 min
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 9460.25 ave 9469 max 9449 min
Nghost: 9460.25 ave 9469 max 9449 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 395975 ave 397239 max 394616 min
Neighs: 395968.0 ave 397233 max 394606 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1583901
Ave neighs/atom = 49.4969
Total # of neighbors = 1583871
Ave neighs/atom = 49.495969
Neighbor list builds = 37
Dangerous builds = 12
Total wall time: 0:00:03

48
bench/POTENTIALS/log.16Mar18.fene.1 → bench/POTENTIALS/log.09Oct20.fene.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# FENE beadspring benchmark
@ -8,7 +7,8 @@ atom_style bond
special_bonds fene
read_data data.fene
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
Reading data file ...
orthogonal box = (-16.796000 -16.796000 -16.796000) to (16.796000 16.796000 16.796000)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
@ -18,8 +18,13 @@ read_data data.fene
1 = max bonds/atom
reading bonds ...
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 1.0 1.0
special bond factors coul: 0.0 1.0 1.0
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.003 seconds
read_data CPU = 0.054 seconds
neighbor 0.4 bin
neigh_modify delay 5 every 1
@ -49,36 +54,37 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.18 | 13.18 | 13.18 Mbytes
WARNING: Communication cutoff 1.52 is shorter than a bond length based estimate of 1.855. This may lead to errors. (src/comm.cpp:667)
Per MPI rank memory allocation (min/avg/max) = 13.20 | 13.20 | 13.20 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9729966 0.4361122 20.507698 22.40326 4.6548819
Loop time of 0.66285 on 1 procs for 100 steps with 32000 atoms
Loop time of 0.648089 on 1 procs for 100 steps with 32000 atoms
Performance: 156415.445 tau/day, 150.864 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 159978.044 tau/day, 154.300 timesteps/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 | 0.13075 | 0.13075 | 0.13075 | 0.0 | 19.73
Bond | 0.046363 | 0.046363 | 0.046363 | 0.0 | 6.99
Neigh | 0.3172 | 0.3172 | 0.3172 | 0.0 | 47.85
Comm | 0.016553 | 0.016553 | 0.016553 | 0.0 | 2.50
Output | 0.00010395 | 0.00010395 | 0.00010395 | 0.0 | 0.02
Modify | 0.14515 | 0.14515 | 0.14515 | 0.0 | 21.90
Other | | 0.006728 | | | 1.02
Pair | 0.12174 | 0.12174 | 0.12174 | 0.0 | 18.78
Bond | 0.050688 | 0.050688 | 0.050688 | 0.0 | 7.82
Neigh | 0.33136 | 0.33136 | 0.33136 | 0.0 | 51.13
Comm | 0.014753 | 0.014753 | 0.014753 | 0.0 | 2.28
Output | 9.8467e-05 | 9.8467e-05 | 9.8467e-05 | 0.0 | 0.02
Modify | 0.12378 | 0.12378 | 0.12378 | 0.0 | 19.10
Other | | 0.005668 | | | 0.87
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9493 ave 9493 max 9493 min
Nghost: 9493.00 ave 9493 max 9493 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 155873 ave 155873 max 155873 min
Neighs: 155873.0 ave 155873 max 155873 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 155873
Ave neighs/atom = 4.87103
Ave special neighs/atom = 1.98
Ave neighs/atom = 4.8710312
Ave special neighs/atom = 1.9800000
Neighbor list builds = 20
Dangerous builds = 20
Total wall time: 0:00:00

48
bench/POTENTIALS/log.16Mar18.fene.4 → bench/POTENTIALS/log.09Oct20.fene.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# FENE beadspring benchmark
@ -8,7 +7,8 @@ atom_style bond
special_bonds fene
read_data data.fene
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
Reading data file ...
orthogonal box = (-16.796000 -16.796000 -16.796000) to (16.796000 16.796000 16.796000)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
@ -18,8 +18,13 @@ read_data data.fene
1 = max bonds/atom
reading bonds ...
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 1.0 1.0
special bond factors coul: 0.0 1.0 1.0
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.048 seconds
neighbor 0.4 bin
neigh_modify delay 5 every 1
@ -49,36 +54,37 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.605 | 4.605 | 4.606 Mbytes
WARNING: Communication cutoff 1.52 is shorter than a bond length based estimate of 1.855. This may lead to errors. (src/comm.cpp:667)
Per MPI rank memory allocation (min/avg/max) = 4.779 | 4.780 | 4.780 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9736748 0.44378481 20.502389 22.40664 4.7809557
Loop time of 0.184782 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.179123 on 4 procs for 100 steps with 32000 atoms
Performance: 561093.346 tau/day, 541.178 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 578819.228 tau/day, 558.275 timesteps/s
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 | 0.033747 | 0.034391 | 0.035036 | 0.3 | 18.61
Bond | 0.012475 | 0.012579 | 0.012812 | 0.1 | 6.81
Neigh | 0.083916 | 0.083953 | 0.084022 | 0.0 | 45.43
Comm | 0.012409 | 0.01363 | 0.014534 | 0.7 | 7.38
Output | 4.1246e-05 | 5.9545e-05 | 0.00010443 | 0.0 | 0.03
Modify | 0.036675 | 0.037876 | 0.038357 | 0.4 | 20.50
Other | | 0.002294 | | | 1.24
Pair | 0.031898 | 0.032311 | 0.032864 | 0.2 | 18.04
Bond | 0.01335 | 0.013471 | 0.013588 | 0.1 | 7.52
Neigh | 0.087105 | 0.087195 | 0.087282 | 0.0 | 48.68
Comm | 0.010541 | 0.011533 | 0.012463 | 0.7 | 6.44
Output | 3.8624e-05 | 5.6028e-05 | 0.00010157 | 0.0 | 0.03
Modify | 0.031766 | 0.03233 | 0.033015 | 0.3 | 18.05
Other | | 0.002227 | | | 1.24
Nlocal: 8000 ave 8023 max 7978 min
Nlocal: 8000.00 ave 8023 max 7978 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 4158.75 ave 4175 max 4145 min
Nghost: 4158.75 ave 4175 max 4145 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 38940 ave 39184 max 38640 min
Neighs: 38940.0 ave 39184 max 38640 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 155760
Ave neighs/atom = 4.8675
Ave special neighs/atom = 1.98
Ave neighs/atom = 4.8675000
Ave special neighs/atom = 1.9800000
Neighbor list builds = 20
Dangerous builds = 20
Total wall time: 0:00:00

47
bench/POTENTIALS/log.16Mar18.gb.1 → bench/POTENTIALS/log.09Oct20.gb.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Gay-Berne benchmark
# biaxial ellipsoid mesogens in isotropic phase
@ -18,13 +17,15 @@ atom_style ellipsoid
#set group all quat/random 982381
read_data data.gb
orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
Reading data file ...
orthogonal box = (2.1957493 2.1957493 2.1957493) to (50.812373 50.812373 50.812373)
1 by 1 by 1 MPI processor grid
reading atoms ...
32768 atoms
reading velocities ...
32768 velocities
32768 ellipsoids
read_data CPU = 0.097 seconds
compute rot all temp/asphere
group spheroid type 1
@ -63,41 +64,41 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 28.91 | 28.91 | 28.91 Mbytes
Per MPI rank memory allocation (min/avg/max) = 28.98 | 28.98 | 28.98 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.4 0.50438568 0 4.1042758 6.7818168 114909.09
20 2.7357818 0.26045557 0 4.364003 6.8299368 111715.16
40 2.9201296 0.22570735 0 4.605768 7.0767907 109473.23
60 2.9820039 0.19733812 0 4.6702075 7.1507065 108393.77
80 3.0148529 0.15114819 0 4.6732895 7.1699502 107672.24
100 3.0206703 0.10567623 0 4.6365433 7.154345 107184.83
Loop time of 43.7894 on 1 procs for 100 steps with 32768 atoms
20 2.7357797 0.26044978 0 4.363994 6.8299173 111715.2
40 2.9201268 0.2257049 0 4.6057615 7.0767796 109473.26
60 2.9820022 0.19733756 0 4.6702044 7.1507023 108393.79
80 3.014852 0.15114765 0 4.6732876 7.1699472 107672.25
100 3.0206698 0.105676 0 4.6365424 7.1543436 107184.84
Loop time of 57.1053 on 1 procs for 100 steps with 32768 atoms
Performance: 394.616 tau/day, 2.284 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 302.599 tau/day, 1.751 timesteps/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 | 42.881 | 42.881 | 42.881 | 0.0 | 97.93
Neigh | 0.35071 | 0.35071 | 0.35071 | 0.0 | 0.80
Comm | 0.065153 | 0.065153 | 0.065153 | 0.0 | 0.15
Output | 0.00054383 | 0.00054383 | 0.00054383 | 0.0 | 0.00
Modify | 0.47852 | 0.47852 | 0.47852 | 0.0 | 1.09
Other | | 0.01337 | | | 0.03
Pair | 56.246 | 56.246 | 56.246 | 0.0 | 98.50
Neigh | 0.31058 | 0.31058 | 0.31058 | 0.0 | 0.54
Comm | 0.066039 | 0.066039 | 0.066039 | 0.0 | 0.12
Output | 0.00048757 | 0.00048757 | 0.00048757 | 0.0 | 0.00
Modify | 0.46972 | 0.46972 | 0.46972 | 0.0 | 0.82
Other | | 0.01198 | | | 0.02
Nlocal: 32768 ave 32768 max 32768 min
Nlocal: 32768.0 ave 32768 max 32768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 25669 ave 25669 max 25669 min
Nghost: 25669.0 ave 25669 max 25669 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.30433e+06 ave 2.30433e+06 max 2.30433e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2304332
Ave neighs/atom = 70.3226
Total # of neighbors = 2304331
Ave neighs/atom = 70.322601
Neighbor list builds = 6
Dangerous builds = 3
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:44
Total wall time: 0:00:57

