diff --git a/bench/log.15Feb16.chain.fixed.icc.1 b/bench/log.6Oct16.chain.fixed.icc.1
similarity index 71%
rename from bench/log.15Feb16.chain.fixed.icc.1
rename to bench/log.6Oct16.chain.fixed.icc.1
index 553241bf22..d1279b8ca1 100644
--- a/bench/log.15Feb16.chain.fixed.icc.1
+++ b/bench/log.6Oct16.chain.fixed.icc.1
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# FENE beadspring benchmark
units lj
@@ -43,25 +43,25 @@ Neighbor list info ...
master list distance cutoff = 1.52
ghost atom cutoff = 1.52
binsize = 0.76 -> bins = 45 45 45
-Memory usage per processor = 11.5189 Mbytes
+Memory usage per processor = 12.0423 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9729966 0.4361122 20.507698 22.40326 4.6548819
-Loop time of 0.978585 on 1 procs for 100 steps with 32000 atoms
+Loop time of 0.977647 on 1 procs for 100 steps with 32000 atoms
-Performance: 105948.895 tau/day, 102.188 timesteps/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 106050.541 tau/day, 102.286 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 | 0.19562 | 0.19562 | 0.19562 | 0.0 | 19.99
-Bond | 0.087475 | 0.087475 | 0.087475 | 0.0 | 8.94
-Neigh | 0.44861 | 0.44861 | 0.44861 | 0.0 | 45.84
-Comm | 0.032932 | 0.032932 | 0.032932 | 0.0 | 3.37
-Output | 0.00010395 | 0.00010395 | 0.00010395 | 0.0 | 0.01
-Modify | 0.19413 | 0.19413 | 0.19413 | 0.0 | 19.84
-Other | | 0.01972 | | | 2.02
+Pair | 0.19421 | 0.19421 | 0.19421 | 0.0 | 19.86
+Bond | 0.08741 | 0.08741 | 0.08741 | 0.0 | 8.94
+Neigh | 0.45791 | 0.45791 | 0.45791 | 0.0 | 46.84
+Comm | 0.032649 | 0.032649 | 0.032649 | 0.0 | 3.34
+Output | 0.00012207 | 0.00012207 | 0.00012207 | 0.0 | 0.01
+Modify | 0.18071 | 0.18071 | 0.18071 | 0.0 | 18.48
+Other | | 0.02464 | | | 2.52
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/bench/log.15Feb16.chain.fixed.icc.4 b/bench/log.6Oct16.chain.fixed.icc.4
similarity index 71%
rename from bench/log.15Feb16.chain.fixed.icc.4
rename to bench/log.6Oct16.chain.fixed.icc.4
index 1ff445b27a..ce088d20a6 100644
--- a/bench/log.15Feb16.chain.fixed.icc.4
+++ b/bench/log.6Oct16.chain.fixed.icc.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# FENE beadspring benchmark
units lj
@@ -43,25 +43,25 @@ Neighbor list info ...
master list distance cutoff = 1.52
ghost atom cutoff = 1.52
binsize = 0.76 -> bins = 45 45 45
-Memory usage per processor = 3.91518 Mbytes
+Memory usage per processor = 4.14663 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.97145835 0.43803883 20.502691 22.397872 4.626988
-Loop time of 0.271187 on 4 procs for 100 steps with 32000 atoms
+Loop time of 0.269205 on 4 procs for 100 steps with 32000 atoms
-Performance: 382319.453 tau/day, 368.749 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 385133.446 tau/day, 371.464 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.048621 | 0.050076 | 0.051229 | 0.4 | 18.47
-Bond | 0.022254 | 0.022942 | 0.023567 | 0.3 | 8.46
-Neigh | 0.11873 | 0.11881 | 0.11887 | 0.0 | 43.81
-Comm | 0.019066 | 0.021357 | 0.024297 | 1.3 | 7.88
-Output | 5.0068e-05 | 5.5015e-05 | 6.1035e-05 | 0.1 | 0.02
-Modify | 0.048737 | 0.050198 | 0.051231 | 0.4 | 18.51
-Other | | 0.007751 | | | 2.86
+Pair | 0.049383 | 0.049756 | 0.049988 | 0.1 | 18.48
+Bond | 0.022701 | 0.022813 | 0.022872 | 0.0 | 8.47
+Neigh | 0.11982 | 0.12002 | 0.12018 | 0.0 | 44.58
+Comm | 0.020274 | 0.021077 | 0.022348 | 0.5 | 7.83
+Output | 5.3167e-05 | 5.6148e-05 | 6.3181e-05 | 0.1 | 0.02
+Modify | 0.046276 | 0.046809 | 0.047016 | 0.1 | 17.39
+Other | | 0.008669 | | | 3.22
Nlocal: 8000 ave 8030 max 7974 min
Histogram: 1 0 0 1 0 1 0 0 0 1
diff --git a/bench/log.15Feb16.chain.scaled.icc.4 b/bench/log.6Oct16.chain.scaled.icc.4
similarity index 74%
rename from bench/log.15Feb16.chain.scaled.icc.4
rename to bench/log.6Oct16.chain.scaled.icc.4
index df541d404c..2f2d47d78b 100644
--- a/bench/log.15Feb16.chain.scaled.icc.4
+++ b/bench/log.6Oct16.chain.scaled.icc.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# FENE beadspring benchmark
variable x index 1
@@ -59,25 +59,25 @@ Neighbor list info ...
