diff --git a/examples/min/log.5Oct16.min.box.g++.1 b/examples/min/log.27Nov18.min.box.g++.1
similarity index 84%
rename from examples/min/log.5Oct16.min.box.g++.1
rename to examples/min/log.27Nov18.min.box.g++.1
index 29294567aef1722d02651e2368d6f6816f42b27c..7e2151c6cb665593878474e40de15c477ceb71e5 100644
--- a/examples/min/log.5Oct16.min.box.g++.1
+++ b/examples/min/log.27Nov18.min.box.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 2d Lennard-Jones melt and subsequent energy minimization,
# followed by box relaxation to a target stress state
#
@@ -14,6 +15,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
+ Time spent = 0.000453234 secs
mass 1 1.0
velocity all create 5.0 87287 loop geom
@@ -40,13 +42,18 @@ thermo 100
run 1000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 22 22 1
-Memory usage per processor = 2.47843 Mbytes
+ binsize = 1.4, bins = 22 22 1
+ 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/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.056 | 3.056 | 3.056 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
@@ -59,20 +66,20 @@ Step Temp E_pair E_mol TotEng Press
800 3.3016275 -0.76569171 0 2.5318087 15.639335
900 3.4639203 -0.92788002 0 2.5317104 14.765912
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
-Loop time of 0.202646 on 1 procs for 1000 steps with 800 atoms
+Loop time of 0.210142 on 1 procs for 1000 steps with 800 atoms
-Performance: 2131796.155 tau/day, 4934.713 timesteps/s
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 2055749.118 tau/day, 4758.679 timesteps/s
+98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.12926 | 0.12926 | 0.12926 | 0.0 | 63.79
-Neigh | 0.051169 | 0.051169 | 0.051169 | 0.0 | 25.25
-Comm | 0.0044918 | 0.0044918 | 0.0044918 | 0.0 | 2.22
-Output | 9.3222e-05 | 9.3222e-05 | 9.3222e-05 | 0.0 | 0.05
-Modify | 0.011879 | 0.011879 | 0.011879 | 0.0 | 5.86
-Other | | 0.005755 | | | 2.84
+Pair | 0.12951 | 0.12951 | 0.12951 | 0.0 | 61.63
+Neigh | 0.053642 | 0.053642 | 0.053642 | 0.0 | 25.53
+Comm | 0.0062521 | 0.0062521 | 0.0062521 | 0.0 | 2.98
+Output | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 0.06
+Modify | 0.0142 | 0.0142 | 0.0142 | 0.0 | 6.76
+Other | | 0.006405 | | | 3.05
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -98,7 +105,7 @@ thermo 50
# atoms only
minimize 1.0e-6 0.001 1000 10000
-Memory usage per processor = 3.60343 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.79078181 0 -0.79078181 12.79527
1050 0 -2.8361415 0 -2.8361415 -1.1950285
@@ -111,9 +118,9 @@ Step Temp E_pair E_mol TotEng Press
1400 0 -2.9131297 0 -2.9131297 -1.0962069
1450 0 -2.9167506 0 -2.9167506 -1.0259809
1475 0 -2.9169436 0 -2.9169436 -1.0125744
-Loop time of 0.232023 on 1 procs for 475 steps with 800 atoms
+Loop time of 0.234897 on 1 procs for 475 steps with 800 atoms
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -127,12 +134,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.18865 | 0.18865 | 0.18865 | 0.0 | 81.30
-Neigh | 0.020881 | 0.020881 | 0.020881 | 0.0 | 9.00
-Comm | 0.0028429 | 0.0028429 | 0.0028429 | 0.0 | 1.23
-Output | 7.0095e-05 | 7.0095e-05 | 7.0095e-05 | 0.0 | 0.03
-Modify | 0.0020018 | 0.0020018 | 0.0020018 | 0.0 | 0.86
-Other | | 0.01758 | | | 7.58
+Pair | 0.18533 | 0.18533 | 0.18533 | 0.0 | 78.90
+Neigh | 0.02206 | 0.02206 | 0.02206 | 0.0 | 9.39
+Comm | 0.0041955 | 0.0041955 | 0.0041955 | 0.0 | 1.79
+Output | 0.000108 | 0.000108 | 0.000108 | 0.0 | 0.05
+Modify | 0.002362 | 0.002362 | 0.002362 | 0.0 | 1.01
+Other | | 0.02084 | | | 8.87
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -156,7 +163,7 @@ thermo_style custom step temp pe pxx pyy pxy f_3 v_emin
# anisotropic volume relaxation to hydrostatic target
minimize 0.0 10.0e0 10000 100000
-Memory usage per processor = 3.60343 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
1475 0 -2.9169436 -1.0208231 -1.0043256 0.042048233 0 -2.9169436
1500 0 -2.9112018 1.4420862 1.4721681 0.065929095 -0.087730988 -2.9989327
@@ -164,9 +171,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
1600 0 -2.924265 1.4545702 1.5281333 0.053590255 -0.12032598 -3.044591
1650 0 -2.9289538 1.4528452 1.5692678 0.038096542 -0.12516914 -3.054123
1699 0 -2.9334511 1.4447667 1.5587557 0.044510608 -0.12731783 -3.060769
-Loop time of 0.109303 on 1 procs for 224 steps with 800 atoms
+Loop time of 0.112146 on 1 procs for 224 steps with 800 atoms
-99.7% CPU use with 1 MPI tasks x no OpenMP threads
+97.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -180,12 +187,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.086675 | 0.086675 | 0.086675 | 0.0 | 79.30
-Neigh | 0.0040114 | 0.0040114 | 0.0040114 | 0.0 | 3.67
-Comm | 0.0010419 | 0.0010419 | 0.0010419 | 0.0 | 0.95
-Output | 9.4891e-05 | 9.4891e-05 | 9.4891e-05 | 0.0 | 0.09
-Modify | 0.00085473 | 0.00085473 | 0.00085473 | 0.0 | 0.78
-Other | | 0.01662 | | | 15.21
+Pair | 0.084376 | 0.084376 | 0.084376 | 0.0 | 75.24
+Neigh | 0.0042746 | 0.0042746 | 0.0042746 | 0.0 | 3.81
+Comm | 0.0015385 | 0.0015385 | 0.0015385 | 0.0 | 1.37
+Output | 0.0001235 | 0.0001235 | 0.0001235 | 0.0 | 0.11
+Modify | 0.0011208 | 0.0011208 | 0.0011208 | 0.0 | 1.00
+Other | | 0.02071 | | | 18.47
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -202,13 +209,13 @@ Dangerous builds = 0
fix 3 all box/relax aniso 1.5 vmax 1.0e-3
minimize 0.0 10.0 10000 100000
-Memory usage per processor = 3.60343 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
1699 0 -2.9334511 1.4447667 1.5587557 0.044510608 0 -2.9334511
1700 0 -2.9335996 1.4982915 1.4969508 0.044657372 9.09619e-05 -2.9335086
-Loop time of 0.000785828 on 1 procs for 1 steps with 800 atoms
+Loop time of 0.000793934 on 1 procs for 1 steps with 800 atoms
-127.3% CPU use with 1 MPI tasks x no OpenMP threads
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -222,12 +229,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.00063896 | 0.00063896 | 0.00063896 | 0.0 | 81.31
+Pair | 0.00061846 | 0.00061846 | 0.00061846 | 0.0 | 77.90
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 | 0.0 | 0.76
+Comm | 1.0014e-05 | 1.0014e-05 | 1.0014e-05 | 0.0 | 1.26
Output | 0 | 0 | 0 | 0.0 | 0.00
-Modify | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 | 0.0 | 0.79
-Other | | 0.0001347 | | | 17.14
+Modify | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.96
+Other | | 0.0001578 | | | 19.88
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -246,7 +253,7 @@ Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3
minimize 0.0 10.0 10000 100000
-Memory usage per processor = 3.60343 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
1700 0 -2.9335996 1.4982915 1.4969508 0.044657372 -3.5527137e-17 -2.9335996
1750 0 -2.9306696 0.95043712 1.984164 0.04474671 -0.014282691 -2.9449523
@@ -254,9 +261,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
1850 0 -2.935585 0.98224846 1.9920507 0.047038767 -0.021070874 -2.9566559
1900 0 -2.9380757 0.96811097 1.9677247 0.068809483 -0.024274947 -2.9623506
1913 0 -2.9391305 0.98238419 1.9782761 0.074400364 -0.025108208 -2.9642387
-Loop time of 0.0971339 on 1 procs for 213 steps with 800 atoms
+Loop time of 0.0997889 on 1 procs for 213 steps with 800 atoms
-100.9% CPU use with 1 MPI tasks x no OpenMP threads
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -270,12 +277,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.076124 | 0.076124 | 0.076124 | 0.0 | 78.37
-Neigh | 0.0027554 | 0.0027554 | 0.0027554 | 0.0 | 2.84
-Comm | 0.00085568 | 0.00085568 | 0.00085568 | 0.0 | 0.88
-Output | 0.00012589 | 0.00012589 | 0.00012589 | 0.0 | 0.13
-Modify | 0.00077486 | 0.00077486 | 0.00077486 | 0.0 | 0.80
-Other | | 0.0165 | | | 16.98
+Pair | 0.074305 | 0.074305 | 0.074305 | 0.0 | 74.46
+Neigh | 0.0028846 | 0.0028846 | 0.0028846 | 0.0 | 2.89
+Comm | 0.0012925 | 0.0012925 | 0.0012925 | 0.0 | 1.30
+Output | 0.00016117 | 0.00016117 | 0.00016117 | 0.0 | 0.16
+Modify | 0.00090647 | 0.00090647 | 0.00090647 | 0.0 | 0.91
+Other | | 0.02024 | | | 20.28
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -290,7 +297,7 @@ Neighbor list builds = 11
Dangerous builds = 0
minimize 0.0 1.0 10000 100000
-Memory usage per processor = 3.60343 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
1913 0 -2.9391305 0.98238419 1.9782761 0.074400364 7.1054274e-17 -2.9391305
1950 0 -2.9397224 0.98880561 2.0105792 0.10042798 -0.0026601558 -2.9423825
@@ -382,9 +389,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
6250 0 -3.0378032 0.99964291 1.9971778 0.033045048 -0.037140636 -3.0749439
6300 0 -3.0377782 0.9965492 1.9980669 0.032201395 -0.037170252 -3.0749485
6314 0 -3.0377854 0.99649081 1.9975871 0.032243768 -0.037163869 -3.0749493
-Loop time of 2.27089 on 1 procs for 4401 steps with 800 atoms
+Loop time of 2.33993 on 1 procs for 4401 steps with 800 atoms
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -398,12 +405,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 1.8251 | 1.8251 | 1.8251 | 0.0 | 80.37
-Neigh | 0.027037 | 0.027037 | 0.027037 | 0.0 | 1.19
-Comm | 0.019059 | 0.019059 | 0.019059 | 0.0 | 0.84
-Output | 0.0027676 | 0.0027676 | 0.0027676 | 0.0 | 0.12
-Modify | 0.018233 | 0.018233 | 0.018233 | 0.0 | 0.80
-Other | | 0.3786 | | | 16.67
+Pair | 1.7909 | 1.7909 | 1.7909 | 0.0 | 76.54
+Neigh | 0.028373 | 0.028373 | 0.028373 | 0.0 | 1.21
