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update log files for peptide, peri, pour and python examples

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This commit is contained in:
Axel Kohlmeyer
2018-11-29 14:51:25 -05:00
parent cef4164460
commit 46bf4b7efb
39 changed files with 1843 additions and 1353 deletions
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92
examples/peptide/log.5Oct16.peptide.g++.1 → examples/peptide/log.27Nov18.peptide.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide # Solvated 5-mer peptide
units real units real
@ -70,7 +71,7 @@ group peptide type <= 12
run 300 run 300
PPPM initialization ... PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725 G vector (1/distance) = 0.268725
grid = 15 15 15 grid = 15 15 15
stencil order = 5 stencil order = 5
@ -79,12 +80,17 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
using double precision FFTs using double precision FFTs
3d grid and FFT values/proc = 10648 3375 3d grid and FFT values/proc = 10648 3375
Neighbor list info ... Neighbor list info ...
1 neighbor list requests
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 = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta) on step 0 SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05 4 1.111 1.44264e-05
6 0.996998 7.26967e-06 6 0.996998 7.26967e-06
@ -94,13 +100,13 @@ SHAKE stats (type/ave/delta) on step 0
14 0.96 0 14 0.96 0
18 0.957206 4.37979e-05 18 0.957206 4.37979e-05
31 104.519 0.00396029 31 104.519 0.00396029
Memory usage per processor = 15.5934 Mbytes Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- ---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112
---------------- Step 50 ----- CPU = 0.9457 (sec) ---------------- ---------------- Step 50 ----- CPU = 1.0190 (sec) ----------------
TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745 TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745
PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365 PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785 E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785
@ -114,77 +120,77 @@ SHAKE stats (type/ave/delta) on step 100
14 0.96 0 14 0.96 0
18 0.957201 5.3796e-06 18 0.957201 5.3796e-06
31 104.52 0.000502278 31 104.52 0.000502278
---------------- Step 100 ----- CPU = 1.9163 (sec) ---------------- ---------------- Step 100 ----- CPU = 2.0505 (sec) ----------------
TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663 TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663
PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429 PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273
E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6819 E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6819
---------------- Step 150 ----- CPU = 2.9286 (sec) ---------------- ---------------- Step 150 ----- CPU = 3.1208 (sec) ----------------
TotEng = -5287.2798 KinEng = 1098.6028 Temp = 273.0737 TotEng = -5287.2799 KinEng = 1098.6028 Temp = 273.0737
PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594 PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594
E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675 E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675
E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1829 E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1829
SHAKE stats (type/ave/delta) on step 200 SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18698e-07 4 1.111 2.18698e-07
6 0.997 1.50562e-07 6 0.997 1.50563e-07
8 1.08 6.57498e-08 8 1.08 6.57499e-08
10 1.111 5.54188e-07 10 1.111 5.54188e-07
12 1.08 1.98839e-07 12 1.08 1.9884e-07
14 0.96 0 14 0.96 0
18 0.957201 3.59627e-06 18 0.957201 3.59627e-06
31 104.52 0.000388335 31 104.52 0.000388335
---------------- Step 200 ----- CPU = 3.8703 (sec) ---------------- ---------------- Step 200 ----- CPU = 4.1320 (sec) ----------------
TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421 TotEng = -5308.4468 KinEng = 1100.4873 Temp = 273.5421
PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040 PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040
E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221 E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221
E_coul = 26736.1319 E_long = -33902.3837 Press = -1470.3400 E_coul = 26736.1319 E_long = -33902.3837 Press = -1470.3401
---------------- Step 250 ----- CPU = 4.8652 (sec) ---------------- ---------------- Step 250 ----- CPU = 5.2131 (sec) ----------------
TotEng = -5294.1569 KinEng = 1071.0938 Temp = 266.2359 TotEng = -5294.1568 KinEng = 1071.0940 Temp = 266.2360
PotEng = -6365.2507 E_bond = 14.2013 E_angle = 39.1996 PotEng = -6365.2508 E_bond = 14.2013 E_angle = 39.1996
E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4590 E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4590
E_coul = 26714.0040 E_long = -33908.7139 Press = -189.6059 E_coul = 26714.0039 E_long = -33908.7139 Press = -189.6057
SHAKE stats (type/ave/delta) on step 300 SHAKE stats (type/ave/delta) on step 300
4 1.111 3.79044e-06 4 1.111 3.79043e-06
6 0.997001 3.6052e-06 6 0.997001 3.6052e-06
8 1.08 2.09369e-06 8 1.08 2.09369e-06
10 1.111 5.6484e-06 10 1.111 5.6484e-06
12 1.08 2.10677e-06 12 1.08 2.10676e-06
14 0.96 0 14 0.96 0
18 0.957202 7.72576e-06 18 0.957202 7.72571e-06
31 104.52 0.000806204 31 104.52 0.000806203
---------------- Step 300 ----- CPU = 5.8596 (sec) ---------------- ---------------- Step 300 ----- CPU = 6.2919 (sec) ----------------
TotEng = -5251.3637 KinEng = 1123.7718 Temp = 279.3298 TotEng = -5251.3662 KinEng = 1123.7719 Temp = 279.3299
PotEng = -6375.1355 E_bond = 14.2206 E_angle = 38.4274 PotEng = -6375.1381 E_bond = 14.2206 E_angle = 38.4274
E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3473 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3476
E_coul = 26745.4074 E_long = -33909.0791 Press = -471.5505 E_coul = 26745.4045 E_long = -33909.0791 Press = -471.5904
Loop time of 5.85959 on 1 procs for 300 steps with 2004 atoms Loop time of 6.29195 on 1 procs for 300 steps with 2004 atoms
Performance: 8.847 ns/day, 2.713 hours/ns, 51.198 timesteps/s Performance: 8.239 ns/day, 2.913 hours/ns, 47.680 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads 99.0% 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 | 4.6289 | 4.6289 | 4.6289 | 0.0 | 79.00 Pair | 4.8228 | 4.8228 | 4.8228 | 0.0 | 76.65
Bond | 0.013405 | 0.013405 | 0.013405 | 0.0 | 0.23 Bond | 0.0094063 | 0.0094063 | 0.0094063 | 0.0 | 0.15
Kspace | 0.47821 | 0.47821 | 0.47821 | 0.0 | 8.16 Kspace | 0.523 | 0.523 | 0.523 | 0.0 | 8.31
Neigh | 0.64447 | 0.64447 | 0.64447 | 0.0 | 11.00 Neigh | 0.82602 | 0.82602 | 0.82602 | 0.0 | 13.13
Comm | 0.026137 | 0.026137 | 0.026137 | 0.0 | 0.45 Comm | 0.03742 | 0.03742 | 0.03742 | 0.0 | 0.59
Output | 0.00018501 | 0.00018501 | 0.00018501 | 0.0 | 0.00 Output | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.00
Modify | 0.062095 | 0.062095 | 0.062095 | 0.0 | 1.06 Modify | 0.068182 | 0.068182 | 0.068182 | 0.0 | 1.08
Other | | 0.006195 | | | 0.11 Other | | 0.00493 | | | 0.08
Nlocal: 2004 ave 2004 max 2004 min Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11185 ave 11185 max 11185 min Nghost: 11185 ave 11185 max 11185 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708018 ave 708018 max 708018 min Neighs: 708019 ave 708019 max 708019 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 = 708018 Total # of neighbors = 708019
Ave neighs/atom = 353.302 Ave neighs/atom = 353.303
Ave special neighs/atom = 2.34032 Ave special neighs/atom = 2.34032
Neighbor list builds = 26 Neighbor list builds = 26
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:05 Total wall time: 0:00:06

100
examples/peptide/log.5Oct16.peptide.g++.4 → examples/peptide/log.27Nov18.peptide.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide # Solvated 5-mer peptide
units real units real
@ -70,7 +71,7 @@ group peptide type <= 12
run 300 run 300
PPPM initialization ... PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725 G vector (1/distance) = 0.268725
grid = 15 15 15 grid = 15 15 15
stencil order = 5 stencil order = 5
@ -79,12 +80,17 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
using double precision FFTs using double precision FFTs
3d grid and FFT values/proc = 4312 960 3d grid and FFT values/proc = 4312 960
Neighbor list info ... Neighbor list info ...
1 neighbor list requests
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 = 12 master list distance cutoff = 12
ghost atom cutoff = 12 ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5 binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta) on step 0 SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05 4 1.111 1.44264e-05
6 0.996998 7.26967e-06 6 0.996998 7.26967e-06
@ -94,13 +100,13 @@ SHAKE stats (type/ave/delta) on step 0
14 0.96 0 14 0.96 0
18 0.957206 4.37979e-05 18 0.957206 4.37979e-05
31 104.519 0.00396029 31 104.519 0.00396029
Memory usage per processor = 14.8928 Mbytes Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- ---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112
---------------- Step 50 ----- CPU = 0.2741 (sec) ---------------- ---------------- Step 50 ----- CPU = 0.2858 (sec) ----------------
TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745 TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745
PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365 PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785 E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785
@ -114,65 +120,65 @@ SHAKE stats (type/ave/delta) on step 100
14 0.96 0 14 0.96 0
18 0.957201 5.3796e-06 18 0.957201 5.3796e-06
31 104.52 0.000502278 31 104.52 0.000502278
---------------- Step 100 ----- CPU = 0.5371 (sec) ---------------- ---------------- Step 100 ----- CPU = 0.5744 (sec) ----------------
TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663 TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663
PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429 PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273
E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6819 E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6820
---------------- Step 150 ----- CPU = 0.8054 (sec) ---------------- ---------------- Step 150 ----- CPU = 0.8756 (sec) ----------------
TotEng = -5287.2799 KinEng = 1098.6028 Temp = 273.0737 TotEng = -5287.2798 KinEng = 1098.6028 Temp = 273.0737
PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594 PotEng = -6385.8826 E_bond = 17.4925 E_angle = 32.8594
E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675 E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675
E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1830 E_coul = 26717.2656 E_long = -33907.2821 Press = -333.1828
SHAKE stats (type/ave/delta) on step 200 SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18699e-07 4 1.111 2.18699e-07
6 0.997 1.50563e-07 6 0.997 1.50563e-07
8 1.08 6.57501e-08 8 1.08 6.575e-08
10 1.111 5.54188e-07 10 1.111 5.54187e-07
12 1.08 1.98841e-07 12 1.08 1.9884e-07
14 0.96 0 14 0.96 0
18 0.957201 3.59627e-06 18 0.957201 3.59627e-06
31 104.52 0.000388336 31 104.52 0.000388335
---------------- Step 200 ----- CPU = 1.0652 (sec) ---------------- ---------------- Step 200 ----- CPU = 1.1602 (sec) ----------------
TotEng = -5308.4465 KinEng = 1100.4875 Temp = 273.5422 TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421
PotEng = -6408.9340 E_bond = 18.2714 E_angle = 33.3040 PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040
E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221 E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221
E_coul = 26736.1321 E_long = -33902.3837 Press = -1470.3400 E_coul = 26736.1320 E_long = -33902.3837 Press = -1470.3400
---------------- Step 250 ----- CPU = 1.3409 (sec) ---------------- ---------------- Step 250 ----- CPU = 1.4629 (sec) ----------------
TotEng = -5294.1570 KinEng = 1071.0939 Temp = 266.2360 TotEng = -5294.1567 KinEng = 1071.0938 Temp = 266.2359
PotEng = -6365.2509 E_bond = 14.2013 E_angle = 39.1996 PotEng = -6365.2505 E_bond = 14.2013 E_angle = 39.1996
E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4591 E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4589
E_coul = 26714.0037 E_long = -33908.7139 Press = -189.6059 E_coul = 26714.0043 E_long = -33908.7139 Press = -189.6068
SHAKE stats (type/ave/delta) on step 300 SHAKE stats (type/ave/delta) on step 300
4 1.111 3.79043e-06 4 1.111 3.79043e-06
6 0.997001 3.60519e-06 6 0.997001 3.6052e-06
8 1.08 2.09368e-06 8 1.08 2.09369e-06
10 1.111 5.64839e-06 10 1.111 5.6484e-06
12 1.08 2.10676e-06 12 1.08 2.10677e-06
14 0.96 0 14 0.96 0
18 0.957202 7.72573e-06 18 0.957202 7.72579e-06
31 104.52 0.000806208 31 104.52 0.000806203
---------------- Step 300 ----- CPU = 1.6199 (sec) ---------------- ---------------- Step 300 ----- CPU = 1.7662 (sec) ----------------
TotEng = -5251.3639 KinEng = 1123.7721 Temp = 279.3299 TotEng = -5251.3662 KinEng = 1123.7712 Temp = 279.3297
PotEng = -6375.1360 E_bond = 14.2206 E_angle = 38.4274 PotEng = -6375.1374 E_bond = 14.2206 E_angle = 38.4274
E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3470 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3474
E_coul = 26745.4071 E_long = -33909.0790 Press = -471.5569 E_coul = 26745.4053 E_long = -33909.0790 Press = -471.5904
Loop time of 1.61992 on 4 procs for 300 steps with 2004 atoms Loop time of 1.76629 on 4 procs for 300 steps with 2004 atoms
Performance: 32.002 ns/day, 0.750 hours/ns, 185.194 timesteps/s Performance: 29.350 ns/day, 0.818 hours/ns, 169.847 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads 98.8% 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 | 1.1484 | 1.17 | 1.1865 | 1.5 | 72.23 Pair | 1.2044 | 1.2351 | 1.2721 | 2.3 | 69.92
Bond | 0.0011752 | 0.003831 | 0.0069602 | 4.0 | 0.24 Bond | 0.0013924 | 0.0034139 | 0.0057151 | 3.2 | 0.19
Kspace | 0.16316 | 0.1798 | 0.20413 | 3.9 | 11.10 Kspace | 0.17476 | 0.21195 | 0.2407 | 5.3 | 12.00
Neigh | 0.16885 | 0.16895 | 0.16902 | 0.0 | 10.43 Neigh | 0.21273 | 0.21286 | 0.21293 | 0.0 | 12.05
Comm | 0.046479 | 0.047215 | 0.047759 | 0.2 | 2.91 Comm | 0.042942 | 0.046074 | 0.047584 | 0.9 | 2.61
Output | 0.00024033 | 0.00025702 | 0.00030375 | 0.2 | 0.02 Output | 0.00025845 | 0.00033492 | 0.00055695 | 0.0 | 0.02
Modify | 0.04556 | 0.045949 | 0.046353 | 0.2 | 2.84 Modify | 0.049944 | 0.051619 | 0.054278 | 0.8 | 2.92
Other | | 0.003923 | | | 0.24 Other | | 0.004988 | | | 0.28
Nlocal: 501 ave 508 max 490 min Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1 Histogram: 1 0 0 0 0 0 1 1 0 1

45
examples/peri/log.6Jul17.peri.eps.g++.1 → examples/peri/log.27Nov18.peri.eps.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile # small Peridynamic cylinder hit by projectile
@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 region target create_atoms 1 region target
Created 3487 atoms Created 3487 atoms
Time spent = 0.00100374 secs
pair_style peri/eps pair_style peri/eps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8 pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8
@ -72,44 +73,44 @@ Peridynamic bonds:
Per MPI rank memory allocation (min/avg/max) = 50.29 | 50.29 | 50.29 Mbytes Per MPI rank memory allocation (min/avg/max) = 50.29 | 50.29 | 50.29 Mbytes
Step Temp E_pair E_mol TotEng Press Volume Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07 0 0 0 0 0 0 5.0030006e-07
100 8.3466308e+24 247103.03 0 849681.45 8.0295601e+11 5.0030006e-07 100 9.7403734e+24 248692.93 0 951891.49 9.3703576e+11 5.0030006e-07
200 1.1784921e+27 1098605.6 0 86178912 1.0246967e+14 5.5353162e-07 200 1.220493e+27 1011231.9 0 89123756 1.0636834e+14 5.5224782e-07
300 2.6263212e+27 4118581.6 0 1.9372377e+08 1.662415e+14 7.6036043e-07 300 2.7274231e+27 4549425.2 0 2.0145358e+08 1.7250255e+14 7.6097098e-07
400 3.3085888e+27 9397203.3 0 2.4825816e+08 1.561692e+14 1.0196674e-06 400 3.3665092e+27 13347641 0 2.5639011e+08 1.5828139e+14 1.0236725e-06
500 3.9151799e+27 18408722 0 3.0106204e+08 1.5298661e+14 1.2317127e-06 500 3.8995641e+27 14196430 0 2.9572238e+08 1.5145191e+14 1.2392314e-06
600 6.2936721e+27 11346143 0 4.6571282e+08 1.9645007e+14 1.5419242e-06 600 4.6668832e+27 23135807 0 3.6005775e+08 1.478168e+14 1.5195473e-06
700 1.2721597e+28 3830223.2 0 9.2225588e+08 3.0235577e+14 2.0250441e-06 700 1.1847301e+28 8126622 0 8.6343315e+08 2.9204301e+14 1.9524671e-06
800 1.3190107e+28 2831668.7 0 9.5508099e+08 2.4853932e+14 2.5542553e-06 800 1.2328889e+28 4646514.3 0 8.9472087e+08 2.2467312e+14 2.6410944e-06
900 1.3166045e+28 1911868.6 0 9.524241e+08 1.9729649e+14 3.2117896e-06 900 1.2277283e+28 2668877.7 0 8.8901759e+08 1.671177e+14 3.5358262e-06
1000 1.3159578e+28 1995827.6 0 9.5204114e+08 1.6722163e+14 3.7875695e-06 1000 1.2260912e+28 1587002.9 0 8.8675386e+08 1.29707e+14 4.5495712e-06
Loop time of 72.5574 on 1 procs for 1000 steps with 3487 atoms Loop time of 34.8143 on 1 procs for 1000 steps with 3487 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 96.7% 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 | 71.779 | 71.779 | 71.779 | 0.0 | 98.93 Pair | 34.045 | 34.045 | 34.045 | 0.0 | 97.79
Neigh | 0.5596 | 0.5596 | 0.5596 | 0.0 | 0.77 Neigh | 0.63254 | 0.63254 | 0.63254 | 0.0 | 1.82
Comm | 0.0040631 | 0.0040631 | 0.0040631 | 0.0 | 0.01 Comm | 0.0025852 | 0.0025852 | 0.0025852 | 0.0 | 0.01
Output | 0.00056624 | 0.00056624 | 0.00056624 | 0.0 | 0.00 Output | 0.00035906 | 0.00035906 | 0.00035906 | 0.0 | 0.00
Modify | 0.18403 | 0.18403 | 0.18403 | 0.0 | 0.25 Modify | 0.11784 | 0.11784 | 0.11784 | 0.0 | 0.34
Other | | 0.03016 | | | 0.04 Other | | 0.01593 | | | 0.05
Nlocal: 3487 ave 3487 max 3487 min Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min Nghost: 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
Neighs: 569177 ave 569177 max 569177 min Neighs: 546591 ave 546591 max 546591 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 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 = 1209076 Total # of neighbors = 1209076
Ave neighs/atom = 346.738 Ave neighs/atom = 346.738
Neighbor list builds = 40 Neighbor list builds = 45
Dangerous builds = 0 Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:12 Total wall time: 0:00:34