master list distance cutoff = 1.52
ghost atom cutoff = 1.52
binsize = 0.76 -> bins = 89 89 45
-Memory usage per processor = 12.8735 Mbytes
+Memory usage per processor = 13.2993 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97027498 0.44484087 20.494523 22.394765 4.6721833
100 0.97682955 0.44239968 20.500229 22.407862 4.6527025
-Loop time of 1.20889 on 4 procs for 100 steps with 128000 atoms
+Loop time of 1.14845 on 4 procs for 100 steps with 128000 atoms
-Performance: 85764.410 tau/day, 82.720 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 90277.919 tau/day, 87.074 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.21738 | 0.23306 | 0.23926 | 1.9 | 19.28
-Bond | 0.094536 | 0.10196 | 0.10534 | 1.4 | 8.43
-Neigh | 0.52311 | 0.52392 | 0.52519 | 0.1 | 43.34
-Comm | 0.090161 | 0.10022 | 0.12557 | 4.7 | 8.29
-Output | 0.00012207 | 0.00017327 | 0.00019598 | 0.2 | 0.01
-Modify | 0.19662 | 0.20262 | 0.20672 | 0.8 | 16.76
-Other | | 0.04694 | | | 3.88
+Pair | 0.2203 | 0.22207 | 0.22386 | 0.3 | 19.34
+Bond | 0.094861 | 0.095302 | 0.095988 | 0.1 | 8.30
+Neigh | 0.52127 | 0.5216 | 0.52189 | 0.0 | 45.42
+Comm | 0.079585 | 0.082159 | 0.084366 | 0.7 | 7.15
+Output | 0.00013304 | 0.00015306 | 0.00018501 | 0.2 | 0.01
+Modify | 0.18351 | 0.18419 | 0.1856 | 0.2 | 16.04
+Other | | 0.04298 | | | 3.74
Nlocal: 32000 ave 32015 max 31983 min
Histogram: 1 0 1 0 0 0 0 0 1 1
diff --git a/bench/log.15Feb16.chute.fixed.icc.1 b/bench/log.6Oct16.chute.fixed.icc.1
similarity index 72%
rename from bench/log.15Feb16.chute.fixed.icc.1
rename to bench/log.6Oct16.chute.fixed.icc.1
index e256524152..9f53d44092 100644
--- a/bench/log.15Feb16.chute.fixed.icc.1
+++ b/bench/log.6Oct16.chute.fixed.icc.1
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@@ -47,24 +47,24 @@ Neighbor list info ...
master list distance cutoff = 1.1
ghost atom cutoff = 1.1
binsize = 0.55 -> bins = 73 37 68
-Memory usage per processor = 15.567 Mbytes
-Step Atoms KinEng 1 Volume
+Memory usage per processor = 16.0904 Mbytes
+Step Atoms KinEng c_1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
-Loop time of 0.550482 on 1 procs for 100 steps with 32000 atoms
+Loop time of 0.534174 on 1 procs for 100 steps with 32000 atoms
-Performance: 1569.534 tau/day, 181.659 timesteps/s
-100.1% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1617.451 tau/day, 187.205 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.33849 | 0.33849 | 0.33849 | 0.0 | 61.49
-Neigh | 0.040353 | 0.040353 | 0.040353 | 0.0 | 7.33
-Comm | 0.018023 | 0.018023 | 0.018023 | 0.0 | 3.27
-Output | 0.00020385 | 0.00020385 | 0.00020385 | 0.0 | 0.04
-Modify | 0.13155 | 0.13155 | 0.13155 | 0.0 | 23.90
-Other | | 0.02186 | | | 3.97
+Pair | 0.33346 | 0.33346 | 0.33346 | 0.0 | 62.43
+Neigh | 0.043902 | 0.043902 | 0.043902 | 0.0 | 8.22
+Comm | 0.018391 | 0.018391 | 0.018391 | 0.0 | 3.44
+Output | 0.00022411 | 0.00022411 | 0.00022411 | 0.0 | 0.04
+Modify | 0.11666 | 0.11666 | 0.11666 | 0.0 | 21.84
+Other | | 0.02153 | | | 4.03
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/bench/log.15Feb16.chute.fixed.icc.4 b/bench/log.6Oct16.chute.fixed.icc.4
similarity index 72%
rename from bench/log.15Feb16.chute.fixed.icc.4
rename to bench/log.6Oct16.chute.fixed.icc.4
index 8252408833..a75a7c1f01 100644
--- a/bench/log.15Feb16.chute.fixed.icc.4
+++ b/bench/log.6Oct16.chute.fixed.icc.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@@ -47,24 +47,24 @@ Neighbor list info ...