49
bench/POTENTIALS/log.16Mar18.gb.4 → bench/POTENTIALS/log.09Oct20.gb.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Gay-Berne benchmark
# biaxial ellipsoid mesogens in isotropic phase
@ -18,13 +17,15 @@ atom_style ellipsoid
#set group all quat/random 982381
read_data data.gb
orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
Reading data file ...
orthogonal box = (2.1957493 2.1957493 2.1957493) to (50.812373 50.812373 50.812373)
1 by 2 by 2 MPI processor grid
reading atoms ...
32768 atoms
reading velocities ...
32768 velocities
32768 ellipsoids
read_data CPU = 0.079 seconds
compute rot all temp/asphere
group spheroid type 1
@ -63,41 +64,41 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes
Per MPI rank memory allocation (min/avg/max) = 11.99 | 11.99 | 12.00 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.4 0.50438568 0 4.1042758 6.7818168 114909.09
20 2.7357818 0.26045557 0 4.364003 6.8299368 111715.16
40 2.9201296 0.22570735 0 4.605768 7.0767907 109473.23
60 2.9820039 0.19733812 0 4.6702075 7.1507065 108393.77
80 3.0148529 0.15114819 0 4.6732895 7.1699502 107672.24
100 3.0206703 0.10567623 0 4.6365433 7.154345 107184.83
Loop time of 11.3124 on 4 procs for 100 steps with 32768 atoms
20 2.7357797 0.26044978 0 4.363994 6.8299173 111715.2
40 2.9201268 0.2257049 0 4.6057615 7.0767796 109473.26
60 2.9820022 0.19733756 0 4.6702044 7.1507023 108393.79
80 3.014852 0.15114765 0 4.6732876 7.1699472 107672.25
100 3.0206698 0.105676 0 4.6365424 7.1543436 107184.84
Loop time of 14.9338 on 4 procs for 100 steps with 32768 atoms
Performance: 1527.522 tau/day, 8.840 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 1157.109 tau/day, 6.696 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.778 | 10.849 | 10.934 | 2.0 | 95.90
Neigh | 0.088265 | 0.08871 | 0.089238 | 0.1 | 0.78
Comm | 0.1384 | 0.22518 | 0.29662 | 14.1 | 1.99
Output | 0.00020599 | 0.00024837 | 0.00036836 | 0.0 | 0.00
Modify | 0.13828 | 0.13899 | 0.13984 | 0.2 | 1.23
Other | | 0.01053 | | | 0.09
Pair | 14.317 | 14.457 | 14.545 | 2.5 | 96.81
Neigh | 0.080048 | 0.080928 | 0.082009 | 0.3 | 0.54
Comm | 0.15948 | 0.24734 | 0.38914 | 18.9 | 1.66
Output | 0.00018859 | 0.00034791 | 0.00082254 | 0.0 | 0.00
Modify | 0.137 | 0.13804 | 0.13981 | 0.3 | 0.92
Other | | 0.01041 | | | 0.07
Nlocal: 8192 ave 8215 max 8166 min
Nlocal: 8192.00 ave 8215 max 8166 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 11972.5 ave 11984 max 11959 min
Nghost: 11972.5 ave 11984 max 11959 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 576083 ave 579616 max 572161 min
Neighs: 576083.0 ave 579616 max 572161 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 2304332
Ave neighs/atom = 70.3226
Total # of neighbors = 2304331
Ave neighs/atom = 70.322601
Neighbor list builds = 6
Dangerous builds = 3
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:11
Total wall time: 0:00:15

35
bench/POTENTIALS/log.16Mar18.granular.1 → bench/POTENTIALS/log.09Oct20.granular.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# granular chute flow
@ -10,12 +9,14 @@ newton off
comm_modify vel yes
read_data data.granular
orthogonal box = (0 0 0) to (40 20 37.2886)
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.000000 20.000000 37.288600)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.050 seconds
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
@ -52,34 +53,34 @@ Neighbor list info ...
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 23.36 | 23.36 | 23.36 Mbytes
Per MPI rank memory allocation (min/avg/max) = 23.37 | 23.37 | 23.37 Mbytes
Step Atoms KinEng c_1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
Loop time of 0.292816 on 1 procs for 100 steps with 32000 atoms
Loop time of 0.274779 on 1 procs for 100 steps with 32000 atoms
Performance: 2950.657 tau/day, 341.511 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 3144.341 tau/day, 363.928 timesteps/s
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 | 0.17449 | 0.17449 | 0.17449 | 0.0 | 59.59
Neigh | 0.031927 | 0.031927 | 0.031927 | 0.0 | 10.90
Comm | 0.010195 | 0.010195 | 0.010195 | 0.0 | 3.48
Output | 0.00019121 | 0.00019121 | 0.00019121 | 0.0 | 0.07
Modify | 0.064463 | 0.064463 | 0.064463 | 0.0 | 22.01
Other | | 0.01155 | | | 3.94
Pair | 0.16956 | 0.16956 | 0.16956 | 0.0 | 61.71
Neigh | 0.027646 | 0.027646 | 0.027646 | 0.0 | 10.06
Comm | 0.010068 | 0.010068 | 0.010068 | 0.0 | 3.66
Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.06
Modify | 0.056372 | 0.056372 | 0.056372 | 0.0 | 20.52
Other | | 0.01096 | | | 3.99
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5463 ave 5463 max 5463 min
Nghost: 5463.00 ave 5463 max 5463 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 115133 ave 115133 max 115133 min
Neighs: 115133.0 ave 115133 max 115133 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 115133
Ave neighs/atom = 3.59791
Ave neighs/atom = 3.5979062
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:00

35
bench/POTENTIALS/log.16Mar18.granular.4 → bench/POTENTIALS/log.09Oct20.granular.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# granular chute flow
@ -10,12 +9,14 @@ newton off
comm_modify vel yes
read_data data.granular
orthogonal box = (0 0 0) to (40 20 37.2886)
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.000000 20.000000 37.288600)
2 by 1 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
read_data CPU = 0.052 seconds
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
@ -52,34 +53,34 @@ Neighbor list info ...
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.41 | 10.42 | 10.42 Mbytes
Per MPI rank memory allocation (min/avg/max) = 10.59 | 10.59 | 10.60 Mbytes
Step Atoms KinEng c_1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
Loop time of 0.0903978 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.0952788 on 4 procs for 100 steps with 32000 atoms
Performance: 9557.751 tau/day, 1106.221 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 9068.124 tau/day, 1049.551 timesteps/s
95.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.046331 | 0.049088 | 0.052195 | 1.2 | 54.30
Neigh | 0.0090401 | 0.0091327 | 0.0091863 | 0.1 | 10.10
Comm | 0.0073855 | 0.0080023 | 0.0086699 | 0.6 | 8.85
Output | 7.1049e-05 | 0.00010067 | 0.00012088 | 0.0 | 0.11
Modify | 0.017226 | 0.017449 | 0.01803 | 0.3 | 19.30
Other | | 0.006625 | | | 7.33
Pair | 0.044316 | 0.047274 | 0.049681 | 1.0 | 49.62
Neigh | 0.0079038 | 0.0079354 | 0.0079608 | 0.0 | 8.33
Comm | 0.0082569 | 0.0089372 | 0.0094819 | 0.5 | 9.38
Output | 6.9857e-05 | 9.3222e-05 | 0.00010514 | 0.0 | 0.10
Modify | 0.015689 | 0.016034 | 0.016789 | 0.4 | 16.83
Other | | 0.015 | | | 15.75
Nlocal: 8000 ave 8008 max 7992 min
Nlocal: 8000.00 ave 8008 max 7992 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2439 ave 2450 max 2428 min
Nghost: 2439.00 ave 2450 max 2428 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 29500.5 ave 30488 max 28513 min
Neighs: 29500.5 ave 30488 max 28513 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 118002
Ave neighs/atom = 3.68756
Ave neighs/atom = 3.6875625
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:00

33
bench/POTENTIALS/log.16Mar18.lj.1 → bench/POTENTIALS/log.09Oct20.lj.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
@ -7,14 +6,14 @@ units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (33.591924 33.591924 33.591924)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00183916 secs
create_atoms CPU = 0.002 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
@ -44,30 +43,30 @@ Per MPI rank memory allocation (min/avg/max) = 15.82 | 15.82 | 15.82 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.75745998 -5.7584998 0 -4.6223453 0.20729996
Loop time of 1.721 on 1 procs for 100 steps with 32000 atoms
Loop time of 1.59245 on 1 procs for 100 steps with 32000 atoms
Performance: 25101.720 tau/day, 58.106 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 27127.959 tau/day, 62.796 timesteps/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 | 1.2551 | 1.2551 | 1.2551 | 0.0 | 72.93
Neigh | 0.41825 | 0.41825 | 0.41825 | 0.0 | 24.30
Comm | 0.015347 | 0.015347 | 0.015347 | 0.0 | 0.89
Output | 0.00010729 | 0.00010729 | 0.00010729 | 0.0 | 0.01
Modify | 0.023436 | 0.023436 | 0.023436 | 0.0 | 1.36
Other | | 0.008766 | | | 0.51
Pair | 1.1654 | 1.1654 | 1.1654 | 0.0 | 73.18
Neigh | 0.38321 | 0.38321 | 0.38321 | 0.0 | 24.06
Comm | 0.014476 | 0.014476 | 0.014476 | 0.0 | 0.91
Output | 9.5844e-05 | 9.5844e-05 | 9.5844e-05 | 0.0 | 0.01
Modify | 0.021453 | 0.021453 | 0.021453 | 0.0 | 1.35
Other | | 0.007799 | | | 0.49
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19669 ave 19669 max 19669 min
Nghost: 19669.0 ave 19669 max 19669 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20318e+06 ave 1.20318e+06 max 1.20318e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1203176
Ave neighs/atom = 37.5992
Ave neighs/atom = 37.599250
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:01