53
examples/peri/log.6Jul17.peri.eps.g++.4 → examples/peri/log.27Nov18.peri.eps.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile # small Peridynamic cylinder hit by projectile
@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
2 by 1 by 2 MPI processor grid 2 by 1 by 2 MPI processor grid
create_atoms 1 region target create_atoms 1 region target
Created 3487 atoms Created 3487 atoms
Time spent = 0.000587225 secs
pair_style peri/eps pair_style peri/eps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8 pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8
@ -72,44 +73,44 @@ Peridynamic bonds:
Per MPI rank memory allocation (min/avg/max) = 44.77 | 45.04 | 45.14 Mbytes Per MPI rank memory allocation (min/avg/max) = 44.77 | 45.04 | 45.14 Mbytes
Step Temp E_pair E_mol TotEng Press Volume Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07 0 0 0 0 0 0 5.0030006e-07
100 8.3466308e+24 247103.03 0 849681.45 8.0295601e+11 5.0030006e-07 100 2.3613868e+26 2297417.8 0 19345263 2.2716828e+13 5.0030006e-07
200 1.1784921e+27 1098605.6 0 86178912 1.0246967e+14 5.5353162e-07 200 3.9573281e+27 28896934 0 3.1459311e+08 3.6928392e+14 5.1576607e-07
300 2.6263212e+27 4118581.6 0 1.9372377e+08 1.662415e+14 7.6036043e-07 300 8.7809254e+27 38915502 0 6.7284747e+08 6.4053658e+14 6.5979263e-07
400 3.3085888e+27 9397203.3 0 2.4825816e+08 1.561692e+14 1.0196674e-06 400 1.3210949e+28 35344681 0 9.8909868e+08 7.0953264e+14 8.9613355e-07
500 3.9151799e+27 18408722 0 3.0106204e+08 1.5298661e+14 1.2317127e-06 500 1.7324732e+28 21092574 0 1.2718379e+09 7.4083646e+14 1.1255254e-06
600 6.2936721e+27 11346143 0 4.6571282e+08 1.9645007e+14 1.5419242e-06 600 2.1194595e+28 11349855 0 1.5414769e+09 6.6250164e+14 1.5397467e-06
700 1.2721597e+28 3830223.2 0 9.2225588e+08 3.0235577e+14 2.0250441e-06 700 2.316318e+28 2515600.8 0 1.6747631e+09 5.0111859e+14 2.2246862e-06
800 1.3190107e+28 2831668.7 0 9.5508099e+08 2.4853932e+14 2.5542553e-06 800 2.363319e+28 1731461.2 0 1.7079109e+09 4.0277805e+14 2.8240193e-06
900 1.3166045e+28 1911869.3 0 9.524241e+08 1.9729649e+14 3.2117896e-06 900 2.3668922e+28 870525.69 0 1.7096296e+09 3.1718257e+14 3.5915363e-06
1000 1.3159578e+28 1995833.9 0 9.5204114e+08 1.6722163e+14 3.7875695e-06 1000 2.3654433e+28 789707.52 0 1.7085028e+09 2.5538989e+14 4.4577935e-06
Loop time of 29.6266 on 4 procs for 1000 steps with 3487 atoms Loop time of 5.11902 on 4 procs for 1000 steps with 3487 atoms
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads 90.5% 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 | 25.905 | 26.18 | 26.326 | 3.2 | 88.37 Pair | 3.1161 | 3.9019 | 4.7582 | 30.3 | 76.22
Neigh | 0.15352 | 0.1872 | 0.22394 | 7.6 | 0.63 Neigh | 0.0701 | 0.080061 | 0.089326 | 3.0 | 1.56
Comm | 3.0374 | 3.1471 | 3.3731 | 7.5 | 10.62 Comm | 0.22296 | 1.0644 | 1.8357 | 57.0 | 20.79
Output | 0.00047588 | 0.00062978 | 0.00097752 | 0.0 | 0.00 Output | 0.00028729 | 0.00058514 | 0.0013847 | 0.0 | 0.01
Modify | 0.073521 | 0.081854 | 0.093222 | 2.7 | 0.28 Modify | 0.041605 | 0.043229 | 0.044626 | 0.6 | 0.84
Other | | 0.02989 | | | 0.10 Other | | 0.02887 | | | 0.56
Nlocal: 871.75 ave 908 max 838 min Nlocal: 871.75 ave 947 max 799 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 1368.25 ave 1402 max 1332 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 142294 ave 159233 max 124729 min
Histogram: 2 0 0 0 0 0 0 0 0 2 Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1011 ave 1087 max 936 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91271.8 ave 92650 max 90045 min
Histogram: 1 1 0 0 0 0 1 0 0 1
FullNghs: 302269 ave 346070 max 260820 min FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 1209076 Total # of neighbors = 1209076
Ave neighs/atom = 346.738 Ave neighs/atom = 346.738
Neighbor list builds = 40 Neighbor list builds = 24
Dangerous builds = 0 Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:29 Total wall time: 0:00:05

43
examples/peri/log.6Jul17.peri.lps.g++.1 → examples/peri/log.27Nov18.peri.lps.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile # small Peridynamic cylinder hit by projectile
@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 region target create_atoms 1 region target
Created 3487 atoms Created 3487 atoms
Time spent = 0.00101972 secs
pair_style peri/lps pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
@ -72,35 +73,35 @@ Peridynamic bonds:
Per MPI rank memory allocation (min/avg/max) = 34.91 | 34.91 | 34.91 Mbytes Per MPI rank memory allocation (min/avg/max) = 34.91 | 34.91 | 34.91 Mbytes
Step Temp E_pair E_mol TotEng Press Volume Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07 0 0 0 0 0 0 5.0030006e-07
100 1.684629e+24 133446.65 0 255067.11 1.6206343e+11 5.0030006e-07 100 2.0851116e+24 132640.06 0 283173.04 2.0059034e+11 5.0030006e-07
200 1.1380148e+27 684478.05 0 82842557 9.9178307e+13 5.5225839e-07 200 1.1421456e+27 733330.77 0 83189631 9.9580342e+13 5.5202528e-07
300 2.5659218e+27 5944645.9 0 1.9118934e+08 1.6231114e+14 7.6086254e-07 300 2.5694547e+27 6192900.7 0 1.9169265e+08 1.6253438e+14 7.6086363e-07
400 2.9916164e+27 13677434 0 2.2965481e+08 1.4081705e+14 1.0224963e-06 400 3.0375813e+27 7013786 0 2.2630957e+08 1.4286927e+14 1.0232935e-06
500 3.3570343e+27 11130894 0 2.5348933e+08 1.2577633e+14 1.2846002e-06 500 3.4006176e+27 5347550.9 0 2.5085245e+08 1.2727968e+14 1.2859078e-06
600 3.9506165e+27 6986672.5 0 2.9219831e+08 1.2659956e+14 1.5019096e-06 600 3.7690314e+27 8040942.9 0 2.8014319e+08 1.2082801e+14 1.5013199e-06
700 7.8366157e+27 11716082 0 5.7747436e+08 1.9480124e+14 1.9361899e-06 700 7.6688193e+27 8282231 0 5.6192658e+08 1.9074258e+14 1.935049e-06
800 8.2483231e+27 4671647.2 0 6.0015282e+08 1.7040064e+14 2.3297298e-06 800 8.2147783e+27 3439316.5 0 5.9649874e+08 1.6954721e+14 2.3319342e-06
900 8.2720965e+27 1249680.9 0 5.9844715e+08 1.4117116e+14 2.8202052e-06 900 8.1767735e+27 1827759 0 5.9214346e+08 1.38875e+14 2.8337987e-06
1000 8.2441462e+27 2278265.6 0 5.9745788e+08 1.234652e+14 3.213751e-06 1000 8.1478191e+27 1415059 0 5.8964042e+08 1.2086486e+14 3.2445347e-06
Loop time of 62.3833 on 1 procs for 1000 steps with 3487 atoms Loop time of 27.5943 on 1 procs for 1000 steps with 3487 atoms
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads 99.0% 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 | 61.608 | 61.608 | 61.608 | 0.0 | 98.76 Pair | 26.946 | 26.946 | 26.946 | 0.0 | 97.65
Neigh | 0.57177 | 0.57177 | 0.57177 | 0.0 | 0.92 Neigh | 0.52412 | 0.52412 | 0.52412 | 0.0 | 1.90
Comm | 0.0030825 | 0.0030825 | 0.0030825 | 0.0 | 0.00 Comm | 0.001683 | 0.001683 | 0.001683 | 0.0 | 0.01
Output | 0.00051951 | 0.00051951 | 0.00051951 | 0.0 | 0.00 Output | 0.00032282 | 0.00032282 | 0.00032282 | 0.0 | 0.00
Modify | 0.17278 | 0.17278 | 0.17278 | 0.0 | 0.28 Modify | 0.10716 | 0.10716 | 0.10716 | 0.0 | 0.39
Other | | 0.02745 | | | 0.04 Other | | 0.01544 | | | 0.06
Nlocal: 3487 ave 3487 max 3487 min Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min Nghost: 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
Neighs: 576568 ave 576568 max 576568 min Neighs: 578212 ave 578212 max 578212 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -112,4 +113,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:02 Total wall time: 0:00:27

55
examples/peri/log.6Jul17.peri.lps.g++.4 → examples/peri/log.27Nov18.peri.lps.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile # small Peridynamic cylinder hit by projectile
@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
2 by 1 by 2 MPI processor grid 2 by 1 by 2 MPI processor grid
create_atoms 1 region target create_atoms 1 region target
Created 3487 atoms Created 3487 atoms
Time spent = 0.000591278 secs
pair_style peri/lps pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
@ -72,44 +73,44 @@ Peridynamic bonds:
Per MPI rank memory allocation (min/avg/max) = 29.4 | 29.66 | 29.76 Mbytes Per MPI rank memory allocation (min/avg/max) = 29.4 | 29.66 | 29.76 Mbytes
Step Temp E_pair E_mol TotEng Press Volume Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07 0 0 0 0 0 0 5.0030006e-07
100 1.684629e+24 133446.65 0 255067.11 1.6206343e+11 5.0030006e-07 100 2.1708413e+26 2019616.1 0 17691833 2.0883757e+13 5.0030006e-07
200 1.1380148e+27 684478.05 0 82842557 9.9178307e+13 5.5225839e-07 200 2.6858201e+27 23091889 0 2.1699255e+08 2.5837916e+14 5.0030006e-07
300 2.5659218e+27 5944645.9 0 1.9118934e+08 1.6231114e+14 7.6086254e-07 300 7.7773248e+27 36337377 0 5.9781519e+08 5.5903929e+14 6.6957466e-07
400 2.9916164e+27 13677434 0 2.2965481e+08 1.4081705e+14 1.0224963e-06 400 1.2392524e+28 26946130 0 9.2161463e+08 5.8015586e+14 1.0280783e-06
500 3.3570343e+27 11130894 0 2.5348933e+08 1.2577633e+14 1.2846002e-06 500 1.6748989e+28 24398485 0 1.2335785e+09 5.5317919e+14 1.4572494e-06
600 3.9506165e+27 6986672.5 0 2.9219831e+08 1.2659956e+14 1.5019096e-06 600 2.1137718e+28 12455731 0 1.5384766e+09 5.144781e+14 1.9774354e-06
700 7.8366157e+27 11716082 0 5.7747436e+08 1.9480124e+14 1.9361899e-06 700 2.2843381e+28 3012521.8 0 1.6521724e+09 4.1591669e+14 2.6434138e-06
800 8.2483231e+27 4671647.2 0 6.0015282e+08 1.7040064e+14 2.3297298e-06 800 2.30994e+28 1986584 0 1.6696295e+09 3.1911076e+14 3.4839376e-06
900 8.2720965e+27 1249680.9 0 5.9844715e+08 1.4117116e+14 2.8202052e-06 900 2.3325118e+28 935517.5 0 1.684874e+09 2.5083968e+14 4.4754707e-06
1000 8.2441489e+27 2277476.2 0 5.9745729e+08 1.2346524e+14 3.213751e-06 1000 2.3453028e+28 646658.88 0 1.6938195e+09 1.9996924e+14 5.6447777e-06
Loop time of 23.2656 on 4 procs for 1000 steps with 3487 atoms Loop time of 3.68562 on 4 procs for 1000 steps with 3487 atoms
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads 97.8% 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 | 20.801 | 21.119 | 21.525 | 6.3 | 90.78 Pair | 2.3895 | 2.9098 | 3.4454 | 22.8 | 78.95
Neigh | 0.13851 | 0.18557 | 0.22747 | 8.5 | 0.80 Neigh | 0.089031 | 0.10631 | 0.12931 | 5.1 | 2.88
Comm | 1.5175 | 1.8689 | 2.1386 | 18.0 | 8.03 Comm | 0.084373 | 0.61215 | 1.1154 | 48.5 | 16.61
Output | 0.00049806 | 0.00059026 | 0.00071931 | 0.0 | 0.00 Output | 0.00026274 | 0.00058717 | 0.0014296 | 0.0 | 0.02
Modify | 0.063441 | 0.066235 | 0.069135 | 0.9 | 0.28 Modify | 0.030758 | 0.032229 | 0.034897 | 0.9 | 0.87
Other | | 0.02496 | | | 0.11 Other | | 0.02456 | | | 0.67
Nlocal: 871.75 ave 939 max 805 min Nlocal: 871.75 ave 955 max 804 min
Histogram: 1 0 0 0 1 1 0 0 0 1 Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1343.25 ave 1410 max 1276 min Nghost: 1052.5 ave 1144 max 960 min
Histogram: 1 0 0 0 1 1 0 0 0 1 Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 144142 ave 176488 max 113797 min Neighs: 94652.8 ave 98974 max 91771 min
Histogram: 1 0 1 0 0 0 1 0 0 1 Histogram: 1 1 0 0 1 0 0 0 0 1
FullNghs: 302269 ave 346070 max 260820 min FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 1209076 Total # of neighbors = 1209076
Ave neighs/atom = 346.738 Ave neighs/atom = 346.738
Neighbor list builds = 37 Neighbor list builds = 31
Dangerous builds = 0 Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:23 Total wall time: 0:00:03

29
examples/peri/log.6Jul17.peri.pmb.g++.1 → examples/peri/log.27Nov18.peri.pmb.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile # small Peridynamic cylinder hit by projectile
@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 region target create_atoms 1 region target
Created 3487 atoms Created 3487 atoms
Time spent = 0.000993729 secs
pair_style peri/pmb pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
@ -79,28 +80,28 @@ Step Temp E_pair E_mol TotEng Press Volume
500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06 500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06 600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06 700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
800 1.2424839e+28 2407365.1 0 8.994088e+08 2.3787786e+14 2.5138992e-06 800 1.2424839e+28 2407361.6 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358397e+28 4532424.3 0 8.9673716e+08 1.9097316e+14 3.1145903e-06 900 1.2358395e+28 4532520.6 0 8.9673706e+08 1.9097312e+14 3.1145903e-06
1000 1.2341048e+28 3219355.8 0 8.9417154e+08 1.5968585e+14 3.7196039e-06 1000 1.2341057e+28 3219939.5 0 8.9417279e+08 1.5968597e+14 3.7196039e-06
Loop time of 28.565 on 1 procs for 1000 steps with 3487 atoms Loop time of 15.3451 on 1 procs for 1000 steps with 3487 atoms
99.5% 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: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 27.721 | 27.721 | 27.721 | 0.0 | 97.04 Pair | 14.575 | 14.575 | 14.575 | 0.0 | 94.98
Neigh | 0.66353 | 0.66353 | 0.66353 | 0.0 | 2.32 Neigh | 0.65203 | 0.65203 | 0.65203 | 0.0 | 4.25
Comm | 0.0027969 | 0.0027969 | 0.0027969 | 0.0 | 0.01 Comm | 0.0019367 | 0.0019367 | 0.0019367 | 0.0 | 0.01
Output | 0.00042295 | 0.00042295 | 0.00042295 | 0.0 | 0.00 Output | 0.00032711 | 0.00032711 | 0.00032711 | 0.0 | 0.00
Modify | 0.1566 | 0.1566 | 0.1566 | 0.0 | 0.55 Modify | 0.10225 | 0.10225 | 0.10225 | 0.0 | 0.67
Other | | 0.02086 | | | 0.07 Other | | 0.01342 | | | 0.09
Nlocal: 3487 ave 3487 max 3487 min Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min Nghost: 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
Neighs: 567132 ave 567132 max 567132 min Neighs: 567140 ave 567140 max 567140 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -112,4 +113,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:28 Total wall time: 0:00:15

39
examples/peri/log.6Jul17.peri.pmb.g++.4 → examples/peri/log.27Nov18.peri.pmb.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile # small Peridynamic cylinder hit by projectile
@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
2 by 1 by 2 MPI processor grid 2 by 1 by 2 MPI processor grid
create_atoms 1 region target create_atoms 1 region target
Created 3487 atoms Created 3487 atoms
Time spent = 0.000591755 secs
pair_style peri/pmb pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
@ -79,29 +80,29 @@ Step Temp E_pair E_mol TotEng Press Volume
500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06 500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06 600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06 700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
800 1.2424839e+28 2407365.2 0 8.994088e+08 2.3787786e+14 2.5138992e-06 800 1.2424839e+28 2407361.5 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358397e+28 4532423 0 8.9673716e+08 1.9097316e+14 3.1145903e-06 900 1.2358395e+28 4532520.1 0 8.9673706e+08 1.9097312e+14 3.1145903e-06
1000 1.2341048e+28 3219408.7 0 8.9417158e+08 1.5968585e+14 3.7196039e-06 1000 1.2341057e+28 3219974.3 0 8.9417286e+08 1.5968598e+14 3.7196039e-06
Loop time of 9.59889 on 4 procs for 1000 steps with 3487 atoms Loop time of 4.86638 on 4 procs for 1000 steps with 3487 atoms
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads 98.2% 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 | 7.9131 | 8.1341 | 8.3286 | 6.7 | 84.74 Pair | 3.524 | 3.9207 | 4.4499 | 17.8 | 80.57
Neigh | 0.19736 | 0.22539 | 0.25643 | 5.6 | 2.35 Neigh | 0.12891 | 0.16928 | 0.21015 | 9.0 | 3.48
Comm | 0.92843 | 1.1536 | 1.402 | 18.4 | 12.02 Comm | 0.1204 | 0.70321 | 1.1349 | 46.1 | 14.45
Output | 0.00053358 | 0.00059688 | 0.00070548 | 0.0 | 0.01 Output | 0.00028253 | 0.00053787 | 0.0012429 | 0.0 | 0.01
Modify | 0.060774 | 0.06358 | 0.068375 | 1.2 | 0.66 Modify | 0.03231 | 0.033227 | 0.034578 | 0.5 | 0.68
Other | | 0.02165 | | | 0.23 Other | | 0.03944 | | | 0.81
Nlocal: 871.75 ave 920 max 829 min Nlocal: 871.75 ave 920 max 824 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 1343.25 ave 1386 max 1295 min Nghost: 1343.25 ave 1391 max 1295 min
Histogram: 1 0 0 0 0 2 0 0 0 1 Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 141783 ave 157099 max 127518 min Neighs: 141785 ave 170754 max 115891 min
Histogram: 2 0 0 0 0 0 0 0 1 1 Histogram: 1 1 0 0 0 0 0 1 0 1
FullNghs: 302269 ave 346070 max 260820 min FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 0 2 0 0 0 0 1
@ -112,4 +113,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09 Total wall time: 0:00:04

45
examples/peri/log.6Jul17.peri.ves.g++.1 → examples/peri/log.27Nov18.peri.ves.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile # small Peridynamic cylinder hit by projectile
@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 region target create_atoms 1 region target
Created 3487 atoms Created 3487 atoms
Time spent = 0.000948906 secs
pair_style peri/ves pair_style peri/ves
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001 pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
@ -72,44 +73,44 @@ Peridynamic bonds:
Per MPI rank memory allocation (min/avg/max) = 65.41 | 65.41 | 65.41 Mbytes Per MPI rank memory allocation (min/avg/max) = 65.41 | 65.41 | 65.41 Mbytes
Step Temp E_pair E_mol TotEng Press Volume Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07 0 0 0 0 0 0 5.0030006e-07
100 8.3392177e+24 247040.57 0 849083.8 8.0224286e+11 5.0030006e-07 100 9.7323839e+24 248625.39 0 951247.15 9.3626715e+11 5.0030006e-07
200 1.1849022e+27 1158030.5 0 86701105 1.0301578e+14 5.5359205e-07 200 1.2061753e+27 1013477.4 0 88092352 1.0509747e+14 5.5236899e-07
300 2.6287222e+27 4389155.1 0 1.9416767e+08 1.6636212e+14 7.6050375e-07 300 2.7144154e+27 3853028.1 0 1.998181e+08 1.7162586e+14 7.6121038e-07
400 3.2718778e+27 7458219 0 2.4366885e+08 1.5439709e+14 1.0199269e-06 400 3.40253e+27 12536380 0 2.5817934e+08 1.5995767e+14 1.0237832e-06
500 3.8413187e+27 6151611.4 0 2.8347258e+08 1.5008974e+14 1.2318007e-06 500 3.9896399e+27 9604773.5 0 2.9763367e+08 1.5530851e+14 1.2363731e-06
600 6.1409926e+27 18424316 0 4.6176842e+08 1.9507512e+14 1.5151227e-06 600 5.1484768e+27 20065080 0 3.9175529e+08 1.6320898e+14 1.5182588e-06
700 1.0046131e+28 11478344 0 7.3675086e+08 2.4228512e+14 1.9956447e-06 700 1.1341683e+28 8156461.7 0 8.269603e+08 2.765964e+14 1.9735225e-06
800 1.0402132e+28 4421233.6 0 7.5539495e+08 2.0512303e+14 2.4407262e-06 800 1.1679489e+28 4475262.6 0 8.4766672e+08 2.1589017e+14 2.6037667e-06
900 1.0419515e+28 7223261.3 0 7.594519e+08 1.6647307e+14 3.0124137e-06 900 1.1714785e+28 2839888 0 8.4857954e+08 1.7092697e+14 3.2986395e-06
1000 1.0503737e+28 2621490.6 0 7.6093049e+08 1.4315634e+14 3.5313793e-06 1000 1.1716494e+28 1690965.6 0 8.4755402e+08 1.3801485e+14 4.0858554e-06
Loop time of 77.2175 on 1 procs for 1000 steps with 3487 atoms Loop time of 27.0077 on 1 procs for 1000 steps with 3487 atoms
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads 99.5% 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 | 76.421 | 76.421 | 76.421 | 0.0 | 98.97 Pair | 26.294 | 26.294 | 26.294 | 0.0 | 97.36
Neigh | 0.56616 | 0.56616 | 0.56616 | 0.0 | 0.73 Neigh | 0.5863 | 0.5863 | 0.5863 | 0.0 | 2.17
Comm | 0.0038247 | 0.0038247 | 0.0038247 | 0.0 | 0.00 Comm | 0.0051315 | 0.0051315 | 0.0051315 | 0.0 | 0.02
Output | 0.00051951 | 0.00051951 | 0.00051951 | 0.0 | 0.00 Output | 0.00033832 | 0.00033832 | 0.00033832 | 0.0 | 0.00
Modify | 0.19434 | 0.19434 | 0.19434 | 0.0 | 0.25 Modify | 0.10736 | 0.10736 | 0.10736 | 0.0 | 0.40
Other | | 0.03197 | | | 0.04 Other | | 0.01489 | | | 0.06
Nlocal: 3487 ave 3487 max 3487 min Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min Nghost: 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
Neighs: 561942 ave 561942 max 561942 min Neighs: 539960 ave 539960 max 539960 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 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 = 1209076 Total # of neighbors = 1209076
Ave neighs/atom = 346.738 Ave neighs/atom = 346.738
Neighbor list builds = 37 Neighbor list builds = 42
Dangerous builds = 0 Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:17 Total wall time: 0:00:27