+Comm | 0.029514 | 0.029514 | 0.029514 | 0.0 | 1.26
+Output | 0.0037448 | 0.0037448 | 0.0037448 | 0.0 | 0.16
+Modify | 0.021746 | 0.021746 | 0.021746 | 0.0 | 0.93
+Other | | 0.4657 | | | 19.90
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -418,7 +425,7 @@ Neighbor list builds = 109
Dangerous builds = 0
minimize 0.0 1.0e-2 10000 100000
-Memory usage per processor = 3.60343 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
6314 0 -3.0377854 0.99649081 1.9975871 0.032243768 3.5527137e-17 -3.0377854
6350 0 -3.0377426 0.9995618 1.9997582 0.032364722 -4.5395813e-05 -3.037788
@@ -454,9 +461,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
7850 0 -3.0378352 1.0000397 2.0000524 0.033753896 -7.5318252e-05 -3.0379105
7900 0 -3.0378354 1.0000486 2.0000488 0.033742064 -7.5113089e-05 -3.0379105
7904 0 -3.0378356 1.0000321 2.0000425 0.033740786 -7.491864e-05 -3.0379105
-Loop time of 0.831561 on 1 procs for 1590 steps with 800 atoms
+Loop time of 0.85351 on 1 procs for 1590 steps with 800 atoms
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -470,12 +477,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.67727 | 0.67727 | 0.67727 | 0.0 | 81.45
-Neigh | 0.0004921 | 0.0004921 | 0.0004921 | 0.0 | 0.06
-Comm | 0.0065284 | 0.0065284 | 0.0065284 | 0.0 | 0.79
-Output | 0.0010114 | 0.0010114 | 0.0010114 | 0.0 | 0.12
-Modify | 0.0067346 | 0.0067346 | 0.0067346 | 0.0 | 0.81
-Other | | 0.1395 | | | 16.78
+Pair | 0.66264 | 0.66264 | 0.66264 | 0.0 | 77.64
+Neigh | 0.00052071 | 0.00052071 | 0.00052071 | 0.0 | 0.06
+Comm | 0.010136 | 0.010136 | 0.010136 | 0.0 | 1.19
+Output | 0.0012524 | 0.0012524 | 0.0012524 | 0.0 | 0.15
+Modify | 0.0080862 | 0.0080862 | 0.0080862 | 0.0 | 0.95
+Other | | 0.1709 | | | 20.02
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -494,7 +501,7 @@ Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 nreset 100
minimize 0.0 1.0e-4 10000 100000
-Memory usage per processor = 3.60343 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
7904 0 -3.0378356 1.0000321 2.0000425 0.033740786 0 -3.0378356
7950 0 -3.0378364 1.000001 2.0000015 0.03373689 8.3404927e-07 -3.0378356
@@ -515,9 +522,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
8700 0 -3.0378364 1 1.9999997 0.033725586 4.9116894e-09 -3.0378364
8750 0 -3.0378364 0.99999991 2 0.033725386 7.3634181e-10 -3.0378364
8753 0 -3.0378364 1 2 0.033725385 -1.0901182e-09 -3.0378364
-Loop time of 0.445577 on 1 procs for 849 steps with 800 atoms
+Loop time of 0.457836 on 1 procs for 849 steps with 800 atoms
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -531,12 +538,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.36325 | 0.36325 | 0.36325 | 0.0 | 81.52
+Pair | 0.3559 | 0.3559 | 0.3559 | 0.0 | 77.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0034921 | 0.0034921 | 0.0034921 | 0.0 | 0.78
-Output | 0.00052595 | 0.00052595 | 0.00052595 | 0.0 | 0.12
-Modify | 0.0036132 | 0.0036132 | 0.0036132 | 0.0 | 0.81
-Other | | 0.07469 | | | 16.76
+Comm | 0.0054362 | 0.0054362 | 0.0054362 | 0.0 | 1.19
+Output | 0.00070548 | 0.00070548 | 0.00070548 | 0.0 | 0.15
+Modify | 0.004298 | 0.004298 | 0.004298 | 0.0 | 0.94
+Other | | 0.09149 | | | 19.98
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/min/log.5Oct16.min.box.g++.4 b/examples/min/log.27Nov18.min.box.g++.4
similarity index 84%
rename from examples/min/log.5Oct16.min.box.g++.4
rename to examples/min/log.27Nov18.min.box.g++.4
index 090b5ad79cce044db4873812aa99d8530722fa05..f6dacb01293cd963cc0d0209a3eebc38cc27334c 100644
--- a/examples/min/log.5Oct16.min.box.g++.4
+++ b/examples/min/log.27Nov18.min.box.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 2d Lennard-Jones melt and subsequent energy minimization,
# followed by box relaxation to a target stress state
#
@@ -14,6 +15,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
+ Time spent = 0.000339985 secs
mass 1 1.0
velocity all create 5.0 87287 loop geom
@@ -40,13 +42,18 @@ thermo 100
run 1000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 22 22 1
-Memory usage per processor = 2.47676 Mbytes
+ binsize = 1.4, bins = 22 22 1
+ 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/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.049 | 3.049 | 3.049 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
@@ -59,20 +66,20 @@ Step Temp E_pair E_mol TotEng Press
800 3.3016408 -0.76570603 0 2.5318077 15.639259
900 3.4621697 -0.92610292 0 2.5317391 14.773473
1000 3.3058424 -0.77076863 0 2.5309414 15.708171
-Loop time of 0.066087 on 4 procs for 1000 steps with 800 atoms
+Loop time of 0.0739716 on 4 procs for 1000 steps with 800 atoms
-Performance: 6536837.061 tau/day, 15131.567 timesteps/s
-98.3% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 5840081.570 tau/day, 13518.707 timesteps/s
+96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.032169 | 0.032534 | 0.032995 | 0.2 | 49.23
-Neigh | 0.013092 | 0.013286 | 0.01348 | 0.1 | 20.10
-Comm | 0.011925 | 0.012799 | 0.013343 | 0.5 | 19.37
-Output | 0.00017333 | 0.00018448 | 0.00021172 | 0.1 | 0.28
-Modify | 0.0029421 | 0.0029953 | 0.0030239 | 0.1 | 4.53
-Other | | 0.004288 | | | 6.49
+Pair | 0.031443 | 0.032581 | 0.034717 | 0.7 | 44.04
+Neigh | 0.01403 | 0.014414 | 0.01483 | 0.2 | 19.49
+Comm | 0.013565 | 0.015975 | 0.01834 | 1.4 | 21.60
+Output | 0.00017476 | 0.00018531 | 0.00020695 | 0.0 | 0.25
+Modify | 0.0037742 | 0.0043355 | 0.0058382 | 1.3 | 5.86
+Other | | 0.006481 | | | 8.76
Nlocal: 200 ave 202 max 196 min
Histogram: 1 0 0 0 0 0 0 0 2 1
@@ -98,7 +105,7 @@ thermo 50
# atoms only
minimize 1.0e-6 0.001 1000 10000
-Memory usage per processor = 3.60176 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.77076863 0 -0.77076863 12.920868
1050 0 -2.8318266 0 -2.8318266 -1.1892931
@@ -107,9 +114,9 @@ Step Temp E_pair E_mol TotEng Press
1200 0 -2.8831122 0 -2.8831122 -1.1004001
1250 0 -2.8877971 0 -2.8877971 -1.0596414
1300 0 -2.8887969 0 -2.8887969 -1.0448381
-Loop time of 0.0501025 on 4 procs for 300 steps with 800 atoms
+Loop time of 0.0533715 on 4 procs for 300 steps with 800 atoms
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
+96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -123,12 +130,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.030059 | 0.030357 | 0.030755 | 0.2 | 60.59
-Neigh | 0.0037379 | 0.0037849 | 0.0038264 | 0.1 | 7.55
-Comm | 0.0061991 | 0.0067289 | 0.0071735 | 0.5 | 13.43
-Output | 7.3195e-05 | 7.7724e-05 | 8.9407e-05 | 0.1 | 0.16
-Modify | 0.00036192 | 0.00037038 | 0.00037956 | 0.0 | 0.74
-Other | | 0.008784 | | | 17.53
+Pair | 0.029885 | 0.031269 | 0.033625 | 0.8 | 58.59
+Neigh | 0.0038524 | 0.0040049 | 0.0040805 | 0.1 | 7.50
+Comm | 0.0062668 | 0.0087315 | 0.010314 | 1.7 | 16.36
+Output | 7.9632e-05 | 8.3268e-05 | 9.346e-05 | 0.0 | 0.16
+Modify | 0.00043797 | 0.00044793 | 0.00045705 | 0.0 | 0.84
+Other | | 0.008835 | | | 16.55
Nlocal: 200 ave 202 max 196 min
Histogram: 1 0 0 0 0 0 1 0 0 2
@@ -152,15 +159,15 @@ thermo_style custom step temp pe pxx pyy pxy f_3 v_emin
# anisotropic volume relaxation to hydrostatic target
minimize 0.0 10.0e0 10000 100000
-Memory usage per processor = 3.60176 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
1300 0 -2.8887969 -0.93904343 -1.1506328 -0.0037265764 0 -2.8887969
1350 0 -2.889313 1.555657 1.4414453 -0.025585726 -0.10933729 -2.9986503
1400 0 -2.8958621 1.5320803 1.476774 0.0041557664 -0.1208966 -3.0167587
1403 0 -2.8962558 1.5290172 1.4743135 0.00471395 -0.12088872 -3.0171446
-Loop time of 0.0163901 on 4 procs for 103 steps with 800 atoms
+Loop time of 0.0172202 on 4 procs for 103 steps with 800 atoms
-97.6% CPU use with 4 MPI tasks x no OpenMP threads
+96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -174,12 +181,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0086238 | 0.0087494 | 0.0088425 | 0.1 | 53.38
-Neigh | 0.00099087 | 0.0010223 | 0.0010412 | 0.1 | 6.24
-Comm | 0.0017323 | 0.0018613 | 0.002028 | 0.3 | 11.36
-Output | 7.3195e-05 | 7.4625e-05 | 7.8917e-05 | 0.0 | 0.46
-Modify | 9.7513e-05 | 0.00010496 | 0.00011063 | 0.1 | 0.64
-Other | | 0.004578 | | | 27.93
+Pair | 0.0085471 | 0.0087811 | 0.0090215 | 0.2 | 50.99
+Neigh | 0.0010307 | 0.0011456 | 0.0013525 | 0.4 | 6.65
+Comm | 0.0017407 | 0.0020964 | 0.0024772 | 0.6 | 12.17
+Output | 7.5102e-05 | 7.695e-05 | 8.1301e-05 | 0.0 | 0.45
+Modify | 0.00012064 | 0.0001241 | 0.00012684 | 0.0 | 0.72
+Other | | 0.004996 | | | 29.01
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 0 0 0 2 0 0 0 1
@@ -196,13 +203,13 @@ Dangerous builds = 0
fix 3 all box/relax aniso 1.5 vmax 1.0e-3
minimize 0.0 10.0 10000 100000
-Memory usage per processor = 3.60176 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
1403 0 -2.8962558 1.5290172 1.4743135 0.00471395 0 -2.8962558
1404 0 -2.8963678 1.49615 1.499767 0.0037848845 9.6365079e-05 -2.8962714
-Loop time of 0.000319898 on 4 procs for 1 steps with 800 atoms
+Loop time of 0.000330448 on 4 procs for 1 steps with 800 atoms
-0.0% CPU use with 4 MPI tasks x no OpenMP threads
+96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -216,12 +223,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.00016475 | 0.0001657 | 0.00016618 | 0.0 | 51.80
+Pair | 0.00016141 | 0.00016457 | 0.00016809 | 0.0 | 49.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 2.9802e-05 | 3.1531e-05 | 3.4094e-05 | 0.0 | 9.86