37
bench/POTENTIALS/log.16Mar18.lj.4 → bench/POTENTIALS/log.09Oct20.lj.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
@ -7,14 +6,14 @@ units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (33.591924 33.591924 33.591924)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000587225 secs
create_atoms CPU = 0.001 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
@ -40,34 +39,34 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.88 | 6.88 | 6.88 Mbytes
Per MPI rank memory allocation (min/avg/max) = 6.881 | 6.881 | 6.881 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.75745998 -5.7584998 0 -4.6223453 0.20729996
Loop time of 0.469936 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.452443 on 4 procs for 100 steps with 32000 atoms
Performance: 91927.316 tau/day, 212.795 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 95481.741 tau/day, 221.023 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.32713 | 0.32917 | 0.33317 | 0.4 | 70.05
Neigh | 0.10836 | 0.10931 | 0.11007 | 0.2 | 23.26
Comm | 0.015526 | 0.020355 | 0.022399 | 2.0 | 4.33
Output | 4.2439e-05 | 5.8353e-05 | 0.00010061 | 0.0 | 0.01
Modify | 0.0071156 | 0.0072448 | 0.007309 | 0.1 | 1.54
Other | | 0.003793 | | | 0.81
Pair | 0.31149 | 0.3132 | 0.31493 | 0.2 | 69.22
Neigh | 0.1006 | 0.10164 | 0.10385 | 0.4 | 22.47
Comm | 0.02195 | 0.025904 | 0.028603 | 1.6 | 5.73
Output | 4.3631e-05 | 7.534e-05 | 0.00015879 | 0.0 | 0.02
Modify | 0.0067751 | 0.0073788 | 0.0088398 | 1.0 | 1.63
Other | | 0.004243 | | | 0.94
Nlocal: 8000 ave 8041 max 7958 min
Nlocal: 8000.00 ave 8041 max 7958 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 9011 ave 9065 max 8961 min
Nghost: 9011.00 ave 9065 max 8961 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 300794 ave 304843 max 297317 min
Neighs: 300794.0 ave 304843 max 297317 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 1203176
Ave neighs/atom = 37.5992
Ave neighs/atom = 37.599250
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:00

41
bench/POTENTIALS/log.16Mar18.meamc.1 → bench/POTENTIALS/log.09Oct20.meamc.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
@ -7,17 +6,19 @@ units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00184226 secs
create_atoms CPU = 0.002 seconds
pair_style meam/c
pair_coeff * * library.meam Ni4 Ni.meam Ni4
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam with DATE: 2007-06-11
velocity all create 1600.0 376847 loop geom
@ -47,37 +48,37 @@ Neighbor list info ...
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 55.91 | 55.91 | 55.91 Mbytes
Per MPI rank memory allocation (min/avg/max) = 55.92 | 55.92 | 55.92 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.431
100 895.50973 -139454.3 0 -135750.3 31804.185
Loop time of 22.9343 on 1 procs for 100 steps with 32000 atoms
Loop time of 21.655 on 1 procs for 100 steps with 32000 atoms
Performance: 1.884 ns/day, 12.741 hours/ns, 4.360 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 1.995 ns/day, 12.031 hours/ns, 4.618 timesteps/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 | 22.397 | 22.397 | 22.397 | 0.0 | 97.66
Neigh | 0.48781 | 0.48781 | 0.48781 | 0.0 | 2.13
Comm | 0.013967 | 0.013967 | 0.013967 | 0.0 | 0.06
Output | 0.00022793 | 0.00022793 | 0.00022793 | 0.0 | 0.00
Modify | 0.025412 | 0.025412 | 0.025412 | 0.0 | 0.11
Other | | 0.009448 | | | 0.04
Pair | 21.181 | 21.181 | 21.181 | 0.0 | 97.81
Neigh | 0.42787 | 0.42787 | 0.42787 | 0.0 | 1.98
Comm | 0.013557 | 0.013557 | 0.013557 | 0.0 | 0.06
Output | 0.00020766 | 0.00020766 | 0.00020766 | 0.0 | 0.00
Modify | 0.023456 | 0.023456 | 0.023456 | 0.0 | 0.11
Other | | 0.008504 | | | 0.04
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13576 ave 13576 max 13576 min
Nghost: 13576.0 ave 13576 max 13576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 780360 ave 780360 max 780360 min
Neighs: 780360.0 ave 780360 max 780360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Ave neighs/atom = 48.772500
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:23
Total wall time: 0:00:21

39
bench/POTENTIALS/log.16Mar18.meamc.4 → bench/POTENTIALS/log.09Oct20.meamc.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
@ -7,17 +6,19 @@ units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
Lattice spacing in x,y,z = 3.5200000 3.5200000 3.5200000
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (70.400000 70.400000 70.400000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00058651 secs
create_atoms CPU = 0.001 seconds
pair_style meam/c
pair_coeff * * library.meam Ni4 Ni.meam Ni4
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam with DATE: 2007-06-11
velocity all create 1600.0 376847 loop geom
@ -47,37 +48,37 @@ Neighbor list info ...
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.41 | 17.41 | 17.41 Mbytes
Per MPI rank memory allocation (min/avg/max) = 17.42 | 17.42 | 17.42 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.431
100 895.50973 -139454.3 0 -135750.3 31804.185
Loop time of 6.45947 on 4 procs for 100 steps with 32000 atoms
Loop time of 6.34746 on 4 procs for 100 steps with 32000 atoms
Performance: 6.688 ns/day, 3.589 hours/ns, 15.481 timesteps/s
Performance: 6.806 ns/day, 3.526 hours/ns, 15.754 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.22 | 6.2385 | 6.265 | 0.7 | 96.58
Neigh | 0.12657 | 0.12691 | 0.12721 | 0.1 | 1.96
Comm | 0.052339 | 0.07915 | 0.097897 | 5.9 | 1.23
Output | 9.7752e-05 | 0.0001151 | 0.00016594 | 0.0 | 0.00
Modify | 0.010194 | 0.010291 | 0.010442 | 0.1 | 0.16
Other | | 0.004529 | | | 0.07
Pair | 6.0585 | 6.1109 | 6.1535 | 1.4 | 96.27
Neigh | 0.11286 | 0.11651 | 0.12455 | 1.4 | 1.84
Comm | 0.058046 | 0.099641 | 0.15569 | 11.7 | 1.57
Output | 9.0122e-05 | 0.00016046 | 0.0003624 | 0.0 | 0.00
Modify | 0.010822 | 0.011674 | 0.014224 | 1.4 | 0.18
Other | | 0.008601 | | | 0.14
Nlocal: 8000 ave 8045 max 7947 min
Nlocal: 8000.00 ave 8045 max 7947 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 6066.75 ave 6120 max 6021 min
Nghost: 6066.75 ave 6120 max 6021 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 195090 ave 196403 max 193697 min
Neighs: 195090.0 ave 196403 max 193697 min
Histogram: 1 0 0 1 0 0 0 1 0 1
FullNghs: 390180 ave 392616 max 387490 min
FullNghs: 390180.0 ave 392616 max 387490 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Ave neighs/atom = 48.772500
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:06

33
bench/POTENTIALS/log.16Mar18.peri.1 → bench/POTENTIALS/log.09Oct20.peri.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Crack growth in notched 3D Peridynamic block
@ -58,11 +57,11 @@ region plate block 0 0.01975 0 0.01575 ${myzmin} ${myzmax} units bo
region plate block 0 0.01975 0 0.01575 0 ${myzmax} units box
region plate block 0 0.01975 0 0.01575 0 0.01225 units box
create_box 3 plate
Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (0.01975 0.01575 0.01225)
1 by 1 by 1 MPI processor grid
create_atoms 1 region plate
Created 32000 atoms
Time spent = 0.00362897 secs
create_atoms CPU = 0.004 seconds
pair_style peri/pmb
@ -101,8 +100,10 @@ region topright block 0.009875 0.01975 0.01075 0.01575 ${myzmin} ${myzmax}
region topright block 0.009875 0.01975 0.01075 0.01575 0 ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 0.01575 0 0.01225 units box
set region topleft type 2
Setting atom values ...
5000 settings made for type
set region topright type 3
Setting atom values ...
5000 settings made for type
pair_coeff 1 1 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
@ -129,11 +130,13 @@ pair_coeff 1 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 1 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
set group all density ${mydensity}
set group all density 2440
Setting atom values ...
32000 settings made for density
variable myvolume equal ($h)^3
variable myvolume equal (0.0005)^3
set group all volume ${myvolume}
set group all volume 1.25e-10
Setting atom values ...
32000 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
@ -184,23 +187,23 @@ Step Temp E_pair E_mol TotEng Press Volume
60 9.8975313e+26 5.7284448e+08 0 1.2287455e+09 1.2048543e+14 3.6292128e-06
80 9.3888573e+26 4.0928092e+08 0 1.0314725e+09 1.1429321e+14 3.6292128e-06
100 8.3930314e+26 3.8522361e+08 0 9.4142265e+08 1.0217075e+14 3.6292128e-06
Loop time of 11.0398 on 1 procs for 100 steps with 32000 atoms
Loop time of 10.1036 on 1 procs for 100 steps with 32000 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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 | 11.005 | 11.005 | 11.005 | 0.0 | 99.68
Pair | 10.07 | 10.07 | 10.07 | 0.0 | 99.67
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.6042e-05 | 6.6042e-05 | 6.6042e-05 | 0.0 | 0.00
Output | 0.00057292 | 0.00057292 | 0.00057292 | 0.0 | 0.01
Modify | 0.0256 | 0.0256 | 0.0256 | 0.0 | 0.23
Other | | 0.008592 | | | 0.08
Comm | 6.6519e-05 | 6.6519e-05 | 6.6519e-05 | 0.0 | 0.00
Output | 0.00051737 | 0.00051737 | 0.00051737 | 0.0 | 0.01
Modify | 0.024288 | 0.024288 | 0.024288 | 0.0 | 0.24
Other | | 0.008486 | | | 0.08
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.74442e+06 ave 6.74442e+06 max 6.74442e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -208,10 +211,10 @@ FullNghs: 1.34888e+07 ave 1.34888e+07 max 1.34888e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13488836
Ave neighs/atom = 421.526
Ave neighs/atom = 421.52612
Neighbor list builds = 0
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