55
examples/peri/log.6Jul17.peri.ves.g++.4 → examples/peri/log.27Nov18.peri.ves.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (6 Jul 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# small Peridynamic cylinder hit by projectile # small Peridynamic cylinder hit by projectile
@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
2 by 1 by 2 MPI processor grid 2 by 1 by 2 MPI processor grid
create_atoms 1 region target create_atoms 1 region target
Created 3487 atoms Created 3487 atoms
Time spent = 0.000587225 secs
pair_style peri/ves pair_style peri/ves
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001 pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
@ -72,44 +73,44 @@ Peridynamic bonds:
Per MPI rank memory allocation (min/avg/max) = 59.9 | 60.16 | 60.26 Mbytes Per MPI rank memory allocation (min/avg/max) = 59.9 | 60.16 | 60.26 Mbytes
Step Temp E_pair E_mol TotEng Press Volume Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07 0 0 0 0 0 0 5.0030006e-07
100 8.3392177e+24 247040.57 0 849083.8 8.0224286e+11 5.0030006e-07 100 2.3611484e+26 2297126.2 0 19343251 2.2714535e+13 5.0030006e-07
200 1.1849022e+27 1158030.5 0 86701105 1.0301578e+14 5.5359205e-07 200 3.9696282e+27 27477818 0 3.1406199e+08 3.7046187e+14 5.1572409e-07
300 2.6287222e+27 4389155.1 0 1.9416767e+08 1.6636212e+14 7.6050375e-07 300 8.8025822e+27 32485477 0 6.6798094e+08 7.1158578e+14 5.9537958e-07
400 3.2718778e+27 7458219 0 2.4366885e+08 1.5439709e+14 1.0199269e-06 400 1.3288413e+28 37587857 0 9.9693436e+08 7.7688957e+14 8.2323713e-07
500 3.8413187e+27 6151611.4 0 2.8347258e+08 1.5008974e+14 1.2318007e-06 500 1.777552e+28 24842920 0 1.3081325e+09 7.3838229e+14 1.1586497e-06
600 6.1409926e+27 18424316 0 4.6176842e+08 1.9507512e+14 1.5151227e-06 600 2.1408855e+28 11023553 0 1.5566189e+09 6.4536834e+14 1.5966028e-06
700 1.0046131e+28 11478344 0 7.3675086e+08 2.4228512e+14 1.9956447e-06 700 2.2659932e+28 3494159 0 1.63941e+09 4.9466351e+14 2.2047524e-06
800 1.0402132e+28 4421233.6 0 7.5539495e+08 2.0512303e+14 2.4407262e-06 800 2.285628e+28 2220143.6 0 1.6523112e+09 3.8214902e+14 2.8786171e-06
900 1.0419515e+28 7223258.7 0 7.594519e+08 1.6647307e+14 3.0124137e-06 900 2.2903476e+28 904133.04 0 1.6544025e+09 2.790555e+14 3.9502258e-06
1000 1.0503738e+28 2621480.4 0 7.6093057e+08 1.4315636e+14 3.5313793e-06 1000 2.29097e+28 617974.86 0 1.6545656e+09 2.2599918e+14 4.8789193e-06
Loop time of 25.9768 on 4 procs for 1000 steps with 3487 atoms Loop time of 3.73704 on 4 procs for 1000 steps with 3487 atoms
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads 98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 22.455 | 23.348 | 24.175 | 14.1 | 89.88 Pair | 2.3248 | 2.876 | 3.5364 | 25.9 | 76.96
Neigh | 0.14472 | 0.18294 | 0.2299 | 8.6 | 0.70 Neigh | 0.072288 | 0.081806 | 0.091866 | 3.1 | 2.19
Comm | 1.4715 | 2.3485 | 3.2075 | 44.8 | 9.04 Comm | 0.078943 | 0.72589 | 1.2634 | 50.3 | 19.42
Output | 0.000489 | 0.00059682 | 0.0007987 | 0.0 | 0.00 Output | 0.00028825 | 0.00057435 | 0.001307 | 0.0 | 0.02
Modify | 0.063634 | 0.071411 | 0.076907 | 1.9 | 0.27 Modify | 0.031366 | 0.032767 | 0.035145 | 0.8 | 0.88
Other | | 0.02506 | | | 0.10 Other | | 0.02002 | | | 0.54
Nlocal: 871.75 ave 896 max 852 min Nlocal: 871.75 ave 978 max 770 min
Histogram: 2 0 0 0 0 0 0 1 0 1 Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 1293.25 ave 1313 max 1269 min Nghost: 1004.75 ave 1107 max 906 min
Histogram: 1 0 1 0 0 0 0 0 0 2 Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 140486 ave 167239 max 121255 min Neighs: 90070.2 ave 94639 max 83936 min
Histogram: 2 0 0 0 0 0 1 0 0 1 Histogram: 1 0 0 0 0 1 0 1 0 1
FullNghs: 302269 ave 346070 max 260820 min FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 1209076 Total # of neighbors = 1209076
Ave neighs/atom = 346.738 Ave neighs/atom = 346.738
Neighbor list builds = 37 Neighbor list builds = 25
Dangerous builds = 0 Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:26 Total wall time: 0:00:03

36
examples/pour/log.5Oct16.pour.2d.g++.1 → examples/pour/log.27Nov18.pour.2d.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container # Pour 2d granular particles into container
dimension 2 dimension 2
@ -40,7 +41,7 @@ compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol thermo_style custom step atoms ke c_1 vol
thermo 1000 thermo 1000
thermo_modify lost ignore norm no thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes compute_modify thermo_temp dynamic/dof yes
#dump id all atom 250 dump.pour #dump id all atom 250 dump.pour
@ -52,13 +53,18 @@ compute_modify thermo_temp dynamic yes
run 25000 run 25000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2 master list distance cutoff = 1.2
ghost atom cutoff = 1.2 ghost atom cutoff = 1.2
binsize = 0.6 -> bins = 167 84 2 binsize = 0.6, bins = 167 84 2
Memory usage per processor = 2.75186 Mbytes 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/2d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.804 | 5.804 | 5.804 Mbytes
Step Atoms KinEng c_1 Volume Step Atoms KinEng c_1 Volume
0 0 -0 0 5000 0 0 -0 0 5000
1000 224 201.77464 0 5000 1000 224 201.77464 0 5000
@ -86,20 +92,20 @@ Step Atoms KinEng c_1 Volume
23000 1000 16.115382 7.9435503 5000 23000 1000 16.115382 7.9435503 5000
24000 1000 11.971003 5.9411126 5000 24000 1000 11.971003 5.9411126 5000
25000 1000 10.404117 4.3811155 5000 25000 1000 10.404117 4.3811155 5000
Loop time of 3.00132 on 1 procs for 25000 steps with 1000 atoms Loop time of 2.72875 on 1 procs for 25000 steps with 1000 atoms
Performance: 719682.852 tau/day, 8329.663 timesteps/s Performance: 791570.958 tau/day, 9161.701 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads 98.8% 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 | 1.2554 | 1.2554 | 1.2554 | 0.0 | 41.83 Pair | 0.95597 | 0.95597 | 0.95597 | 0.0 | 35.03
Neigh | 0.4288 | 0.4288 | 0.4288 | 0.0 | 14.29 Neigh | 0.38475 | 0.38475 | 0.38475 | 0.0 | 14.10
Comm | 0.0078034 | 0.0078034 | 0.0078034 | 0.0 | 0.26 Comm | 0.010862 | 0.010862 | 0.010862 | 0.0 | 0.40
Output | 0.0003016 | 0.0003016 | 0.0003016 | 0.0 | 0.01 Output | 0.00054383 | 0.00054383 | 0.00054383 | 0.0 | 0.02
Modify | 1.177 | 1.177 | 1.177 | 0.0 | 39.21 Modify | 1.2364 | 1.2364 | 1.2364 | 0.0 | 45.31
Other | | 0.132 | | | 4.40 Other | | 0.1402 | | | 5.14
Nlocal: 1000 ave 1000 max 1000 min Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -112,4 +118,4 @@ Total # of neighbors = 2374
Ave neighs/atom = 2.374 Ave neighs/atom = 2.374
Neighbor list builds = 2089 Neighbor list builds = 2089
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:03 Total wall time: 0:00:02

34
examples/pour/log.5Oct16.pour.2d.g++.4 → examples/pour/log.27Nov18.pour.2d.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container # Pour 2d granular particles into container
dimension 2 dimension 2
@ -40,7 +41,7 @@ compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol thermo_style custom step atoms ke c_1 vol
thermo 1000 thermo 1000
thermo_modify lost ignore norm no thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes compute_modify thermo_temp dynamic/dof yes
#dump id all atom 250 dump.pour #dump id all atom 250 dump.pour
@ -52,13 +53,18 @@ compute_modify thermo_temp dynamic yes
run 25000 run 25000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2 master list distance cutoff = 1.2
ghost atom cutoff = 1.2 ghost atom cutoff = 1.2
binsize = 0.6 -> bins = 167 84 2 binsize = 0.6, bins = 167 84 2
Memory usage per processor = 2.7174 Mbytes 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/2d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.77 | 5.77 | 5.77 Mbytes
Step Atoms KinEng c_1 Volume Step Atoms KinEng c_1 Volume
0 0 -0 0 5000 0 0 -0 0 5000
1000 224 201.77464 0 5000 1000 224 201.77464 0 5000
@ -86,20 +92,20 @@ Step Atoms KinEng c_1 Volume
23000 1000 11.97674 5.2548063 5000 23000 1000 11.97674 5.2548063 5000
24000 1000 7.8974699 3.7396899 5000 24000 1000 7.8974699 3.7396899 5000
25000 1000 6.1288038 2.2056805 5000 25000 1000 6.1288038 2.2056805 5000
Loop time of 0.974647 on 4 procs for 25000 steps with 1000 atoms Loop time of 0.901039 on 4 procs for 25000 steps with 1000 atoms
Performance: 2216187.157 tau/day, 25650.314 timesteps/s Performance: 2397232.992 tau/day, 27745.752 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads 96.8% 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 | 0.29556 | 0.31544 | 0.33654 | 3.0 | 32.36 Pair | 0.21557 | 0.22754 | 0.23651 | 1.9 | 25.25
Neigh | 0.10012 | 0.10782 | 0.11355 | 1.7 | 11.06 Neigh | 0.098304 | 0.10178 | 0.10595 | 1.0 | 11.30
Comm | 0.081835 | 0.087606 | 0.098412 | 2.2 | 8.99 Comm | 0.051792 | 0.066485 | 0.079589 | 3.8 | 7.38
Output | 0.00039244 | 0.00043273 | 0.0004766 | 0.2 | 0.04 Output | 0.00052619 | 0.00061941 | 0.00082016 | 0.0 | 0.07
Modify | 0.28155 | 0.29814 | 0.31262 | 2.2 | 30.59 Modify | 0.31782 | 0.32767 | 0.33815 | 1.5 | 36.37
Other | | 0.1652 | | | 16.95 Other | | 0.1769 | | | 19.64
Nlocal: 250 ave 267 max 232 min Nlocal: 250 ave 267 max 232 min
Histogram: 1 0 0 0 1 1 0 0 0 1 Histogram: 1 0 0 0 1 1 0 0 0 1

46
examples/pour/log.5Oct16.pour.2d.molecule.g++.1 → examples/pour/log.27Nov18.pour.2d.molecule.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container # Pour 2d granular particles into container
dimension 2 dimension 2
@ -34,11 +35,11 @@ fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NU
molecule object molecule.vshape molecule object molecule.vshape
Read molecule object: Read molecule object:
5 atoms with 1 types 5 atoms with max type 1
0 bonds with 0 types 0 bonds with max type 0
0 angles with 0 types 0 angles with max type 0
0 dihedrals with 0 types 0 dihedrals with max type 0
0 impropers with 0 types 0 impropers with max type 0
fix 3 all rigid/small molecule mol object fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms 0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom 2.23607 = max distance from body owner to body atom
@ -55,7 +56,7 @@ compute 1 all erotate/sphere
compute Tsphere all temp/sphere compute Tsphere all temp/sphere
thermo_style custom step atoms ke c_1 vol thermo_style custom step atoms ke c_1 vol
thermo_modify lost ignore norm no temp Tsphere thermo_modify lost ignore norm no temp Tsphere
compute_modify Tsphere dynamic yes compute_modify Tsphere dynamic/dof yes
thermo 1000 thermo 1000
@ -73,13 +74,18 @@ thermo 1000
run 25000 run 25000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2 master list distance cutoff = 1.2
ghost atom cutoff = 2.5 ghost atom cutoff = 2.5
binsize = 0.6 -> bins = 167 84 2 binsize = 0.6, bins = 167 84 2
Memory usage per processor = 2.75807 Mbytes 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/2d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.81 | 5.81 | 5.81 Mbytes
Step Atoms KinEng c_1 Volume Step Atoms KinEng c_1 Volume
0 0 -0 0 5000 0 0 -0 0 5000
1000 130 259.24123 2.3772821e-30 5000 1000 130 259.24123 2.3772821e-30 5000
@ -106,21 +112,21 @@ Step Atoms KinEng c_1 Volume
22000 1040 1262.0253 1.6097601 5000 22000 1040 1262.0253 1.6097601 5000
23000 1040 1042.7 3.1078701 5000 23000 1040 1042.7 3.1078701 5000
24000 1040 1167.4717 1.4954047 5000 24000 1040 1167.4717 1.4954047 5000
25000 1170 1214.9087 2.4525541 5000 25000 1170 1214.9087 2.4525535 5000
Loop time of 3.19438 on 1 procs for 25000 steps with 1170 atoms Loop time of 3.36515 on 1 procs for 25000 steps with 1170 atoms
Performance: 676187.595 tau/day, 7826.245 timesteps/s Performance: 641872.369 tau/day, 7429.078 timesteps/s
99.8% CPU use with 1 MPI tasks x no 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 | 0.87733 | 0.87733 | 0.87733 | 0.0 | 27.46 Pair | 0.73922 | 0.73922 | 0.73922 | 0.0 | 21.97
Neigh | 0.25913 | 0.25913 | 0.25913 | 0.0 | 8.11 Neigh | 0.22808 | 0.22808 | 0.22808 | 0.0 | 6.78
Comm | 0.0095103 | 0.0095103 | 0.0095103 | 0.0 | 0.30 Comm | 0.013331 | 0.013331 | 0.013331 | 0.0 | 0.40
Output | 0.00043368 | 0.00043368 | 0.00043368 | 0.0 | 0.01 Output | 0.00082207 | 0.00082207 | 0.00082207 | 0.0 | 0.02
Modify | 1.941 | 1.941 | 1.941 | 0.0 | 60.76 Modify | 2.2694 | 2.2694 | 2.2694 | 0.0 | 67.44
Other | | 0.107 | | | 3.35 Other | | 0.1143 | | | 3.40
Nlocal: 1170 ave 1170 max 1170 min Nlocal: 1170 ave 1170 max 1170 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

46
examples/pour/log.5Oct16.pour.2d.molecule.g++.4 → examples/pour/log.27Nov18.pour.2d.molecule.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour 2d granular particles into container # Pour 2d granular particles into container
dimension 2 dimension 2
@ -34,11 +35,11 @@ fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NU
molecule object molecule.vshape molecule object molecule.vshape
Read molecule object: Read molecule object:
5 atoms with 1 types 5 atoms with max type 1
0 bonds with 0 types 0 bonds with max type 0
0 angles with 0 types 0 angles with max type 0
0 dihedrals with 0 types 0 dihedrals with max type 0
0 impropers with 0 types 0 impropers with max type 0
fix 3 all rigid/small molecule mol object fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms 0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom 2.23607 = max distance from body owner to body atom
@ -55,7 +56,7 @@ compute 1 all erotate/sphere
compute Tsphere all temp/sphere compute Tsphere all temp/sphere
thermo_style custom step atoms ke c_1 vol thermo_style custom step atoms ke c_1 vol
thermo_modify lost ignore norm no temp Tsphere thermo_modify lost ignore norm no temp Tsphere
compute_modify Tsphere dynamic yes compute_modify Tsphere dynamic/dof yes
thermo 1000 thermo 1000
@ -73,13 +74,18 @@ thermo 1000
run 25000 run 25000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2 master list distance cutoff = 1.2
ghost atom cutoff = 2.5 ghost atom cutoff = 2.5
binsize = 0.6 -> bins = 167 84 2 binsize = 0.6, bins = 167 84 2
Memory usage per processor = 2.72041 Mbytes 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hertz/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/2d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.773 | 5.773 | 5.773 Mbytes
Step Atoms KinEng c_1 Volume Step Atoms KinEng c_1 Volume
0 0 -0 0 5000 0 0 -0 0 5000
1000 130 259.24123 2.3773387e-30 5000 1000 130 259.24123 2.3773387e-30 5000
@ -106,21 +112,21 @@ Step Atoms KinEng c_1 Volume
22000 1040 1226.7461 1.2299974 5000 22000 1040 1226.7461 1.2299974 5000
23000 1040 1106.7165 3.1057108 5000 23000 1040 1106.7165 3.1057108 5000
24000 1040 1161.9203 2.0994962 5000 24000 1040 1161.9203 2.0994962 5000
25000 1170 1187.5093 2.959617 5000 25000 1170 1187.5093 2.9596172 5000
Loop time of 1.20622 on 4 procs for 25000 steps with 1170 atoms Loop time of 1.4211 on 4 procs for 25000 steps with 1170 atoms
Performance: 1790713.641 tau/day, 20725.852 timesteps/s Performance: 1519946.444 tau/day, 17591.973 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads 94.0% 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 | 0.22275 | 0.23039 | 0.23778 | 1.1 | 19.10 Pair | 0.19053 | 0.21869 | 0.23582 | 3.7 | 15.39
Neigh | 0.064599 | 0.067646 | 0.069656 | 0.7 | 5.61 Neigh | 0.06394 | 0.066575 | 0.070017 | 0.9 | 4.68
Comm | 0.079895 | 0.092342 | 0.10857 | 3.5 | 7.66 Comm | 0.055579 | 0.070079 | 0.080658 | 3.4 | 4.93
Output | 0.00061584 | 0.00065601 | 0.00075412 | 0.2 | 0.05 Output | 0.0012593 | 0.0031545 | 0.0088205 | 5.8 | 0.22
Modify | 0.69333 | 0.69728 | 0.70102 | 0.3 | 57.81 Modify | 0.89034 | 0.9006 | 0.91315 | 0.9 | 63.37
Other | | 0.1179 | | | 9.78 Other | | 0.162 | | | 11.40
Nlocal: 292.5 ave 296 max 285 min Nlocal: 292.5 ave 296 max 285 min
Histogram: 1 0 0 0 0 0 0 0 1 2 Histogram: 1 0 0 0 0 0 0 0 1 2