+Comm | 2.861e-05 | 3.3557e-05 | 3.7193e-05 | 0.0 | 10.16
Output | 0 | 0 | 0 | 0.0 | 0.00
-Modify | 2.1458e-06 | 2.563e-06 | 3.3379e-06 | 0.0 | 0.80
-Other | | 0.0001201 | | | 37.54
+Modify | 2.1458e-06 | 2.3842e-06 | 2.6226e-06 | 0.0 | 0.72
+Other | | 0.0001299 | | | 39.32
Nlocal: 200 ave 202 max 197 min
Histogram: 1 0 0 0 0 0 1 0 1 1
@@ -240,16 +247,16 @@ Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3
minimize 0.0 10.0 10000 100000
-Memory usage per processor = 3.60176 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
1404 0 -2.8963678 1.49615 1.499767 0.0037848845 -7.1054274e-17 -2.8963678
1450 0 -2.8925305 0.94584654 2.0945709 -0.029336194 -0.016086454 -2.9086169
1500 0 -2.8975934 1.0123866 2.009477 -0.036498498 -0.01841842 -2.9160118
1550 0 -2.903576 1.0046986 1.9380791 -0.037683327 -0.020970768 -2.9245468
1592 0 -2.9061298 0.98518925 1.9835783 -0.048932212 -0.024234721 -2.9303646
-Loop time of 0.0294311 on 4 procs for 188 steps with 800 atoms
+Loop time of 0.0321782 on 4 procs for 188 steps with 800 atoms
-101.1% CPU use with 4 MPI tasks x no OpenMP threads
+97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -263,12 +270,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.016194 | 0.016255 | 0.0163 | 0.0 | 55.23
-Neigh | 0.00050688 | 0.0005179 | 0.00053 | 0.0 | 1.76
-Comm | 0.0030935 | 0.0031458 | 0.0031939 | 0.1 | 10.69
-Output | 0.00011897 | 0.00012201 | 0.00013018 | 0.0 | 0.41
-Modify | 0.00016952 | 0.0001781 | 0.00018668 | 0.0 | 0.61
-Other | | 0.009212 | | | 31.30
+Pair | 0.015791 | 0.016377 | 0.01695 | 0.3 | 50.90
+Neigh | 0.00053954 | 0.00056165 | 0.00057793 | 0.0 | 1.75
+Comm | 0.0027378 | 0.0033152 | 0.0039263 | 0.8 | 10.30
+Output | 0.00014901 | 0.00015163 | 0.00015783 | 0.0 | 0.47
+Modify | 0.00021982 | 0.00022542 | 0.0002315 | 0.0 | 0.70
+Other | | 0.01155 | | | 35.88
Nlocal: 200 ave 202 max 196 min
Histogram: 1 0 0 0 0 0 0 0 2 1
@@ -283,7 +290,7 @@ Neighbor list builds = 8
Dangerous builds = 0
minimize 0.0 1.0 10000 100000
-Memory usage per processor = 3.60176 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
1592 0 -2.9061298 0.98518925 1.9835783 -0.048932212 3.5527137e-17 -2.9061298
1600 0 -2.9046586 1.0529014 2.0593731 -0.050860896 -0.0020973121 -2.9067559
@@ -378,9 +385,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
6050 0 -3.0313105 0.9590106 1.959899 0.10814531 -0.084790331 -3.1161008
6100 0 -3.0313244 0.9580272 1.9605104 0.10879691 -0.08493735 -3.1162617
6130 0 -3.0313384 0.95532497 1.9595324 0.10924759 -0.084945274 -3.1162837
-Loop time of 0.833589 on 4 procs for 4538 steps with 800 atoms
+Loop time of 0.937381 on 4 procs for 4538 steps with 800 atoms
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -394,12 +401,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.45739 | 0.47006 | 0.47928 | 1.2 | 56.39
-Neigh | 0.006587 | 0.0068482 | 0.0069439 | 0.2 | 0.82
-Comm | 0.089155 | 0.097262 | 0.11111 | 2.7 | 11.67
-Output | 0.0035946 | 0.0036807 | 0.0039296 | 0.2 | 0.44
-Modify | 0.0051167 | 0.0053424 | 0.005434 | 0.2 | 0.64
-Other | | 0.2504 | | | 30.04
+Pair | 0.45297 | 0.47262 | 0.48939 | 2.1 | 50.42
+Neigh | 0.0071242 | 0.0072536 | 0.0073645 | 0.1 | 0.77
+Comm | 0.12672 | 0.1453 | 0.17041 | 4.8 | 15.50
+Output | 0.0040541 | 0.0063651 | 0.013254 | 5.0 | 0.68
+Modify | 0.0063808 | 0.0065207 | 0.0066283 | 0.1 | 0.70
+Other | | 0.2993 | | | 31.93
Nlocal: 200 ave 203 max 197 min
Histogram: 1 0 0 1 0 0 1 0 0 1
@@ -414,7 +421,7 @@ Neighbor list builds = 104
Dangerous builds = 0
minimize 0.0 1.0e-2 10000 100000
-Memory usage per processor = 3.60176 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
6130 0 -3.0313384 0.95532497 1.9595324 0.10924759 -3.5527137e-17 -3.0313384
6150 0 -3.0304428 0.9947235 1.9969091 0.10935746 -0.00091797415 -3.0313608
@@ -448,9 +455,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
7550 0 -3.0303533 1.0000018 1.9999949 0.10769873 -0.0010415749 -3.0313949
7600 0 -3.0303529 1.0000017 2.0000034 0.10770161 -0.0010419517 -3.0313949
7607 0 -3.0303527 1.0000104 2.0000131 0.10770259 -0.0010421819 -3.0313949
-Loop time of 0.279601 on 4 procs for 1477 steps with 800 atoms
+Loop time of 0.311816 on 4 procs for 1477 steps with 800 atoms
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+96.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -464,12 +471,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.15759 | 0.16061 | 0.16246 | 0.5 | 57.44
+Pair | 0.16143 | 0.16413 | 0.16779 | 0.6 | 52.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.026405 | 0.029149 | 0.033293 | 1.5 | 10.43
-Output | 0.0011969 | 0.0012203 | 0.0012867 | 0.1 | 0.44
-Modify | 0.0017877 | 0.0018381 | 0.0019131 | 0.1 | 0.66
-Other | | 0.08679 | | | 31.04
+Comm | 0.03717 | 0.042433 | 0.05037 | 2.5 | 13.61
+Output | 0.0012872 | 0.0017485 | 0.0031171 | 1.9 | 0.56
+Modify | 0.0022309 | 0.0022756 | 0.002321 | 0.1 | 0.73
+Other | | 0.1012 | | | 32.46
Nlocal: 200 ave 203 max 197 min
Histogram: 1 0 0 1 0 0 1 0 0 1
@@ -488,7 +495,7 @@ Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 nreset 100
minimize 0.0 1.0e-4 10000 100000
-Memory usage per processor = 3.60176 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
7607 0 -3.0303527 1.0000104 2.0000131 0.10770259 3.5527137e-17 -3.0303527
7650 0 -3.030353 0.9999904 2.0000076 0.10770145 2.9878713e-07 -3.0303527
@@ -504,9 +511,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin
8150 0 -3.0303532 1.0000003 2.0000002 0.10770398 -1.4421314e-09 -3.0303532
8200 0 -3.0303532 1.0000001 2.0000001 0.10770407 7.0744514e-10 -3.0303532
8201 0 -3.0303532 0.99999993 2 0.10770406 3.9670625e-09 -3.0303532
-Loop time of 0.118568 on 4 procs for 594 steps with 800 atoms
+Loop time of 0.129036 on 4 procs for 594 steps with 800 atoms
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+95.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
@@ -520,12 +527,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.063769 | 0.065702 | 0.068746 | 0.7 | 55.41
+Pair | 0.06542 | 0.066275 | 0.068163 | 0.4 | 51.36
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.011877 | 0.015052 | 0.017311 | 1.6 | 12.69
-Output | 0.0004735 | 0.00048357 | 0.00051045 | 0.1 | 0.41
-Modify | 0.00073504 | 0.00075912 | 0.00081396 | 0.1 | 0.64
-Other | | 0.03657 | | | 30.84
+Comm | 0.015691 | 0.016819 | 0.018781 | 0.9 | 13.03
+Output | 0.00052595 | 0.00067312 | 0.0011091 | 0.0 | 0.52
+Modify | 0.00091577 | 0.0009293 | 0.0009408 | 0.0 | 0.72
+Other | | 0.04434 | | | 34.36
Nlocal: 200 ave 203 max 197 min
Histogram: 1 0 0 1 0 0 1 0 0 1
diff --git a/examples/min/log.5Oct16.min.g++.1 b/examples/min/log.27Nov18.min.g++.1
similarity index 73%
rename from examples/min/log.5Oct16.min.g++.1
rename to examples/min/log.27Nov18.min.g++.1
index 9d386932749c58f5f91ed3802d63d3a7b10b323c..98c3ca3b930b3011095b36859aef65637e165b1a 100644
--- a/examples/min/log.5Oct16.min.g++.1
+++ b/examples/min/log.27Nov18.min.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
@@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
+ Time spent = 0.000434637 secs
mass 1 1.0
velocity all create 5.0 87287 loop geom
@@ -39,13 +41,18 @@ thermo 100
run 1000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 22 22 1
-Memory usage per processor = 2.47843 Mbytes
+ binsize = 1.4, bins = 22 22 1
+ 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/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.056 | 3.056 | 3.056 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
@@ -58,20 +65,20 @@ Step Temp E_pair E_mol TotEng Press
800 3.3016275 -0.76569171 0 2.5318087 15.639335
900 3.4639203 -0.92788002 0 2.5317104 14.765912
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
-Loop time of 0.201747 on 1 procs for 1000 steps with 800 atoms
+Loop time of 0.206744 on 1 procs for 1000 steps with 800 atoms
-Performance: 2141296.412 tau/day, 4956.705 timesteps/s
-99.6% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 2089538.727 tau/day, 4836.895 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 | 0.12879 | 0.12879 | 0.12879 | 0.0 | 63.84
-Neigh | 0.051049 | 0.051049 | 0.051049 | 0.0 | 25.30
-Comm | 0.0043695 | 0.0043695 | 0.0043695 | 0.0 | 2.17
-Output | 8.1301e-05 | 8.1301e-05 | 8.1301e-05 | 0.0 | 0.04
-Modify | 0.011838 | 0.011838 | 0.011838 | 0.0 | 5.87
-Other | | 0.005622 | | | 2.79
+Pair | 0.12643 | 0.12643 | 0.12643 | 0.0 | 61.15
+Neigh | 0.053694 | 0.053694 | 0.053694 | 0.0 | 25.97
+Comm | 0.0061328 | 0.0061328 | 0.0061328 | 0.0 | 2.97
+Output | 0.00011373 | 0.00011373 | 0.00011373 | 0.0 | 0.06
+Modify | 0.014107 | 0.014107 | 0.014107 | 0.0 | 6.82
+Other | | 0.006263 | | | 3.03
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -91,7 +98,7 @@ neigh_modify delay 0 every 1 check yes
thermo 50
minimize 1.0e-6 0.001 1000 10000
-Memory usage per processor = 3.60343 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
1050 3.3256788 -2.8361415 0 0.48538014 1.6090001
@@ -104,9 +111,9 @@ Step Temp E_pair E_mol TotEng Press
1400 3.3256788 -2.9131297 0 0.40839199 1.7078217
1450 3.3256788 -2.9167506 0 0.40477104 1.7780477
1475 3.3256788 -2.9169436 0 0.4045781 1.7914542
-Loop time of 0.231352 on 1 procs for 475 steps with 800 atoms
+Loop time of 0.233542 on 1 procs for 475 steps with 800 atoms