39
bench/POTENTIALS/log.16Mar18.peri.4 → bench/POTENTIALS/log.09Oct20.peri.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Crack growth in notched 3D Peridynamic block
@ -58,11 +57,11 @@ region plate block 0 0.01975 0 0.01575 ${myzmin} ${myzmax} units bo
region plate block 0 0.01975 0 0.01575 0 ${myzmax} units box
region plate block 0 0.01975 0 0.01575 0 0.01225 units box
create_box 3 plate
Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (0.01975 0.01575 0.01225)
2 by 2 by 1 MPI processor grid
create_atoms 1 region plate
Created 32000 atoms
Time spent = 0.0011344 secs
create_atoms CPU = 0.001 seconds
pair_style peri/pmb
@ -101,8 +100,10 @@ region topright block 0.009875 0.01975 0.01075 0.01575 ${myzmin} ${myzmax}
region topright block 0.009875 0.01975 0.01075 0.01575 0 ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 0.01575 0 0.01225 units box
set region topleft type 2
Setting atom values ...
5000 settings made for type
set region topright type 3
Setting atom values ...
5000 settings made for type
pair_coeff 1 1 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
@ -129,11 +130,13 @@ pair_coeff 1 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 1 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
set group all density ${mydensity}
set group all density 2440
Setting atom values ...
32000 settings made for density
variable myvolume equal ($h)^3
variable myvolume equal (0.0005)^3
set group all volume ${myvolume}
set group all volume 1.25e-10
Setting atom values ...
32000 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
@ -176,7 +179,7 @@ Neighbor list info ...
Peridynamic bonds:
total # of bonds = 3457032
bonds/atom = 108.032
Per MPI rank memory allocation (min/avg/max) = 47.63 | 48.11 | 48.78 Mbytes
Per MPI rank memory allocation (min/avg/max) = 47.70 | 48.18 | 48.85 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.0134233e+27 0 0 1.3342785e+09 2.4509971e+14 3.6292128e-06
20 1.7695805e+27 1.6163291e+08 0 1.3343188e+09 2.1541601e+14 3.6292128e-06
@ -184,34 +187,34 @@ Step Temp E_pair E_mol TotEng Press Volume
60 9.8975313e+26 5.7284448e+08 0 1.2287455e+09 1.2048543e+14 3.6292128e-06
80 9.3888573e+26 4.0928092e+08 0 1.0314725e+09 1.1429321e+14 3.6292128e-06
100 8.3930314e+26 3.8522361e+08 0 9.4142265e+08 1.0217075e+14 3.6292128e-06
Loop time of 2.8928 on 4 procs for 100 steps with 32000 atoms
Loop time of 2.82804 on 4 procs for 100 steps with 32000 atoms
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7472 | 2.7951 | 2.8585 | 2.9 | 96.62
Pair | 2.6021 | 2.6599 | 2.7081 | 2.4 | 94.05
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019592 | 0.083156 | 0.13278 | 17.0 | 2.87
Output | 0.00022125 | 0.00034326 | 0.00058961 | 0.0 | 0.01
Modify | 0.0083542 | 0.0089623 | 0.0095983 | 0.5 | 0.31
Other | | 0.005276 | | | 0.18
Comm | 0.10341 | 0.15313 | 0.21057 | 10.3 | 5.41
Output | 0.00020409 | 0.00041658 | 0.00093699 | 0.0 | 0.01
Modify | 0.008944 | 0.0092288 | 0.0095088 | 0.3 | 0.33
Other | | 0.005395 | | | 0.19
Nlocal: 8000 ave 8000 max 8000 min
Nlocal: 8000.00 ave 8000 max 8000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5125 ave 5125 max 5125 min
Nghost: 5125.00 ave 5125 max 5125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 1.6861e+06 ave 1.77502e+06 max 1.60625e+06 min
Neighs: 1.68610e+06 ave 1.77502e+06 max 1.60625e+06 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 3.37221e+06 ave 3.41832e+06 max 3.3261e+06 min
FullNghs: 3.37221e+06 ave 3.41832e+06 max 3.3261e+06 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 13488836
Ave neighs/atom = 421.526
Ave neighs/atom = 421.52612
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03
Total wall time: 0:00:02

86
bench/POTENTIALS/log.16Mar18.protein.1 → bench/POTENTIALS/log.09Oct20.protein.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Rhodopsin model
@ -17,7 +16,8 @@ pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.protein
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
Reading data file ...
orthogonal box = (-27.500000 -38.500000 -36.364600) to (27.500000 38.500000 36.361500)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
@ -39,16 +39,22 @@ read_data data.protein
56829 dihedrals
reading impropers ...
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
special bonds CPU = 0.011 seconds
read_data CPU = 0.125 seconds
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
find clusters CPU = 0.006 seconds
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
@ -58,13 +64,13 @@ timestep 2.0
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.248835
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.24883488
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.0355478
estimated relative force accuracy = 0.000107051
using double precision FFTs
estimated absolute RMS force accuracy = 0.035547797
estimated relative force accuracy = 0.00010705113
using double precision KISS FFT
3d grid and FFT values/proc = 41070 25600
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
@ -78,46 +84,46 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 140 | 140 | 140 Mbytes
Per MPI rank memory allocation (min/avg/max) = 140.0 | 140.0 | 140.0 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
Volume = 307995.0335
---------------- Step 100 ----- CPU = 23.7567 (sec) ----------------
TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
PotEng = -46882.6482 E_bond = 2567.9789 E_angle = 10781.9556
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
Volume = 308133.9933
Loop time of 23.7568 on 1 procs for 100 steps with 32000 atoms
---------------- Step 100 ----- CPU = 20.0022 (sec) ----------------
TotEng = -25290.7304 KinEng = 21591.9084 Temp = 301.0906
PotEng = -46882.6388 E_bond = 2567.9807 E_angle = 10781.9571
E_dihed = 5198.7492 E_impro = 216.7864 E_vdwl = -1902.6618
E_coul = 206659.5226 E_long = -270404.9730 Press = 6.7406
Volume = 308134.2285
Loop time of 20.0022 on 1 procs for 100 steps with 32000 atoms
Performance: 0.727 ns/day, 32.995 hours/ns, 4.209 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.864 ns/day, 27.781 hours/ns, 4.999 timesteps/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 | 17.905 | 17.905 | 17.905 | 0.0 | 75.37
Bond | 0.73417 | 0.73417 | 0.73417 | 0.0 | 3.09
Kspace | 1.4676 | 1.4676 | 1.4676 | 0.0 | 6.18
Neigh | 2.9907 | 2.9907 | 2.9907 | 0.0 | 12.59
Comm | 0.037427 | 0.037427 | 0.037427 | 0.0 | 0.16
Output | 0.00011754 | 0.00011754 | 0.00011754 | 0.0 | 0.00
Modify | 0.60985 | 0.60985 | 0.60985 | 0.0 | 2.57
Other | | 0.01201 | | | 0.05
Pair | 15 | 15 | 15 | 0.0 | 74.99
Bond | 0.65091 | 0.65091 | 0.65091 | 0.0 | 3.25
Kspace | 1.2144 | 1.2144 | 1.2144 | 0.0 | 6.07
Neigh | 2.6096 | 2.6096 | 2.6096 | 0.0 | 13.05
Comm | 0.035203 | 0.035203 | 0.035203 | 0.0 | 0.18
Output | 0.00010848 | 0.00010848 | 0.00010848 | 0.0 | 0.00
Modify | 0.48116 | 0.48116 | 0.48116 | 0.0 | 2.41
Other | | 0.01032 | | | 0.05
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 47958 ave 47958 max 47958 min
Nghost: 47958.0 ave 47958 max 47958 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Total # of neighbors = 12028093
Ave neighs/atom = 375.87791
Ave special neighs/atom = 7.4318750
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:24
Total wall time: 0:00:20