master list distance cutoff = 1.1
ghost atom cutoff = 1.1
binsize = 0.55 -> bins = 73 37 68
-Memory usage per processor = 6.81783 Mbytes
-Step Atoms KinEng 1 Volume
+Memory usage per processor = 7.04927 Mbytes
+Step Atoms KinEng c_1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
-Loop time of 0.13141 on 4 procs for 100 steps with 32000 atoms
+Loop time of 0.171815 on 4 procs for 100 steps with 32000 atoms
-Performance: 6574.833 tau/day, 760.976 timesteps/s
-99.3% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 5028.653 tau/day, 582.020 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.062505 | 0.067 | 0.07152 | 1.5 | 50.99
-Neigh | 0.010041 | 0.0101 | 0.010178 | 0.1 | 7.69
-Comm | 0.012347 | 0.012895 | 0.013444 | 0.5 | 9.81
-Output | 6.3896e-05 | 0.00010294 | 0.00014091 | 0.3 | 0.08
-Modify | 0.031802 | 0.032348 | 0.032897 | 0.3 | 24.62
-Other | | 0.008965 | | | 6.82
+Pair | 0.093691 | 0.096898 | 0.10005 | 0.8 | 56.40
+Neigh | 0.011976 | 0.012059 | 0.012146 | 0.1 | 7.02
+Comm | 0.016384 | 0.017418 | 0.018465 | 0.8 | 10.14
+Output | 7.7963e-05 | 0.00010747 | 0.00013304 | 0.2 | 0.06
+Modify | 0.031744 | 0.031943 | 0.032167 | 0.1 | 18.59
+Other | | 0.01339 | | | 7.79
Nlocal: 8000 ave 8008 max 7992 min
Histogram: 2 0 0 0 0 0 0 0 0 2
diff --git a/bench/log.15Feb16.chute.scaled.icc.4 b/bench/log.6Oct16.chute.scaled.icc.4
similarity index 73%
rename from bench/log.15Feb16.chute.scaled.icc.4
rename to bench/log.6Oct16.chute.scaled.icc.4
index 0b9807a447..0538e9fbe5 100644
--- a/bench/log.15Feb16.chute.scaled.icc.4
+++ b/bench/log.6Oct16.chute.scaled.icc.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@@ -57,24 +57,24 @@ Neighbor list info ...
master list distance cutoff = 1.1
ghost atom cutoff = 1.1
binsize = 0.55 -> bins = 146 73 68
-Memory usage per processor = 15.7007 Mbytes
-Step Atoms KinEng 1 Volume
+Memory usage per processor = 16.1265 Mbytes
+Step Atoms KinEng c_1 Volume
0 128000 3136556.5 6404.5051 119335.13
100 128000 3137168.3 6284.3873 119338.83
-Loop time of 0.906913 on 4 procs for 100 steps with 128000 atoms
+Loop time of 0.832365 on 4 procs for 100 steps with 128000 atoms
-Performance: 952.683 tau/day, 110.264 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 1038.006 tau/day, 120.140 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.51454 | 0.53094 | 0.55381 | 2.0 | 58.54
-Neigh | 0.042597 | 0.043726 | 0.045801 | 0.6 | 4.82
-Comm | 0.063027 | 0.064657 | 0.067367 | 0.7 | 7.13
-Output | 0.00024891 | 0.00059718 | 0.00086498 | 1.0 | 0.07
-Modify | 0.16508 | 0.17656 | 0.1925 | 2.6 | 19.47
-Other | | 0.09043 | | | 9.97
+Pair | 0.5178 | 0.52208 | 0.52793 | 0.5 | 62.72
+Neigh | 0.047003 | 0.047113 | 0.047224 | 0.0 | 5.66
+Comm | 0.05233 | 0.052988 | 0.053722 | 0.2 | 6.37
+Output | 0.00024986 | 0.00032717 | 0.00036693 | 0.3 | 0.04
+Modify | 0.15517 | 0.15627 | 0.15808 | 0.3 | 18.77
+Other | | 0.0536 | | | 6.44
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -87,4 +87,4 @@ Total # of neighbors = 460532
Ave neighs/atom = 3.59791
Neighbor list builds = 2
Dangerous builds = 0
-Total wall time: 0:00:01
+Total wall time: 0:00:00
diff --git a/bench/log.15Feb16.eam.fixed.icc.1 b/bench/log.6Oct16.eam.fixed.icc.1
similarity index 77%
rename from bench/log.15Feb16.eam.fixed.icc.1
rename to bench/log.6Oct16.eam.fixed.icc.1
index 0408d2c8d7..f5ddfcde0d 100644
--- a/bench/log.15Feb16.eam.fixed.icc.1
+++ b/bench/log.6Oct16.eam.fixed.icc.1
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# bulk Cu lattice
variable x index 1
@@ -49,25 +49,25 @@ Neighbor list info ...
master list distance cutoff = 5.95
ghost atom cutoff = 5.95
binsize = 2.975 -> bins = 25 25 25
-Memory usage per processor = 10.2238 Mbytes
+Memory usage per processor = 11.2238 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
50 781.69049 -109873.35 0 -106640.13 52273.088
100 801.832 -109957.3 0 -106640.77 51322.821
-Loop time of 5.90097 on 1 procs for 100 steps with 32000 atoms
+Loop time of 5.96529 on 1 procs for 100 steps with 32000 atoms
-Performance: 7.321 ns/day, 3.278 hours/ns, 16.946 timesteps/s
+Performance: 7.242 ns/day, 3.314 hours/ns, 16.764 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 | 5.2121 | 5.2121 | 5.2121 | 0.0 | 88.33
-Neigh | 0.58212 | 0.58212 | 0.58212 | 0.0 | 9.86
-Comm | 0.030392 | 0.030392 | 0.030392 | 0.0 | 0.52
-Output | 0.00023389 | 0.00023389 | 0.00023389 | 0.0 | 0.00
-Modify | 0.060871 | 0.060871 | 0.060871 | 0.0 | 1.03
-Other | | 0.01527 | | | 0.26
+Pair | 5.2743 | 5.2743 | 5.2743 | 0.0 | 88.42
+Neigh | 0.59212 | 0.59212 | 0.59212 | 0.0 | 9.93
+Comm | 0.030399 | 0.030399 | 0.030399 | 0.0 | 0.51
+Output | 0.00026202 | 0.00026202 | 0.00026202 | 0.0 | 0.00
+Modify | 0.050487 | 0.050487 | 0.050487 | 0.0 | 0.85
+Other | | 0.01776 | | | 0.30
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/bench/log.15Feb16.eam.fixed.icc.4 b/bench/log.6Oct16.eam.fixed.icc.4
similarity index 77%
rename from bench/log.15Feb16.eam.fixed.icc.4
rename to bench/log.6Oct16.eam.fixed.icc.4
index 6a7c47a58b..3414210acf 100644
--- a/bench/log.15Feb16.eam.fixed.icc.4
+++ b/bench/log.6Oct16.eam.fixed.icc.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# bulk Cu lattice
variable x index 1
@@ -49,25 +49,25 @@ Neighbor list info ...