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -120,12 +127,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.18807 | 0.18807 | 0.18807 | 0.0 | 81.29
-Neigh | 0.02088 | 0.02088 | 0.02088 | 0.0 | 9.03
-Comm | 0.0028048 | 0.0028048 | 0.0028048 | 0.0 | 1.21
-Output | 6.9618e-05 | 6.9618e-05 | 6.9618e-05 | 0.0 | 0.03
-Modify | 0.0020773 | 0.0020773 | 0.0020773 | 0.0 | 0.90
-Other | | 0.01745 | | | 7.54
+Pair | 0.18404 | 0.18404 | 0.18404 | 0.0 | 78.80
+Neigh | 0.02204 | 0.02204 | 0.02204 | 0.0 | 9.44
+Comm | 0.0040922 | 0.0040922 | 0.0040922 | 0.0 | 1.75
+Output | 0.00010443 | 0.00010443 | 0.00010443 | 0.0 | 0.04
+Modify | 0.0023651 | 0.0023651 | 0.0023651 | 0.0 | 1.01
+Other | | 0.0209 | | | 8.95
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/min/log.5Oct16.min.g++.4 b/examples/min/log.27Nov18.min.g++.4
similarity index 71%
rename from examples/min/log.5Oct16.min.g++.4
rename to examples/min/log.27Nov18.min.g++.4
index c58633b77c8bebe554ae62c8a0dcfbc53aa5bdd4..43171cd28db394610c736aadd1d64059bea43594 100644
--- a/examples/min/log.5Oct16.min.g++.4
+++ b/examples/min/log.27Nov18.min.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
@@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
+ Time spent = 0.000340223 secs
mass 1 1.0
velocity all create 5.0 87287 loop geom
@@ -39,13 +41,18 @@ thermo 100
run 1000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 22 22 1
-Memory usage per processor = 2.47676 Mbytes
+ binsize = 1.4, bins = 22 22 1
+ 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/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.049 | 3.049 | 3.049 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
@@ -58,20 +65,20 @@ Step Temp E_pair E_mol TotEng Press
800 3.3016408 -0.76570603 0 2.5318077 15.639259
900 3.4621697 -0.92610292 0 2.5317391 14.773473
1000 3.3058424 -0.77076863 0 2.5309414 15.708171
-Loop time of 0.162444 on 4 procs for 1000 steps with 800 atoms
+Loop time of 0.0730537 on 4 procs for 1000 steps with 800 atoms
-Performance: 2659379.051 tau/day, 6155.970 timesteps/s
-78.3% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 5913456.756 tau/day, 13688.557 timesteps/s
+95.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.032602 | 0.033969 | 0.034999 | 0.5 | 20.91
-Neigh | 0.013433 | 0.013719 | 0.013862 | 0.1 | 8.45
-Comm | 0.08291 | 0.088224 | 0.099287 | 2.2 | 54.31
-Output | 0.00084209 | 0.00093055 | 0.00097394 | 0.2 | 0.57
-Modify | 0.0030942 | 0.0033001 | 0.0035179 | 0.3 | 2.03
-Other | | 0.0223 | | | 13.73
+Pair | 0.031481 | 0.031893 | 0.032234 | 0.2 | 43.66
+Neigh | 0.014234 | 0.014466 | 0.014672 | 0.1 | 19.80
+Comm | 0.017078 | 0.01775 | 0.018055 | 0.3 | 24.30
+Output | 0.00017548 | 0.00027454 | 0.00056386 | 0.0 | 0.38
+Modify | 0.0038447 | 0.0038754 | 0.0038893 | 0.0 | 5.30
+Other | | 0.004795 | | | 6.56
Nlocal: 200 ave 202 max 196 min
Histogram: 1 0 0 0 0 0 0 0 2 1
@@ -91,7 +98,7 @@ neigh_modify delay 0 every 1 check yes
thermo 50
minimize 1.0e-6 0.001 1000 10000
-Memory usage per processor = 3.60176 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3058424 -0.77076863 0 2.5309414 15.708171
1050 3.3058424 -2.8318266 0 0.46988351 1.5980106
@@ -100,9 +107,9 @@ Step Temp E_pair E_mol TotEng Press
1200 3.3058424 -2.8831122 0 0.41859789 1.6869035
1250 3.3058424 -2.8877971 0 0.413913 1.7276622
1300 3.3058424 -2.8887969 0 0.41291311 1.7424655
-Loop time of 0.048058 on 4 procs for 300 steps with 800 atoms
+Loop time of 0.055995 on 4 procs for 300 steps with 800 atoms
-98.8% CPU use with 4 MPI tasks x no OpenMP threads
+96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -116,12 +123,12 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.03076 | 0.031581 | 0.032226 | 0.3 | 65.71
-Neigh | 0.0037913 | 0.0038914 | 0.0039353 | 0.1 | 8.10
-Comm | 0.004194 | 0.0049016 | 0.0058777 | 1.0 | 10.20
-Output | 6.3181e-05 | 6.6817e-05 | 7.7009e-05 | 0.1 | 0.14
-Modify | 0.00035 | 0.00036556 | 0.0003829 | 0.1 | 0.76
-Other | | 0.007252 | | | 15.09
+Pair | 0.029709 | 0.030492 | 0.031057 | 0.3 | 54.45
+Neigh | 0.0040245 | 0.0042111 | 0.0046084 | 0.4 | 7.52
+Comm | 0.010827 | 0.011703 | 0.012587 | 0.6 | 20.90
+Output | 9.8228e-05 | 0.00024104 | 0.00066733 | 0.0 | 0.43
+Modify | 0.0004456 | 0.00045222 | 0.00045633 | 0.0 | 0.81
+Other | | 0.008895 | | | 15.89
Nlocal: 200 ave 202 max 196 min
Histogram: 1 0 0 0 0 0 1 0 0 2
diff --git a/examples/msst/log.5Oct16.msst.g++.1 b/examples/msst/log.27Nov18.msst.g++.1
similarity index 79%
rename from examples/msst/log.5Oct16.msst.g++.1
rename to examples/msst/log.27Nov18.msst.g++.1
index 64af9958968bbbaeac68070cc059be6c952b033a..4b18e67702697132f5be95737399c33e0155fc40 100644
--- a/examples/msst/log.5Oct16.msst.g++.1
+++ b/examples/msst/log.27Nov18.msst.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# LJ test of msst shock dynamics
# Energy in eV, time in ps, distance in angstroms.
@@ -20,6 +21,7 @@ Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
+ Time spent = 0.00902033 secs
mass 1 40.00
@@ -37,13 +39,18 @@ thermo 10
run 100
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 17 17 17
-Memory usage per processor = 8.03726 Mbytes
+ binsize = 6, bins = 17 17 17
+ 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) = 17.86 | 17.86 | 17.86 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -1943.9014 0 -134.75058 992.06384
10 586.44651 -1917.3971 0 -149.11346 1306.17
@@ -56,20 +63,20 @@ Step Temp E_pair E_mol TotEng Press
80 300.28534 -1056.589 0 -151.15321 8324.8812
90 305.83368 -1073.3097 0 -151.14426 8175.2478
100 304.06857 -1067.9843 0 -151.14112 8191.234
-Loop time of 3.5066 on 1 procs for 100 steps with 23328 atoms
+Loop time of 3.49498 on 1 procs for 100 steps with 23328 atoms
-Performance: 4.928 ns/day, 4.870 hours/ns, 28.518 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 4.944 ns/day, 4.854 hours/ns, 28.612 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 3.3534 | 3.3534 | 3.3534 | 0.0 | 95.63
-Neigh | 0.066456 | 0.066456 | 0.066456 | 0.0 | 1.90
-Comm | 0.01981 | 0.01981 | 0.01981 | 0.0 | 0.56
-Output | 0.00096083 | 0.00096083 | 0.00096083 | 0.0 | 0.03
-Modify | 0.037752 | 0.037752 | 0.037752 | 0.0 | 1.08
-Other | | 0.02825 | | | 0.81
+Pair | 3.354 | 3.354 | 3.354 | 0.0 | 95.97
+Neigh | 0.074059 | 0.074059 | 0.074059 | 0.0 | 2.12
+Comm | 0.020118 | 0.020118 | 0.020118 | 0.0 | 0.58
+Output | 0.0010924 | 0.0010924 | 0.0010924 | 0.0 | 0.03
+Modify | 0.034063 | 0.034063 | 0.034063 | 0.0 | 0.97
+Other | | 0.01168 | | | 0.33
Nlocal: 23328 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -118,7 +125,7 @@ Fix MSST v0 = 8.97521e+05
Fix MSST p0 = 8.10679e+03
Fix MSST e0 = to be -1.51141e+02
Fix MSST initial strain rate of -3.20112e-02 established by reducing temperature by factor of 1.00000e-02
-Memory usage per processor = 8.04369 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 18.99 | 18.99 | 18.99 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
100 301.02788 907.67474 -1058.8159 96.4602 96.4602 96.4602 8242.1214 8202.9779 8095.8693 -151.14112 1.5203428 -10.919311 0 0 9.1684318
110 297.71411 897.68288 -1048.8859 96.4602 96.4602 96.399397 8347.6253 8303.7121 8220.7572 -151.20299 1.439058 28.652258 0.017649501 -0.55980494 5.7336721
@@ -131,20 +138,20 @@ Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lg
180 304.99 919.62151 -1071.3588 96.4602 96.4602 96.022824 8461.5542 8343.1436 8484.9824 -151.73733 0.99203387 -235.51793 0.12695926 -4.4693063 -15.685622
190 305.1148 919.99782 -1071.7807 96.4602 96.4602 95.9748 8498.7562 8371.4217 8514.4473 -151.78288 0.93937416 -273.43964 0.1408996 -5.0266132 -18.403999
200 306.45829 924.0488 -1075.8787 96.4602 96.4602 95.927931 8488.9509 8385.2408 8529.6443 -151.82991 0.88654815 -324.00777 0.15450451 -5.583645 -21.055149
-Loop time of 4.74363 on 1 procs for 100 steps with 23328 atoms
+Loop time of 5.50267 on 1 procs for 100 steps with 23328 atoms
-Performance: 3.643 ns/day, 6.588 hours/ns, 21.081 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 3.140 ns/day, 7.643 hours/ns, 18.173 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 3.366 | 3.366 | 3.366 | 0.0 | 70.96
-Neigh | 0.13476 | 0.13476 | 0.13476 | 0.0 | 2.84
-Comm | 0.017403 | 0.017403 | 0.017403 | 0.0 | 0.37
-Output | 0.011465 | 0.011465 | 0.011465 | 0.0 | 0.24
-Modify | 1.1866 | 1.1866 | 1.1866 | 0.0 | 25.01
-Other | | 0.02743 | | | 0.58
+Pair | 4.7512 | 4.7512 | 4.7512 | 0.0 | 86.34
+Neigh | 0.14916 | 0.14916 | 0.14916 | 0.0 | 2.71
+Comm | 0.020737 | 0.020737 | 0.020737 | 0.0 | 0.38
+Output | 0.010999 | 0.010999 | 0.010999 | 0.0 | 0.20
+Modify | 0.55965 | 0.55965 | 0.55965 | 0.0 | 10.17
+Other | | 0.01089 | | | 0.20
Nlocal: 23328 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -157,4 +164,4 @@ Total # of neighbors = 2183494
Ave neighs/atom = 93.5997
Neighbor list builds = 2
Dangerous builds = 0
-Total wall time: 0:00:08
+Total wall time: 0:00:09
diff --git a/examples/msst/log.5Oct16.msst.g++.4 b/examples/msst/log.27Nov18.msst.g++.4
similarity index 79%
rename from examples/msst/log.5Oct16.msst.g++.4
rename to examples/msst/log.27Nov18.msst.g++.4
index 6026141acea6566481e2c771e59c04c89f8fa7e4..c2ed0fcb5e4226cd090fd14eb3a64bb6f94edaad 100644
--- a/examples/msst/log.5Oct16.msst.g++.4
+++ b/examples/msst/log.27Nov18.msst.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# LJ test of msst shock dynamics