88
bench/POTENTIALS/log.16Mar18.protein.4 → bench/POTENTIALS/log.09Oct20.protein.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# Rhodopsin model
@ -17,7 +16,8 @@ pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.protein
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
Reading data file ...
orthogonal box = (-27.500000 -38.500000 -36.364600) to (27.500000 38.500000 36.361500)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
@ -39,16 +39,22 @@ read_data data.protein
56829 dihedrals
reading impropers ...
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
special bonds CPU = 0.005 seconds
read_data CPU = 0.210 seconds
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
find clusters CPU = 0.003 seconds
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
@ -58,13 +64,13 @@ timestep 2.0
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.248835
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.24883488
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.0355478
estimated relative force accuracy = 0.000107051
using double precision FFTs
estimated absolute RMS force accuracy = 0.035547797
estimated relative force accuracy = 0.00010705113
using double precision KISS FFT
3d grid and FFT values/proc = 13230 6400
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
@ -78,46 +84,46 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 49.07 | 49.17 | 49.46 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.25 | 49.35 | 49.64 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
Volume = 307995.0335
---------------- Step 100 ----- CPU = 6.3997 (sec) ----------------
TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
PotEng = -46882.6483 E_bond = 2567.9789 E_angle = 10781.9556
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
Volume = 308133.9933
Loop time of 6.39977 on 4 procs for 100 steps with 32000 atoms
---------------- Step 100 ----- CPU = 5.5375 (sec) ----------------
TotEng = -25290.7303 KinEng = 21591.9085 Temp = 301.0906
PotEng = -46882.6388 E_bond = 2567.9807 E_angle = 10781.9571
E_dihed = 5198.7492 E_impro = 216.7864 E_vdwl = -1902.6618
E_coul = 206659.5225 E_long = -270404.9730 Press = 6.7406
Volume = 308134.2285
Loop time of 5.53765 on 4 procs for 100 steps with 32000 atoms
Performance: 2.700 ns/day, 8.889 hours/ns, 15.626 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 3.120 ns/day, 7.691 hours/ns, 18.058 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4434 | 4.5321 | 4.6846 | 4.3 | 70.82
Bond | 0.17894 | 0.18568 | 0.19951 | 1.9 | 2.90
Kspace | 0.4651 | 0.61064 | 0.69123 | 11.1 | 9.54
Neigh | 0.7739 | 0.77394 | 0.774 | 0.0 | 12.09
Comm | 0.057676 | 0.069183 | 0.07901 | 3.0 | 1.08
Output | 5.6505e-05 | 6.6578e-05 | 9.4414e-05 | 0.0 | 0.00
Modify | 0.21444 | 0.21866 | 0.22524 | 0.9 | 3.42
Other | | 0.009451 | | | 0.15
Pair | 3.8921 | 3.9427 | 4.0762 | 3.9 | 71.20
Bond | 0.16218 | 0.16829 | 0.17972 | 1.7 | 3.04
Kspace | 0.35196 | 0.48475 | 0.53996 | 11.1 | 8.75
Neigh | 0.69975 | 0.69981 | 0.69988 | 0.0 | 12.64
Comm | 0.04908 | 0.049445 | 0.049767 | 0.1 | 0.89
Output | 5.1737e-05 | 8.5056e-05 | 0.00018382 | 0.0 | 0.00
Modify | 0.18393 | 0.18474 | 0.18528 | 0.1 | 3.34
Other | | 0.007858 | | | 0.14
Nlocal: 8000 ave 8143 max 7933 min
Nlocal: 8000.00 ave 8143 max 7933 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 22733.5 ave 22769 max 22693 min
Nghost: 22733.5 ave 22769 max 22693 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Total # of neighbors = 12028093
Ave neighs/atom = 375.87791
Ave special neighs/atom = 7.4318750
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:06
Total wall time: 0:00:05

96
bench/POTENTIALS/log.09Oct20.reaxc.1 Normal file
View File

@ -0,0 +1,96 @@
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4910650 9.4910650 6.9912300)
1 by 1 by 1 MPI processor grid
reading atoms ...
58 atoms
read_data CPU = 0.000 seconds
replicate 7 8 10
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (66.437455 75.928520 69.912300)
1 by 1 by 1 MPI processor grid
32480 atoms
replicate CPU = 0.002 seconds
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 1727.0 | 1727.0 | 1727.0 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5638 -3203096.6
10 299.37479 28983.59 -3232075.2 21746.783 -23987.396 7610.3039 -3203091.6
20 295.58549 28616.733 -3231710.1 18178.443 -10872.027 10603.19 -3203093.3
30 289.48845 28026.456 -3231123.3 12146.101 4985.2572 13364.258 -3203096.8
40 282.66408 27365.763 -3230467.5 4284.1187 18132.512 14133.51 -3203101.7
50 274.97007 26620.878 -3229730.4 -3718.933 25520.016 12551.903 -3203109.5
60 266.11301 25763.393 -3228883.8 -9271.3498 27307.451 9753.2362 -3203120.4
70 259.32635 25106.351 -3228237.2 -11150.623 24238.509 6578.531 -3203130.8
80 260.33969 25204.456 -3228344.2 -9576.4144 16737.758 3454.6426 -3203139.7
90 269.9021 26130.229 -3229275.5 -5905.8652 5246.3236 467.53439 -3203145.2
100 280.76723 27182.123 -3230330.6 -1363.6002 -8133.2093 -1689.6535 -3203148.5
Loop time of 213.234 on 1 procs for 100 steps with 32480 atoms
Performance: 0.004 ns/day, 5923.154 hours/ns, 0.469 timesteps/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 | 157 | 157 | 157 | 0.0 | 73.63
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.024997 | 0.024997 | 0.024997 | 0.0 | 0.01
Output | 0.0022025 | 0.0022025 | 0.0022025 | 0.0 | 0.00
Modify | 56.19 | 56.19 | 56.19 | 0.0 | 26.35
Other | | 0.01211 | | | 0.01
Nlocal: 32480.0 ave 32480 max 32480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45128.0 ave 45128 max 45128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.27781e+07 ave 1.27781e+07 max 1.27781e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12778082
Ave neighs/atom = 393.41385
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:03:37

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LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4910650 9.4910650 6.9912300)
2 by 2 by 1 MPI processor grid
reading atoms ...
58 atoms
read_data CPU = 0.000 seconds
replicate 7 8 10
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (66.437455 75.928520 69.912300)
1 by 2 by 2 MPI processor grid
32480 atoms
replicate CPU = 0.001 seconds
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 647.0 | 647.0 | 647.0 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5638 -3203096.6
10 299.37479 28983.59 -3232075.2 21746.771 -23987.411 7610.2901 -3203091.6
20 295.58551 28616.736 -3231710.1 18178.439 -10871.954 10603.303 -3203093.3
30 289.48844 28026.456 -3231123.2 12146.289 4985.5678 13364.519 -3203096.8
40 282.66406 27365.762 -3230467.4 4284.8179 18133.406 14134.156 -3203101.7
50 274.97009 26620.88 -3229730.3 -3718.6796 25520.338 12552.205 -3203109.5
60 266.11302 25763.394 -3228883.8 -9271.5644 27307.146 9753.1034 -3203120.4
70 259.32636 25106.352 -3228237.1 -11150.66 24238.705 6578.7141 -3203130.8
80 260.33966 25204.454 -3228344.1 -9576.2474 16737.753 3454.7607 -3203139.7
90 269.90207 26130.226 -3229275.5 -5905.8809 5246.1687 467.42114 -3203145.2
100 280.76722 27182.122 -3230330.6 -1363.4752 -8133.2096 -1689.5922 -3203148.5
Loop time of 69.1187 on 4 procs for 100 steps with 32480 atoms
Performance: 0.013 ns/day, 1919.965 hours/ns, 1.447 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 45.964 | 48.533 | 51.423 | 29.3 | 70.22
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.19604 | 3.0913 | 5.6647 | 116.3 | 4.47
Output | 0.00074649 | 0.0011722 | 0.0023553 | 2.0 | 0.00
Modify | 17.48 | 17.485 | 17.489 | 0.1 | 25.30
Other | | 0.008528 | | | 0.01
Nlocal: 8120.00 ave 8120 max 8120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 21992.0 ave 21992 max 21992 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3.48274e+06 ave 3.48274e+06 max 3.48274e+06 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13930976
Ave neighs/atom = 428.90936
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:10

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LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
Reading data file ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000 seconds
replicate 17 16 2
Replicating atoms ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
1 by 1 by 1 MPI processor grid
32640 atoms
replicate CPU = 0.002 seconds
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.rebo C H
Reading rebo potential file CH.rebo with DATE: 2018-7-3
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebo, 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) = 34.21 | 34.21 | 34.21 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.83 0 -137177.16 2463.0748
10 179.37985 -137931.27 0 -137174.48 15655.936
20 206.87654 -138046.99 0 -137174.19 -24042.627
30 150.80122 -137807.43 0 -137171.21 -16524.118
40 173.24945 -137902.35 0 -137171.42 -5716.9119
50 151.80455 -137812.36 0 -137171.91 3480.4584
60 199.08777 -138013.82 0 -137173.88 17881.372
70 217.85748 -138093.86 0 -137174.73 -12270.999
80 202.37482 -138029.39 0 -137175.59 -7622.7319
90 194.90628 -137997.05 0 -137174.75 -32267.471
100 185.17818 -137954.51 0 -137173.26 -6901.7499
Loop time of 4.83649 on 1 procs for 100 steps with 32640 atoms
Performance: 0.893 ns/day, 26.869 hours/ns, 20.676 timesteps/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 | 3.3248 | 3.3248 | 3.3248 | 0.0 | 68.74
Neigh | 1.4583 | 1.4583 | 1.4583 | 0.0 | 30.15
Comm | 0.01934 | 0.01934 | 0.01934 | 0.0 | 0.40
Output | 0.0011871 | 0.0011871 | 0.0011871 | 0.0 | 0.02
Modify | 0.023516 | 0.023516 | 0.023516 | 0.0 | 0.49
Other | | 0.009316 | | | 0.19
Nlocal: 32640.0 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26460.0 ave 26460 max 26460 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4902134
Ave neighs/atom = 150.18793
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:05