master list distance cutoff = 5.95
ghost atom cutoff = 5.95
binsize = 2.975 -> bins = 25 25 25
-Memory usage per processor = 5.09629 Mbytes
+Memory usage per processor = 5.59629 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
50 781.69049 -109873.35 0 -106640.13 52273.088
100 801.832 -109957.3 0 -106640.77 51322.821
-Loop time of 1.58019 on 4 procs for 100 steps with 32000 atoms
+Loop time of 1.64562 on 4 procs for 100 steps with 32000 atoms
-Performance: 27.338 ns/day, 0.878 hours/ns, 63.284 timesteps/s
+Performance: 26.252 ns/day, 0.914 hours/ns, 60.767 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 1.3617 | 1.366 | 1.3723 | 0.4 | 86.45
-Neigh | 0.15123 | 0.15232 | 0.15374 | 0.2 | 9.64
-Comm | 0.033429 | 0.041275 | 0.047066 | 2.7 | 2.61
-Output | 0.00011301 | 0.0001573 | 0.000211 | 0.3 | 0.01
-Modify | 0.014694 | 0.015085 | 0.015421 | 0.2 | 0.95
-Other | | 0.005342 | | | 0.34
+Pair | 1.408 | 1.4175 | 1.4341 | 0.9 | 86.14
+Neigh | 0.15512 | 0.15722 | 0.16112 | 0.6 | 9.55
+Comm | 0.029105 | 0.049986 | 0.061822 | 5.8 | 3.04
+Output | 0.00010991 | 0.00011539 | 0.00012302 | 0.0 | 0.01
+Modify | 0.013383 | 0.013573 | 0.013883 | 0.2 | 0.82
+Other | | 0.007264 | | | 0.44
Nlocal: 8000 ave 8008 max 7993 min
Histogram: 2 0 0 0 0 0 0 0 1 1
diff --git a/bench/log.15Feb16.eam.scaled.icc.4 b/bench/log.6Oct16.eam.scaled.icc.4
similarity index 77%
rename from bench/log.15Feb16.eam.scaled.icc.4
rename to bench/log.6Oct16.eam.scaled.icc.4
index 2c1cd3273e..8a2ec90b78 100644
--- a/bench/log.15Feb16.eam.scaled.icc.4
+++ b/bench/log.6Oct16.eam.scaled.icc.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# bulk Cu lattice
variable x index 1
@@ -49,25 +49,25 @@ Neighbor list info ...
master list distance cutoff = 5.95
ghost atom cutoff = 5.95
binsize = 2.975 -> bins = 49 49 25
-Memory usage per processor = 10.1402 Mbytes
+Memory usage per processor = 11.1402 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -453120 0 -426647.73 18704.012
50 779.50001 -439457.02 0 -426560.06 52355.276
100 797.97828 -439764.76 0 -426562.07 51474.74
-Loop time of 6.46849 on 4 procs for 100 steps with 128000 atoms
+Loop time of 6.60121 on 4 procs for 100 steps with 128000 atoms
-Performance: 6.679 ns/day, 3.594 hours/ns, 15.460 timesteps/s
+Performance: 6.544 ns/day, 3.667 hours/ns, 15.149 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 5.581 | 5.5997 | 5.6265 | 0.8 | 86.57
-Neigh | 0.65287 | 0.658 | 0.66374 | 0.5 | 10.17
-Comm | 0.075706 | 0.11015 | 0.13655 | 7.2 | 1.70
-Output | 0.00026488 | 0.00028312 | 0.00029302 | 0.1 | 0.00
-Modify | 0.069607 | 0.072407 | 0.074555 | 0.7 | 1.12
-Other | | 0.02794 | | | 0.43
+Pair | 5.6676 | 5.7011 | 5.7469 | 1.3 | 86.36
+Neigh | 0.66423 | 0.67119 | 0.68082 | 0.7 | 10.17
+Comm | 0.079367 | 0.13668 | 0.1791 | 10.5 | 2.07
+Output | 0.00026989 | 0.00028622 | 0.00031209 | 0.1 | 0.00
+Modify | 0.060046 | 0.062203 | 0.065009 | 0.9 | 0.94
+Other | | 0.02974 | | | 0.45
Nlocal: 32000 ave 32092 max 31914 min
Histogram: 1 0 0 1 0 1 0 0 0 1
diff --git a/bench/log.15Feb16.lj.fixed.icc.1 b/bench/log.6Oct16.lj.fixed.icc.1
similarity index 78%
rename from bench/log.15Feb16.lj.fixed.icc.1
rename to bench/log.6Oct16.lj.fixed.icc.1
index e889fba225..b08ca3b6b8 100644
--- a/bench/log.15Feb16.lj.fixed.icc.1
+++ b/bench/log.6Oct16.lj.fixed.icc.1
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# 3d Lennard-Jones melt
variable x index 1
@@ -50,20 +50,20 @@ Memory usage per processor = 8.21387 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
-Loop time of 2.26309 on 1 procs for 100 steps with 32000 atoms
+Loop time of 2.26185 on 1 procs for 100 steps with 32000 atoms
-Performance: 19088.920 tau/day, 44.187 timesteps/s
+Performance: 19099.377 tau/day, 44.212 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 | 1.9341 | 1.9341 | 1.9341 | 0.0 | 85.46
-Neigh | 0.2442 | 0.2442 | 0.2442 | 0.0 | 10.79
-Comm | 0.024158 | 0.024158 | 0.024158 | 0.0 | 1.07
-Output | 0.00011611 | 0.00011611 | 0.00011611 | 0.0 | 0.01