56
examples/pour/log.5Oct16.pour.g++.1 → examples/pour/log.27Nov18.pour.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour granular particles into chute container, then induce flow # Pour granular particles into chute container, then induce flow
atom_style sphere atom_style sphere
@ -36,7 +37,7 @@ compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol thermo_style custom step atoms ke c_1 vol
thermo 1000 thermo 1000
thermo_modify lost ignore norm no thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes compute_modify thermo_temp dynamic/dof yes
#dump id all atom 1000 dump.pour #dump id all atom 1000 dump.pour
@ -48,13 +49,18 @@ compute_modify thermo_temp dynamic yes
run 25000 run 25000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2 master list distance cutoff = 1.2
ghost atom cutoff = 1.2 ghost atom cutoff = 1.2
binsize = 0.6 -> bins = 34 34 28 binsize = 0.6, bins = 34 34 28
Memory usage per processor = 2.90017 Mbytes 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.955 | 5.955 | 5.955 Mbytes
Step Atoms KinEng c_1 Volume Step Atoms KinEng c_1 Volume
0 0 -0 0 6600 0 0 -0 0 6600
1000 402 768.04606 0 6600 1000 402 768.04606 0 6600
@ -82,20 +88,20 @@ Step Atoms KinEng c_1 Volume
23000 3000 446.47658 39.719019 6600 23000 3000 446.47658 39.719019 6600
24000 3000 331.57201 24.034747 6600 24000 3000 331.57201 24.034747 6600
25000 3000 239.90493 18.457205 6600 25000 3000 239.90493 18.457205 6600
Loop time of 9.8391 on 1 procs for 25000 steps with 3000 atoms Loop time of 8.66761 on 1 procs for 25000 steps with 3000 atoms
Performance: 219532.250 tau/day, 2540.883 timesteps/s Performance: 249203.592 tau/day, 2884.301 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads 99.7% 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 | 5.5009 | 5.5009 | 5.5009 | 0.0 | 55.91 Pair | 4.5311 | 4.5311 | 4.5311 | 0.0 | 52.28
Neigh | 1.57 | 1.57 | 1.57 | 0.0 | 15.96 Neigh | 1.4556 | 1.4556 | 1.4556 | 0.0 | 16.79
Comm | 0.20079 | 0.20079 | 0.20079 | 0.0 | 2.04 Comm | 0.2322 | 0.2322 | 0.2322 | 0.0 | 2.68
Output | 0.00048852 | 0.00048852 | 0.00048852 | 0.0 | 0.00 Output | 0.00084257 | 0.00084257 | 0.00084257 | 0.0 | 0.01
Modify | 2.2916 | 2.2916 | 2.2916 | 0.0 | 23.29 Modify | 2.1642 | 2.1642 | 2.1642 | 0.0 | 24.97
Other | | 0.2752 | | | 2.80 Other | | 0.2837 | | | 3.27
Nlocal: 3000 ave 3000 max 3000 min Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -112,7 +118,7 @@ Dangerous builds = 0
unfix ins unfix ins
fix 2 all gravity 1.0 chute 26.0 fix 2 all gravity 1.0 chute 26.0
run 25000 run 25000
Memory usage per processor = 7.31316 Mbytes Per MPI rank memory allocation (min/avg/max) = 13.24 | 13.24 | 13.24 Mbytes
Step Atoms KinEng c_1 Volume Step Atoms KinEng c_1 Volume
25000 3000 239.90493 18.457205 6600 25000 3000 239.90493 18.457205 6600
26000 3000 86.453151 19.990229 6600 26000 3000 86.453151 19.990229 6600
@ -140,20 +146,20 @@ Step Atoms KinEng c_1 Volume
48000 3000 16184.643 202.00907 6600 48000 3000 16184.643 202.00907 6600
49000 3000 17573.204 215.30429 6600 49000 3000 17573.204 215.30429 6600
50000 3000 19117.749 232.28939 6600 50000 3000 19117.749 232.28939 6600
Loop time of 18.9367 on 1 procs for 25000 steps with 3000 atoms Loop time of 16.4345 on 1 procs for 25000 steps with 3000 atoms
Performance: 114064.182 tau/day, 1320.187 timesteps/s Performance: 131430.508 tau/day, 1521.186 timesteps/s
99.9% CPU use with 1 MPI tasks x no 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 | 12.058 | 12.058 | 12.058 | 0.0 | 63.68 Pair | 9.893 | 9.893 | 9.893 | 0.0 | 60.20
Neigh | 2.3177 | 2.3177 | 2.3177 | 0.0 | 12.24 Neigh | 2.1448 | 2.1448 | 2.1448 | 0.0 | 13.05
Comm | 0.4221 | 0.4221 | 0.4221 | 0.0 | 2.23 Comm | 0.47991 | 0.47991 | 0.47991 | 0.0 | 2.92
Output | 0.00076723 | 0.00076723 | 0.00076723 | 0.0 | 0.00 Output | 0.0011523 | 0.0011523 | 0.0011523 | 0.0 | 0.01
Modify | 3.6817 | 3.6817 | 3.6817 | 0.0 | 19.44 Modify | 3.4635 | 3.4635 | 3.4635 | 0.0 | 21.07
Other | | 0.4563 | | | 2.41 Other | | 0.4522 | | | 2.75
Nlocal: 3000 ave 3000 max 3000 min Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -166,4 +172,4 @@ Total # of neighbors = 13997
Ave neighs/atom = 4.66567 Ave neighs/atom = 4.66567
Neighbor list builds = 836 Neighbor list builds = 836
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:28 Total wall time: 0:00:25

54
examples/pour/log.5Oct16.pour.g++.4 → examples/pour/log.27Nov18.pour.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Pour granular particles into chute container, then induce flow # Pour granular particles into chute container, then induce flow
atom_style sphere atom_style sphere
@ -36,7 +37,7 @@ compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol thermo_style custom step atoms ke c_1 vol
thermo 1000 thermo 1000
thermo_modify lost ignore norm no thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes compute_modify thermo_temp dynamic/dof yes
#dump id all atom 1000 dump.pour #dump id all atom 1000 dump.pour
@ -48,13 +49,18 @@ compute_modify thermo_temp dynamic yes
run 25000 run 25000
Neighbor list info ... Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2 master list distance cutoff = 1.2
ghost atom cutoff = 1.2 ghost atom cutoff = 1.2
binsize = 0.6 -> bins = 34 34 28 binsize = 0.6, bins = 34 34 28
Memory usage per processor = 2.7753 Mbytes 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.83 | 5.83 | 5.83 Mbytes
Step Atoms KinEng c_1 Volume Step Atoms KinEng c_1 Volume
0 0 -0 0 6600 0 0 -0 0 6600
1000 402 768.04606 0 6600 1000 402 768.04606 0 6600
@ -82,20 +88,20 @@ Step Atoms KinEng c_1 Volume
23000 3000 456.26221 36.394458 6600 23000 3000 456.26221 36.394458 6600
24000 3000 334.38331 26.256087 6600 24000 3000 334.38331 26.256087 6600
25000 3000 233.7217 18.768345 6600 25000 3000 233.7217 18.768345 6600
Loop time of 3.00537 on 4 procs for 25000 steps with 3000 atoms Loop time of 2.79912 on 4 procs for 25000 steps with 3000 atoms
Performance: 718714.211 tau/day, 8318.452 timesteps/s Performance: 771671.423 tau/day, 8931.382 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads 97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 1.328 | 1.3659 | 1.4112 | 2.9 | 45.45 Pair | 1.0916 | 1.1431 | 1.1982 | 4.0 | 40.84
Neigh | 0.39528 | 0.40948 | 0.42265 | 1.6 | 13.62 Neigh | 0.37439 | 0.39186 | 0.41149 | 2.6 | 14.00
Comm | 0.36134 | 0.36901 | 0.37668 | 0.9 | 12.28 Comm | 0.32241 | 0.32795 | 0.33831 | 1.1 | 11.72
Output | 0.00052094 | 0.00060934 | 0.0006752 | 0.2 | 0.02 Output | 0.00068283 | 0.0029467 | 0.0094671 | 6.9 | 0.11
Modify | 0.5892 | 0.60403 | 0.61671 | 1.3 | 20.10 Modify | 0.5813 | 0.5952 | 0.60947 | 1.5 | 21.26
Other | | 0.2564 | | | 8.53 Other | | 0.3381 | | | 12.08
Nlocal: 750 ave 765 max 730 min Nlocal: 750 ave 765 max 730 min
Histogram: 1 0 0 0 1 0 0 0 1 1 Histogram: 1 0 0 0 1 0 0 0 1 1
@ -112,7 +118,7 @@ Dangerous builds = 0
unfix ins unfix ins
fix 2 all gravity 1.0 chute 26.0 fix 2 all gravity 1.0 chute 26.0
run 25000 run 25000
Memory usage per processor = 7.16682 Mbytes Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.39 | 13.06 Mbytes
Step Atoms KinEng c_1 Volume Step Atoms KinEng c_1 Volume
25000 3000 233.7217 18.768345 6600 25000 3000 233.7217 18.768345 6600
26000 3000 80.58756 21.114703 6600 26000 3000 80.58756 21.114703 6600
@ -140,20 +146,20 @@ Step Atoms KinEng c_1 Volume
48000 3000 15555.796 204.40316 6600 48000 3000 15555.796 204.40316 6600
49000 3000 16694.338 208.98934 6600 49000 3000 16694.338 208.98934 6600
50000 3000 17936.665 192.19442 6600 50000 3000 17936.665 192.19442 6600
Loop time of 5.5877 on 4 procs for 25000 steps with 3000 atoms Loop time of 5.65089 on 4 procs for 25000 steps with 3000 atoms
Performance: 386563.121 tau/day, 4474.110 timesteps/s Performance: 382240.368 tau/day, 4424.078 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads 94.3% 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 | 2.9862 | 3.0411 | 3.0685 | 1.9 | 54.42 Pair | 2.5656 | 2.5853 | 2.6068 | 0.9 | 45.75
Neigh | 0.58638 | 0.60065 | 0.61313 | 1.2 | 10.75 Neigh | 0.57736 | 0.59939 | 0.61824 | 1.9 | 10.61
Comm | 0.49186 | 0.50314 | 0.51344 | 1.2 | 9.00 Comm | 0.58146 | 0.63908 | 0.70461 | 5.5 | 11.31
Output | 0.00076151 | 0.0010245 | 0.0012021 | 0.5 | 0.02 Output | 0.00081015 | 0.002184 | 0.0061922 | 5.0 | 0.04
Modify | 0.93086 | 0.95139 | 0.96527 | 1.3 | 17.03 Modify | 0.91975 | 0.93371 | 0.95875 | 1.5 | 16.52
Other | | 0.4904 | | | 8.78 Other | | 0.8912 | | | 15.77
Nlocal: 750 ave 758 max 741 min Nlocal: 750 ave 758 max 741 min
Histogram: 1 0 0 0 0 2 0 0 0 1 Histogram: 1 0 0 0 0 2 0 0 0 1

100
examples/python/log.27Nov18.fix_python_invoke.g++.1 Normal file
View File

@ -0,0 +1,100 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000678539 secs
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
python end_of_step_callback here """
from __future__ import print_function
from lammps import lammps
def end_of_step_callback(lmp):
L = lammps(ptr=lmp)
t = L.extract_global("ntimestep", 0)
print("### END OF STEP ###", t)
def post_force_callback(lmp, v):
L = lammps(ptr=lmp)
t = L.extract_global("ntimestep", 0)
print("### POST_FORCE ###", t)
"""
fix 1 all nve
fix 2 all python/invoke 50 end_of_step end_of_step_callback
fix 3 all python/invoke 50 post_force post_force_callback
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 0.732007 on 1 procs for 250 steps with 4000 atoms
Performance: 147539.519 tau/day, 341.527 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 | 0.60651 | 0.60651 | 0.60651 | 0.0 | 82.86
Neigh | 0.092702 | 0.092702 | 0.092702 | 0.0 | 12.66
Comm | 0.013686 | 0.013686 | 0.013686 | 0.0 | 1.87
Output | 0.00016069 | 0.00016069 | 0.00016069 | 0.0 | 0.02
Modify | 0.016055 | 0.016055 | 0.016055 | 0.0 | 2.19
Other | | 0.00289 | | | 0.39
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000408888 secs
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
python end_of_step_callback here """
from __future__ import print_function
from lammps import lammps
def end_of_step_callback(lmp):
L = lammps(ptr=lmp)
t = L.extract_global("ntimestep", 0)
print("### END OF STEP ###", t)
def post_force_callback(lmp, v):
L = lammps(ptr=lmp)
t = L.extract_global("ntimestep", 0)
print("### POST_FORCE ###", t)
"""
fix 1 all nve
fix 2 all python/invoke 50 end_of_step end_of_step_callback
fix 3 all python/invoke 50 post_force post_force_callback
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.227907 on 4 procs for 250 steps with 4000 atoms
Performance: 473877.870 tau/day, 1096.940 timesteps/s
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15923 | 0.16507 | 0.17227 | 1.2 | 72.43
Neigh | 0.02438 | 0.025177 | 0.025757 | 0.4 | 11.05
Comm | 0.022418 | 0.030157 | 0.036685 | 2.9 | 13.23
Output | 0.00052595 | 0.00092125 | 0.0011675 | 0.0 | 0.40
Modify | 0.0053911 | 0.0057266 | 0.006294 | 0.5 | 2.51
Other | | 0.0008523 | | | 0.37
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000658989 secs
mass * 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all python/move py_nve.NVE
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 12.0574 on 1 procs for 250 steps with 4000 atoms
Performance: 8957.186 tau/day, 20.734 timesteps/s
98.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.61686 | 0.61686 | 0.61686 | 0.0 | 5.12
Neigh | 0.094026 | 0.094026 | 0.094026 | 0.0 | 0.78
Comm | 0.015743 | 0.015743 | 0.015743 | 0.0 | 0.13
Output | 0.00021815 | 0.00021815 | 0.00021815 | 0.0 | 0.00
Modify | 11.328 | 11.328 | 11.328 | 0.0 | 93.95
Other | | 0.002812 | | | 0.02
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:12

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.00041604 secs
mass * 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all python/move py_nve.NVE
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 3.60532 on 4 procs for 250 steps with 4000 atoms
Performance: 29955.711 tau/day, 69.342 timesteps/s
95.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.15953 | 0.16556 | 0.16945 | 0.9 | 4.59
Neigh | 0.024014 | 0.024431 | 0.024704 | 0.2 | 0.68
Comm | 0.10837 | 0.26844 | 0.38063 | 19.1 | 7.45
Output | 0.00021553 | 0.0063262 | 0.0088348 | 4.5 | 0.18
Modify | 3.0299 | 3.138 | 3.3038 | 5.7 | 87.04
Other | | 0.002585 | | | 0.07
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:03

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000703096 secs
mass * 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all python/move py_nve.NVE_Opt
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 0.806998 on 1 procs for 250 steps with 4000 atoms
Performance: 133829.286 tau/day, 309.790 timesteps/s
95.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.60639 | 0.60639 | 0.60639 | 0.0 | 75.14
Neigh | 0.092807 | 0.092807 | 0.092807 | 0.0 | 11.50
Comm | 0.013782 | 0.013782 | 0.013782 | 0.0 | 1.71
Output | 0.00021243 | 0.00021243 | 0.00021243 | 0.0 | 0.03
Modify | 0.091672 | 0.091672 | 0.091672 | 0.0 | 11.36
Other | | 0.00213 | | | 0.26
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000407457 secs
mass * 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all python/move py_nve.NVE_Opt
thermo 50
run 250
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.283796 on 4 procs for 250 steps with 4000 atoms
Performance: 380554.630 tau/day, 880.913 timesteps/s
93.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.16068 | 0.16297 | 0.167 | 0.6 | 57.42
Neigh | 0.024281 | 0.02511 | 0.027018 | 0.7 | 8.85
Comm | 0.033199 | 0.035637 | 0.03814 | 1.3 | 12.56
Output | 0.00044489 | 0.00057381 | 0.00065589 | 0.0 | 0.20
Modify | 0.056902 | 0.058489 | 0.06128 | 0.7 | 20.61
Other | | 0.001018 | | | 0.36
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
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
pair_style hybrid/overlay coul/cut 12.0 python 12.0
pair_coeff * * coul/cut
pair_coeff * * python py_pot.LJCutSPCE OW NULL
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 1.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
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
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
# create combined lj/coul table for all atom types
# generate tabulated potential from python variant
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
# switch to tabulated potential
pair_style table linear 2000 pppm
pair_coeff 1 1 spce.table OW-OW
WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
pair_coeff 1 2 spce.table OW-HW
WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
pair_coeff 2 2 spce.table HW-HW
WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
thermo 10
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 = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, 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) = 25.18 | 25.18 | 25.18 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -18173.499 0 -18173.499 -2019.6011
10 146.87683 -19431.334 0 -18118.336 -4804.774
20 183.13008 -19192.694 0 -17555.612 -5105.075
30 205.91102 -18124.567 0 -16283.836 -4052.5955
40 241.34432 -18154.089 0 -15996.604 -3187.3994
50 265.93905 -19712.779 0 -17335.431 -2716.3264
60 273.67861 -21092.479 0 -18645.943 -2266.2648
70 288.39213 -19794.592 0 -17216.526 -1207.5782
80 300.36209 -20235.73 0 -17550.658 -1345.2669
90 303.8567 -21670.331 0 -18954.02 -2207.0831
100 304.10875 -19847.214 0 -17128.649 -1431.7749
Loop time of 5.78394 on 1 procs for 100 steps with 4500 atoms
Performance: 1.494 ns/day, 16.066 hours/ns, 17.289 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 | 5.4417 | 5.4417 | 5.4417 | 0.0 | 94.08
Bond | 9.5844e-05 | 9.5844e-05 | 9.5844e-05 | 0.0 | 0.00
Neigh | 0.26895 | 0.26895 | 0.26895 | 0.0 | 4.65
Comm | 0.019179 | 0.019179 | 0.019179 | 0.0 | 0.33
Output | 0.00039768 | 0.00039768 | 0.00039768 | 0.0 | 0.01
Modify | 0.050508 | 0.050508 | 0.050508 | 0.0 | 0.87
Other | | 0.003098 | | | 0.05
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21269 ave 21269 max 21269 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.59772e+06 ave 2.59772e+06 max 2.59772e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2597720
Ave neighs/atom = 577.271
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:06

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
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
pair_style hybrid/overlay coul/cut 12.0 python 12.0
pair_coeff * * coul/cut
pair_coeff * * python py_pot.LJCutSPCE OW NULL
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 1.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
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
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
# create combined lj/coul table for all atom types
# generate tabulated potential from python variant
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
# switch to tabulated potential
pair_style table linear 2000 pppm
pair_coeff 1 1 spce.table OW-OW
WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
pair_coeff 1 2 spce.table OW-HW
WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
pair_coeff 2 2 spce.table HW-HW
WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
thermo 10
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 = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, 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) = 10.01 | 10.01 | 10.01 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -18173.499 0 -18173.499 -2019.6011
10 146.87683 -19431.334 0 -18118.336 -4804.774
20 183.13008 -19192.694 0 -17555.612 -5105.075
30 205.91102 -18124.567 0 -16283.836 -4052.5955
40 241.34432 -18154.089 0 -15996.604 -3187.3994
50 265.93905 -19712.779 0 -17335.431 -2716.3264
60 273.67861 -21092.479 0 -18645.943 -2266.2648
70 288.39213 -19794.592 0 -17216.526 -1207.5782
80 300.36209 -20235.73 0 -17550.658 -1345.2669
90 303.8567 -21670.331 0 -18954.02 -2207.0831
100 304.10875 -19847.214 0 -17128.649 -1431.7749
Loop time of 1.64676 on 4 procs for 100 steps with 4500 atoms
Performance: 5.247 ns/day, 4.574 hours/ns, 60.725 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 | 1.4241 | 1.4506 | 1.5134 | 3.0 | 88.09
Bond | 9.8705e-05 | 0.00010312 | 0.00010729 | 0.0 | 0.01
Neigh | 0.071698 | 0.071712 | 0.07172 | 0.0 | 4.35
Comm | 0.027696 | 0.090501 | 0.11691 | 12.1 | 5.50
Output | 0.00032783 | 0.00048846 | 0.00096679 | 0.0 | 0.03
Modify | 0.030543 | 0.030691 | 0.030788 | 0.1 | 1.86
Other | | 0.002627 | | | 0.16
Nlocal: 1125 ave 1163 max 1097 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 12265.5 ave 12299 max 12233 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 649430 ave 681781 max 630283 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 2597720
Ave neighs/atom = 577.271
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:01

