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update BOP input and log files

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Axel Kohlmeyer
2018-03-21 19:45:52 -04:00
parent 9f785a4f0b
commit 07a8e31623
3 changed files with 49 additions and 45 deletions
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2
bench/POTENTIALS/in.bop
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@ -13,7 +13,7 @@ create_box 2 box
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2 create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
pair_style bop pair_style bop
pair_coeff * * CdTe.bop Cd Te pair_coeff * * CdTe.bop.table Cd Te
mass 1 112.4 mass 1 112.4
mass 2 127.6 mass 2 127.6

42
bench/POTENTIALS/log.16Mar18.bop.1
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@ -14,10 +14,12 @@ Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2 create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
Created 32000 atoms Created 32000 atoms
Time spent = 0.00193691 secs Time spent = 0.00191426 secs
pair_style bop pair_style bop
pair_coeff * * CdTe.bop Cd Te 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
mass 1 112.4 mass 1 112.4
mass 2 127.6 mass 2 127.6
@ -36,33 +38,33 @@ run 100
Neighbor list info ... Neighbor list info ...
update every 1 steps, delay 5 steps, check yes update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.1 master list distance cutoff = 5
ghost atom cutoff = 14.7 ghost atom cutoff = 14.7
binsize = 1.05, bins = 131 131 66 binsize = 2.5, bins = 55 55 28
1 neighbor lists, perpetual/occasional/extra = 1 0 0 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair bop, perpetual (1) pair bop, perpetual
attributes: full, newton on, ghost attributes: full, newton on, ghost
pair build: full/bin/ghost pair build: full/bin/ghost
stencil: full/ghost/bin/3d stencil: full/ghost/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 27.17 | 27.17 | 27.17 Mbytes Per MPI rank memory allocation (min/avg/max) = 19.39 | 19.39 | 19.39 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 1000 0 0 4136.1954 3468.3214 0 1000 -69539.487 0 -65403.292 3473.2595
100 1000 0 0 4136.1954 3468.3214 100 572.16481 -67769.936 0 -65403.35 1838.6993
Loop time of 0.486724 on 1 procs for 100 steps with 32000 atoms Loop time of 24.1696 on 1 procs for 100 steps with 32000 atoms
Performance: 17.751 ns/day, 1.352 hours/ns, 205.455 timesteps/s Performance: 0.357 ns/day, 67.138 hours/ns, 4.137 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.064003 | 0.064003 | 0.064003 | 0.0 | 13.15 Pair | 23.355 | 23.355 | 23.355 | 0.0 | 96.63
Neigh | 0.36615 | 0.36615 | 0.36615 | 0.0 | 75.23 Neigh | 0.7545 | 0.7545 | 0.7545 | 0.0 | 3.12
Comm | 0.024469 | 0.024469 | 0.024469 | 0.0 | 5.03 Comm | 0.026978 | 0.026978 | 0.026978 | 0.0 | 0.11
Output | 0.00010872 | 0.00010872 | 0.00010872 | 0.0 | 0.02 Output | 0.0001111 | 0.0001111 | 0.0001111 | 0.0 | 0.00
Modify | 0.023037 | 0.023037 | 0.023037 | 0.0 | 4.73 Modify | 0.024145 | 0.024145 | 0.024145 | 0.0 | 0.10
Other | | 0.008954 | | | 1.84 Other | | 0.009326 | | | 0.04
Nlocal: 32000 ave 32000 max 32000 min Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -70,11 +72,11 @@ Nghost: 35071 ave 35071 max 35071 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min FullNghs: 141288 ave 141288 max 141288 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0 Total # of neighbors = 141288
Ave neighs/atom = 0 Ave neighs/atom = 4.41525
Neighbor list builds = 14 Neighbor list builds = 14
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:00 Total wall time: 0:00:24

50
bench/POTENTIALS/log.16Mar18.bop.4
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@ -14,10 +14,12 @@ Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
2 by 2 by 1 MPI processor grid 2 by 2 by 1 MPI processor grid
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2 create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
Created 32000 atoms Created 32000 atoms
Time spent = 0.000608683 secs Time spent = 0.000597477 secs
pair_style bop pair_style bop
pair_coeff * * CdTe.bop Cd Te 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
mass 1 112.4 mass 1 112.4
mass 2 127.6 mass 2 127.6
@ -36,45 +38,45 @@ run 100
Neighbor list info ... Neighbor list info ...
update every 1 steps, delay 5 steps, check yes update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.1 master list distance cutoff = 5
ghost atom cutoff = 14.7 ghost atom cutoff = 14.7
binsize = 1.05, bins = 131 131 66 binsize = 2.5, bins = 55 55 28
1 neighbor lists, perpetual/occasional/extra = 1 0 0 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair bop, perpetual (1) pair bop, perpetual
attributes: full, newton on, ghost attributes: full, newton on, ghost
pair build: full/bin/ghost pair build: full/bin/ghost
stencil: full/ghost/bin/3d stencil: full/ghost/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.5 | 11.5 | 11.5 Mbytes Per MPI rank memory allocation (min/avg/max) = 8.497 | 8.497 | 8.497 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 1000 0 0 4136.1954 3468.3214 0 1000 -69539.487 0 -65403.292 3473.2595
100 1000 0 0 4136.1954 3468.3214 100 572.16481 -67769.936 0 -65403.35 1838.6993
Loop time of 0.203971 on 4 procs for 100 steps with 32000 atoms Loop time of 6.50033 on 4 procs for 100 steps with 32000 atoms
Performance: 42.359 ns/day, 0.567 hours/ns, 490.266 timesteps/s 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 99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.023027 | 0.023097 | 0.023184 | 0.0 | 11.32 Pair | 5.7879 | 5.975 | 6.1607 | 5.4 | 91.92
Neigh | 0.14493 | 0.14556 | 0.14659 | 0.2 | 71.36 Neigh | 0.27603 | 0.27621 | 0.27647 | 0.0 | 4.25
Comm | 0.020405 | 0.021607 | 0.022162 | 0.5 | 10.59 Comm | 0.049869 | 0.23531 | 0.42241 | 27.2 | 3.62
Output | 4.8161e-05 | 4.9949e-05 | 5.4359e-05 | 0.0 | 0.02 Output | 4.9829e-05 | 5.9724e-05 | 8.5592e-05 | 0.0 | 0.00
Modify | 0.0089087 | 0.009183 | 0.0093095 | 0.2 | 4.50 Modify | 0.0089927 | 0.0090921 | 0.0092406 | 0.1 | 0.14
Other | | 0.004473 | | | 2.19 Other | | 0.004665 | | | 0.07
Nlocal: 8000 ave 8022 max 7985 min Nlocal: 8000 ave 8006 max 7994 min
Histogram: 1 1 0 0 1 0 0 0 0 1 Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 15171 ave 15186 max 15149 min Nghost: 15171 ave 15177 max 15165 min
Histogram: 1 0 0 0 0 1 0 0 1 1 Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 0 ave 0 max 0 min FullNghs: 35322 ave 35412 max 35267 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 0 Total # of neighbors = 141288
Ave neighs/atom = 0 Ave neighs/atom = 4.41525
Neighbor list builds = 14 Neighbor list builds = 14
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:00 Total wall time: 0:00:06