-Modify | 0.053222 | 0.053222 | 0.053222 | 0.0 | 2.35
-Other | | 0.007258 | | | 0.32
+Pair | 1.9328 | 1.9328 | 1.9328 | 0.0 | 85.45
+Neigh | 0.2558 | 0.2558 | 0.2558 | 0.0 | 11.31
+Comm | 0.024061 | 0.024061 | 0.024061 | 0.0 | 1.06
+Output | 0.00012612 | 0.00012612 | 0.00012612 | 0.0 | 0.01
+Modify | 0.040887 | 0.040887 | 0.040887 | 0.0 | 1.81
+Other | | 0.008214 | | | 0.36
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/bench/log.15Feb16.lj.fixed.icc.4 b/bench/log.6Oct16.lj.fixed.icc.4
similarity index 76%
rename from bench/log.15Feb16.lj.fixed.icc.4
rename to bench/log.6Oct16.lj.fixed.icc.4
index 53cdcdbee6..9eee300a94 100644
--- a/bench/log.15Feb16.lj.fixed.icc.4
+++ b/bench/log.6Oct16.lj.fixed.icc.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# 3d Lennard-Jones melt
variable x index 1
@@ -50,20 +50,20 @@ Memory usage per processor = 4.09506 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
-Loop time of 0.640733 on 4 procs for 100 steps with 32000 atoms
+Loop time of 0.635957 on 4 procs for 100 steps with 32000 atoms
-Performance: 67422.779 tau/day, 156.071 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 67929.172 tau/day, 157.243 timesteps/s
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.49487 | 0.51733 | 0.5322 | 1.9 | 80.74
-Neigh | 0.061131 | 0.063685 | 0.065433 | 0.6 | 9.94
-Comm | 0.02457 | 0.042349 | 0.069598 | 8.1 | 6.61
-Output | 5.9843e-05 | 6.3181e-05 | 6.6996e-05 | 0.0 | 0.01
-Modify | 0.012961 | 0.013863 | 0.014491 | 0.5 | 2.16
-Other | | 0.003448 | | | 0.54
+Pair | 0.51335 | 0.51822 | 0.52569 | 0.7 | 81.49
+Neigh | 0.063695 | 0.064309 | 0.065397 | 0.3 | 10.11
+Comm | 0.027525 | 0.03629 | 0.041959 | 3.1 | 5.71
+Output | 6.3896e-05 | 6.6698e-05 | 7.081e-05 | 0.0 | 0.01
+Modify | 0.012472 | 0.01254 | 0.012618 | 0.1 | 1.97
+Other | | 0.004529 | | | 0.71
Nlocal: 8000 ave 8037 max 7964 min
Histogram: 2 0 0 0 0 0 0 0 1 1
diff --git a/bench/log.15Feb16.lj.scaled.icc.4 b/bench/log.6Oct16.lj.scaled.icc.4
similarity index 78%
rename from bench/log.15Feb16.lj.scaled.icc.4
rename to bench/log.6Oct16.lj.scaled.icc.4
index 7676040c54..4599879e59 100644
--- a/bench/log.15Feb16.lj.scaled.icc.4
+++ b/bench/log.6Oct16.lj.scaled.icc.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# 3d Lennard-Jones melt
variable x index 1
@@ -50,20 +50,20 @@ Memory usage per processor = 8.13678 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6133849 -5.0196788
100 0.75841891 -5.759957 0 -4.6223375 0.20008866
-Loop time of 2.57914 on 4 procs for 100 steps with 128000 atoms
+Loop time of 2.55762 on 4 procs for 100 steps with 128000 atoms
-Performance: 16749.768 tau/day, 38.773 timesteps/s
+Performance: 16890.677 tau/day, 39.099 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 2.042 | 2.1092 | 2.1668 | 3.1 | 81.78
-Neigh | 0.23982 | 0.24551 | 0.25233 | 1.0 | 9.52
-Comm | 0.067088 | 0.13887 | 0.22681 | 15.7 | 5.38
-Output | 0.00013185 | 0.00021666 | 0.00027108 | 0.4 | 0.01
-Modify | 0.060348 | 0.071269 | 0.077063 | 2.5 | 2.76
-Other | | 0.01403 | | | 0.54
+Pair | 2.0583 | 2.0988 | 2.1594 | 2.6 | 82.06
+Neigh | 0.24411 | 0.24838 | 0.25585 | 0.9 | 9.71
+Comm | 0.066397 | 0.13872 | 0.1863 | 11.9 | 5.42
+Output | 0.00012994 | 0.00021023 | 0.00025702 | 0.3 | 0.01
+Modify | 0.055533 | 0.058343 | 0.061791 | 1.2 | 2.28
+Other | | 0.0132 | | | 0.52
Nlocal: 32000 ave 32060 max 31939 min
Histogram: 1 0 1 0 0 0 0 1 0 1
diff --git a/bench/log.15Feb16.rhodo.fixed.icc.1 b/bench/log.6Oct16.rhodo.fixed.icc.1
similarity index 63%
rename from bench/log.15Feb16.rhodo.fixed.icc.1
rename to bench/log.6Oct16.rhodo.fixed.icc.1
index 994c69e585..65596d3285 100644
--- a/bench/log.15Feb16.rhodo.fixed.icc.1
+++ b/bench/log.6Oct16.rhodo.fixed.icc.1
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# Rhodopsin model
units real
@@ -56,6 +56,7 @@ timestep 2.0
run 100
PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.248835
grid = 25 32 32
stencil order = 5
@@ -70,41 +71,41 @@ Neighbor list info ...