111
examples/python/log.4May17.pair_python_hybrid.g++.1 → examples/python/log.27Nov18.pair_python_hybrid.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones hybrid # 3d Lennard-Jones hybrid
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4000 atoms Created 4000 atoms
Time spent = 0.00073123 secs
mass * 1.0 mass * 1.0
region half block -0.1 4.9 0 10 0 10 region half block -0.1 4.9 0 10 0 10
set region half type 2 set region half type 2
@ -53,7 +54,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes Per MPI rank memory allocation (min/avg/max) = 4.484 | 4.484 | 4.484 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504 0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064 50 1.6758903 -4.7955425 0 -2.2823355 5.670064
@ -61,20 +62,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6324555 -4.7286791 0 -2.280608 5.9589514 150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365 250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 10.0384 on 1 procs for 250 steps with 4000 atoms Loop time of 5.56562 on 1 procs for 250 steps with 4000 atoms
Performance: 10758.705 tau/day, 24.904 timesteps/s Performance: 19404.856 tau/day, 44.919 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads 99.0% 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 | 9.913 | 9.913 | 9.913 | 0.0 | 98.75 Pair | 5.4305 | 5.4305 | 5.4305 | 0.0 | 97.57
Neigh | 0.095569 | 0.095569 | 0.095569 | 0.0 | 0.95 Neigh | 0.10441 | 0.10441 | 0.10441 | 0.0 | 1.88
Comm | 0.012686 | 0.012686 | 0.012686 | 0.0 | 0.13 Comm | 0.013915 | 0.013915 | 0.013915 | 0.0 | 0.25
Output | 0.00027537 | 0.00027537 | 0.00027537 | 0.0 | 0.00 Output | 0.00019979 | 0.00019979 | 0.00019979 | 0.0 | 0.00
Modify | 0.01386 | 0.01386 | 0.01386 | 0.0 | 0.14 Modify | 0.014502 | 0.014502 | 0.014502 | 0.0 | 0.26
Other | | 0.003027 | | | 0.03 Other | | 0.002061 | | | 0.04
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -89,14 +90,60 @@ Neighbor list builds = 12
Dangerous builds not checked Dangerous builds not checked
write_data hybrid.data write_data hybrid.data
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
write_restart hybrid.restart write_restart hybrid.restart
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
clear clear
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
read_restart hybrid.restart read_restart hybrid.restart
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796) orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
restoring pair style hybrid from restart
4000 atoms 4000 atoms
pair_style hybrid lj/cut 2.5 python 2.5 pair_style hybrid lj/cut 2.5 python 2.5
@ -129,7 +176,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.245 | 4.245 | 4.245 Mbytes Per MPI rank memory allocation (min/avg/max) = 4.281 | 4.281 | 4.281 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
250 1.6275257 -4.7224992 0 -2.281821 5.9567365 250 1.6275257 -4.7224992 0 -2.281821 5.9567365
300 1.645592 -4.7496711 0 -2.2819002 5.8734193 300 1.645592 -4.7496711 0 -2.2819002 5.8734193
@ -137,20 +184,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6540555 -4.7622999 0 -2.281837 5.8200413 400 1.6540555 -4.7622999 0 -2.281837 5.8200413
450 1.6264734 -4.7200865 0 -2.2809863 5.9546991 450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
500 1.6366891 -4.7350979 0 -2.2806781 5.9369284 500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
Loop time of 10.0803 on 1 procs for 250 steps with 4000 atoms Loop time of 5.56525 on 1 procs for 250 steps with 4000 atoms
Performance: 10713.932 tau/day, 24.801 timesteps/s Performance: 19406.123 tau/day, 44.922 timesteps/s
98.7% CPU use with 1 MPI tasks x 1 OpenMP threads 99.0% 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 | 9.8479 | 9.8479 | 9.8479 | 0.0 | 97.69 Pair | 5.3122 | 5.3122 | 5.3122 | 0.0 | 95.45
Neigh | 0.20002 | 0.20002 | 0.20002 | 0.0 | 1.98 Neigh | 0.21918 | 0.21918 | 0.21918 | 0.0 | 3.94
Comm | 0.01437 | 0.01437 | 0.01437 | 0.0 | 0.14 Comm | 0.015959 | 0.015959 | 0.015959 | 0.0 | 0.29
Output | 0.00024033 | 0.00024033 | 0.00024033 | 0.0 | 0.00 Output | 0.00018764 | 0.00018764 | 0.00018764 | 0.0 | 0.00
Modify | 0.013422 | 0.013422 | 0.013422 | 0.0 | 0.13 Modify | 0.014443 | 0.014443 | 0.014443 | 0.0 | 0.26
Other | | 0.004348 | | | 0.04 Other | | 0.00326 | | | 0.06
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -211,7 +258,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.745 | 3.745 | 3.745 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.781 | 3.781 | 3.781 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 1.6275257 -4.7224992 0 -2.281821 5.9567365 0 1.6275257 -4.7224992 0 -2.281821 5.9567365
50 1.6454666 -4.7497515 0 -2.2821686 5.8729175 50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
@ -219,20 +266,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6537193 -4.7627023 0 -2.2827434 5.8177704 150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
200 1.6258731 -4.7205017 0 -2.2823017 5.952511 200 1.6258731 -4.7205017 0 -2.2823017 5.952511
250 1.6370862 -4.7373176 0 -2.2823022 5.925807 250 1.6370862 -4.7373176 0 -2.2823022 5.925807
Loop time of 9.93686 on 1 procs for 250 steps with 4000 atoms Loop time of 5.44427 on 1 procs for 250 steps with 4000 atoms
Performance: 10868.626 tau/day, 25.159 timesteps/s Performance: 19837.379 tau/day, 45.920 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads 99.0% 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 | 9.8119 | 9.8119 | 9.8119 | 0.0 | 98.74 Pair | 5.3082 | 5.3082 | 5.3082 | 0.0 | 97.50
Neigh | 0.096041 | 0.096041 | 0.096041 | 0.0 | 0.97 Neigh | 0.10536 | 0.10536 | 0.10536 | 0.0 | 1.94
Comm | 0.01243 | 0.01243 | 0.01243 | 0.0 | 0.13 Comm | 0.01346 | 0.01346 | 0.01346 | 0.0 | 0.25
Output | 0.00028133 | 0.00028133 | 0.00028133 | 0.0 | 0.00 Output | 0.00019431 | 0.00019431 | 0.00019431 | 0.0 | 0.00
Modify | 0.013261 | 0.013261 | 0.013261 | 0.0 | 0.13 Modify | 0.015079 | 0.015079 | 0.015079 | 0.0 | 0.28
Other | | 0.002994 | | | 0.03 Other | | 0.002012 | | | 0.04
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -247,4 +294,4 @@ Neighbor list builds = 12
Dangerous builds not checked Dangerous builds not checked
shell rm hybrid.data hybrid.restart shell rm hybrid.data hybrid.restart
Total wall time: 0:00:30 Total wall time: 0:00:16

111
examples/python/log.4May17.pair_python_hybrid.g++.4 → examples/python/log.27Nov18.pair_python_hybrid.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones hybrid # 3d Lennard-Jones hybrid
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4000 atoms Created 4000 atoms
Time spent = 0.000420809 secs
mass * 1.0 mass * 1.0
region half block -0.1 4.9 0 10 0 10 region half block -0.1 4.9 0 10 0 10
set region half type 2 set region half type 2
@ -53,7 +54,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.953 | 3.953 | 3.953 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.968 | 3.968 | 3.968 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504 0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
@ -61,20 +62,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 2.71748 on 4 procs for 250 steps with 4000 atoms Loop time of 1.53377 on 4 procs for 250 steps with 4000 atoms
Performance: 39742.745 tau/day, 91.997 timesteps/s Performance: 70414.718 tau/day, 162.997 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads 98.8% 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 | 2.4777 | 2.5639 | 2.6253 | 3.9 | 94.35 Pair | 1.3644 | 1.406 | 1.4448 | 3.2 | 91.67
Neigh | 0.024626 | 0.025331 | 0.02598 | 0.3 | 0.93 Neigh | 0.027066 | 0.027591 | 0.028437 | 0.3 | 1.80
Comm | 0.061933 | 0.12297 | 0.20987 | 18.0 | 4.53 Comm | 0.055296 | 0.095109 | 0.13733 | 12.4 | 6.20
Output | 0.00026131 | 0.00027591 | 0.00031352 | 0.0 | 0.01 Output | 0.00022817 | 0.00030088 | 0.00042033 | 0.0 | 0.02
Modify | 0.0036087 | 0.0036573 | 0.0037553 | 0.1 | 0.13 Modify | 0.0037878 | 0.0038549 | 0.0040336 | 0.2 | 0.25
Other | | 0.001337 | | | 0.05 Other | | 0.0008861 | | | 0.06
Nlocal: 1000 ave 1010 max 982 min Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2 Histogram: 1 0 0 0 0 0 1 0 0 2
@ -89,14 +90,60 @@ Neighbor list builds = 12
Dangerous builds not checked Dangerous builds not checked
write_data hybrid.data write_data hybrid.data
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
write_restart hybrid.restart write_restart hybrid.restart
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair python, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
clear clear
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
read_restart hybrid.restart read_restart hybrid.restart
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796) orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
restoring pair style hybrid from restart
4000 atoms 4000 atoms
pair_style hybrid lj/cut 2.5 python 2.5 pair_style hybrid lj/cut 2.5 python 2.5
@ -129,7 +176,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.612 | 3.612 | 3.612 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.626 | 3.626 | 3.626 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
250 1.6323462 -4.7292062 0 -2.2812991 5.9762168 250 1.6323462 -4.7292062 0 -2.2812991 5.9762168
300 1.6451788 -4.7488091 0 -2.2816578 5.8375485 300 1.6451788 -4.7488091 0 -2.2816578 5.8375485
@ -137,20 +184,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084 400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898 450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
500 1.643316 -4.7454222 0 -2.2810644 5.8454817 500 1.643316 -4.7454222 0 -2.2810644 5.8454817
Loop time of 2.75827 on 4 procs for 250 steps with 4000 atoms Loop time of 1.51785 on 4 procs for 250 steps with 4000 atoms
Performance: 39155.038 tau/day, 90.637 timesteps/s Performance: 71153.411 tau/day, 164.707 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads 98.9% 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 | 2.3631 | 2.5412 | 2.6672 | 7.2 | 92.13 Pair | 1.2893 | 1.3741 | 1.416 | 4.2 | 90.53
Neigh | 0.050358 | 0.052316 | 0.053312 | 0.5 | 1.90 Neigh | 0.055474 | 0.056676 | 0.057363 | 0.3 | 3.73
Comm | 0.032793 | 0.15893 | 0.33904 | 29.1 | 5.76 Comm | 0.039187 | 0.081666 | 0.16742 | 17.6 | 5.38
Output | 0.00018525 | 0.00020212 | 0.00024509 | 0.0 | 0.01 Output | 0.00014877 | 0.0002687 | 0.00061893 | 0.0 | 0.02
Modify | 0.0034482 | 0.0035321 | 0.0036578 | 0.1 | 0.13 Modify | 0.003741 | 0.0037862 | 0.0038075 | 0.0 | 0.25
Other | | 0.002039 | | | 0.07 Other | | 0.001315 | | | 0.09
Nlocal: 1000 ave 1012 max 983 min Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1 Histogram: 1 0 0 0 0 0 2 0 0 1
@ -211,7 +258,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.126 | 3.126 | 3.126 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 1.6323462 -4.7292062 0 -2.2812991 5.9762168 0 1.6323462 -4.7292062 0 -2.2812991 5.9762168
50 1.6450626 -4.7488948 0 -2.2819177 5.8370409 50 1.6450626 -4.7488948 0 -2.2819177 5.8370409
@ -219,20 +266,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273 150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228 200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819 250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
Loop time of 2.71936 on 4 procs for 250 steps with 4000 atoms Loop time of 1.53622 on 4 procs for 250 steps with 4000 atoms
Performance: 39715.257 tau/day, 91.933 timesteps/s Performance: 70302.534 tau/day, 162.737 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads 97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 2.3769 | 2.5432 | 2.6447 | 6.6 | 93.52 Pair | 1.2893 | 1.3875 | 1.4506 | 5.1 | 90.32
Neigh | 0.024088 | 0.025093 | 0.025748 | 0.4 | 0.92 Neigh | 0.026512 | 0.02714 | 0.027651 | 0.2 | 1.77
Comm | 0.044614 | 0.14598 | 0.31339 | 27.5 | 5.37 Comm | 0.053684 | 0.11665 | 0.21515 | 17.6 | 7.59
Output | 0.00026488 | 0.00028872 | 0.00034189 | 0.0 | 0.01 Output | 0.00017214 | 0.00029582 | 0.0006547 | 0.0 | 0.02
Modify | 0.0034099 | 0.0035709 | 0.0036535 | 0.2 | 0.13 Modify | 0.0037682 | 0.0037964 | 0.0038147 | 0.0 | 0.25
Other | | 0.001215 | | | 0.04 Other | | 0.0008581 | | | 0.06
Nlocal: 1000 ave 1013 max 989 min Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1 Histogram: 1 0 0 1 0 1 0 0 0 1
@ -247,4 +294,4 @@ Neighbor list builds = 12
Dangerous builds not checked Dangerous builds not checked
shell rm hybrid.data hybrid.restart shell rm hybrid.data hybrid.restart
Total wall time: 0:00:08 Total wall time: 0:00:04

60
examples/python/log.4May17.pair_python_long.g++.1 → examples/python/log.27Nov18.pair_python_long.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
units real units real
atom_style full atom_style full
@ -48,8 +48,8 @@ fix 2 all nvt temp 300.0 300.0 100.0
# create only lj/cut table for the oxygen atoms from python # create only lj/cut table for the oxygen atoms from python
shell rm -f spce.table shell rm -f spce.table
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
Neighbor list info ... Neighbor list info ...
update every 1 steps, delay 10 steps, check yes update every 1 steps, delay 10 steps, check yes
@ -69,11 +69,13 @@ pair_style hybrid/overlay coul/long 12.0 table linear 2000
kspace_style pppm 1.0e-6 kspace_style pppm 1.0e-6
pair_coeff * * coul/long pair_coeff * * coul/long
pair_coeff 1 1 table spce.table OW-OW pair_coeff 1 1 table spce.table OW-OW
WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
thermo 10 thermo 10
run 100 run 100
PPPM initialization ... PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.279652 G vector (1/distance) = 0.279652
grid = 40 40 40 grid = 40 40 40
stencil order = 5 stencil order = 5
@ -98,35 +100,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 36.47 | 36.47 | 36.47 Mbytes Per MPI rank memory allocation (min/avg/max) = 36.57 | 36.57 | 36.57 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -16690.032 0 -16690.032 -1268.9538 0 0 -16690.019 0 -16690.019 -1268.9124
10 120.58553 -17767.504 0 -16689.536 -4063.8589 10 120.58553 -17767.489 0 -16689.521 -4063.8136
20 136.11736 -17882.557 0 -16665.742 -5124.6758 20 136.11736 -17882.538 0 -16665.724 -5124.6194
30 137.00764 -17872.318 0 -16647.545 -5337.2022 30 137.00764 -17872.302 0 -16647.529 -5337.1515
40 153.38868 -17999.269 0 -16628.059 -5213.6001 40 153.38867 -17999.256 0 -16628.046 -5213.5616
50 167.70342 -18103.06 0 -16603.883 -4460.6632 50 167.70342 -18103.046 0 -16603.87 -4460.6216
60 163.07134 -18034.856 0 -16577.088 -3285.0037 60 163.07134 -18034.842 0 -16577.074 -3284.9621
70 169.59286 -18064.636 0 -16548.57 -2606.407 70 169.59286 -18064.622 0 -16548.556 -2606.3642
80 182.92893 -18153.499 0 -16518.215 -2385.5152 80 182.92892 -18153.485 0 -16518.202 -2385.4747
90 191.2793 -18195.356 0 -16485.425 -2235.3701 90 191.2793 -18195.343 0 -16485.411 -2235.3292
100 194.68587 -18192.458 0 -16452.073 -1948.3746 100 194.68587 -18192.446 0 -16452.061 -1948.3379
Loop time of 7.90705 on 1 procs for 100 steps with 4500 atoms Loop time of 7.00522 on 1 procs for 100 steps with 4500 atoms
Performance: 1.093 ns/day, 21.964 hours/ns, 12.647 timesteps/s Performance: 1.233 ns/day, 19.459 hours/ns, 14.275 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads 98.3% 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 | 6.0343 | 6.0343 | 6.0343 | 0.0 | 76.32 Pair | 5.5664 | 5.5664 | 5.5664 | 0.0 | 79.46
Bond | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.00 Bond | 0.00011444 | 0.00011444 | 0.00011444 | 0.0 | 0.00
Kspace | 1.5311 | 1.5311 | 1.5311 | 0.0 | 19.36 Kspace | 1.0814 | 1.0814 | 1.0814 | 0.0 | 15.44
Neigh | 0.246 | 0.246 | 0.246 | 0.0 | 3.11 Neigh | 0.28011 | 0.28011 | 0.28011 | 0.0 | 4.00
Comm | 0.023937 | 0.023937 | 0.023937 | 0.0 | 0.30 Comm | 0.020573 | 0.020573 | 0.020573 | 0.0 | 0.29
Output | 0.00060368 | 0.00060368 | 0.00060368 | 0.0 | 0.01 Output | 0.00045538 | 0.00045538 | 0.00045538 | 0.0 | 0.01
Modify | 0.065543 | 0.065543 | 0.065543 | 0.0 | 0.83 Modify | 0.052692 | 0.052692 | 0.052692 | 0.0 | 0.75
Other | | 0.005364 | | | 0.07 Other | | 0.003407 | | | 0.05
Nlocal: 4500 ave 4500 max 4500 min Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -135,7 +137,7 @@ Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 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 = 2601769 Total # of neighbors = 2601768
Ave neighs/atom = 578.171 Ave neighs/atom = 578.171
Ave special neighs/atom = 2 Ave special neighs/atom = 2
Neighbor list builds = 3 Neighbor list builds = 3
@ -143,4 +145,4 @@ Dangerous builds = 0
shell rm spce.table shell rm spce.table
Total wall time: 0:00:08 Total wall time: 0:00:07

60
examples/python/log.4May17.pair_python_long.g++.4 → examples/python/log.27Nov18.pair_python_long.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
units real units real
atom_style full atom_style full
@ -48,8 +48,8 @@ fix 2 all nvt temp 300.0 300.0 100.0
# create only lj/cut table for the oxygen atoms from python # create only lj/cut table for the oxygen atoms from python
shell rm -f spce.table shell rm -f spce.table
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308)
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
Neighbor list info ... Neighbor list info ...
update every 1 steps, delay 10 steps, check yes update every 1 steps, delay 10 steps, check yes
@ -69,11 +69,13 @@ pair_style hybrid/overlay coul/long 12.0 table linear 2000
kspace_style pppm 1.0e-6 kspace_style pppm 1.0e-6
pair_coeff * * coul/long pair_coeff * * coul/long
pair_coeff 1 1 table spce.table OW-OW pair_coeff 1 1 table spce.table OW-OW
WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (src/pair_table.cpp:481)
thermo 10 thermo 10
run 100 run 100
PPPM initialization ... PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.279652 G vector (1/distance) = 0.279652
grid = 40 40 40 grid = 40 40 40
stencil order = 5 stencil order = 5
@ -98,44 +100,44 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.45 | 13.45 Mbytes Per MPI rank memory allocation (min/avg/max) = 13.5 | 13.5 | 13.5 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -16690.032 0 -16690.032 -1268.9538 0 0 -16690.019 0 -16690.019 -1268.9124
10 120.58553 -17767.504 0 -16689.536 -4063.8589 10 120.58553 -17767.489 0 -16689.521 -4063.8136
20 136.11736 -17882.557 0 -16665.742 -5124.6758 20 136.11736 -17882.538 0 -16665.724 -5124.6194
30 137.00764 -17872.318 0 -16647.545 -5337.2022 30 137.00764 -17872.302 0 -16647.529 -5337.1515
40 153.38868 -17999.269 0 -16628.059 -5213.6001 40 153.38867 -17999.256 0 -16628.046 -5213.5616
50 167.70342 -18103.06 0 -16603.883 -4460.6632 50 167.70342 -18103.046 0 -16603.87 -4460.6216
60 163.07134 -18034.856 0 -16577.088 -3285.0037 60 163.07134 -18034.842 0 -16577.074 -3284.9621
70 169.59286 -18064.636 0 -16548.57 -2606.407 70 169.59286 -18064.622 0 -16548.556 -2606.3642
80 182.92893 -18153.499 0 -16518.215 -2385.5152 80 182.92892 -18153.485 0 -16518.202 -2385.4747
90 191.2793 -18195.356 0 -16485.425 -2235.3701 90 191.2793 -18195.343 0 -16485.411 -2235.3292
100 194.68587 -18192.458 0 -16452.073 -1948.3746 100 194.68587 -18192.446 0 -16452.061 -1948.3379
Loop time of 2.36748 on 4 procs for 100 steps with 4500 atoms Loop time of 2.26946 on 4 procs for 100 steps with 4500 atoms
Performance: 3.649 ns/day, 6.576 hours/ns, 42.239 timesteps/s Performance: 3.807 ns/day, 6.304 hours/ns, 44.063 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads 95.8% 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 | 1.5309 | 1.5977 | 1.6926 | 4.7 | 67.49 Pair | 1.4676 | 1.53 | 1.6054 | 4.5 | 67.42
Bond | 9.9182e-05 | 0.00012749 | 0.00016403 | 0.0 | 0.01 Bond | 9.7752e-05 | 0.00012088 | 0.00013947 | 0.0 | 0.01
Kspace | 0.52158 | 0.61232 | 0.67676 | 7.3 | 25.86 Kspace | 0.51974 | 0.59375 | 0.65496 | 7.2 | 26.16
Neigh | 0.066937 | 0.06702 | 0.067093 | 0.0 | 2.83 Neigh | 0.075271 | 0.075279 | 0.075287 | 0.0 | 3.32
Comm | 0.035882 | 0.039862 | 0.042244 | 1.2 | 1.68 Comm | 0.028602 | 0.029937 | 0.031052 | 0.5 | 1.32
Output | 0.0004003 | 0.00044602 | 0.00057578 | 0.0 | 0.02 Output | 0.00035477 | 0.00062722 | 0.0014365 | 0.0 | 0.03
Modify | 0.046088 | 0.046227 | 0.046315 | 0.0 | 1.95 Modify | 0.03581 | 0.035956 | 0.036059 | 0.1 | 1.58
Other | | 0.003775 | | | 0.16 Other | | 0.003819 | | | 0.17
Nlocal: 1125 ave 1154 max 1092 min Nlocal: 1125 ave 1154 max 1092 min
Histogram: 1 0 0 0 1 0 0 1 0 1 Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost: 12256.2 ave 12296 max 12213 min Nghost: 12256.2 ave 12296 max 12213 min
Histogram: 1 0 1 0 0 0 0 0 1 1 Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 650442 ave 678831 max 626373 min Neighs: 650442 ave 678830 max 626373 min
Histogram: 1 0 0 0 2 0 0 0 0 1 Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 2601769 Total # of neighbors = 2601768
Ave neighs/atom = 578.171 Ave neighs/atom = 578.171
Ave special neighs/atom = 2 Ave special neighs/atom = 2
Neighbor list builds = 3 Neighbor list builds = 3