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bench/POTENTIALS/log.09Oct20.rebo.4 Normal file
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LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
Reading data file ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (2.1000000 2.1000000 25.579000)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000 seconds
replicate 17 16 2
Replicating atoms ...
orthogonal box = (-2.1000000 -2.1000000 0.0000000) to (69.300000 65.100000 51.158000)
2 by 2 by 1 MPI processor grid
32640 atoms
replicate CPU = 0.001 seconds
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.rebo C H
Reading rebo potential file CH.rebo with DATE: 2018-7-3
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebo, 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) = 11.80 | 12.00 | 12.19 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.83 0 -137177.16 2463.0748
10 179.37985 -137931.27 0 -137174.48 15655.936
20 206.87654 -138046.99 0 -137174.19 -24042.627
30 150.80122 -137807.43 0 -137171.21 -16524.118
40 173.24945 -137902.35 0 -137171.42 -5716.9119
50 151.80455 -137812.36 0 -137171.91 3480.4584
60 199.08777 -138013.82 0 -137173.88 17881.372
70 217.85748 -138093.86 0 -137174.73 -12270.999
80 202.37482 -138029.39 0 -137175.59 -7622.7319
90 194.90628 -137997.05 0 -137174.75 -32267.471
100 185.17818 -137954.51 0 -137173.26 -6901.7499
Loop time of 1.74701 on 4 procs for 100 steps with 32640 atoms
Performance: 2.473 ns/day, 9.706 hours/ns, 57.241 timesteps/s
94.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.89836 | 0.96998 | 1.054 | 6.0 | 55.52
Neigh | 0.453 | 0.47091 | 0.50316 | 2.8 | 26.96
Comm | 0.15706 | 0.27291 | 0.36547 | 14.5 | 15.62
Output | 0.00047016 | 0.00073808 | 0.0015287 | 0.0 | 0.04
Modify | 0.0093558 | 0.010209 | 0.011958 | 1.0 | 0.58
Other | | 0.02227 | | | 1.27
Nlocal: 8160.00 ave 8163 max 8157 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11605.8 ave 11615 max 11593 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.22553e+06 ave 1.22735e+06 max 1.22455e+06 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 4902134
Ave neighs/atom = 150.18793
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:01

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bench/POTENTIALS/log.09Oct20.spce.1 Normal file
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LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
Reading data file ...
orthogonal box = (0.02645 0.02645 0.02641) to (35.532800 35.532800 35.473600)
1 by 1 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.009 seconds
replicate 2 4 1
Replicating atoms ...
orthogonal box = (0.02645 0.02645 0.02641) to (71.039150 142.05185 35.473600)
1 by 1 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.005 seconds
replicate CPU = 0.012 seconds
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.5
special bond factors coul: 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.005 seconds
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
find clusters CPU = 0.005 seconds
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.2688011
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.033101471
estimated relative force accuracy = 9.9684097e-05
using double precision KISS FFT
3d grid and FFT values/proc = 91977 55296
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.8
ghost atom cutoff = 11.8
binsize = 5.9, bins = 13 25 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 105.4 | 105.4 | 105.4 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 516.17807
50 264.98553 -136986.74 0 -118030.61 -440.29256
100 274.45966 -136364.57 0 -116730.69 -128.61948
Loop time of 18.5133 on 1 procs for 100 steps with 36000 atoms
Performance: 0.933 ns/day, 25.713 hours/ns, 5.402 timesteps/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 | 14.557 | 14.557 | 14.557 | 0.0 | 78.63
Bond | 7.1764e-05 | 7.1764e-05 | 7.1764e-05 | 0.0 | 0.00
Kspace | 1.7651 | 1.7651 | 1.7651 | 0.0 | 9.53
Neigh | 1.8703 | 1.8703 | 1.8703 | 0.0 | 10.10
Comm | 0.042219 | 0.042219 | 0.042219 | 0.0 | 0.23
Output | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.00
Modify | 0.26983 | 0.26983 | 0.26983 | 0.0 | 1.46
Other | | 0.008397 | | | 0.05
Nlocal: 36000.0 ave 36000 max 36000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 56963.0 ave 56963 max 56963 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.24625e+07 ave 1.24625e+07 max 1.24625e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12462451
Ave neighs/atom = 346.17919
Ave special neighs/atom = 2.0000000
Neighbor list builds = 9
Dangerous builds = 6
Total wall time: 0:00:19

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LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
Reading data file ...
orthogonal box = (0.02645 0.02645 0.02641) to (35.532800 35.532800 35.473600)
2 by 2 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.008 seconds
replicate 2 4 1
Replicating atoms ...
orthogonal box = (0.02645 0.02645 0.02641) to (71.039150 142.05185 35.473600)
1 by 4 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
replicate CPU = 0.005 seconds
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.5
special bond factors coul: 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.004 seconds
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
find clusters CPU = 0.003 seconds
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
G vector (1/distance) = 0.2688011
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.033101471
estimated relative force accuracy = 9.9684097e-05
using double precision KISS FFT
3d grid and FFT values/proc = 27993 13824
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.8
ghost atom cutoff = 11.8
binsize = 5.9, bins = 13 25 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 37.90 | 37.90 | 37.90 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 516.17807
50 264.98553 -136986.74 0 -118030.61 -440.29255
100 274.45966 -136364.57 0 -116730.69 -128.61954
Loop time of 5.44355 on 4 procs for 100 steps with 36000 atoms
Performance: 3.174 ns/day, 7.560 hours/ns, 18.370 timesteps/s
95.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.82 | 3.8744 | 3.9155 | 1.8 | 71.17
Bond | 7.8917e-05 | 8.6784e-05 | 9.4891e-05 | 0.0 | 0.00
Kspace | 0.79192 | 0.83671 | 0.88328 | 3.5 | 15.37
Neigh | 0.51754 | 0.5178 | 0.51789 | 0.0 | 9.51
Comm | 0.069774 | 0.078783 | 0.088247 | 2.3 | 1.45
Output | 9.0361e-05 | 0.00015712 | 0.00035048 | 0.0 | 0.00
Modify | 0.12822 | 0.13016 | 0.13486 | 0.8 | 2.39
Other | | 0.005435 | | | 0.10
Nlocal: 9000.00 ave 9002 max 8998 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 24134.2 ave 24184 max 24062 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 3.11561e+06 ave 3.11676e+06 max 3.11446e+06 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 12462451
Ave neighs/atom = 346.17919
Ave special neighs/atom = 2.0000000
Neighbor list builds = 9
Dangerous builds = 6
Total wall time: 0:00:05

40
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@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Stillinger-Weber
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00191712 secs
create_atoms CPU = 0.002 seconds
pair_style sw
pair_coeff * * Si.sw Si
Reading sw potential file Si.sw with DATE: 2007-06-11
mass 1 28.06
velocity all create 1000.0 376847 loop geom
@ -46,32 +46,32 @@ Per MPI rank memory allocation (min/avg/max) = 12.52 | 12.52 | 12.52 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -138771.2 0 -134635 6866.6499
100 508.80533 -136736.12 0 -134631.6 6361.7858
Loop time of 5.66634 on 1 procs for 100 steps with 32000 atoms
Loop time of 3.9309 on 1 procs for 100 steps with 32000 atoms
Performance: 1.525 ns/day, 15.740 hours/ns, 17.648 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 2.198 ns/day, 10.919 hours/ns, 25.439 timesteps/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 | 5.5464 | 5.5464 | 5.5464 | 0.0 | 97.88
Neigh | 0.075834 | 0.075834 | 0.075834 | 0.0 | 1.34
Comm | 0.0092049 | 0.0092049 | 0.0092049 | 0.0 | 0.16
Output | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.00
Modify | 0.024666 | 0.024666 | 0.024666 | 0.0 | 0.44
Other | | 0.01014 | | | 0.18
Pair | 3.8206 | 3.8206 | 3.8206 | 0.0 | 97.19
Neigh | 0.067368 | 0.067368 | 0.067368 | 0.0 | 1.71
Comm | 0.0091503 | 0.0091503 | 0.0091503 | 0.0 | 0.23
Output | 0.0001049 | 0.0001049 | 0.0001049 | 0.0 | 0.00
Modify | 0.023839 | 0.023839 | 0.023839 | 0.0 | 0.61
Other | | 0.009882 | | | 0.25
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12495 ave 12495 max 12495 min
Nghost: 12495.0 ave 12495 max 12495 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 894818 ave 894818 max 894818 min
FullNghs: 894818.0 ave 894818 max 894818 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 894818
Ave neighs/atom = 27.9631
Ave neighs/atom = 27.963062
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:05
Total wall time: 0:00:03

38
bench/POTENTIALS/log.16Mar18.sw.4 → bench/POTENTIALS/log.09Oct20.sw.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Stillinger-Weber
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000604153 secs
create_atoms CPU = 0.001 seconds
pair_style sw
pair_coeff * * Si.sw Si
Reading sw potential file Si.sw with DATE: 2007-06-11
mass 1 28.06
velocity all create 1000.0 376847 loop geom
@ -46,32 +46,32 @@ Per MPI rank memory allocation (min/avg/max) = 4.104 | 4.104 | 4.104 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -138771.2 0 -134635 6866.6499
100 508.80533 -136736.12 0 -134631.6 6361.7858
Loop time of 1.47105 on 4 procs for 100 steps with 32000 atoms
Loop time of 1.04386 on 4 procs for 100 steps with 32000 atoms
Performance: 5.873 ns/day, 4.086 hours/ns, 67.978 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 8.277 ns/day, 2.900 hours/ns, 95.798 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3788 | 1.3929 | 1.4053 | 0.8 | 94.69
Neigh | 0.019134 | 0.019502 | 0.019816 | 0.2 | 1.33
Comm | 0.024183 | 0.035734 | 0.049122 | 4.7 | 2.43
Output | 5.1975e-05 | 6.6102e-05 | 0.00010204 | 0.0 | 0.00
Modify | 0.0063825 | 0.0064374 | 0.0064764 | 0.0 | 0.44
Other | | 0.01638 | | | 1.11
Pair | 0.96496 | 0.97632 | 0.9978 | 1.3 | 93.53
Neigh | 0.01732 | 0.017998 | 0.019718 | 0.7 | 1.72
Comm | 0.012035 | 0.036398 | 0.049588 | 7.7 | 3.49
Output | 4.5061e-05 | 5.5015e-05 | 7.7248e-05 | 0.0 | 0.01
Modify | 0.0070148 | 0.0070775 | 0.0071096 | 0.0 | 0.68
Other | | 0.006012 | | | 0.58
Nlocal: 8000 ave 8015 max 7978 min
Nlocal: 8000.00 ave 8015 max 7978 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 4995 ave 5017 max 4980 min
Nghost: 4995.00 ave 5017 max 4980 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 223704 ave 224108 max 223131 min
FullNghs: 223704.0 ave 224108 max 223131 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 894818
Ave neighs/atom = 27.9631
Ave neighs/atom = 27.963062
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:01