# Energy in eV, time in ps, distance in angstroms.
@@ -20,6 +21,7 @@ Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
1 by 2 by 2 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
+ Time spent = 0.00104165 secs
mass 1 40.00
@@ -37,13 +39,18 @@ thermo 10
run 100
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 17 17 17
-Memory usage per processor = 5.24184 Mbytes
+ binsize = 6, bins = 17 17 17
+ 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) = 7.784 | 7.784 | 7.784 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -1943.9014 0 -134.75058 992.06384
10 586.47212 -1917.4465 0 -149.08565 1305.7368
@@ -56,20 +63,20 @@ Step Temp E_pair E_mol TotEng Press
80 299.37658 -1053.8476 0 -151.1519 8352.9467
90 304.24026 -1068.4941 0 -151.13319 8218.1594
100 301.9683 -1061.6332 0 -151.12284 8244.1277
-Loop time of 0.933851 on 4 procs for 100 steps with 23328 atoms
+Loop time of 0.978562 on 4 procs for 100 steps with 23328 atoms
-Performance: 18.504 ns/day, 1.297 hours/ns, 107.083 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 17.659 ns/day, 1.359 hours/ns, 102.191 timesteps/s
+97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.83046 | 0.85727 | 0.86953 | 1.7 | 91.80
-Neigh | 0.01685 | 0.017314 | 0.017519 | 0.2 | 1.85
-Comm | 0.028471 | 0.041764 | 0.070721 | 8.3 | 4.47
-Output | 0.00049806 | 0.00062126 | 0.00067735 | 0.3 | 0.07
-Modify | 0.0090787 | 0.009689 | 0.0099437 | 0.4 | 1.04
-Other | | 0.007188 | | | 0.77
+Pair | 0.86406 | 0.88129 | 0.89922 | 1.4 | 90.06
+Neigh | 0.019231 | 0.019453 | 0.019816 | 0.2 | 1.99
+Comm | 0.043947 | 0.06197 | 0.079005 | 5.1 | 6.33
+Output | 0.00057197 | 0.00082499 | 0.0015628 | 0.0 | 0.08
+Modify | 0.0091414 | 0.0092927 | 0.0094769 | 0.1 | 0.95
+Other | | 0.005727 | | | 0.59
Nlocal: 5832 ave 5850 max 5813 min
Histogram: 1 0 0 0 1 1 0 0 0 1
@@ -118,7 +125,7 @@ Fix MSST v0 = 8.97521e+05
Fix MSST p0 = 8.18624e+03
Fix MSST e0 = to be -1.51123e+02
Fix MSST initial strain rate of -3.19005e-02 established by reducing temperature by factor of 1.00000e-02
-Memory usage per processor = 5.24184 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 8.534 | 8.534 | 8.534 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
100 298.94862 901.40524 -1052.5281 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034
110 296.49826 894.01679 -1045.224 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557
@@ -131,20 +138,20 @@ Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lg
180 305.86343 922.25514 -1073.9633 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462
190 307.44054 927.01052 -1078.7892 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801
200 308.43619 930.01265 -1081.8521 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378
-Loop time of 1.23008 on 4 procs for 100 steps with 23328 atoms
+Loop time of 1.57102 on 4 procs for 100 steps with 23328 atoms
-Performance: 14.048 ns/day, 1.708 hours/ns, 81.295 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 10.999 ns/day, 2.182 hours/ns, 63.653 timesteps/s
+97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.83631 | 0.84345 | 0.85189 | 0.8 | 68.57
-Neigh | 0.033866 | 0.03409 | 0.034339 | 0.1 | 2.77
-Comm | 0.029796 | 0.038609 | 0.045779 | 3.5 | 3.14
-Output | 0.0036259 | 0.0036446 | 0.0036905 | 0.0 | 0.30
-Modify | 0.30399 | 0.30447 | 0.30495 | 0.1 | 24.75
-Other | | 0.00582 | | | 0.47
+Pair | 1.2237 | 1.2543 | 1.3264 | 3.7 | 79.84
+Neigh | 0.038648 | 0.039684 | 0.041811 | 0.6 | 2.53
+Comm | 0.026617 | 0.10771 | 0.14194 | 14.3 | 6.86
+Output | 0.0035126 | 0.0045422 | 0.0076261 | 2.6 | 0.29
+Modify | 0.15787 | 0.15969 | 0.16403 | 0.6 | 10.16
+Other | | 0.005042 | | | 0.32
Nlocal: 5832 ave 5874 max 5803 min
Histogram: 2 0 0 0 0 1 0 0 0 1
diff --git a/examples/nb3b/log.5Oct16.nb3b.g++.1 b/examples/nb3b/log.27Nov18.nb3b.g++.1
similarity index 71%
rename from examples/nb3b/log.5Oct16.nb3b.g++.1
rename to examples/nb3b/log.27Nov18.nb3b.g++.1
index a156b3400c40924a79d7ab2053e5a972826640f9..d4a8cffc42f490b8eb3714d8c9f07017d72e8df3 100644
--- a/examples/nb3b/log.5Oct16.nb3b.g++.1
+++ b/examples/nb3b/log.27Nov18.nb3b.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# test of NB3B pair style with pair hybrid and KSpace solver
units real
@@ -57,26 +58,46 @@ thermo 50
### Minimize forces in structure ###
minimize 1.0e-06 1.0e-08 1000 10000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
EwaldDisp initialization ...
-WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216)
- G vector = 0.269426
-WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216)
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218)
+ G vector = 0.269426 accuracy = 0.0332064
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218)
Neighbor list info ...
- 4 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 4 4 4
+ binsize = 6, bins = 4 4 4
+ 4 neighbor lists, perpetual/occasional/extra = 4 0 0
+ (1) pair nb3b/harmonic, perpetual
+ attributes: full, newton on
+ pair build: full/bin
+ stencil: full/bin/3d
+ bin: standard
+ (2) pair lj/cut/coul/long, perpetual, half/full from (1)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (3) pair nb3b/harmonic, perpetual, copy from (1)
+ attributes: full, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+ (4) pair lj/cut/coul/long, perpetual, copy from (2)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
vectors: nbox = 6, nkvec = 478
-Memory usage per processor = 17.039 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 32.37 | 32.37 | 32.37 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72822 22.5907 22.359 23.4708 0 0 0 11855.229
4 -61506.604 0 0 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 1657.43 22.5907 22.359 23.4708 0 0 0 11855.229
-Loop time of 0.434716 on 1 procs for 4 steps with 1400 atoms
+Loop time of 0.562063 on 1 procs for 4 steps with 1400 atoms
-98.4% CPU use with 1 MPI tasks x no OpenMP threads
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -90,14 +111,14 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.35925 | 0.35925 | 0.35925 | 0.0 | 82.64
-Bond | 0.00031662 | 0.00031662 | 0.00031662 | 0.0 | 0.07
-Kspace | 0.074097 | 0.074097 | 0.074097 | 0.0 | 17.04
+Pair | 0.47517 | 0.47517 | 0.47517 | 0.0 | 84.54
+Bond | 0.00020051 | 0.00020051 | 0.00020051 | 0.0 | 0.04
+Kspace | 0.085509 | 0.085509 | 0.085509 | 0.0 | 15.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.00059676 | 0.00059676 | 0.00059676 | 0.0 | 0.14
+Comm | 0.00077796 | 0.00077796 | 0.00077796 | 0.0 | 0.14
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 0.0004592 | | | 0.11
+Other | | 0.0004046 | | | 0.07
Nlocal: 1400 ave 1400 max 1400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -123,38 +144,31 @@ fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
run 100
EwaldDisp initialization ...
-WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216)
- G vector = 0.269426
-WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216)
-Neighbor list info ...
- 4 neighbor list requests
- update every 1 steps, delay 5 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12
- ghost atom cutoff = 12
- binsize = 6 -> bins = 4 4 4
-Memory usage per processor = 16.664 Mbytes
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218)
+ G vector = 0.269426 accuracy = 0.0332064
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218)
+Per MPI rank memory allocation (min/avg/max) = 31.99 | 31.99 | 31.99 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
4 -60263.898 1242.7057 298 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 6449.1472 22.5907 22.359 23.4708 0 0 0 11855.229
50 -58769.885 1186.4036 284.49881 -59956.289 309.92499 0 0 0 6168.8458 -20249.062 -46185.998 21737.807 22.5907 22.359 23.4708 0 0 0 11855.229
100 -58865.196 1242.7057 298 -60107.902 371.56168 0 0 0 6422.4016 -20716.005 -46185.86 22887.006 22.5907 22.359 23.4708 0 0 0 11855.229
104 -58865.334 1260.1244 302.177 -60125.458 386.24491 0 0 0 6377.3686 -20705.327 -46183.745 19154.01 22.5907 22.359 23.4708 0 0 0 11855.229
-Loop time of 7.88523 on 1 procs for 100 steps with 1400 atoms
+Loop time of 10.7036 on 1 procs for 100 steps with 1400 atoms
-Performance: 1.096 ns/day, 21.903 hours/ns, 12.682 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.807 ns/day, 29.732 hours/ns, 9.343 timesteps/s
+99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 6.9318 | 6.9318 | 6.9318 | 0.0 | 87.91
-Bond | 0.0063558 | 0.0063558 | 0.0063558 | 0.0 | 0.08
-Kspace | 0.81841 | 0.81841 | 0.81841 | 0.0 | 10.38
-Neigh | 0.1015 | 0.1015 | 0.1015 | 0.0 | 1.29
-Comm | 0.013201 | 0.013201 | 0.013201 | 0.0 | 0.17
-Output | 9.7752e-05 | 9.7752e-05 | 9.7752e-05 | 0.0 | 0.00
-Modify | 0.0064344 | 0.0064344 | 0.0064344 | 0.0 | 0.08
-Other | | 0.007411 | | | 0.09
+Pair | 9.5983 | 9.5983 | 9.5983 | 0.0 | 89.67
+Bond | 0.0037653 | 0.0037653 | 0.0037653 | 0.0 | 0.04
+Kspace | 0.95057 | 0.95057 | 0.95057 | 0.0 | 8.88
+Neigh | 0.11977 | 0.11977 | 0.11977 | 0.0 | 1.12
+Comm | 0.018144 | 0.018144 | 0.018144 | 0.0 | 0.17
+Output | 0.00011969 | 0.00011969 | 0.00011969 | 0.0 | 0.00
+Modify | 0.0061135 | 0.0061135 | 0.0061135 | 0.0 | 0.06
+Other | | 0.006855 | | | 0.06
Nlocal: 1400 ave 1400 max 1400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -170,4 +184,4 @@ Ave neighs/atom = 850.439
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0
-Total wall time: 0:00:08
+Total wall time: 0:00:11
diff --git a/examples/nb3b/log.5Oct16.nb3b.g++.4 b/examples/nb3b/log.27Nov18.nb3b.g++.4
similarity index 71%
rename from examples/nb3b/log.5Oct16.nb3b.g++.4
rename to examples/nb3b/log.27Nov18.nb3b.g++.4
index f63a40486d6639db7efd35c2f370e0ff3dcb6cad..e2c1f778443ed72d6551210f7f3a3b0f4ae4b46b 100644
--- a/examples/nb3b/log.5Oct16.nb3b.g++.4
+++ b/examples/nb3b/log.27Nov18.nb3b.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# test of NB3B pair style with pair hybrid and KSpace solver
units real
@@ -57,26 +58,46 @@ thermo 50
### Minimize forces in structure ###
minimize 1.0e-06 1.0e-08 1000 10000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
EwaldDisp initialization ...
-WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216)
- G vector = 0.269426
-WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216)
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218)
+ G vector = 0.269426 accuracy = 0.0332064
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218)
Neighbor list info ...
- 4 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 4 4 4
+ binsize = 6, bins = 4 4 4
+ 4 neighbor lists, perpetual/occasional/extra = 4 0 0
+ (1) pair nb3b/harmonic, perpetual
+ attributes: full, newton on
+ pair build: full/bin
+ stencil: full/bin/3d
+ bin: standard
+ (2) pair lj/cut/coul/long, perpetual, half/full from (1)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (3) pair nb3b/harmonic, perpetual, copy from (1)
+ attributes: full, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+ (4) pair lj/cut/coul/long, perpetual, copy from (2)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
vectors: nbox = 6, nkvec = 478
-Memory usage per processor = 16.9507 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 20.64 | 21.18 | 22.02 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72822 22.5907 22.359 23.4708 0 0 0 11855.229
4 -61506.604 0 0 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 1657.43 22.5907 22.359 23.4708 0 0 0 11855.229
-Loop time of 0.129448 on 4 procs for 4 steps with 1400 atoms
+Loop time of 0.164255 on 4 procs for 4 steps with 1400 atoms
-99.4% CPU use with 4 MPI tasks x no OpenMP threads
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
@@ -90,14 +111,14 @@ Minimization stats:
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.082641 | 0.0934 | 0.10605 | 3.3 | 72.15
-Bond | 7.2002e-05 | 7.9215e-05 | 8.6546e-05 | 0.1 | 0.06
-Kspace | 0.021445 | 0.032612 | 0.04218 | 4.9 | 25.19
+Pair | 0.11101 | 0.12473 | 0.13747 | 3.3 | 75.93
+Bond | 5.8889e-05 | 6.2823e-05 | 6.6757e-05 | 0.0 | 0.04
+Kspace | 0.025273 | 0.036047 | 0.047969 | 5.3 | 21.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0015318 | 0.0030052 | 0.0042045 | 2.1 | 2.32
+Comm | 0.001081 | 0.0030527 | 0.0048478 | 2.8 | 1.86
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
-Other | | 0.0003518 | | | 0.27
+Other | | 0.000367 | | | 0.22
Nlocal: 350 ave 399 max 305 min
Histogram: 1 1 0 0 0 0 0 0 1 1
@@ -123,38 +144,31 @@ fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
run 100
EwaldDisp initialization ...
-WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216)
- G vector = 0.269426
-WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216)
-Neighbor list info ...