67
examples/python/log.4May17.pair_python_melt.g++.1 → examples/python/log.27Nov18.pair_python_melt.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt # 3d Lennard-Jones melt
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4000 atoms Created 4000 atoms
Time spent = 0.000694513 secs
mass * 1.0 mass * 1.0
velocity all create 3.0 87287 velocity all create 3.0 87287
@ -39,7 +40,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504 0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064 50 1.6758903 -4.7955425 0 -2.2823355 5.670064
@ -47,20 +48,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6324555 -4.7286791 0 -2.280608 5.9589514 150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365 250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 20.9283 on 1 procs for 250 steps with 4000 atoms Loop time of 11.5979 on 1 procs for 250 steps with 4000 atoms
Performance: 5160.475 tau/day, 11.946 timesteps/s Performance: 9312.020 tau/day, 21.556 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads 99.1% 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 | 20.809 | 20.809 | 20.809 | 0.0 | 99.43 Pair | 11.474 | 11.474 | 11.474 | 0.0 | 98.94
Neigh | 0.088638 | 0.088638 | 0.088638 | 0.0 | 0.42 Neigh | 0.092903 | 0.092903 | 0.092903 | 0.0 | 0.80
Comm | 0.013424 | 0.013424 | 0.013424 | 0.0 | 0.06 Comm | 0.01373 | 0.01373 | 0.01373 | 0.0 | 0.12
Output | 0.0002737 | 0.0002737 | 0.0002737 | 0.0 | 0.00 Output | 0.00021935 | 0.00021935 | 0.00021935 | 0.0 | 0.00
Modify | 0.014334 | 0.014334 | 0.014334 | 0.0 | 0.07 Modify | 0.014506 | 0.014506 | 0.014506 | 0.0 | 0.13
Other | | 0.003089 | | | 0.01 Other | | 0.002072 | | | 0.02
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -81,8 +82,10 @@ clear
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
read_restart melt.restart read_restart melt.restart
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796) orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
pair style python stores no restart info
4000 atoms 4000 atoms
pair_style python 2.5 pair_style python 2.5
@ -104,7 +107,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.36 | 3.36 | 3.36 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.396 | 3.396 | 3.396 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
250 1.6275257 -4.7224992 0 -2.281821 5.9567365 250 1.6275257 -4.7224992 0 -2.281821 5.9567365
300 1.645592 -4.7496711 0 -2.2819002 5.8734193 300 1.645592 -4.7496711 0 -2.2819002 5.8734193
@ -112,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6540555 -4.7622999 0 -2.281837 5.8200413 400 1.6540555 -4.7622999 0 -2.281837 5.8200413
450 1.6264734 -4.7200865 0 -2.2809863 5.9546991 450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
500 1.6366891 -4.7350979 0 -2.2806781 5.9369284 500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
Loop time of 21.1422 on 1 procs for 250 steps with 4000 atoms Loop time of 11.6299 on 1 procs for 250 steps with 4000 atoms
Performance: 5108.279 tau/day, 11.825 timesteps/s Performance: 9286.409 tau/day, 21.496 timesteps/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads 99.7% 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 | 20.925 | 20.925 | 20.925 | 0.0 | 98.97 Pair | 11.403 | 11.403 | 11.403 | 0.0 | 98.05
Neigh | 0.18452 | 0.18452 | 0.18452 | 0.0 | 0.87 Neigh | 0.19289 | 0.19289 | 0.19289 | 0.0 | 1.66
Comm | 0.014836 | 0.014836 | 0.014836 | 0.0 | 0.07 Comm | 0.015828 | 0.015828 | 0.015828 | 0.0 | 0.14
Output | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.00 Output | 0.00018644 | 0.00018644 | 0.00018644 | 0.0 | 0.00
Modify | 0.01366 | 0.01366 | 0.01366 | 0.0 | 0.06 Modify | 0.014582 | 0.014582 | 0.014582 | 0.0 | 0.13
Other | | 0.004355 | | | 0.02 Other | | 0.003107 | | | 0.03
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -175,7 +178,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.86 | 2.86 | 2.86 Mbytes Per MPI rank memory allocation (min/avg/max) = 2.896 | 2.896 | 2.896 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 1.6275257 -4.7224992 0 -2.281821 5.9567365 0 1.6275257 -4.7224992 0 -2.281821 5.9567365
50 1.6454666 -4.7497515 0 -2.2821686 5.8729175 50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
@ -183,20 +186,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6537193 -4.7627023 0 -2.2827434 5.8177704 150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
200 1.6258731 -4.7205017 0 -2.2823017 5.952511 200 1.6258731 -4.7205017 0 -2.2823017 5.952511
250 1.6370862 -4.7373176 0 -2.2823022 5.925807 250 1.6370862 -4.7373176 0 -2.2823022 5.925807
Loop time of 21.1026 on 1 procs for 250 steps with 4000 atoms Loop time of 11.6243 on 1 procs for 250 steps with 4000 atoms
Performance: 5117.845 tau/day, 11.847 timesteps/s Performance: 9290.855 tau/day, 21.507 timesteps/s
98.7% 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 | 20.984 | 20.984 | 20.984 | 0.0 | 99.44 Pair | 11.501 | 11.501 | 11.501 | 0.0 | 98.94
Neigh | 0.088639 | 0.088639 | 0.088639 | 0.0 | 0.42 Neigh | 0.093333 | 0.093333 | 0.093333 | 0.0 | 0.80
Comm | 0.012881 | 0.012881 | 0.012881 | 0.0 | 0.06 Comm | 0.013483 | 0.013483 | 0.013483 | 0.0 | 0.12
Output | 0.00028563 | 0.00028563 | 0.00028563 | 0.0 | 0.00 Output | 0.00020981 | 0.00020981 | 0.00020981 | 0.0 | 0.00
Modify | 0.013523 | 0.013523 | 0.013523 | 0.0 | 0.06 Modify | 0.014475 | 0.014475 | 0.014475 | 0.0 | 0.12
Other | | 0.003033 | | | 0.01 Other | | 0.001968 | | | 0.02
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -211,4 +214,4 @@ Neighbor list builds = 12
Dangerous builds not checked Dangerous builds not checked
shell rm melt.data melt.restart shell rm melt.data melt.restart
Total wall time: 0:01:05 Total wall time: 0:00:35

67
examples/python/log.4May17.pair_python_melt.g++.4 → examples/python/log.27Nov18.pair_python_melt.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt # 3d Lennard-Jones melt
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4000 atoms Created 4000 atoms
Time spent = 0.000413418 secs
mass * 1.0 mass * 1.0
velocity all create 3.0 87287 velocity all create 3.0 87287
@ -39,7 +40,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504 0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
@ -47,20 +48,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 5.65922 on 4 procs for 250 steps with 4000 atoms Loop time of 3.21263 on 4 procs for 250 steps with 4000 atoms
Performance: 19083.895 tau/day, 44.176 timesteps/s Performance: 33617.340 tau/day, 77.818 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads 98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 5.4529 | 5.5207 | 5.5575 | 1.7 | 97.55 Pair | 2.9309 | 2.9942 | 3.1071 | 3.9 | 93.20
Neigh | 0.023164 | 0.023376 | 0.023883 | 0.2 | 0.41 Neigh | 0.024111 | 0.024518 | 0.024765 | 0.2 | 0.76
Comm | 0.073318 | 0.1099 | 0.17804 | 12.2 | 1.94 Comm | 0.075799 | 0.1889 | 0.25258 | 15.5 | 5.88
Output | 0.00023365 | 0.00026143 | 0.00030684 | 0.0 | 0.00 Output | 0.00018406 | 0.00030106 | 0.00065088 | 0.0 | 0.01
Modify | 0.0036483 | 0.0037143 | 0.003896 | 0.2 | 0.07 Modify | 0.0038259 | 0.0038511 | 0.0038726 | 0.0 | 0.12
Other | | 0.001274 | | | 0.02 Other | | 0.0009047 | | | 0.03
Nlocal: 1000 ave 1010 max 982 min Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2 Histogram: 1 0 0 0 0 0 1 0 0 2
@ -81,8 +82,10 @@ clear
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
read_restart melt.restart read_restart melt.restart
restoring atom style atomic from restart
orthogonal box = (0 0 0) to (16.796 16.796 16.796) orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
pair style python stores no restart info
4000 atoms 4000 atoms
pair_style python 2.5 pair_style python 2.5
@ -104,7 +107,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.815 | 2.816 | 2.816 Mbytes Per MPI rank memory allocation (min/avg/max) = 2.829 | 2.83 | 2.83 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
250 1.6323462 -4.7292062 0 -2.2812991 5.9762168 250 1.6323462 -4.7292062 0 -2.2812991 5.9762168
300 1.6451788 -4.7488091 0 -2.2816578 5.8375485 300 1.6451788 -4.7488091 0 -2.2816578 5.8375485
@ -112,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084 400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898 450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
500 1.643316 -4.7454222 0 -2.2810644 5.8454817 500 1.643316 -4.7454222 0 -2.2810644 5.8454817
Loop time of 5.70169 on 4 procs for 250 steps with 4000 atoms Loop time of 3.16401 on 4 procs for 250 steps with 4000 atoms
Performance: 18941.760 tau/day, 43.847 timesteps/s Performance: 34133.894 tau/day, 79.014 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads 99.0% 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 | 5.3919 | 5.4905 | 5.6136 | 3.7 | 96.30 Pair | 2.9254 | 2.9723 | 3.0639 | 3.2 | 93.94
Neigh | 0.046791 | 0.047817 | 0.048795 | 0.3 | 0.84 Neigh | 0.04915 | 0.050266 | 0.050704 | 0.3 | 1.59
Comm | 0.034221 | 0.1575 | 0.25635 | 22.1 | 2.76 Comm | 0.044051 | 0.13579 | 0.18379 | 15.0 | 4.29
Output | 0.00020409 | 0.00023448 | 0.00026131 | 0.0 | 0.00 Output | 0.00016141 | 0.00028008 | 0.00063109 | 0.0 | 0.01
Modify | 0.0035028 | 0.0035674 | 0.0036926 | 0.1 | 0.06 Modify | 0.0037544 | 0.003895 | 0.0041802 | 0.3 | 0.12
Other | | 0.002079 | | | 0.04 Other | | 0.001474 | | | 0.05
Nlocal: 1000 ave 1012 max 983 min Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1 Histogram: 1 0 0 0 0 0 2 0 0 1
@ -175,7 +178,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.315 | 2.316 | 2.316 Mbytes Per MPI rank memory allocation (min/avg/max) = 2.329 | 2.33 | 2.33 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 1.6323462 -4.7292062 0 -2.2812991 5.9762168 0 1.6323462 -4.7292062 0 -2.2812991 5.9762168
50 1.6450626 -4.7488948 0 -2.2819177 5.8370409 50 1.6450626 -4.7488948 0 -2.2819177 5.8370409
@ -183,20 +186,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273 150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228 200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819 250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
Loop time of 5.69568 on 4 procs for 250 steps with 4000 atoms Loop time of 3.16461 on 4 procs for 250 steps with 4000 atoms
Performance: 18961.751 tau/day, 43.893 timesteps/s Performance: 34127.383 tau/day, 78.999 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads 98.7% 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 | 5.4041 | 5.5245 | 5.6139 | 3.2 | 96.99 Pair | 2.9135 | 2.9842 | 3.0594 | 3.1 | 94.30
Neigh | 0.022658 | 0.022986 | 0.023398 | 0.2 | 0.40 Neigh | 0.024132 | 0.024319 | 0.024553 | 0.1 | 0.77
Comm | 0.053521 | 0.14309 | 0.26385 | 20.2 | 2.51 Comm | 0.075955 | 0.15106 | 0.22174 | 13.9 | 4.77
Output | 0.00027037 | 0.00029504 | 0.00033665 | 0.0 | 0.01 Output | 0.00016856 | 0.00028443 | 0.00062919 | 0.0 | 0.01
Modify | 0.0035288 | 0.0035585 | 0.0035827 | 0.0 | 0.06 Modify | 0.0037944 | 0.0038335 | 0.0038977 | 0.1 | 0.12
Other | | 0.001275 | | | 0.02 Other | | 0.0008717 | | | 0.03
Nlocal: 1000 ave 1013 max 989 min Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1 Histogram: 1 0 0 1 0 1 0 0 0 1
@ -211,4 +214,4 @@ Neighbor list builds = 12
Dangerous builds not checked Dangerous builds not checked
shell rm melt.data melt.restart shell rm melt.data melt.restart
Total wall time: 0:00:17 Total wall time: 0:00:09

30
examples/python/log.4May17.pair_python_spce.g++.1 → examples/python/log.27Nov18.pair_python_spce.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
units real units real
atom_style full atom_style full
@ -52,7 +52,7 @@ fix 2 all nvt temp 300.0 300.0 100.0
thermo 10 thermo 10
run 100 run 100
PPPM initialization ... PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.279652 G vector (1/distance) = 0.279652
grid = 40 40 40 grid = 40 40 40
stencil order = 5 stencil order = 5
@ -77,7 +77,7 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 41.05 | 41.05 | 41.05 Mbytes Per MPI rank memory allocation (min/avg/max) = 41.15 | 41.15 | 41.15 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -16692.369 0 -16692.369 -1289.222 0 0 -16692.369 0 -16692.369 -1289.222
10 120.56861 -17769.719 0 -16691.902 -4082.7098 10 120.56861 -17769.719 0 -16691.902 -4082.7098
@ -90,22 +90,22 @@ Step Temp E_pair E_mol TotEng Press
80 182.94811 -18155.978 0 -16520.523 -2393.3156 80 182.94811 -18155.978 0 -16520.523 -2393.3156
90 191.29902 -18197.887 0 -16487.779 -2242.7104 90 191.29902 -18197.887 0 -16487.779 -2242.7104
100 194.70949 -18195.021 0 -16454.425 -1955.2916 100 194.70949 -18195.021 0 -16454.425 -1955.2916
Loop time of 23.5385 on 1 procs for 100 steps with 4500 atoms Loop time of 15.3744 on 1 procs for 100 steps with 4500 atoms
Performance: 0.367 ns/day, 65.385 hours/ns, 4.248 timesteps/s Performance: 0.562 ns/day, 42.707 hours/ns, 6.504 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads 98.8% 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 | 21.642 | 21.642 | 21.642 | 0.0 | 91.94 Pair | 13.914 | 13.914 | 13.914 | 0.0 | 90.50
Bond | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.00 Bond | 0.00013375 | 0.00013375 | 0.00013375 | 0.0 | 0.00
Kspace | 1.5436 | 1.5436 | 1.5436 | 0.0 | 6.56 Kspace | 1.0852 | 1.0852 | 1.0852 | 0.0 | 7.06
Neigh | 0.25623 | 0.25623 | 0.25623 | 0.0 | 1.09 Neigh | 0.29811 | 0.29811 | 0.29811 | 0.0 | 1.94
Comm | 0.024325 | 0.024325 | 0.024325 | 0.0 | 0.10 Comm | 0.020503 | 0.020503 | 0.020503 | 0.0 | 0.13
Output | 0.00064301 | 0.00064301 | 0.00064301 | 0.0 | 0.00 Output | 0.00045133 | 0.00045133 | 0.00045133 | 0.0 | 0.00
Modify | 0.065919 | 0.065919 | 0.065919 | 0.0 | 0.28 Modify | 0.052513 | 0.052513 | 0.052513 | 0.0 | 0.34
Other | | 0.005401 | | | 0.02 Other | | 0.00348 | | | 0.02
Nlocal: 4500 ave 4500 max 4500 min Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -119,4 +119,4 @@ Ave neighs/atom = 578.169
Ave special neighs/atom = 2 Ave special neighs/atom = 2
Neighbor list builds = 3 Neighbor list builds = 3
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:24 Total wall time: 0:00:15

30
examples/python/log.4May17.pair_python_spce.g++.4 → examples/python/log.27Nov18.pair_python_spce.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
units real units real
atom_style full atom_style full
@ -52,7 +52,7 @@ fix 2 all nvt temp 300.0 300.0 100.0
thermo 10 thermo 10
run 100 run 100
PPPM initialization ... PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.279652 G vector (1/distance) = 0.279652
grid = 40 40 40 grid = 40 40 40
stencil order = 5 stencil order = 5
@ -77,7 +77,7 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 14.59 | 14.59 | 14.59 Mbytes Per MPI rank memory allocation (min/avg/max) = 14.64 | 14.64 | 14.64 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 0 -16692.369 0 -16692.369 -1289.222 0 0 -16692.369 0 -16692.369 -1289.222
10 120.56861 -17769.719 0 -16691.902 -4082.7098 10 120.56861 -17769.719 0 -16691.902 -4082.7098
@ -90,22 +90,22 @@ Step Temp E_pair E_mol TotEng Press
80 182.94811 -18155.978 0 -16520.523 -2393.3156 80 182.94811 -18155.978 0 -16520.523 -2393.3156
90 191.29902 -18197.887 0 -16487.779 -2242.7104 90 191.29902 -18197.887 0 -16487.779 -2242.7104
100 194.70949 -18195.021 0 -16454.425 -1955.2916 100 194.70949 -18195.021 0 -16454.425 -1955.2916
Loop time of 6.4942 on 4 procs for 100 steps with 4500 atoms Loop time of 4.36104 on 4 procs for 100 steps with 4500 atoms
Performance: 1.330 ns/day, 18.039 hours/ns, 15.398 timesteps/s Performance: 1.981 ns/day, 12.114 hours/ns, 22.930 timesteps/s
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads 97.7% 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 | 5.4084 | 5.572 | 5.8013 | 7.2 | 85.80 Pair | 3.5019 | 3.6105 | 3.738 | 4.4 | 82.79
Bond | 0.00012994 | 0.0001421 | 0.00016356 | 0.0 | 0.00 Bond | 0.00010133 | 0.00013196 | 0.00017118 | 0.0 | 0.00
Kspace | 0.52942 | 0.75773 | 0.92078 | 19.5 | 11.67 Kspace | 0.47082 | 0.59641 | 0.70417 | 10.8 | 13.68
Neigh | 0.071055 | 0.07116 | 0.071278 | 0.0 | 1.10 Neigh | 0.081036 | 0.081042 | 0.081047 | 0.0 | 1.86
Comm | 0.040311 | 0.041255 | 0.041817 | 0.3 | 0.64 Comm | 0.030113 | 0.03092 | 0.03135 | 0.3 | 0.71
Output | 0.00040603 | 0.00048071 | 0.00058675 | 0.0 | 0.01 Output | 0.00034952 | 0.00064117 | 0.001514 | 0.0 | 0.01
Modify | 0.047507 | 0.047629 | 0.047772 | 0.1 | 0.73 Modify | 0.036583 | 0.037553 | 0.038021 | 0.3 | 0.86
Other | | 0.003771 | | | 0.06 Other | | 0.00388 | | | 0.09
Nlocal: 1125 ave 1154 max 1092 min Nlocal: 1125 ave 1154 max 1092 min
Histogram: 1 0 0 0 1 0 0 1 0 1 Histogram: 1 0 0 0 1 0 0 1 0 1
@ -119,4 +119,4 @@ Ave neighs/atom = 578.169
Ave special neighs/atom = 2 Ave special neighs/atom = 2
Neighbor list builds = 3 Neighbor list builds = 3
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:06 Total wall time: 0:00:04

27
examples/python/log.4May17.pair_python_table.g++.1 → examples/python/log.27Nov18.pair_python_table.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt # 3d Lennard-Jones melt
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4000 atoms Created 4000 atoms
Time spent = 0.000697136 secs
mass * 1.0 mass * 1.0
velocity all create 3.0 87287 velocity all create 3.0 87287
@ -38,7 +39,7 @@ Neighbor list info ...
pair_style table linear 2000 pair_style table linear 2000
pair_coeff 1 1 lj_1_1.table LJ pair_coeff 1 1 lj_1_1.table LJ
WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr. WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476) Should only be flagged at inflection points (src/pair_table.cpp:481)
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify every 20 delay 0 check no neigh_modify every 20 delay 0 check no
@ -59,7 +60,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 3 -6.7733629 0 -2.2744879 -3.7032813 0 3 -6.7733629 0 -2.2744879 -3.7032813
50 1.6758731 -4.7953067 0 -2.2821255 5.6706553 50 1.6758731 -4.7953067 0 -2.2821255 5.6706553
@ -67,20 +68,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.632425 -4.7284533 0 -2.2804279 5.9595684 150 1.632425 -4.7284533 0 -2.2804279 5.9595684
200 1.6631578 -4.7749889 0 -2.2808759 5.7365839 200 1.6631578 -4.7749889 0 -2.2808759 5.7365839
250 1.6277062 -4.7224727 0 -2.2815238 5.9572913 250 1.6277062 -4.7224727 0 -2.2815238 5.9572913
Loop time of 0.996739 on 1 procs for 250 steps with 4000 atoms Loop time of 0.94897 on 1 procs for 250 steps with 4000 atoms
Performance: 108353.298 tau/day, 250.818 timesteps/s Performance: 113807.650 tau/day, 263.444 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads 99.6% 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 | 0.87985 | 0.87985 | 0.87985 | 0.0 | 88.27 Pair | 0.82415 | 0.82415 | 0.82415 | 0.0 | 86.85
Neigh | 0.08799 | 0.08799 | 0.08799 | 0.0 | 8.83 Neigh | 0.093798 | 0.093798 | 0.093798 | 0.0 | 9.88
Comm | 0.012301 | 0.012301 | 0.012301 | 0.0 | 1.23 Comm | 0.013542 | 0.013542 | 0.013542 | 0.0 | 1.43
Output | 0.00013161 | 0.00013161 | 0.00013161 | 0.0 | 0.01 Output | 0.00017834 | 0.00017834 | 0.00017834 | 0.0 | 0.02
Modify | 0.013656 | 0.013656 | 0.013656 | 0.0 | 1.37 Modify | 0.014418 | 0.014418 | 0.014418 | 0.0 | 1.52
Other | | 0.002808 | | | 0.28 Other | | 0.002882 | | | 0.30
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -96,4 +97,4 @@ Dangerous builds not checked
shell rm lj_1_1.table shell rm lj_1_1.table
Total wall time: 0:00:01 Total wall time: 0:00:00