42
bench/POTENTIALS/log.16Mar18.tersoff.1 → bench/POTENTIALS/log.09Oct20.tersoff.1
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Tersoff
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.0019412 secs
create_atoms CPU = 0.002 seconds
pair_style tersoff
pair_coeff * * Si.tersoff Si
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
mass 1 28.06
velocity all create 1000.0 376847 loop geom
@ -42,36 +42,36 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.1 | 11.1 | 11.1 Mbytes
Per MPI rank memory allocation (min/avg/max) = 11.11 | 11.11 | 11.11 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -148173.19 0 -144036.99 7019.4434
100 430.57813 -145815.61 0 -144034.65 -14550.734
Loop time of 8.53088 on 1 procs for 100 steps with 32000 atoms
Loop time of 4.71424 on 1 procs for 100 steps with 32000 atoms
Performance: 1.013 ns/day, 23.697 hours/ns, 11.722 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 1.833 ns/day, 13.095 hours/ns, 21.212 timesteps/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 | 8.4236 | 8.4236 | 8.4236 | 0.0 | 98.74
Neigh | 0.065852 | 0.065852 | 0.065852 | 0.0 | 0.77
Comm | 0.0078607 | 0.0078607 | 0.0078607 | 0.0 | 0.09
Output | 0.00010872 | 0.00010872 | 0.00010872 | 0.0 | 0.00
Modify | 0.023968 | 0.023968 | 0.023968 | 0.0 | 0.28
Other | | 0.009521 | | | 0.11
Pair | 4.612 | 4.612 | 4.612 | 0.0 | 97.83
Neigh | 0.060618 | 0.060618 | 0.060618 | 0.0 | 1.29
Comm | 0.008847 | 0.008847 | 0.008847 | 0.0 | 0.19
Output | 9.9659e-05 | 9.9659e-05 | 9.9659e-05 | 0.0 | 0.00
Modify | 0.023234 | 0.023234 | 0.023234 | 0.0 | 0.49
Other | | 0.00941 | | | 0.20
Nlocal: 32000 ave 32000 max 32000 min
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11537 ave 11537 max 11537 min
Nghost: 11537.0 ave 11537 max 11537 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 530500 ave 530500 max 530500 min
FullNghs: 530500.0 ave 530500 max 530500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 530500
Ave neighs/atom = 16.5781
Ave neighs/atom = 16.578125
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:08
Total wall time: 0:00:04

42
bench/POTENTIALS/log.16Mar18.tersoff.4 → bench/POTENTIALS/log.09Oct20.tersoff.4
View File

@ -1,5 +1,4 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (9 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Tersoff
@ -7,17 +6,18 @@ units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (108.62000 108.62000 54.310000)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000605822 secs
create_atoms CPU = 0.001 seconds
pair_style tersoff
pair_coeff * * Si.tersoff Si
Reading tersoff potential file Si.tersoff with DATE: 2007-10-25
mass 1 28.06
velocity all create 1000.0 376847 loop geom
@ -42,36 +42,36 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.753 | 3.753 | 3.753 Mbytes
Per MPI rank memory allocation (min/avg/max) = 3.754 | 3.754 | 3.754 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -148173.19 0 -144036.99 7019.4434
100 430.57813 -145815.61 0 -144034.65 -14550.734
Loop time of 2.16161 on 4 procs for 100 steps with 32000 atoms
Loop time of 1.32053 on 4 procs for 100 steps with 32000 atoms
Performance: 3.997 ns/day, 6.004 hours/ns, 46.262 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 6.543 ns/day, 3.668 hours/ns, 75.727 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1122 | 2.1165 | 2.122 | 0.2 | 97.91
Neigh | 0.016894 | 0.016915 | 0.016955 | 0.0 | 0.78
Comm | 0.012348 | 0.017858 | 0.022105 | 2.7 | 0.83
Output | 4.7684e-05 | 6.2048e-05 | 9.9421e-05 | 0.0 | 0.00
Modify | 0.0064063 | 0.0064579 | 0.0065169 | 0.0 | 0.30
Other | | 0.003793 | | | 0.18
Pair | 1.1729 | 1.2118 | 1.2453 | 2.3 | 91.77
Neigh | 0.015989 | 0.016319 | 0.016708 | 0.3 | 1.24
Comm | 0.046884 | 0.078767 | 0.11602 | 8.9 | 5.96
Output | 3.9816e-05 | 7.0453e-05 | 0.00015831 | 0.0 | 0.01
Modify | 0.0070612 | 0.0071967 | 0.0073555 | 0.1 | 0.54
Other | | 0.006331 | | | 0.48
Nlocal: 8000 ave 8005 max 7993 min
Nlocal: 8000.00 ave 8005 max 7993 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 4580.25 ave 4593 max 4567 min
Nghost: 4580.25 ave 4593 max 4567 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 132625 ave 132785 max 132562 min
FullNghs: 132625.0 ave 132785 max 132562 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 530500
Ave neighs/atom = 16.5781
Ave neighs/atom = 16.578125
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:01

87
bench/POTENTIALS/log.16Mar18.airebo.1
View File

@ -1,87 +0,0 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00154901 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, 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) = 106.4 | 106.4 | 106.4 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139299.7 0 -138034.03 7998.7287
10 161.33916 -138711.85 0 -138031.17 33242.273
20 208.59505 -138911.77 0 -138031.73 -3199.2371
30 139.73485 -138617.76 0 -138028.23 10890.529
40 142.15332 -138628.03 0 -138028.3 14614.022
50 114.21945 -138509.87 0 -138027.98 24700.885
60 164.9432 -138725.08 0 -138029.19 35135.722
70 162.14928 -138714.86 0 -138030.77 5666.4609
80 157.17575 -138694.81 0 -138031.7 19838.161
90 196.16354 -138859.65 0 -138032.05 -7942.9718
100 178.30378 -138783.8 0 -138031.55 31012.15
Loop time of 60.9424 on 1 procs for 100 steps with 32640 atoms
Performance: 0.071 ns/day, 338.569 hours/ns, 1.641 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 55.299 | 55.299 | 55.299 | 0.0 | 90.74
Neigh | 5.5777 | 5.5777 | 5.5777 | 0.0 | 9.15
Comm | 0.027658 | 0.027658 | 0.027658 | 0.0 | 0.05
Output | 0.0011463 | 0.0011463 | 0.0011463 | 0.0 | 0.00
Modify | 0.024684 | 0.024684 | 0.024684 | 0.0 | 0.04
Other | | 0.012 | | | 0.02
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48190 ave 48190 max 48190 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: 2.22179e+07 ave 2.22179e+07 max 2.22179e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22217870
Ave neighs/atom = 680.695
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:01:02

87
bench/POTENTIALS/log.16Mar18.airebo.4
View File

@ -1,87 +0,0 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.00070262 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, 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) = 29.37 | 29.75 | 30.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139299.7 0 -138034.03 7998.7287
10 161.33916 -138711.85 0 -138031.17 33242.273
20 208.59505 -138911.77 0 -138031.73 -3199.2371
30 139.73485 -138617.76 0 -138028.23 10890.529
40 142.15332 -138628.03 0 -138028.3 14614.022
50 114.21945 -138509.87 0 -138027.98 24700.885
60 164.9432 -138725.08 0 -138029.19 35135.722
70 162.14928 -138714.86 0 -138030.77 5666.4609
80 157.17575 -138694.81 0 -138031.7 19838.161
90 196.16354 -138859.65 0 -138032.05 -7942.9718
100 178.30378 -138783.8 0 -138031.55 31012.15
Loop time of 16.768 on 4 procs for 100 steps with 32640 atoms
Performance: 0.258 ns/day, 93.156 hours/ns, 5.964 timesteps/s
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 | 14.538 | 14.589 | 14.654 | 1.3 | 87.00
Neigh | 1.8853 | 1.8992 | 1.9159 | 0.8 | 11.33
Comm | 0.18073 | 0.25896 | 0.31361 | 10.6 | 1.54
Output | 0.00050807 | 0.0040419 | 0.0077746 | 5.6 | 0.02
Modify | 0.0094635 | 0.0096973 | 0.0099616 | 0.2 | 0.06
Other | | 0.007481 | | | 0.04
Nlocal: 8160 ave 8174 max 8146 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 22614.5 ave 22629 max 22601 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5.55447e+06 ave 5.56557e+06 max 5.54193e+06 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 22217870
Ave neighs/atom = 680.695
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:17