- 4 neighbor list requests
- update every 1 steps, delay 5 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12
- ghost atom cutoff = 12
- binsize = 6 -> bins = 4 4 4
-Memory usage per processor = 16.5757 Mbytes
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218)
+ G vector = 0.269426 accuracy = 0.0332064
+WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218)
+Per MPI rank memory allocation (min/avg/max) = 20.26 | 20.8 | 21.65 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
4 -60263.898 1242.7057 298 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 6449.1472 22.5907 22.359 23.4708 0 0 0 11855.229
50 -58769.885 1186.4036 284.49881 -59956.289 309.92499 0 0 0 6168.8458 -20249.062 -46185.998 21737.807 22.5907 22.359 23.4708 0 0 0 11855.229
100 -58865.196 1242.7057 298 -60107.902 371.56168 0 0 0 6422.4016 -20716.005 -46185.86 22887.006 22.5907 22.359 23.4708 0 0 0 11855.229
104 -58865.334 1260.1244 302.177 -60125.458 386.24491 0 0 0 6377.3686 -20705.327 -46183.745 19154.01 22.5907 22.359 23.4708 0 0 0 11855.229
-Loop time of 2.3186 on 4 procs for 100 steps with 1400 atoms
+Loop time of 3.0299 on 4 procs for 100 steps with 1400 atoms
-Performance: 3.726 ns/day, 6.441 hours/ns, 43.129 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 2.852 ns/day, 8.416 hours/ns, 33.004 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 1.7054 | 1.8352 | 1.9875 | 8.4 | 79.15
-Bond | 0.0015972 | 0.0017807 | 0.0019476 | 0.3 | 0.08
-Kspace | 0.21511 | 0.22245 | 0.23383 | 1.6 | 9.59
-Neigh | 0.026175 | 0.026182 | 0.026186 | 0.0 | 1.13
-Comm | 0.062151 | 0.21516 | 0.34573 | 24.7 | 9.28
-Output | 0.0001421 | 0.00016701 | 0.00020218 | 0.2 | 0.01
-Modify | 0.0021067 | 0.0031134 | 0.0037572 | 1.2 | 0.13
-Other | | 0.01456 | | | 0.63
+Pair | 2.424 | 2.5288 | 2.6552 | 6.3 | 83.46
+Bond | 0.0011241 | 0.0011699 | 0.0011907 | 0.1 | 0.04
+Kspace | 0.24584 | 0.25484 | 0.26259 | 1.5 | 8.41
+Neigh | 0.031059 | 0.031067 | 0.031075 | 0.0 | 1.03
+Comm | 0.070014 | 0.19745 | 0.30262 | 22.7 | 6.52
+Output | 0.00011683 | 0.0002265 | 0.00050616 | 0.0 | 0.01
+Modify | 0.0022085 | 0.0030763 | 0.0039916 | 1.3 | 0.10
+Other | | 0.01331 | | | 0.44
Nlocal: 350 ave 357 max 340 min
Histogram: 1 0 0 0 0 0 1 1 0 1
@@ -170,4 +184,4 @@ Ave neighs/atom = 850.439
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0
-Total wall time: 0:00:02
+Total wall time: 0:00:03
diff --git a/examples/nemd/log.27Nov18.nemd.g++.1 b/examples/nemd/log.27Nov18.nemd.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..c0989db969672766bfd6ea10b8ccd2c7c059eeed
--- /dev/null
+++ b/examples/nemd/log.27Nov18.nemd.g++.1
@@ -0,0 +1,137 @@
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
+# 2d NEMD simulation
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000332355 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+#dump 1 all custom 5000 dump.nemd id type x y z
+
+#dump 2 all image 1000 image.*.jpg type type adiam 1.2
+#dump_modify 2 pad 5
+
+#dump 3 all movie 1000 movie.mpg type type adiam 1.2
+#dump_modify 3 pad 5
+
+thermo 1000
+
+run 50000
+Neighbor list info ...
+ 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 = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1.44 0 0 1.431 1.2080502 189.52855
+ 1000 1.1326992 0.25863754 0 1.3842573 6.0588079 189.52855
+ 2000 0.99104643 0.37634349 0 1.3611959 7.8993387 189.52855
+ 3000 1.0749743 0.21908728 0 1.2873429 6.2659517 189.52855
+ 4000 1.0986742 0.27147022 0 1.3632777 5.8778262 189.52855
+ 5000 1.071838 0.23413372 0 1.2992728 5.9120887 189.52855
+ 6000 1.0013194 0.26923671 0 1.2642979 6.2802759 189.52855
+ 7000 0.94110685 0.3224557 0 1.2576806 6.1864166 189.52855
+ 8000 0.97391513 0.28793383 0 1.255762 6.5071893 189.52855
+ 9000 0.95346063 0.31050593 0 1.2580074 6.3321512 189.52855
+ 10000 0.96236447 0.26298203 0 1.2193317 6.4083918 189.52855
+ 11000 0.9511149 0.27571527 0 1.2208857 6.0949768 189.52855
+ 12000 1.0186935 0.18134918 0 1.1936758 5.1269128 189.52855
+ 13000 0.96350682 0.23171507 0 1.1892 5.7367267 189.52855
+ 14000 0.94740402 0.27357945 0 1.2150622 6.0156532 189.52855
+ 15000 0.87951545 0.27745111 0 1.1514696 6.297405 189.52855
+ 16000 0.93216196 0.27020559 0 1.1965415 6.6188833 189.52855
+ 17000 0.94109936 0.24756193 0 1.1827794 5.8993088 189.52855
+ 18000 0.97325239 0.27996398 0 1.2471335 6.1486561 189.52855
+ 19000 1.0494686 0.27132686 0 1.3142363 6.6757065 189.52855
+ 20000 1.0391862 0.25195457 0 1.2846459 6.143235 189.52855
+ 21000 0.96407137 0.27359166 0 1.2316376 5.9577116 189.52855
+ 22000 0.97954534 0.31920255 0 1.2926257 6.5320163 189.52855
+ 23000 0.97585473 0.24154424 0 1.2112999 6.0839179 189.52855
+ 24000 1.0522109 0.1646952 0 1.2103298 5.0388687 189.52855
+ 25000 0.93707172 0.25655806 0 1.1877731 5.819887 189.52855
+ 26000 0.89798775 0.26629627 0 1.1586716 6.0393558 189.52855
+ 27000 0.93259926 0.24542428 0 1.1721948 5.3560986 189.52855
+ 28000 0.8428223 0.20784302 0 1.0453977 4.956911 189.52855
+ 29000 0.81653505 0.21924932 0 1.030681 5.271501 189.52855
+ 30000 0.90157811 0.15070734 0 1.0466506 4.476142 189.52855
+ 31000 0.86580039 0.21115151 0 1.0715407 5.0056915 189.52855
+ 32000 0.89768096 0.28377249 0 1.1758429 5.8449711 189.52855
+ 33000 1.0504011 0.29009694 0 1.333933 6.1319155 189.52855
+ 34000 1.2009765 0.19137934 0 1.3848498 4.9643885 189.52855
+ 35000 1.208705 0.27071222 0 1.4718628 6.2162389 189.52855
+ 36000 1.2211309 0.28389521 0 1.497394 6.5090715 189.52855
+ 37000 1.1384381 0.42795547 0 1.5592783 8.5129272 189.52855
+ 38000 1.2198334 0.34335732 0 1.5555668 7.2940883 189.52855
+ 39000 1.1562045 0.35783089 0 1.5068091 7.340999 189.52855
+ 40000 1.2145924 0.28410558 0 1.4911068 6.234986 189.52855
+ 41000 1.1240878 0.34663237 0 1.4636946 7.1720193 189.52855
+ 42000 1.2491422 0.26815889 0 1.509494 6.1390803 189.52855
+ 43000 1.1387564 0.33755832 0 1.4691975 7.0577597 189.52855
+ 44000 1.0031598 0.4081807 0 1.4050708 8.2732113 189.52855
+ 45000 1.0166213 0.29131017 0 1.3015776 6.1907807 189.52855
+ 46000 0.96251302 0.31483519 0 1.2713325 6.6987235 189.52855
+ 47000 0.89809294 0.30909884 0 1.2015787 6.3997583 189.52855
+ 48000 0.86736217 0.31917648 0 1.1811176 7.1584774 189.52855
+ 49000 0.91979053 0.21099403 0 1.1250359 5.4968259 189.52855
+ 50000 0.87079959 0.24059333 0 1.1059504 5.6039305 189.52855
+Loop time of 1.54353 on 1 procs for 50000 steps with 160 atoms
+
+Performance: 13993916.675 tau/day, 32393.326 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 | 0.20172 | 0.20172 | 0.20172 | 0.0 | 13.07
+Neigh | 0.16634 | 0.16634 | 0.16634 | 0.0 | 10.78
+Comm | 0.068928 | 0.068928 | 0.068928 | 0.0 | 4.47
+Output | 0.00059891 | 0.00059891 | 0.00059891 | 0.0 | 0.04
+Modify | 1.0123 | 1.0123 | 1.0123 | 0.0 | 65.59
+Other | | 0.09361 | | | 6.06
+
+Nlocal: 160 ave 160 max 160 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 73 ave 73 max 73 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 353 ave 353 max 353 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 353
+Ave neighs/atom = 2.20625
+Neighbor list builds = 5273
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/nemd/log.27Nov18.nemd.g++.4 b/examples/nemd/log.27Nov18.nemd.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..68543882b72f1b645abf1f1952caa14d832cdfed
--- /dev/null
+++ b/examples/nemd/log.27Nov18.nemd.g++.4
@@ -0,0 +1,137 @@
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
+# 2d NEMD simulation
+
+units lj
+atom_style atomic
+dimension 2
+
+lattice sq2 0.8442
+Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
+region box prism 0 10 0 8 -0.5 0.5 0 0 0
+create_box 2 box
+Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
+ 2 by 2 by 1 MPI processor grid
+create_atoms 1 box
+Created 160 atoms
+ Time spent = 0.000308275 secs
+mass * 1.0
+
+velocity all create 1.44 87287 loop geom
+
+region slice block 4 6 INF INF INF INF
+set region slice type 2
+ 40 settings made for type
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0 every 1
+
+fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
+fix 2 all deform 1 xy erate 0.01 remap v
+
+#dump 1 all custom 5000 dump.nemd id type x y z
+
+#dump 2 all image 1000 image.*.jpg type type adiam 1.2
+#dump_modify 2 pad 5
+
+#dump 3 all movie 1000 movie.mpg type type adiam 1.2
+#dump_modify 3 pad 5
+
+thermo 1000
+
+run 50000
+Neighbor list info ...