25
examples/python/log.4May17.pair_python_table.g++.4 → examples/python/log.27Nov18.pair_python_table.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (4 May 2017) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt # 3d Lennard-Jones melt
@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4000 atoms Created 4000 atoms
Time spent = 0.000404596 secs
mass * 1.0 mass * 1.0
velocity all create 3.0 87287 velocity all create 3.0 87287
@ -38,7 +39,7 @@ Neighbor list info ...
pair_style table linear 2000 pair_style table linear 2000
pair_coeff 1 1 lj_1_1.table LJ pair_coeff 1 1 lj_1_1.table LJ
WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr. WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:476) Should only be flagged at inflection points (src/pair_table.cpp:481)
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify every 20 delay 0 check no neigh_modify every 20 delay 0 check no
@ -59,7 +60,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 3 -6.7733629 0 -2.2744879 -3.7032813 0 3 -6.7733629 0 -2.2744879 -3.7032813
50 1.675395 -4.7945736 0 -2.2821094 5.6620623 50 1.675395 -4.7945736 0 -2.2821094 5.6620623
@ -67,20 +68,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6595852 -4.7697199 0 -2.2809644 5.7837898 150 1.6595852 -4.7697199 0 -2.2809644 5.7837898
200 1.6371471 -4.7363942 0 -2.2812874 5.924977 200 1.6371471 -4.7363942 0 -2.2812874 5.924977
250 1.6315623 -4.7278268 0 -2.2810951 5.9807196 250 1.6315623 -4.7278268 0 -2.2810951 5.9807196
Loop time of 0.291846 on 4 procs for 250 steps with 4000 atoms Loop time of 0.285577 on 4 procs for 250 steps with 4000 atoms
Performance: 370058.286 tau/day, 856.616 timesteps/s Performance: 378181.086 tau/day, 875.419 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads 96.5% 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 | 0.22586 | 0.23364 | 0.24085 | 1.3 | 80.06 Pair | 0.2111 | 0.21779 | 0.22447 | 1.0 | 76.26
Neigh | 0.022808 | 0.023235 | 0.023602 | 0.2 | 7.96 Neigh | 0.024165 | 0.024465 | 0.0247 | 0.1 | 8.57
Comm | 0.022573 | 0.030065 | 0.038092 | 3.9 | 10.30 Comm | 0.03147 | 0.038356 | 0.044902 | 2.5 | 13.43
Output | 0.00013423 | 0.00014067 | 0.00015759 | 0.0 | 0.05 Output | 0.00016117 | 0.00022227 | 0.00040102 | 0.0 | 0.08
Modify | 0.0035079 | 0.0035501 | 0.0036008 | 0.1 | 1.22 Modify | 0.0037565 | 0.0038704 | 0.0040345 | 0.2 | 1.36
Other | | 0.001211 | | | 0.42 Other | | 0.0008699 | | | 0.30
Nlocal: 1000 ave 1010 max 981 min Nlocal: 1000 ave 1010 max 981 min
Histogram: 1 0 0 0 0 0 1 0 0 2 Histogram: 1 0 0 0 0 0 1 0 0 2

231
examples/python/log.5Oct16.python.g++.1 → examples/python/log.27Nov18.python.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt with Python functions added # 3d Lennard-Jones melt with Python functions added
units lj units lj
@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4000 atoms Created 4000 atoms
Time spent = 0.00072813 secs
mass 1 1.0 mass 1 1.0
velocity all create 1.44 87287 loop geom velocity all create 1.44 87287 loop geom
@ -26,30 +28,35 @@ fix 1 all nve
run 10 run 10
Neighbor list info ... Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8 master list distance cutoff = 2.8
ghost atom cutoff = 2.8 ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 12 12 12 binsize = 1.4, bins = 12 12 12
Memory usage per processor = 2.69271 Mbytes 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.721 | 3.721 | 3.721 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732 0 1.44 -6.7733681 0 -4.6139081 -5.0199732
10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638 10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638
Loop time of 0.0323398 on 1 procs for 10 steps with 4000 atoms Loop time of 0.0312054 on 1 procs for 10 steps with 4000 atoms
Performance: 133581.484 tau/day, 309.216 timesteps/s Performance: 138437.508 tau/day, 320.457 timesteps/s
102.0% CPU use with 1 MPI tasks x no OpenMP threads 99.7% 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 | 0.024638 | 0.024638 | 0.024638 | 0.0 | 76.18 Pair | 0.022328 | 0.022328 | 0.022328 | 0.0 | 71.55
Neigh | 0.0063899 | 0.0063899 | 0.0063899 | 0.0 | 19.76 Neigh | 0.0073318 | 0.0073318 | 0.0073318 | 0.0 | 23.50
Comm | 0.00049949 | 0.00049949 | 0.00049949 | 0.0 | 1.54 Comm | 0.0006578 | 0.0006578 | 0.0006578 | 0.0 | 2.11
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.06 Output | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.09
Modify | 0.00050044 | 0.00050044 | 0.00050044 | 0.0 | 1.55 Modify | 0.00057721 | 0.00057721 | 0.00057721 | 0.0 | 1.85
Other | | 0.0002944 | | | 0.91 Other | | 0.0002832 | | | 0.91
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -67,13 +74,14 @@ Dangerous builds = 0
# example of catching a syntax error # example of catching a syntax error
python simple here """ python simple here """
from __future__ import print_function
def simple(): def simple():
import exceptions foo = 0
print "Inside simple function" print("Inside simple function")
try: try:
foo += 1 foo += 1
except Exception, e: except Exception as e:
print "FOO error:",e print("FOO error:", e)
""" """
python simple invoke python simple invoke
@ -110,31 +118,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.0 pair_style lj/cut 1.0
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65 -> bins = 26 26 26
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
10 1.1259767 0.016557378 0 1.7051002 1.2784679 10 1.1259767 0.016557378 0 1.7051002 1.2784679
20 0.87608998 0.39300382 0 1.7068103 6.0488236 20 0.87608998 0.39300382 0 1.7068103 6.0488236
Loop time of 0.0046258 on 1 procs for 10 steps with 4000 atoms Loop time of 0.00488138 on 1 procs for 10 steps with 4000 atoms
Performance: 933893.067 tau/day, 2161.790 timesteps/s Performance: 884995.276 tau/day, 2048.600 timesteps/s
86.4% CPU use with 1 MPI tasks x no OpenMP threads 99.7% 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 | 0.001574 | 0.001574 | 0.001574 | 0.0 | 34.03 Pair | 0.0017166 | 0.0017166 | 0.0017166 | 0.0 | 35.17
Neigh | 0.0020421 | 0.0020421 | 0.0020421 | 0.0 | 44.14 Neigh | 0.0020256 | 0.0020256 | 0.0020256 | 0.0 | 41.50
Comm | 0.00025463 | 0.00025463 | 0.00025463 | 0.0 | 5.50 Comm | 0.00028539 | 0.00028539 | 0.00028539 | 0.0 | 5.85
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.39 Output | 2.6703e-05 | 2.6703e-05 | 2.6703e-05 | 0.0 | 0.55
Modify | 0.00049615 | 0.00049615 | 0.00049615 | 0.0 | 10.73 Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 11.76
Other | | 0.000241 | | | 5.21 Other | | 0.0002532 | | | 5.19
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -151,31 +152,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.1 pair_style lj/cut 1.1
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.4
ghost atom cutoff = 1.4
binsize = 0.7 -> bins = 24 24 24
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
20 0.87608998 -0.33042884 0 0.9833776 8.5817494 20 0.87608998 -0.33042884 0 0.9833776 8.5817494
30 1.0155079 -0.83166219 0 0.69121891 7.9905553 30 1.0155079 -0.83166219 0 0.69121891 7.9905553
Loop time of 0.00619817 on 1 procs for 10 steps with 4000 atoms Loop time of 0.00647616 on 1 procs for 10 steps with 4000 atoms
Performance: 696980.162 tau/day, 1613.380 timesteps/s Performance: 667061.565 tau/day, 1544.124 timesteps/s
96.8% CPU use with 1 MPI tasks x no 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 | 0.0029786 | 0.0029786 | 0.0029786 | 0.0 | 48.06 Pair | 0.0030439 | 0.0030439 | 0.0030439 | 0.0 | 47.00
Neigh | 0.002203 | 0.002203 | 0.002203 | 0.0 | 35.54 Neigh | 0.002295 | 0.002295 | 0.002295 | 0.0 | 35.44
Comm | 0.00025678 | 0.00025678 | 0.00025678 | 0.0 | 4.14 Comm | 0.00028467 | 0.00028467 | 0.00028467 | 0.0 | 4.40
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.29 Output | 2.3842e-05 | 2.3842e-05 | 2.3842e-05 | 0.0 | 0.37
Modify | 0.00049472 | 0.00049472 | 0.00049472 | 0.0 | 7.98 Modify | 0.0005753 | 0.0005753 | 0.0005753 | 0.0 | 8.88
Other | | 0.0002472 | | | 3.99 Other | | 0.0002534 | | | 3.91
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -192,31 +186,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.2 pair_style lj/cut 1.2
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.5
ghost atom cutoff = 1.5
binsize = 0.75 -> bins = 23 23 23
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
30 1.0155079 -2.0616558 0 -0.53877467 7.6238572 30 1.0155079 -2.0616558 0 -0.53877467 7.6238572
40 1.0490928 -2.1868324 0 -0.61358669 7.2084131 40 1.0490928 -2.1868324 0 -0.61358669 7.2084131
Loop time of 0.00750899 on 1 procs for 10 steps with 4000 atoms Loop time of 0.00802207 on 1 procs for 10 steps with 4000 atoms
Performance: 575310.153 tau/day, 1331.736 timesteps/s Performance: 538514.378 tau/day, 1246.561 timesteps/s
93.2% CPU use with 1 MPI tasks x no OpenMP threads 99.1% 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 | 0.004189 | 0.004189 | 0.004189 | 0.0 | 55.79 Pair | 0.0044219 | 0.0044219 | 0.0044219 | 0.0 | 55.12
Neigh | 0.0022991 | 0.0022991 | 0.0022991 | 0.0 | 30.62 Neigh | 0.0024219 | 0.0024219 | 0.0024219 | 0.0 | 30.19
Comm | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 3.45 Comm | 0.00030112 | 0.00030112 | 0.00030112 | 0.0 | 3.75
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.24 Output | 2.5749e-05 | 2.5749e-05 | 2.5749e-05 | 0.0 | 0.32
Modify | 0.00049615 | 0.00049615 | 0.00049615 | 0.0 | 6.61 Modify | 0.00059366 | 0.00059366 | 0.00059366 | 0.0 | 7.40
Other | | 0.0002475 | | | 3.30 Other | | 0.0002577 | | | 3.21
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -233,31 +220,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.3 pair_style lj/cut 1.3
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.6
ghost atom cutoff = 1.6
binsize = 0.8 -> bins = 21 21 21
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
40 1.0490928 -3.0667608 0 -1.493515 6.2796311 40 1.0490928 -3.0667608 0 -1.493515 6.2796311
50 1.0764484 -3.1173704 0 -1.5031014 6.0850409 50 1.0764484 -3.1173704 0 -1.5031014 6.0850409
Loop time of 0.00869107 on 1 procs for 10 steps with 4000 atoms Loop time of 0.00908327 on 1 procs for 10 steps with 4000 atoms
Performance: 497061.786 tau/day, 1150.606 timesteps/s Performance: 475599.593 tau/day, 1100.925 timesteps/s
103.5% CPU use with 1 MPI tasks x no OpenMP threads 99.9% 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 | 0.0049038 | 0.0049038 | 0.0049038 | 0.0 | 56.42 Pair | 0.0049157 | 0.0049157 | 0.0049157 | 0.0 | 54.12
Neigh | 0.0027289 | 0.0027289 | 0.0027289 | 0.0 | 31.40 Neigh | 0.0029771 | 0.0029771 | 0.0029771 | 0.0 | 32.78
Comm | 0.00028753 | 0.00028753 | 0.00028753 | 0.0 | 3.31 Comm | 0.00033617 | 0.00033617 | 0.00033617 | 0.0 | 3.70
Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.23 Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.25
Modify | 0.00049758 | 0.00049758 | 0.00049758 | 0.0 | 5.73 Modify | 0.00057578 | 0.00057578 | 0.00057578 | 0.0 | 6.34
Other | | 0.0002532 | | | 2.91 Other | | 0.0002553 | | | 2.81
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -274,31 +254,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.4 pair_style lj/cut 1.4
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7
ghost atom cutoff = 1.7
binsize = 0.85 -> bins = 20 20 20
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
50 1.0764484 -3.6112241 0 -1.9969552 5.4223348 50 1.0764484 -3.6112241 0 -1.9969552 5.4223348
60 1.1101013 -3.6616014 0 -1.9968657 5.2348251 60 1.1101013 -3.6616014 0 -1.9968657 5.2348251
Loop time of 0.00934482 on 1 procs for 10 steps with 4000 atoms Loop time of 0.0096159 on 1 procs for 10 steps with 4000 atoms
Performance: 462288.386 tau/day, 1070.112 timesteps/s Performance: 449256.007 tau/day, 1039.944 timesteps/s
96.3% CPU use with 1 MPI tasks x no OpenMP threads 99.9% 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 | 0.0055761 | 0.0055761 | 0.0055761 | 0.0 | 59.67 Pair | 0.0054793 | 0.0054793 | 0.0054793 | 0.0 | 56.98
Neigh | 0.002676 | 0.002676 | 0.002676 | 0.0 | 28.64 Neigh | 0.0028973 | 0.0028973 | 0.0028973 | 0.0 | 30.13
Comm | 0.00032163 | 0.00032163 | 0.00032163 | 0.0 | 3.44 Comm | 0.00038075 | 0.00038075 | 0.00038075 | 0.0 | 3.96
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.19 Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.24
Modify | 0.00049901 | 0.00049901 | 0.00049901 | 0.0 | 5.34 Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 5.97
Other | | 0.0002542 | | | 2.72 Other | | 0.0002615 | | | 2.72
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -315,31 +288,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.5 pair_style lj/cut 1.5
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9 -> bins = 19 19 19
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
60 1.1101013 -3.9655053 0 -2.3007696 4.7849008 60 1.1101013 -3.9655053 0 -2.3007696 4.7849008
70 1.1122144 -3.9657095 0 -2.297805 4.8014106 70 1.1122144 -3.9657095 0 -2.297805 4.8014106
Loop time of 0.0103869 on 1 procs for 10 steps with 4000 atoms Loop time of 0.0107083 on 1 procs for 10 steps with 4000 atoms
Performance: 415906.746 tau/day, 962.747 timesteps/s Performance: 403424.172 tau/day, 933.852 timesteps/s
96.3% CPU use with 1 MPI tasks x no OpenMP threads 99.9% 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 | 0.0063703 | 0.0063703 | 0.0063703 | 0.0 | 61.33 Pair | 0.0062652 | 0.0062652 | 0.0062652 | 0.0 | 58.51
Neigh | 0.002893 | 0.002893 | 0.002893 | 0.0 | 27.85 Neigh | 0.0031667 | 0.0031667 | 0.0031667 | 0.0 | 29.57
Comm | 0.00034499 | 0.00034499 | 0.00034499 | 0.0 | 3.32 Comm | 0.00041771 | 0.00041771 | 0.00041771 | 0.0 | 3.90
Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.17 Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.21
Modify | 0.00050139 | 0.00050139 | 0.00050139 | 0.0 | 4.83 Modify | 0.0005734 | 0.0005734 | 0.0005734 | 0.0 | 5.35
Other | | 0.0002594 | | | 2.50 Other | | 0.0002627 | | | 2.45
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -356,31 +322,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.6 pair_style lj/cut 1.6
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.9
ghost atom cutoff = 1.9
binsize = 0.95 -> bins = 18 18 18
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
70 1.1122144 -4.1752688 0 -2.5073643 4.4755409 70 1.1122144 -4.1752688 0 -2.5073643 4.4755409
80 1.117224 -4.1831357 0 -2.5077187 4.446079 80 1.117224 -4.1831357 0 -2.5077187 4.446079
Loop time of 0.0116282 on 1 procs for 10 steps with 4000 atoms Loop time of 0.0121632 on 1 procs for 10 steps with 4000 atoms
Performance: 371512.205 tau/day, 859.982 timesteps/s Performance: 355170.795 tau/day, 822.155 timesteps/s
103.2% CPU use with 1 MPI tasks x no OpenMP threads 99.9% 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 | 0.0074186 | 0.0074186 | 0.0074186 | 0.0 | 63.80 Pair | 0.0074623 | 0.0074623 | 0.0074623 | 0.0 | 61.35
Neigh | 0.0030658 | 0.0030658 | 0.0030658 | 0.0 | 26.37 Neigh | 0.0033951 | 0.0033951 | 0.0033951 | 0.0 | 27.91
Comm | 0.00036025 | 0.00036025 | 0.00036025 | 0.0 | 3.10 Comm | 0.00043678 | 0.00043678 | 0.00043678 | 0.0 | 3.59
Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.15 Output | 2.408e-05 | 2.408e-05 | 2.408e-05 | 0.0 | 0.20
Modify | 0.0005033 | 0.0005033 | 0.0005033 | 0.0 | 4.33 Modify | 0.00057578 | 0.00057578 | 0.00057578 | 0.0 | 4.73
Other | | 0.000263 | | | 2.26 Other | | 0.0002692 | | | 2.21
Nlocal: 4000 ave 4000 max 4000 min Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