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 10 13 13
-Memory usage per processor = 91.7487 Mbytes
+Memory usage per processor = 93.2721 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
-E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035
+E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
Volume = 307995.0335
----------------- Step 50 ----- CPU = 17.6362 (sec) ----------------
-TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230
-PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975
-E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754
-E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701
-Volume = 308031.5639
----------------- Step 100 ----- CPU = 35.9089 (sec) ----------------
-TotEng = -25290.7593 KinEng = 21592.0117 Temp = 301.0920
-PotEng = -46882.7709 E_bond = 2567.9807 E_angle = 10781.9408
-E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783
-E_coul = 206659.2326 E_long = -270404.9733 Press = 6.9960
-Volume = 308133.9888
-Loop time of 35.9089 on 1 procs for 100 steps with 32000 atoms
+---------------- Step 50 ----- CPU = 17.2007 (sec) ----------------
+TotEng = -25330.0321 KinEng = 21501.0036 Temp = 299.8230
+PotEng = -46831.0357 E_bond = 2471.7033 E_angle = 10836.5108
+E_dihed = 5239.6316 E_impro = 227.1219 E_vdwl = -1993.2763
+E_coul = 206797.6655 E_long = -270410.3927 Press = 237.6866
+Volume = 308031.5640
+---------------- Step 100 ----- CPU = 35.0315 (sec) ----------------
+TotEng = -25290.7387 KinEng = 21591.9096 Temp = 301.0906
+PotEng = -46882.6484 E_bond = 2567.9789 E_angle = 10781.9556
+E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
+E_coul = 206659.5006 E_long = -270404.9733 Press = 6.7898
+Volume = 308133.9933
+Loop time of 35.0316 on 1 procs for 100 steps with 32000 atoms
-Performance: 0.481 ns/day, 49.874 hours/ns, 2.785 timesteps/s
+Performance: 0.493 ns/day, 48.655 hours/ns, 2.855 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 | 25.731 | 25.731 | 25.731 | 0.0 | 71.66
-Bond | 1.2771 | 1.2771 | 1.2771 | 0.0 | 3.56
-Kspace | 3.2094 | 3.2094 | 3.2094 | 0.0 | 8.94
-Neigh | 4.4538 | 4.4538 | 4.4538 | 0.0 | 12.40
-Comm | 0.068507 | 0.068507 | 0.068507 | 0.0 | 0.19
-Output | 0.00025916 | 0.00025916 | 0.00025916 | 0.0 | 0.00
-Modify | 1.1417 | 1.1417 | 1.1417 | 0.0 | 3.18
-Other | | 0.027 | | | 0.08
+Pair | 25.021 | 25.021 | 25.021 | 0.0 | 71.42
+Bond | 1.2834 | 1.2834 | 1.2834 | 0.0 | 3.66
+Kspace | 3.2116 | 3.2116 | 3.2116 | 0.0 | 9.17
+Neigh | 4.2767 | 4.2767 | 4.2767 | 0.0 | 12.21
+Comm | 0.069283 | 0.069283 | 0.069283 | 0.0 | 0.20
+Output | 0.00028205 | 0.00028205 | 0.00028205 | 0.0 | 0.00
+Modify | 1.14 | 1.14 | 1.14 | 0.0 | 3.25
+Other | | 0.02938 | | | 0.08
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -113,9 +114,9 @@ Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 12028107
+Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
-Total wall time: 0:00:37
+Total wall time: 0:00:36
diff --git a/bench/log.15Feb16.rhodo.fixed.icc.4 b/bench/log.6Oct16.rhodo.fixed.icc.4
similarity index 60%
rename from bench/log.15Feb16.rhodo.fixed.icc.4
rename to bench/log.6Oct16.rhodo.fixed.icc.4
index dfa5b065f9..50526063f1 100644
--- a/bench/log.15Feb16.rhodo.fixed.icc.4
+++ b/bench/log.6Oct16.rhodo.fixed.icc.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# Rhodopsin model
units real
@@ -56,6 +56,7 @@ timestep 2.0
run 100
PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.248835
grid = 25 32 32
stencil order = 5
@@ -70,52 +71,52 @@ Neighbor list info ...