+ 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 = 24 19 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton/tri
+ stencil: half/bin/2d/newton/tri
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 1.44 0 0 1.431 1.2080502 189.52855
+ 1000 1.1682693 0.24486562 0 1.4058332 5.8092954 189.52855
+ 2000 1.0928734 0.27609364 0 1.3621366 6.2237017 189.52855
+ 3000 1.09088 0.24816112 0 1.3322231 5.7001547 189.52855
+ 4000 1.0110684 0.29868377 0 1.303433 7.3312319 189.52855
+ 5000 0.91033678 0.28330698 0 1.1879542 6.1840352 189.52855
+ 6000 0.93416074 0.22661127 0 1.1549335 5.3619735 189.52855
+ 7000 0.93305734 0.19203739 0 1.1192631 5.2497547 189.52855
+ 8000 0.88944438 0.19421381 0 1.0780992 4.9733446 189.52855
+ 9000 0.86949257 0.21207681 0 1.0761351 5.4687076 189.52855
+ 10000 0.80088203 0.24071142 0 1.0365879 5.334545 189.52855
+ 11000 0.88899727 0.19972767 0 1.0831687 4.8832207 189.52855
+ 12000 0.93045817 0.17883252 0 1.1034753 4.9081709 189.52855
+ 13000 0.9724196 0.19089684 0 1.1572388 5.3460903 189.52855
+ 14000 0.93902186 0.25513773 0 1.1882907 6.3338337 189.52855
+ 15000 0.91879903 0.31605547 0 1.229112 6.2085671 189.52855
+ 16000 0.9860058 0.26863362 0 1.2484769 6.514688 189.52855
+ 17000 1.0354756 0.23445357 0 1.2634574 6.1519296 189.52855
+ 18000 1.0244774 0.27511827 0 1.2931927 6.2230002 189.52855
+ 19000 1.1581216 0.21558936 0 1.3664727 5.5458237 189.52855
+ 20000 1.0552168 0.29344488 0 1.3420666 6.4880315 189.52855
+ 21000 0.97925435 0.31583414 0 1.2889681 6.7584093 189.52855
+ 22000 1.0112494 0.26246834 0 1.2673974 5.4112008 189.52855
+ 23000 1.0463332 0.26049752 0 1.3002911 6.1359606 189.52855
+ 24000 1.1130319 0.19848564 0 1.3045611 5.7088487 189.52855
+ 25000 1.0355662 0.28048951 0 1.3095834 6.4596476 189.52855
+ 26000 1.0823932 0.21784218 0 1.2934704 5.106334 189.52855
+ 27000 0.99719525 0.32679678 0 1.3177596 6.7399277 189.52855
+ 28000 1.0665868 0.25002709 0 1.3099477 6.2732557 189.52855
+ 29000 1.0312798 0.30650087 0 1.3313351 7.0581024 189.52855
+ 30000 1.0388277 0.29812912 0 1.3304641 6.2533028 189.52855
+ 31000 1.0461658 0.21344416 0 1.2530714 5.3631154 189.52855
+ 32000 1.0233681 0.27545017 0 1.2924222 5.9612896 189.52855
+ 33000 1.1353086 0.20278244 0 1.3309953 5.7619128 189.52855
+ 34000 1.0374791 0.29661216 0 1.327607 6.5124409 189.52855
+ 35000 1.0752783 0.21684443 0 1.2854022 5.4759171 189.52855
+ 36000 1.0383445 0.27068641 0 1.3025412 6.8367218 189.52855
+ 37000 0.97341144 0.24034988 0 1.2076775 6.1335996 189.52855
+ 38000 0.9285918 0.2737544 0 1.1965425 5.8750327 189.52855
+ 39000 0.84869423 0.30079207 0 1.144182 6.8909326 189.52855
+ 40000 0.88237131 0.26049171 0 1.1373482 6.3932981 189.52855
+ 41000 0.90368591 0.21064132 0 1.1086792 5.5627232 189.52855
+ 42000 0.93436749 0.20367569 0 1.1322034 5.1420052 189.52855
+ 43000 0.91378588 0.26155533 0 1.16963 6.366756 189.52855
+ 44000 0.91673608 0.25967314 0 1.1706796 6.0846334 189.52855
+ 45000 1.0233334 0.25463562 0 1.2715732 6.0924255 189.52855
+ 46000 0.96184729 0.35422095 0 1.3100567 7.0249175 189.52855
+ 47000 1.134079 0.26196034 0 1.3889514 6.3476756 189.52855
+ 48000 1.0552136 0.303812 0 1.3524305 6.6968927 189.52855
+ 49000 1.1282184 0.2100955 0 1.3312626 5.8658659 189.52855
+ 50000 1.0493816 0.31540438 0 1.3582274 6.6348173 189.52855
+Loop time of 1.09903 on 4 procs for 50000 steps with 160 atoms
+
+Performance: 19653623.953 tau/day, 45494.500 timesteps/s
+94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.057854 | 0.05974 | 0.062726 | 0.7 | 5.44
+Neigh | 0.047791 | 0.049863 | 0.054819 | 1.3 | 4.54
+Comm | 0.3581 | 0.38553 | 0.39784 | 2.6 | 35.08
+Output | 0.001116 | 0.0014414 | 0.0023859 | 1.4 | 0.13
+Modify | 0.41102 | 0.42642 | 0.4493 | 2.3 | 38.80
+Other | | 0.176 | | | 16.02
+
+Nlocal: 40 ave 42 max 39 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost: 36.5 ave 37 max 36 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs: 87.5 ave 94 max 81 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 350
+Ave neighs/atom = 2.1875
+Neighbor list builds = 5276
+Dangerous builds = 0
+Total wall time: 0:00:01
diff --git a/examples/nemd/log.5Oct16.nemd.g++.1 b/examples/nemd/log.5Oct16.nemd.g++.1
deleted file mode 100644
index fb5abee6e29e3c480d3af5edcc570d7c6dcc9329..0000000000000000000000000000000000000000
--- a/examples/nemd/log.5Oct16.nemd.g++.1
+++ /dev/null
@@ -1,130 +0,0 @@
-LAMMPS (5 Oct 2016)
-# 2d NEMD simulation
-
-units lj
-atom_style atomic
-dimension 2
-
-lattice sq2 0.8442
-Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
-region box prism 0 10 0 8 -0.5 0.5 0 0 0
-create_box 2 box
-Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
- 1 by 1 by 1 MPI processor grid
-create_atoms 1 box
-Created 160 atoms
-mass * 1.0
-
-velocity all create 1.44 87287 loop geom
-
-region slice block 4 6 INF INF INF INF
-set region slice type 2
- 40 settings made for type
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 1.0
-
-neighbor 0.3 bin
-neigh_modify delay 0 every 1
-
-fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
-fix 2 all deform 1 xy erate 0.01 remap v
-
-#dump 1 all custom 5000 dump.nemd id type x y z
-
-#dump 2 all image 1000 image.*.jpg type type adiam 1.2
-#dump_modify 2 pad 5
-
-#dump 3 all movie 1000 movie.mpg type type adiam 1.2
-#dump_modify 3 pad 5
-
-thermo 1000
-
-run 50000
-Neighbor list info ...
- 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 = 24 19 3
-Memory usage per processor = 2.49357 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 1.44 0 0 1.431 1.2080502 189.52855
- 1000 1.1326992 0.25863754 0 1.3842573 6.0588079 189.52855
- 2000 1.0158438 0.33502643 0 1.3445212 7.2638652 189.52855
- 3000 1.0968167 0.3149227 0 1.4048843 7.0653223 189.52855
- 4000 1.0070993 0.40611915 0 1.4069241 7.7283521 189.52855
- 5000 1.1153133 0.2674828 0 1.3758254 6.2949171 189.52855
- 6000 1.0170665 0.25843673 0 1.2691466 6.049412 189.52855
- 7000 1.0224605 0.20974914 0 1.2258193 5.5104976 189.52855
- 8000 0.96149374 0.24035439 0 1.1958388 5.4179146 189.52855
- 9000 0.87759014 0.2590493 0 1.1311545 5.8711239 189.52855
- 10000 0.83791968 0.23477897 0 1.0674617 5.666904 189.52855
- 11000 0.87702487 0.22958877 0 1.1011322 5.9068062 189.52855
- 12000 0.81507294 0.26375817 0 1.0737369 5.9166925 189.52855
- 13000 0.85655284 0.24676491 0 1.0979643 5.6918734 189.52855
- 14000 0.84369293 0.27818471 0 1.1166046 6.4146184 189.52855
- 15000 0.90052173 0.19836095 0 1.0932544 5.2690913 189.52855
- 16000 0.83836874 0.26921637 0 1.1023453 5.9579526 189.52855
- 17000 0.90492897 0.21933098 0 1.1186041 5.6042194 189.52855
- 18000 0.90113412 0.24880908 0 1.1443111 6.0634846 189.52855
- 19000 1.0160445 0.17252962 0 1.1822239 5.3149334 189.52855
- 20000 0.96217234 0.2414377 0 1.1975965 5.476653 189.52855
- 21000 0.98229664 0.27569118 0 1.2518485 5.9340174 189.52855
- 22000 1.0551763 0.26997615 0 1.3185576 6.2094112 189.52855
- 23000 1.051999 0.34076639 0 1.3861904 7.082385 189.52855
- 24000 1.1350071 0.23701844 0 1.3649317 6.1829742 189.52855
- 25000 1.0946409 0.33366032 0 1.4214597 7.1907559 189.52855
- 26000 1.1511799 0.24626808 0 1.3902531 5.8469984 189.52855
- 27000 1.1009203 0.25653085 0 1.3505704 6.1504287 189.52855
- 28000 1.0521302 0.2876798 0 1.3332342 5.9906187 189.52855
- 29000 1.0518465 0.21853 0 1.2638025 5.6577549 189.52855
- 30000 0.97264625 0.28758145 0 1.2541487 6.5769804 189.52855
- 31000 1.0133579 0.31575837 0 1.3227828 6.6650893 189.52855
- 32000 1.0714324 0.28757036 0 1.3523063 6.2682059 189.52855
- 33000 1.0739451 0.28062459 0 1.3478575 6.6862746 189.52855
- 34000 1.0056867 0.38289586 0 1.382297 7.1120131 189.52855
- 35000 1.0911349 0.26370939 0 1.3480247 6.1476048 189.52855
- 36000 1.0618618 0.28269593 0 1.3379211 6.9414608 189.52855
- 37000 1.0704991 0.29974994 0 1.3635585 7.0834346 189.52855
- 38000 1.1087507 0.2682201 0 1.3700411 5.8506019 189.52855
- 39000 1.1303733 0.22362416 0 1.3469326 5.2500269 189.52855
- 40000 1.0174248 0.28956571 0 1.3006316 6.4491571 189.52855
- 41000 0.95981887 0.29162143 0 1.2454414 6.4658646 189.52855
- 42000 0.88302144 0.30432252 0 1.1818251 6.7401923 189.52855
- 43000 0.93164419 0.25110308 0 1.1769245 5.9067383 189.52855
- 44000 0.98352598 0.23322873 0 1.2106077 5.5606585 189.52855
- 45000 1.0247245 0.26503082 0 1.2833508 6.533394 189.52855
- 46000 0.93004532 0.32277782 0 1.2470104 6.4689179 189.52855
- 47000 1.0653176 0.29185413 0 1.3505135 6.9534569 189.52855
- 48000 1.0401524 0.3420245 0 1.3756759 6.8016042 189.52855
- 49000 1.0023407 0.31833091 0 1.314407 6.7385662 189.52855
- 50000 1.0566272 0.28657142 0 1.3365947 6.261203 189.52855
-Loop time of 1.14585 on 1 procs for 50000 steps with 160 atoms
-
-Performance: 18850616.224 tau/day, 43635.686 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.19375 | 0.19375 | 0.19375 | 0.0 | 16.91
-Neigh | 0.17407 | 0.17407 | 0.17407 | 0.0 | 15.19
-Comm | 0.046638 | 0.046638 | 0.046638 | 0.0 | 4.07
-Output | 0.0003221 | 0.0003221 | 0.0003221 | 0.0 | 0.03
-Modify | 0.66586 | 0.66586 | 0.66586 | 0.0 | 58.11
-Other | | 0.06522 | | | 5.69
-
-Nlocal: 160 ave 160 max 160 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 71 ave 71 max 71 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 362 ave 362 max 362 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 362
-Ave neighs/atom = 2.2625
-Neighbor list builds = 5256
-Dangerous builds = 0
-Total wall time: 0:00:01
diff --git a/examples/nemd/log.5Oct16.nemd.g++.4 b/examples/nemd/log.5Oct16.nemd.g++.4
deleted file mode 100644
index 7738d64e2e56ffb9a4d504e8e71ca9a07544d497..0000000000000000000000000000000000000000
--- a/examples/nemd/log.5Oct16.nemd.g++.4
+++ /dev/null
@@ -1,130 +0,0 @@
-LAMMPS (5 Oct 2016)
-# 2d NEMD simulation
-
-units lj
-atom_style atomic
-dimension 2
-
-lattice sq2 0.8442
-Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
-region box prism 0 10 0 8 -0.5 0.5 0 0 0
-create_box 2 box
-Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
- 2 by 2 by 1 MPI processor grid
-create_atoms 1 box
-Created 160 atoms
-mass * 1.0
-
-velocity all create 1.44 87287 loop geom
-
-region slice block 4 6 INF INF INF INF
-set region slice type 2
- 40 settings made for type
-
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0 1.0
-
-neighbor 0.3 bin
-neigh_modify delay 0 every 1
-
-fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
-fix 2 all deform 1 xy erate 0.01 remap v
-
-#dump 1 all custom 5000 dump.nemd id type x y z
-
-#dump 2 all image 1000 image.*.jpg type type adiam 1.2
-#dump_modify 2 pad 5
-
-#dump 3 all movie 1000 movie.mpg type type adiam 1.2
-#dump_modify 3 pad 5
-
-thermo 1000
-
-run 50000
-Neighbor list info ...