231
examples/python/log.5Oct16.python.g++.4 → examples/python/log.27Nov18.python.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (5 Oct 2016) LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt with Python functions added # 3d Lennard-Jones melt with Python functions added
units lj units lj
@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 4000 atoms Created 4000 atoms
Time spent = 0.000517368 secs
mass 1 1.0 mass 1 1.0
velocity all create 1.44 87287 loop geom velocity all create 1.44 87287 loop geom
@ -26,30 +28,35 @@ fix 1 all nve
run 10 run 10
Neighbor list info ... Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8 master list distance cutoff = 2.8
ghost atom cutoff = 2.8 ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 12 12 12 binsize = 1.4, bins = 12 12 12
Memory usage per processor = 2.60344 Mbytes 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.205 | 3.205 | 3.205 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732 0 1.44 -6.7733681 0 -4.6139081 -5.0199732
10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638 10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638
Loop time of 0.00930309 on 4 procs for 10 steps with 4000 atoms Loop time of 0.00902343 on 4 procs for 10 steps with 4000 atoms
Performance: 464361.693 tau/day, 1074.911 timesteps/s Performance: 478753.753 tau/day, 1108.226 timesteps/s
96.7% CPU use with 4 MPI tasks x no 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 | 0.0064399 | 0.0064787 | 0.0065157 | 0.0 | 69.64 Pair | 0.0058084 | 0.0058863 | 0.0059605 | 0.1 | 65.23
Neigh | 0.0017071 | 0.0017205 | 0.0017281 | 0.0 | 18.49 Neigh | 0.0019183 | 0.0019591 | 0.0020542 | 0.1 | 21.71
Comm | 0.00073171 | 0.00077122 | 0.00081086 | 0.1 | 8.29 Comm | 0.00081086 | 0.00084025 | 0.00090694 | 0.0 | 9.31
Output | 1.9789e-05 | 2.3663e-05 | 2.9087e-05 | 0.1 | 0.25 Output | 2.1458e-05 | 2.9743e-05 | 4.53e-05 | 0.0 | 0.33
Modify | 0.00012827 | 0.00012904 | 0.00013018 | 0.0 | 1.39 Modify | 0.00015211 | 0.00015229 | 0.00015259 | 0.0 | 1.69
Other | | 0.0001799 | | | 1.93 Other | | 0.0001558 | | | 1.73
Nlocal: 1000 ave 1013 max 989 min Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 1 0 0 1 0 0 0 1 Histogram: 1 0 1 0 0 1 0 0 0 1
@ -67,13 +74,14 @@ Dangerous builds = 0
# example of catching a syntax error # example of catching a syntax error
python simple here """ python simple here """
from __future__ import print_function
def simple(): def simple():
import exceptions foo = 0
print "Inside simple function" print("Inside simple function")
try: try:
foo += 1 foo += 1
except Exception, e: except Exception as e:
print "FOO error:",e print("FOO error:", e)
""" """
python simple invoke python simple invoke
@ -110,31 +118,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.0 pair_style lj/cut 1.0
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65 -> bins = 26 26 26
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
10 1.1259767 0.016557378 0 1.7051002 1.2784679 10 1.1259767 0.016557378 0 1.7051002 1.2784679
20 0.87608998 0.39300382 0 1.7068103 6.0488236 20 0.87608998 0.39300382 0 1.7068103 6.0488236
Loop time of 0.00152922 on 4 procs for 10 steps with 4000 atoms Loop time of 0.00153601 on 4 procs for 10 steps with 4000 atoms
Performance: 2824975.566 tau/day, 6539.295 timesteps/s Performance: 2812478.584 tau/day, 6510.367 timesteps/s
130.8% CPU use with 4 MPI tasks x no OpenMP threads 91.8% 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 | 0.00040293 | 0.0004105 | 0.00041485 | 0.0 | 26.84 Pair | 0.00042677 | 0.00043494 | 0.00044322 | 0.0 | 28.32
Neigh | 0.00057507 | 0.00060332 | 0.00062108 | 0.1 | 39.45 Neigh | 0.00051236 | 0.00051689 | 0.00052524 | 0.0 | 33.65
Comm | 0.0002377 | 0.00025356 | 0.00026774 | 0.1 | 16.58 Comm | 0.00025344 | 0.00026941 | 0.00027728 | 0.0 | 17.54
Output | 1.9073e-05 | 1.9789e-05 | 2.1935e-05 | 0.0 | 1.29 Output | 1.7881e-05 | 2.3544e-05 | 3.9339e-05 | 0.0 | 1.53
Modify | 0.00012994 | 0.00013161 | 0.00013328 | 0.0 | 8.61 Modify | 0.00015187 | 0.00015521 | 0.00016356 | 0.0 | 10.10
Other | | 0.0001104 | | | 7.22 Other | | 0.000136 | | | 8.86
Nlocal: 1000 ave 1015 max 987 min Nlocal: 1000 ave 1015 max 987 min
Histogram: 1 0 0 1 0 1 0 0 0 1 Histogram: 1 0 0 1 0 1 0 0 0 1
@ -151,31 +152,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.1 pair_style lj/cut 1.1
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.4
ghost atom cutoff = 1.4
binsize = 0.7 -> bins = 24 24 24
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
20 0.87608998 -0.33042884 0 0.9833776 8.5817494 20 0.87608998 -0.33042884 0 0.9833776 8.5817494
30 1.0155079 -0.83166219 0 0.69121891 7.9905553 30 1.0155079 -0.83166219 0 0.69121891 7.9905553
Loop time of 0.00186676 on 4 procs for 10 steps with 4000 atoms Loop time of 0.00198567 on 4 procs for 10 steps with 4000 atoms
Performance: 2314172.647 tau/day, 5356.881 timesteps/s Performance: 2175589.035 tau/day, 5036.086 timesteps/s
107.1% CPU use with 4 MPI tasks x no OpenMP threads 98.9% 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 | 0.00075388 | 0.00077951 | 0.00079727 | 0.1 | 41.76 Pair | 0.00076985 | 0.00078291 | 0.00079393 | 0.0 | 39.43
Neigh | 0.00057292 | 0.00058091 | 0.00058484 | 0.0 | 31.12 Neigh | 0.0005703 | 0.00057709 | 0.00058103 | 0.0 | 29.06
Comm | 0.00022578 | 0.00024849 | 0.00028563 | 0.1 | 13.31 Comm | 0.00030351 | 0.00031525 | 0.00033665 | 0.0 | 15.88
Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 1.00 Output | 1.9073e-05 | 2.4378e-05 | 4.0054e-05 | 0.0 | 1.23
Modify | 0.00012493 | 0.00012845 | 0.00013137 | 0.0 | 6.88 Modify | 0.00014806 | 0.00015008 | 0.00015354 | 0.0 | 7.56
Other | | 0.0001107 | | | 5.93 Other | | 0.000136 | | | 6.85
Nlocal: 1000 ave 1019 max 983 min Nlocal: 1000 ave 1019 max 983 min
Histogram: 1 0 1 0 0 0 1 0 0 1 Histogram: 1 0 1 0 0 0 1 0 0 1
@ -192,31 +186,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.2 pair_style lj/cut 1.2
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.5
ghost atom cutoff = 1.5
binsize = 0.75 -> bins = 23 23 23
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
30 1.0155079 -2.0616558 0 -0.53877467 7.6238572 30 1.0155079 -2.0616558 0 -0.53877467 7.6238572
40 1.0490928 -2.1868324 0 -0.61358669 7.2084131 40 1.0490928 -2.1868324 0 -0.61358669 7.2084131
Loop time of 0.00224304 on 4 procs for 10 steps with 4000 atoms Loop time of 0.00232226 on 4 procs for 10 steps with 4000 atoms
Performance: 1925955.918 tau/day, 4458.231 timesteps/s Performance: 1860259.570 tau/day, 4306.156 timesteps/s
89.2% CPU use with 4 MPI tasks x no OpenMP threads 99.4% 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 | 0.0010781 | 0.0011036 | 0.0011303 | 0.1 | 49.20 Pair | 0.0010829 | 0.0010984 | 0.0011158 | 0.0 | 47.30
Neigh | 0.00060606 | 0.00060952 | 0.00061703 | 0.0 | 27.17 Neigh | 0.00060892 | 0.00061285 | 0.00062037 | 0.0 | 26.39
Comm | 0.00023556 | 0.0002715 | 0.00029659 | 0.1 | 12.10 Comm | 0.00027418 | 0.00030226 | 0.00031734 | 0.0 | 13.02
Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 0.83 Output | 1.7881e-05 | 2.3305e-05 | 3.8624e-05 | 0.0 | 1.00
Modify | 0.00012541 | 0.00012833 | 0.00013351 | 0.0 | 5.72 Modify | 0.00014758 | 0.00014979 | 0.0001533 | 0.0 | 6.45
Other | | 0.0001114 | | | 4.97 Other | | 0.0001357 | | | 5.84
Nlocal: 1000 ave 1013 max 984 min Nlocal: 1000 ave 1013 max 984 min
Histogram: 1 0 0 1 0 0 0 0 1 1 Histogram: 1 0 0 1 0 0 0 0 1 1
@ -233,31 +220,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.3 pair_style lj/cut 1.3
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.6
ghost atom cutoff = 1.6
binsize = 0.8 -> bins = 21 21 21
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
40 1.0490928 -3.0667608 0 -1.493515 6.2796311 40 1.0490928 -3.0667608 0 -1.493515 6.2796311
50 1.0764484 -3.1173704 0 -1.5031014 6.0850409 50 1.0764484 -3.1173704 0 -1.5031014 6.0850409
Loop time of 0.00257862 on 4 procs for 10 steps with 4000 atoms Loop time of 0.00268328 on 4 procs for 10 steps with 4000 atoms
Performance: 1675317.210 tau/day, 3878.049 timesteps/s Performance: 1609968.749 tau/day, 3726.780 timesteps/s
77.6% CPU use with 4 MPI tasks x no OpenMP threads 99.5% 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 | 0.0012422 | 0.0012776 | 0.0013103 | 0.1 | 49.55 Pair | 0.0012326 | 0.0012579 | 0.0012789 | 0.1 | 46.88
Neigh | 0.0007019 | 0.00072145 | 0.00073099 | 0.0 | 27.98 Neigh | 0.00073671 | 0.00076056 | 0.00077105 | 0.0 | 28.34
Comm | 0.00027132 | 0.00031221 | 0.00036168 | 0.2 | 12.11 Comm | 0.00031805 | 0.00035089 | 0.0003984 | 0.0 | 13.08
Output | 1.7881e-05 | 1.9133e-05 | 2.1935e-05 | 0.0 | 0.74 Output | 1.7405e-05 | 2.2769e-05 | 3.8147e-05 | 0.0 | 0.85
Modify | 0.00012279 | 0.00012654 | 0.00012875 | 0.0 | 4.91 Modify | 0.00014949 | 0.00015247 | 0.00015497 | 0.0 | 5.68
Other | | 0.0001217 | | | 4.72 Other | | 0.0001387 | | | 5.17
Nlocal: 1000 ave 1013 max 974 min Nlocal: 1000 ave 1013 max 974 min
Histogram: 1 0 0 0 0 0 0 1 0 2 Histogram: 1 0 0 0 0 0 0 1 0 2
@ -274,31 +254,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.4 pair_style lj/cut 1.4
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.7
ghost atom cutoff = 1.7
binsize = 0.85 -> bins = 20 20 20
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
50 1.0764484 -3.6112241 0 -1.9969552 5.4223348 50 1.0764484 -3.6112241 0 -1.9969552 5.4223348
60 1.1101013 -3.6616014 0 -1.9968657 5.2348251 60 1.1101013 -3.6616014 0 -1.9968657 5.2348251
Loop time of 0.00283062 on 4 procs for 10 steps with 4000 atoms Loop time of 0.00504404 on 4 procs for 10 steps with 4000 atoms
Performance: 1526164.943 tau/day, 3532.789 timesteps/s Performance: 856455.812 tau/day, 1982.537 timesteps/s
97.1% CPU use with 4 MPI tasks x no OpenMP threads 88.2% 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 | 0.0014381 | 0.0014688 | 0.0015128 | 0.1 | 51.89 Pair | 0.0013909 | 0.001602 | 0.0021472 | 0.8 | 31.76
Neigh | 0.00070405 | 0.000714 | 0.00071907 | 0.0 | 25.22 Neigh | 0.00074077 | 0.00075352 | 0.00076365 | 0.0 | 14.94
Comm | 0.00032473 | 0.00037426 | 0.0004046 | 0.2 | 13.22 Comm | 0.00083065 | 0.0018672 | 0.0025668 | 1.7 | 37.02
Output | 1.8835e-05 | 1.961e-05 | 2.1935e-05 | 0.0 | 0.69 Output | 2.1458e-05 | 2.7359e-05 | 4.4346e-05 | 0.0 | 0.54
Modify | 0.00012612 | 0.00012892 | 0.00013089 | 0.0 | 4.55 Modify | 0.00014758 | 0.0001505 | 0.00015235 | 0.0 | 2.98
Other | | 0.000125 | | | 4.42 Other | | 0.0006434 | | | 12.76
Nlocal: 1000 ave 1016 max 981 min Nlocal: 1000 ave 1016 max 981 min
Histogram: 1 0 0 0 1 0 1 0 0 1 Histogram: 1 0 0 0 1 0 1 0 0 1
@ -315,31 +288,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.5 pair_style lj/cut 1.5
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.8
ghost atom cutoff = 1.8
binsize = 0.9 -> bins = 19 19 19
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
60 1.1101013 -3.9655053 0 -2.3007696 4.7849008 60 1.1101013 -3.9655053 0 -2.3007696 4.7849008
70 1.1122144 -3.9657095 0 -2.297805 4.8014106 70 1.1122144 -3.9657095 0 -2.297805 4.8014106
Loop time of 0.00313491 on 4 procs for 10 steps with 4000 atoms Loop time of 0.003398 on 4 procs for 10 steps with 4000 atoms
Performance: 1378031.621 tau/day, 3189.888 timesteps/s Performance: 1271335.633 tau/day, 2942.907 timesteps/s
87.7% CPU use with 4 MPI tasks x no OpenMP threads 98.5% 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 | 0.0016167 | 0.001663 | 0.0016985 | 0.1 | 53.05 Pair | 0.0015702 | 0.0016137 | 0.001651 | 0.1 | 47.49
Neigh | 0.00075388 | 0.00076818 | 0.00078201 | 0.0 | 24.50 Neigh | 0.00080371 | 0.00082165 | 0.00084138 | 0.0 | 24.18
Comm | 0.00037456 | 0.00042272 | 0.00048018 | 0.2 | 13.48 Comm | 0.0005908 | 0.00064844 | 0.00071096 | 0.0 | 19.08
Output | 1.7881e-05 | 1.9133e-05 | 2.1935e-05 | 0.0 | 0.61 Output | 1.7643e-05 | 2.3365e-05 | 4.0293e-05 | 0.0 | 0.69
Modify | 0.00012636 | 0.00012881 | 0.00013304 | 0.0 | 4.11 Modify | 0.00014853 | 0.00015211 | 0.00015593 | 0.0 | 4.48
Other | | 0.0001331 | | | 4.25 Other | | 0.0001387 | | | 4.08
Nlocal: 1000 ave 1022 max 982 min Nlocal: 1000 ave 1022 max 982 min
Histogram: 1 0 0 1 0 1 0 0 0 1 Histogram: 1 0 0 1 0 1 0 0 0 1
@ -356,31 +322,24 @@ pair_style lj/cut ${cut}
pair_style lj/cut 1.6 pair_style lj/cut 1.6
pair_coeff * * 1.0 1.0 pair_coeff * * 1.0 1.0
run 10 run 10
Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.9
ghost atom cutoff = 1.9
binsize = 0.95 -> bins = 18 18 18
Memory usage per processor = 2.63679 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
70 1.1122144 -4.1752688 0 -2.5073643 4.4755409 70 1.1122144 -4.1752688 0 -2.5073643 4.4755409
80 1.117224 -4.1831357 0 -2.5077187 4.446079 80 1.117224 -4.1831357 0 -2.5077187 4.446079
Loop time of 0.00345927 on 4 procs for 10 steps with 4000 atoms Loop time of 0.00420767 on 4 procs for 10 steps with 4000 atoms
Performance: 1248816.671 tau/day, 2890.779 timesteps/s Performance: 1026696.317 tau/day, 2376.612 timesteps/s
79.5% CPU use with 4 MPI tasks x no OpenMP threads 95.3% 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 | 0.0019331 | 0.0019561 | 0.0019834 | 0.0 | 56.55 Pair | 0.0019023 | 0.00194 | 0.0019965 | 0.1 | 46.11
Neigh | 0.00081587 | 0.00081897 | 0.00082588 | 0.0 | 23.67 Neigh | 0.00088286 | 0.00088775 | 0.00089431 | 0.0 | 21.10
Comm | 0.00037837 | 0.00040215 | 0.00041842 | 0.1 | 11.63 Comm | 0.0010023 | 0.0010559 | 0.0010967 | 0.1 | 25.09
Output | 1.812e-05 | 1.9312e-05 | 2.1935e-05 | 0.0 | 0.56 Output | 2.0027e-05 | 2.6524e-05 | 4.53e-05 | 0.0 | 0.63
Modify | 0.00012708 | 0.00013059 | 0.00013423 | 0.0 | 3.78 Modify | 0.00014782 | 0.00015038 | 0.00015473 | 0.0 | 3.57
Other | | 0.0001321 | | | 3.82 Other | | 0.0001471 | | | 3.50
Nlocal: 1000 ave 1013 max 987 min Nlocal: 1000 ave 1013 max 987 min
Histogram: 1 0 1 0 0 0 0 1 0 1 Histogram: 1 0 1 0 0 0 0 1 0 1

178
examples/python/log.4May17.pair_python_coulomb.1
View File

@ -1,178 +0,0 @@
LAMMPS (4 May 2017)
using 1 OpenMP thread(s) per MPI task
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
pair_style hybrid/overlay python 12.0 coul/long 12.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff * * python potentials.LJCutSPCE OW NULL
pair_modify table 0
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 1.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
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
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
# create combined lj/coul table for all atom types
# generate tabulated potential from python variant
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
PPPM initialization ...
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.279652
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394206
estimated relative force accuracy = 1.18714e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair python, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
PPPM initialization ...
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.279652
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394206
estimated relative force accuracy = 1.18714e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
PPPM initialization ...
WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.279652
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394206
estimated relative force accuracy = 1.18714e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
# switch to tabulated potential
pair_style table linear 2000 pppm
pair_coeff 1 1 spce.table OW-OW
pair_coeff 1 2 spce.table OW-HW
pair_coeff 2 2 spce.table HW-HW
thermo 10
run 100
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.279652
grid = 40 40 40
stencil order = 5
estimated absolute RMS force accuracy = 0.000394674
estimated relative force accuracy = 1.18855e-06
using double precision FFTs
3d grid and FFT values/proc = 103823 64000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, 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) = 35.26 | 35.26 | 35.26 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -100272.97 0 -100272.97 -1282.0708
10 120.61568 -101350.63 0 -100272.39 -4077.5051
20 136.11379 -101465.43 0 -100248.65 -5136.5677
30 137.01602 -101455.3 0 -100230.46 -5347.8311
40 153.424 -101582.46 0 -100210.93 -5223.1676
50 167.73654 -101686.24 0 -100186.77 -4468.6687
60 163.11642 -101618.16 0 -100159.99 -3291.7815
70 169.64512 -101647.89 0 -100131.35 -2611.638
80 182.9979 -101737.01 0 -100101.11 -2390.6293
90 191.33873 -101778.71 0 -100068.24 -2239.386
100 194.7458 -101775.84 0 -100034.92 -1951.9128
Loop time of 7.60221 on 1 procs for 100 steps with 4500 atoms
Performance: 1.137 ns/day, 21.117 hours/ns, 13.154 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.7401 | 5.7401 | 5.7401 | 0.0 | 75.51
Bond | 0.00017881 | 0.00017881 | 0.00017881 | 0.0 | 0.00
Kspace | 1.5387 | 1.5387 | 1.5387 | 0.0 | 20.24
Neigh | 0.2299 | 0.2299 | 0.2299 | 0.0 | 3.02
Comm | 0.024311 | 0.024311 | 0.024311 | 0.0 | 0.32
Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.01
Modify | 0.063158 | 0.063158 | 0.063158 | 0.0 | 0.83
Other | | 0.005243 | | | 0.07
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21216 ave 21216 max 21216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2601766
Ave neighs/atom = 578.17
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:07

138
examples/python/log.4May17.pair_python_coulomb.g++.1
View File

@ -1,138 +0,0 @@
LAMMPS (4 May 2017)
using 1 OpenMP thread(s) per MPI task
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
pair_style hybrid/overlay coul/cut 12.0 python 12.0
pair_coeff * * coul/cut
pair_coeff * * python py_pot.LJCutSPCE OW NULL
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 1.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
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
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
# create combined lj/coul table for all atom types
# generate tabulated potential from python variant
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
# switch to tabulated potential
pair_style table linear 2000 pppm
pair_coeff 1 1 spce.table OW-OW
pair_coeff 1 2 spce.table OW-HW
pair_coeff 2 2 spce.table HW-HW
thermo 10
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 = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, 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) = 25.08 | 25.08 | 25.08 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -18284.922 0 -18284.922 -2080.7739
10 146.83806 -19552.072 0 -18239.421 -4865.31
20 183.15761 -18706.872 0 -17069.543 -4865.6695
30 205.96203 -18901.541 0 -17060.354 -4454.8634
40 241.62768 -18323.117 0 -16163.099 -3269.1475
50 265.98384 -19883.562 0 -17505.813 -2788.5194
60 274.01897 -21320.575 0 -18870.996 -2387.0708
70 288.7601 -19849.269 0 -17267.913 -1235.818
80 300.64724 -20958.602 0 -18270.981 -1714.7988
90 304.19113 -21580.4 0 -18861.099 -2144.1614
100 304.22027 -21239.014 0 -18519.452 -2092.6759
Loop time of 6.01861 on 1 procs for 100 steps with 4500 atoms
Performance: 1.436 ns/day, 16.718 hours/ns, 16.615 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.698 | 5.698 | 5.698 | 0.0 | 94.67
Bond | 0.0001626 | 0.0001626 | 0.0001626 | 0.0 | 0.00
Neigh | 0.23235 | 0.23235 | 0.23235 | 0.0 | 3.86
Comm | 0.018961 | 0.018961 | 0.018961 | 0.0 | 0.32
Output | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.01
Modify | 0.063452 | 0.063452 | 0.063452 | 0.0 | 1.05
Other | | 0.005146 | | | 0.09
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21285 ave 21285 max 21285 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.59766e+06 ave 2.59766e+06 max 2.59766e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2597662
Ave neighs/atom = 577.258
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:06

138
examples/python/log.4May17.pair_python_coulomb.g++.4
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@ -1,138 +0,0 @@
LAMMPS (4 May 2017)
using 1 OpenMP thread(s) per MPI task
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
pair_style hybrid/overlay coul/cut 12.0 python 12.0
pair_coeff * * coul/cut
pair_coeff * * python py_pot.LJCutSPCE OW NULL
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 1.0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
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
1500 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
# create combined lj/coul table for all atom types
# generate tabulated potential from python variant
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair python, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
# switch to tabulated potential
pair_style table linear 2000 pppm
pair_coeff 1 1 spce.table OW-OW
pair_coeff 1 2 spce.table OW-HW
pair_coeff 2 2 spce.table HW-HW
thermo 10
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 = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, 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) = 9.962 | 9.963 | 9.963 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -18284.922 0 -18284.922 -2080.7739
10 146.83806 -19552.072 0 -18239.421 -4865.31
20 183.15761 -18706.872 0 -17069.543 -4865.6695
30 205.96203 -18901.541 0 -17060.354 -4454.8634
40 241.62768 -18323.117 0 -16163.099 -3269.1475
50 265.98384 -19883.562 0 -17505.813 -2788.5194
60 274.01897 -21320.575 0 -18870.996 -2387.0708
70 288.7601 -19849.269 0 -17267.913 -1235.818
80 300.64724 -20958.602 0 -18270.981 -1714.7988
90 304.19113 -21580.4 0 -18861.099 -2144.1614
100 304.22027 -21239.014 0 -18519.452 -2092.6759
Loop time of 1.7361 on 4 procs for 100 steps with 4500 atoms
Performance: 4.977 ns/day, 4.823 hours/ns, 57.600 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 | 1.4424 | 1.5149 | 1.6066 | 5.3 | 87.26
Bond | 8.9407e-05 | 0.00010258 | 0.00012374 | 0.0 | 0.01
Neigh | 0.064205 | 0.064241 | 0.064295 | 0.0 | 3.70
Comm | 0.023643 | 0.1155 | 0.18821 | 19.2 | 6.65
Output | 0.00038004 | 0.00042355 | 0.00054145 | 0.0 | 0.02
Modify | 0.037507 | 0.037787 | 0.038042 | 0.1 | 2.18
Other | | 0.003148 | | | 0.18
Nlocal: 1125 ave 1162 max 1098 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 12267.8 ave 12302 max 12238 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 649416 ave 681458 max 630541 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 2597662
Ave neighs/atom = 577.258
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
Total wall time: 0:00:01