93
bench/POTENTIALS/log.16Mar18.reaxc.1
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@ -1,93 +0,0 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
1 by 1 by 1 MPI processor grid
reading atoms ...
58 atoms
replicate 7 8 10
orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
1 by 1 by 1 MPI processor grid
32480 atoms
Time spent = 0.00162625 secs
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 1727 | 1727 | 1727 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5637 -3203096.6
10 299.37479 28983.59 -3232075.2 21746.778 -23987.41 7610.2967 -3203091.6
20 295.5855 28616.735 -3231710.1 18178.568 -10871.882 10603.247 -3203093.3
30 289.48845 28026.457 -3231123.2 12146.362 4985.5572 13364.455 -3203096.8
40 282.66404 27365.76 -3230467.5 4284.2794 18132.771 14133.719 -3203101.7
50 274.97005 26620.876 -3229730.4 -3719.11 25519.692 12551.708 -3203109.5
60 266.11301 25763.393 -3228883.8 -9271.4049 27307.216 9753.2509 -3203120.4
70 259.3263 25106.346 -3228237.2 -11150.726 24238.382 6578.5306 -3203130.8
80 260.33956 25204.444 -3228344.2 -9576.6006 16737.65 3454.5747 -3203139.7
90 269.90199 26130.219 -3229275.5 -5906.376 5246.1572 467.31789 -3203145.3
100 280.76717 27182.117 -3230330.6 -1363.8281 -8133.2509 -1689.7711 -3203148.5
Loop time of 437.886 on 1 procs for 100 steps with 32480 atoms
Performance: 0.002 ns/day, 12163.512 hours/ns, 0.228 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 350.29 | 350.29 | 350.29 | 0.0 | 80.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.026264 | 0.026264 | 0.026264 | 0.0 | 0.01
Output | 0.0024614 | 0.0024614 | 0.0024614 | 0.0 | 0.00
Modify | 87.55 | 87.55 | 87.55 | 0.0 | 19.99
Other | | 0.01296 | | | 0.00
Nlocal: 32480 ave 32480 max 32480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45128 ave 45128 max 45128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.27781e+07 ave 1.27781e+07 max 1.27781e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12778082
Ave neighs/atom = 393.414
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:07:24

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
2 by 2 by 1 MPI processor grid
reading atoms ...
58 atoms
replicate 7 8 10
orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
1 by 2 by 2 MPI processor grid
32480 atoms
Time spent = 0.000803709 secs
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 647 | 647 | 647 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5638 -3203096.6
10 299.37479 28983.59 -3232075.2 21746.773 -23987.409 7610.2911 -3203091.6
20 295.58552 28616.737 -3231710.1 18178.576 -10871.874 10603.421 -3203093.3
30 289.48843 28026.455 -3231123.3 12146.158 4985.3436 13364.461 -3203096.8
40 282.66409 27365.764 -3230467.5 4284.5077 18133.151 14133.949 -3203101.7
50 274.97008 26620.879 -3229730.3 -3718.536 25520.328 12552.195 -3203109.5
60 266.11301 25763.393 -3228883.7 -9271.0381 27307.591 9753.5339 -3203120.4
70 259.32631 25106.348 -3228237.1 -11150.314 24238.962 6578.8636 -3203130.8
80 260.33966 25204.453 -3228344.1 -9575.5709 16738.467 3455.2525 -3203139.7
90 269.90213 26130.231 -3229275.5 -5906.0456 5246.2122 467.43473 -3203145.2
100 280.76727 27182.127 -3230330.6 -1363.1733 -8132.8726 -1689.3275 -3203148.4
Loop time of 128.275 on 4 procs for 100 steps with 32480 atoms
Performance: 0.007 ns/day, 3563.196 hours/ns, 0.780 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 92.314 | 97.932 | 103.53 | 44.1 | 76.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.039458 | 5.6409 | 11.263 | 184.0 | 4.40
Output | 0.00086117 | 0.0010868 | 0.0016167 | 0.9 | 0.00
Modify | 24.687 | 24.688 | 24.69 | 0.0 | 19.25
Other | | 0.01323 | | | 0.01
Nlocal: 8120 ave 8120 max 8120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 21992 ave 21992 max 21992 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3.48274e+06 ave 3.48274e+06 max 3.48274e+06 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13930976
Ave neighs/atom = 428.909
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:02:10

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00151849 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebo, 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) = 34.21 | 34.21 | 34.21 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.48 0 -137176.8 2464.5258
10 179.38052 -137930.92 0 -137174.12 15656.95
20 206.87725 -138046.63 0 -137173.83 -24042.005
30 150.80048 -137807.07 0 -137170.86 -16524.069
40 173.25027 -137902 0 -137171.07 -5716.7297
50 151.80552 -137812.01 0 -137171.55 3481.1096
60 199.08762 -138013.46 0 -137173.53 17882.906
70 217.8592 -138093.51 0 -137174.38 -12269.648
80 202.37612 -138029.05 0 -137175.24 -7622.1573
90 194.905 -137996.68 0 -137174.4 -32267.297
100 185.17966 -137954.16 0 -137172.9 -6902.1493
Loop time of 5.17257 on 1 procs for 100 steps with 32640 atoms
Performance: 0.835 ns/day, 28.737 hours/ns, 19.333 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3427 | 3.3427 | 3.3427 | 0.0 | 64.62
Neigh | 1.7764 | 1.7764 | 1.7764 | 0.0 | 34.34
Comm | 0.017914 | 0.017914 | 0.017914 | 0.0 | 0.35
Output | 0.0011199 | 0.0011199 | 0.0011199 | 0.0 | 0.02
Modify | 0.024357 | 0.024357 | 0.024357 | 0.0 | 0.47
Other | | 0.01004 | | | 0.19
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26460 ave 26460 max 26460 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: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4902132
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.000838995 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair rebo, 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) = 11.75 | 11.94 | 12.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.48 0 -137176.8 2464.5258
10 179.38052 -137930.92 0 -137174.12 15656.95
20 206.87725 -138046.63 0 -137173.83 -24042.005
30 150.80048 -137807.07 0 -137170.86 -16524.069
40 173.25027 -137902 0 -137171.07 -5716.7297
50 151.80552 -137812.01 0 -137171.55 3481.1096
60 199.08762 -138013.46 0 -137173.53 17882.906
70 217.8592 -138093.51 0 -137174.38 -12269.648
80 202.37612 -138029.05 0 -137175.24 -7622.1573
90 194.905 -137996.68 0 -137174.4 -32267.297
100 185.17966 -137954.16 0 -137172.9 -6902.1493
Loop time of 1.52214 on 4 procs for 100 steps with 32640 atoms
Performance: 2.838 ns/day, 8.456 hours/ns, 65.697 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.88531 | 0.90632 | 0.92546 | 1.6 | 59.54
Neigh | 0.53954 | 0.54258 | 0.54621 | 0.3 | 35.65
Comm | 0.035654 | 0.058364 | 0.079543 | 7.0 | 3.83
Output | 0.00048494 | 0.00065351 | 0.0011017 | 0.0 | 0.04
Modify | 0.0090034 | 0.0090633 | 0.0091114 | 0.0 | 0.60
Other | | 0.005168 | | | 0.34
Nlocal: 8160 ave 8163 max 8157 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11605.8 ave 11615 max 11593 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.22553e+06 ave 1.22734e+06 max 1.22455e+06 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 4902132
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:01

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bench/POTENTIALS/log.16Mar18.spce.1
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
1 by 1 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
replicate 2 4 1
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
1 by 1 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Time spent = 0.0105426 secs
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268801
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0331015
estimated relative force accuracy = 9.96841e-05
using double precision FFTs
3d grid and FFT values/proc = 91977 55296
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.8
ghost atom cutoff = 11.8
binsize = 5.9, bins = 13 25 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 105.1 | 105.1 | 105.1 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 516.17807
50 264.98553 -136986.74 0 -118030.61 -440.29256
100 274.45966 -136364.57 0 -116730.69 -128.61949
Loop time of 20.172 on 1 procs for 100 steps with 36000 atoms
Performance: 0.857 ns/day, 28.017 hours/ns, 4.957 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.818 | 15.818 | 15.818 | 0.0 | 78.41
Bond | 7.8201e-05 | 7.8201e-05 | 7.8201e-05 | 0.0 | 0.00
Kspace | 1.966 | 1.966 | 1.966 | 0.0 | 9.75
Neigh | 2.0639 | 2.0639 | 2.0639 | 0.0 | 10.23
Comm | 0.043918 | 0.043918 | 0.043918 | 0.0 | 0.22
Output | 0.00025153 | 0.00025153 | 0.00025153 | 0.0 | 0.00
Modify | 0.27056 | 0.27056 | 0.27056 | 0.0 | 1.34
Other | | 0.009522 | | | 0.05
Nlocal: 36000 ave 36000 max 36000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 56963 ave 56963 max 56963 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.24625e+07 ave 1.24625e+07 max 1.24625e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12462451
Ave neighs/atom = 346.179
Ave special neighs/atom = 2
Neighbor list builds = 9
Dangerous builds = 6
Total wall time: 0:00:20

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
2 by 2 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
replicate 2 4 1
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
1 by 4 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Time spent = 0.00535488 secs
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268801
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0331015
estimated relative force accuracy = 9.96841e-05
using double precision FFTs
3d grid and FFT values/proc = 27993 13824
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.8
ghost atom cutoff = 11.8
binsize = 5.9, bins = 13 25 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 37.74 | 37.74 | 37.74 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 516.17807
50 264.98553 -136986.74 0 -118030.61 -440.29256
100 274.45966 -136364.57 0 -116730.69 -128.61949
Loop time of 5.43807 on 4 procs for 100 steps with 36000 atoms
Performance: 3.178 ns/day, 7.553 hours/ns, 18.389 timesteps/s
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 | 4.0016 | 4.0968 | 4.1706 | 3.3 | 75.34
Bond | 7.1049e-05 | 8.5771e-05 | 0.00010586 | 0.0 | 0.00
Kspace | 0.56386 | 0.63614 | 0.73036 | 8.3 | 11.70
Neigh | 0.52575 | 0.52587 | 0.52594 | 0.0 | 9.67
Comm | 0.045847 | 0.047308 | 0.048331 | 0.4 | 0.87
Output | 9.1314e-05 | 0.00012183 | 0.00021172 | 0.0 | 0.00
Modify | 0.12561 | 0.1258 | 0.12605 | 0.1 | 2.31
Other | | 0.005944 | | | 0.11
Nlocal: 9000 ave 9002 max 8998 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 24134.2 ave 24184 max 24062 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 3.11561e+06 ave 3.11676e+06 max 3.11446e+06 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 12462451
Ave neighs/atom = 346.179
Ave special neighs/atom = 2
Neighbor list builds = 9
Dangerous builds = 6
Total wall time: 0:00:05