- 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 = 24 19 3
-Memory usage per processor = 2.49198 Mbytes
-Step Temp E_pair E_mol TotEng Press Volume
- 0 1.44 0 0 1.431 1.2080502 189.52855
- 1000 1.1682693 0.24486562 0 1.4058332 5.8092954 189.52855
- 2000 1.0928734 0.27609364 0 1.3621366 6.2237017 189.52855
- 3000 1.0895801 0.24812344 0 1.3308937 5.6987334 189.52855
- 4000 1.0231536 0.23938192 0 1.2561408 5.6395384 189.52855
- 5000 0.92980496 0.29549086 0 1.2194845 6.7361058 189.52855
- 6000 0.94654468 0.27175873 0 1.2123875 6.1830354 189.52855
- 7000 1.04513 0.19555104 0 1.234149 5.3099904 189.52855
- 8000 0.90165043 0.33774203 0 1.2337571 6.8441345 189.52855
- 9000 1.0559475 0.21527383 0 1.2646217 5.3936713 189.52855
- 10000 1.0316023 0.25162907 0 1.2767839 6.0630699 189.52855
- 11000 1.0057873 0.1929355 0 1.1924366 5.1939416 189.52855
- 12000 0.95976424 0.23631857 0 1.1900843 5.1197849 189.52855
- 13000 0.96228689 0.2359206 0 1.1921932 5.8485377 189.52855
- 14000 0.92347491 0.28934379 0 1.207047 6.7279587 189.52855
- 15000 0.98798195 0.25310368 0 1.2349107 5.5744542 189.52855
- 16000 0.93800257 0.39455603 0 1.3266961 7.5939651 189.52855
- 17000 1.1781148 0.21856228 0 1.3893138 5.8347428 189.52855
- 18000 1.1292943 0.26429204 0 1.3865283 6.0510955 189.52855
- 19000 1.1047406 0.37926848 0 1.4771045 8.1596576 189.52855
- 20000 1.1716353 0.34662527 0 1.5109379 7.4616642 189.52855
- 21000 1.1630831 0.35981763 0 1.5156314 7.1024447 189.52855
- 22000 1.1249714 0.28308559 0 1.4010259 6.4004855 189.52855
- 23000 1.1062056 0.28618757 0 1.3854794 6.4957851 189.52855
- 24000 1.0588756 0.31727536 0 1.369533 6.987661 189.52855
- 25000 1.0379506 0.30773124 0 1.3391947 6.3814122 189.52855
- 26000 1.0316899 0.25596718 0 1.281209 6.4851096 189.52855
- 27000 0.95909019 0.32282679 0 1.2759227 6.480673 189.52855
- 28000 1.0224651 0.24795447 0 1.2640291 5.5846145 189.52855
- 29000 0.98739892 0.24878333 0 1.230011 5.6749101 189.52855
- 30000 1.0099165 0.22964407 0 1.2332486 5.3791167 189.52855
- 31000 0.93350481 0.2879577 0 1.2156281 6.2148818 189.52855
- 32000 0.99089487 0.22340991 0 1.2081117 5.639 189.52855
- 33000 0.89519123 0.26943351 0 1.1590298 6.3869898 189.52855
- 34000 0.891093 0.28473528 0 1.1702589 6.0284238 189.52855
- 35000 0.83575157 0.25811245 0 1.0886406 6.4030425 189.52855
- 36000 0.81108815 0.26558543 0 1.0716043 6.3037393 189.52855
- 37000 0.92476501 0.18404704 0 1.1030323 5.3793557 189.52855
- 38000 0.85121163 0.2792429 0 1.1251345 5.9668051 189.52855
- 39000 0.90345348 0.2399627 0 1.1377696 6.1440023 189.52855
- 40000 0.93871579 0.2217328 0 1.1545816 4.9454727 189.52855
- 41000 1.0132854 0.25226008 0 1.2592124 6.2541531 189.52855
- 42000 0.98600788 0.27213553 0 1.2519809 6.0321859 189.52855
- 43000 1.0635948 0.27086236 0 1.3278097 6.6622232 189.52855
- 44000 1.0332292 0.36613701 0 1.3929085 7.4935675 189.52855
- 45000 1.1168224 0.3374366 0 1.4472788 7.3625776 189.52855
- 46000 1.0725949 0.37916007 0 1.4450513 6.8897095 189.52855
- 47000 1.0940234 0.35474661 0 1.4419324 7.4781317 189.52855
- 48000 1.1093597 0.26705754 0 1.3694837 5.8401116 189.52855
- 49000 1.0803976 0.29555751 0 1.3692026 6.4769008 189.52855
- 50000 1.0150244 0.29822696 0 1.3069075 6.4417197 189.52855
-Loop time of 0.89762 on 4 procs for 50000 steps with 160 atoms
-
-Performance: 24063642.337 tau/day, 55702.876 timesteps/s
-99.3% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.049302 | 0.050204 | 0.051269 | 0.3 | 5.59
-Neigh | 0.047954 | 0.048719 | 0.049847 | 0.3 | 5.43
-Comm | 0.32267 | 0.33536 | 0.34668 | 1.5 | 37.36
-Output | 0.00076675 | 0.00081015 | 0.00093508 | 0.3 | 0.09
-Modify | 0.30312 | 0.31088 | 0.31853 | 1.0 | 34.63
-Other | | 0.1516 | | | 16.89
-
-Nlocal: 40 ave 42 max 38 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Nghost: 35.5 ave 37 max 34 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Neighs: 88.75 ave 96 max 79 min
-Histogram: 1 0 1 0 0 0 0 0 0 2
-
-Total # of neighbors = 355
-Ave neighs/atom = 2.21875
-Neighbor list builds = 5284
-Dangerous builds = 0
-Total wall time: 0:00:00
diff --git a/examples/obstacle/log.5Oct16.obstacle.g++.1 b/examples/obstacle/log.27Nov18.obstacle.g++.1
similarity index 82%
rename from examples/obstacle/log.5Oct16.obstacle.g++.1
rename to examples/obstacle/log.27Nov18.obstacle.g++.1
index 7d1a1a8c7dcd7d671e2120f3720a695c37f03c30..68db45ee7e51b3844745bc084d41264938c25839 100644
--- a/examples/obstacle/log.5Oct16.obstacle.g++.1
+++ b/examples/obstacle/log.27Nov18.obstacle.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 2d LJ obstacle flow
dimension 2
@@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 840 atoms
+ Time spent = 0.0004704 secs
mass 1 1.0
mass 2 1.0
@@ -80,7 +82,7 @@ fix 9 all enforce2d
timestep 0.003
thermo 1000
thermo_modify temp mobile
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
#dump 1 all atom 100 dump.obstacle
@@ -92,13 +94,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474
run 25000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
- binsize = 0.71123 -> bins = 73 32 1
-Memory usage per processor = 2.47903 Mbytes
+ binsize = 0.71123, bins = 73 32 1
+ 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/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.055 | 3.055 | 3.055 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0027471 0 0 0.68849216 0.46317653 1143.0857
1000 1 -0.33689286 0 0.34971312 1.2905426 1286.7728
@@ -126,20 +133,20 @@ Step Temp E_pair E_mol TotEng Press Volume
23000 1 -0.39249509 0 0.29411089 0.97187435 1459.6771
24000 1 -0.33410442 0 0.35250156 0.93960021 1463.5903
25000 1 -0.37437615 0 0.31222983 0.9644765 1464.9391
-Loop time of 1.64517 on 1 procs for 25000 steps with 769 atoms
+Loop time of 1.98053 on 1 procs for 25000 steps with 769 atoms
-Performance: 3938793.608 tau/day, 15195.963 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 3271856.949 tau/day, 12622.905 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 | 0.5054 | 0.5054 | 0.5054 | 0.0 | 30.72
-Neigh | 0.17887 | 0.17887 | 0.17887 | 0.0 | 10.87
-Comm | 0.022527 | 0.022527 | 0.022527 | 0.0 | 1.37
-Output | 0.00023794 | 0.00023794 | 0.00023794 | 0.0 | 0.01
-Modify | 0.85127 | 0.85127 | 0.85127 | 0.0 | 51.74
-Other | | 0.08687 | | | 5.28
+Pair | 0.46219 | 0.46219 | 0.46219 | 0.0 | 23.34
+Neigh | 0.17 | 0.17 | 0.17 | 0.0 | 8.58
+Comm | 0.029093 | 0.029093 | 0.029093 | 0.0 | 1.47
+Output | 0.00041389 | 0.00041389 | 0.00041389 | 0.0 | 0.02
+Modify | 1.22 | 1.22 | 1.22 | 0.0 | 61.60
+Other | | 0.09888 | | | 4.99
Nlocal: 769 ave 769 max 769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/obstacle/log.5Oct16.obstacle.g++.4 b/examples/obstacle/log.27Nov18.obstacle.g++.4
similarity index 82%
rename from examples/obstacle/log.5Oct16.obstacle.g++.4
rename to examples/obstacle/log.27Nov18.obstacle.g++.4
index 5bd84740e4c12133b94e65ab231999fe61661fc5..ed80fabf9b2e76c6a143c293efabb665e70fb098 100644
--- a/examples/obstacle/log.5Oct16.obstacle.g++.4
+++ b/examples/obstacle/log.27Nov18.obstacle.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (27 Nov 2018)
+ using 1 OpenMP thread(s) per MPI task
# 2d LJ obstacle flow
dimension 2
@@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 840 atoms
+ Time spent = 0.000343561 secs
mass 1 1.0
mass 2 1.0
@@ -80,7 +82,7 @@ fix 9 all enforce2d
timestep 0.003
thermo 1000
thermo_modify temp mobile
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
+WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
#dump 1 all atom 100 dump.obstacle
@@ -92,13 +94,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474
run 25000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
- binsize = 0.71123 -> bins = 73 32 1
-Memory usage per processor = 2.47142 Mbytes
+ binsize = 0.71123, bins = 73 32 1
+ 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/2d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.043 | 3.043 | 3.043 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0004177 0 0 0.68689281 0.46210058 1143.0857
1000 1 -0.32494012 0 0.36166587 1.2240503 1282.5239
@@ -126,20 +133,20 @@ Step Temp E_pair E_mol TotEng Press Volume
23000 1 -0.37327871 0 0.31332728 1.0623185 1453.1342
24000 1 -0.40040333 0 0.28620265 0.94983886 1459.4461
25000 1 -0.37645924 0 0.31014674 1.0526044 1458.7191
-Loop time of 0.821326 on 4 procs for 25000 steps with 769 atoms
+Loop time of 0.950647 on 4 procs for 25000 steps with 769 atoms
-Performance: 7889678.376 tau/day, 30438.574 timesteps/s
-99.4% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 6816413.742 tau/day, 26297.893 timesteps/s
+95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.064561 | 0.12703 | 0.20657 | 15.5 | 15.47
-Neigh | 0.036315 | 0.04798 | 0.06249 | 4.4 | 5.84
-Comm | 0.14793 | 0.21791 | 0.27951 | 10.6 | 26.53
-Output | 0.00043583 | 0.00046438 | 0.00054574 | 0.2 | 0.06
-Modify | 0.27754 | 0.31239 | 0.3371 | 3.9 | 38.03
-Other | | 0.1156 | | | 14.07
+Pair | 0.068658 | 0.11988 | 0.18819 | 13.5 | 12.61
+Neigh | 0.034307 | 0.046836 | 0.063159 | 5.0 | 4.93
+Comm | 0.1325 | 0.21714 | 0.27078 | 11.3 | 22.84
+Output | 0.00052547 | 0.00096804 | 0.0022867 | 0.0 | 0.10
+Modify | 0.37752 | 0.41834 | 0.48768 | 6.5 | 44.01
+Other | | 0.1475 | | | 15.51
Nlocal: 192.25 ave 243 max 151 min
Histogram: 1 1 0 0 0 0 1 0 0 1