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 10 13 13
-Memory usage per processor = 36.629 Mbytes
+Memory usage per processor = 37.3604 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
-E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035
+E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
Volume = 307995.0335
----------------- Step 50 ----- CPU = 4.7461 (sec) ----------------
-TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230
-PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975
-E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754
-E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701
-Volume = 308031.5639
----------------- Step 100 ----- CPU = 9.6332 (sec) ----------------
-TotEng = -25290.7591 KinEng = 21592.0117 Temp = 301.0920
-PotEng = -46882.7708 E_bond = 2567.9807 E_angle = 10781.9408
-E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783
-E_coul = 206659.2327 E_long = -270404.9733 Press = 6.9960
-Volume = 308133.9888
-Loop time of 9.63322 on 4 procs for 100 steps with 32000 atoms
+---------------- Step 50 ----- CPU = 4.6056 (sec) ----------------
+TotEng = -25330.0321 KinEng = 21501.0036 Temp = 299.8230
+PotEng = -46831.0357 E_bond = 2471.7033 E_angle = 10836.5108
+E_dihed = 5239.6316 E_impro = 227.1219 E_vdwl = -1993.2763
+E_coul = 206797.6655 E_long = -270410.3927 Press = 237.6866
+Volume = 308031.5640
+---------------- Step 100 ----- CPU = 9.3910 (sec) ----------------
+TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
+PotEng = -46882.6482 E_bond = 2567.9789 E_angle = 10781.9556
+E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
+E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
+Volume = 308133.9933
+Loop time of 9.39107 on 4 procs for 100 steps with 32000 atoms
-Performance: 1.794 ns/day, 13.379 hours/ns, 10.381 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 1.840 ns/day, 13.043 hours/ns, 10.648 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 6.4364 | 6.5993 | 6.7208 | 4.7 | 68.51
-Bond | 0.30755 | 0.32435 | 0.35704 | 3.4 | 3.37
-Kspace | 0.92248 | 1.0782 | 1.2597 | 13.0 | 11.19
-Neigh | 1.1669 | 1.1672 | 1.1675 | 0.0 | 12.12
-Comm | 0.094674 | 0.098065 | 0.10543 | 1.4 | 1.02
-Output | 0.00015521 | 0.00016224 | 0.00018215 | 0.1 | 0.00
-Modify | 0.32982 | 0.34654 | 0.35365 | 1.6 | 3.60
-Other | | 0.01943 | | | 0.20
+Pair | 6.2189 | 6.3266 | 6.6072 | 6.5 | 67.37
+Bond | 0.30793 | 0.32122 | 0.3414 | 2.4 | 3.42
+Kspace | 0.87994 | 1.1644 | 1.2855 | 15.3 | 12.40
+Neigh | 1.1358 | 1.136 | 1.1362 | 0.0 | 12.10
+Comm | 0.08292 | 0.084935 | 0.087077 | 0.5 | 0.90
+Output | 0.00015712 | 0.00016558 | 0.00018501 | 0.1 | 0.00
+Modify | 0.33717 | 0.34246 | 0.34794 | 0.7 | 3.65
+Other | | 0.01526 | | | 0.16
Nlocal: 8000 ave 8143 max 7933 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 22733.5 ave 22769 max 22693 min
Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs: 3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
+Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
-Total # of neighbors = 12028107
+Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
-Total wall time: 0:00:10
+Total wall time: 0:00:09
diff --git a/bench/log.15Feb16.rhodo.scaled.icc.4 b/bench/log.6Oct16.rhodo.scaled.icc.4
similarity index 65%
rename from bench/log.15Feb16.rhodo.scaled.icc.4
rename to bench/log.6Oct16.rhodo.scaled.icc.4
index 73cdb163b0..db445ca72c 100644
--- a/bench/log.15Feb16.rhodo.scaled.icc.4
+++ b/bench/log.6Oct16.rhodo.scaled.icc.4
@@ -1,4 +1,4 @@
-LAMMPS (15 Feb 2016)
+LAMMPS (6 Oct 2016)
# Rhodopsin model
variable x index 1
@@ -77,6 +77,7 @@ timestep 2.0
run 100
PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.248593
grid = 48 60 36
stencil order = 5
@@ -91,52 +92,52 @@ Neighbor list info ...
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 19 26 13
-Memory usage per processor = 95.5339 Mbytes
+Memory usage per processor = 96.9597 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -101425.4887 KinEng = 85779.3251 Temp = 299.0304
PotEng = -187204.8138 E_bond = 10151.9760 E_angle = 43685.4968
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
-E_coul = 827053.5824 E_long = -1080565.6077 Press = -142.3092
+E_coul = 827053.5824 E_long = -1080565.6077 Press = -149.0358
Volume = 1231980.1340
----------------- Step 50 ----- CPU = 18.7806 (sec) ----------------
-TotEng = -101320.2677 KinEng = 86003.4837 Temp = 299.8118
-PotEng = -187323.7514 E_bond = 9887.1072 E_angle = 43346.7922
-E_dihed = 20958.7032 E_impro = 908.4715 E_vdwl = -7973.4457
-E_coul = 826141.3831 E_long = -1080592.7629 Press = 238.0161
-Volume = 1232126.1855
----------------- Step 100 ----- CPU = 38.3684 (sec) ----------------
-TotEng = -101158.1849 KinEng = 86355.6149 Temp = 301.0393
-PotEng = -187513.7998 E_bond = 10272.0693 E_angle = 43128.6454
-E_dihed = 20793.9759 E_impro = 867.0826 E_vdwl = -7586.7186
-E_coul = 825583.7122 E_long = -1080572.5667 Press = 15.2151
-Volume = 1232535.8423
-Loop time of 38.3684 on 4 procs for 100 steps with 128000 atoms
+---------------- Step 50 ----- CPU = 18.1689 (sec) ----------------
+TotEng = -101320.0211 KinEng = 86003.4933 Temp = 299.8118
+PotEng = -187323.5144 E_bond = 9887.1189 E_angle = 43346.8448
+E_dihed = 20958.7108 E_impro = 908.4721 E_vdwl = -7973.4486
+E_coul = 826141.5493 E_long = -1080592.7617 Press = 238.0404
+Volume = 1232126.1814
+---------------- Step 100 ----- CPU = 37.2027 (sec) ----------------
+TotEng = -101157.9546 KinEng = 86355.7413 Temp = 301.0398
+PotEng = -187513.6959 E_bond = 10272.0456 E_angle = 43128.7018
+E_dihed = 20794.0107 E_impro = 867.0928 E_vdwl = -7587.2409
+E_coul = 825584.2416 E_long = -1080572.5474 Press = 15.1729
+Volume = 1232535.8440
+Loop time of 37.2028 on 4 procs for 100 steps with 128000 atoms
-Performance: 0.450 ns/day, 53.289 hours/ns, 2.606 timesteps/s
+Performance: 0.464 ns/day, 51.671 hours/ns, 2.688 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 26.205 | 26.538 | 26.911 | 5.0 | 69.17
-Bond | 1.298 | 1.3125 | 1.3277 | 1.0 | 3.42
-Kspace | 3.7099 | 4.0992 | 4.4422 | 13.3 | 10.68
-Neigh | 4.6137 | 4.6144 | 4.615 | 0.0 | 12.03
-Comm | 0.21398 | 0.21992 | 0.22886 | 1.2 | 0.57
-Output | 0.00030518 | 0.00031543 | 0.00033307 | 0.1 | 0.00
-Modify | 1.5066 | 1.5232 | 1.5388 | 1.0 | 3.97
-Other | | 0.06051 | | | 0.16
+Pair | 25.431 | 25.738 | 25.984 | 4.0 | 69.18
+Bond | 1.2966 | 1.3131 | 1.3226 | 0.9 | 3.53
+Kspace | 3.7563 | 4.0123 | 4.3127 | 10.0 | 10.79
+Neigh | 4.3778 | 4.378 | 4.3782 | 0.0 | 11.77
+Comm | 0.1903 | 0.19549 | 0.20485 | 1.3 | 0.53
+Output | 0.00031805 | 0.00037521 | 0.00039601 | 0.2 | 0.00
+Modify | 1.4861 | 1.5051 | 1.5122 | 0.9 | 4.05
+Other | | 0.05992 | | | 0.16
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 47957 ave 47957 max 47957 min
Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs: 1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
+Neighs: 1.20281e+07 ave 1.20572e+07 max 1.19991e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2
-Total # of neighbors = 48112472
+Total # of neighbors = 48112540
Ave neighs/atom = 375.879
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
-Total wall time: 0:00:39
+Total wall time: 0:00:38
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 21cc9bcccc..471d3e48f4 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
LAMMPS Users Manual
-
+
@@ -21,7 +21,7 @@
LAMMPS Documentation :c,h3
-6 Oct 2016 version :c,h4
+11 Oct 2016 version :c,h4
Version info: :h4
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index 1a49917bdd..8647661210 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@@ -475,9 +475,6 @@ be generated by variable formulas that use comparison or Boolean math
operators or special functions like gmask() and rmask() and grmask().
See the "variable"_variable.html command doc page for details.
-NOTE: The LAST option, discussed below, is not yet implemented. It
-will be soon.
-
The specified value must be a simple numeric value or the word LAST.
If LAST is used, it refers to the value of the attribute the last time
the dump command was invoked to produce a snapshot. This is a way to
diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt
index 1f15169774..dbb4e2d499 100644
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@@ -191,13 +191,18 @@ input script should specify all fixes it will use. However, note that
some fixes store an internal "state" which is written to the restart
file. This allows the fix to continue on with its calculations in a
restarted simulation. To re-enable such a fix, the fix command in the
-new input script must use the same fix-ID and group-ID as was used in
-the input script that wrote the restart file. If a match is found,
-LAMMPS prints a message indicating that the fix is being re-enabled.
-If no match is found before the first run or minimization is performed
-by the new script, the "state" information for the saved fix is
-discarded. See the doc pages for individual fixes for info on which
-ones can be restarted in this manner.
+new input script must be of the same style and use the same fix-ID as
+was used in the input script that wrote the restart file.
+
+If a match is found, LAMMPS prints a message indicating that the fix
+is being re-enabled. If no match is found before the first run or
+minimization is performed by the new script, the "state" information
+for the saved fix is discarded. LAMMPS will also print a list of
+fixes for which the information is being discarded. See the doc pages
+for individual fixes for info on which ones can be restarted in this
+manner. Note that fixes which are created internally by other LAMMPS
+commands (computes, fixes, etc) will have style names which are
+all-capitalized, and IDs which are generated internally.
Likewise, the "computes"_fix.html used for a simulation are not stored
in the restart file. This means the new input script should specify
@@ -213,6 +218,14 @@ re-created fix will be re-enabled with the stored state information as
described in the previous paragraph, so that the compute can continue
its calculations in a consistent manner.
+NOTE: There are a handful of commands which can be used before or
+between runs which require a system initialization. Examples include
+the "balance", "displace_atoms", and "delete_atoms" commands. This is
+because they may migrate atoms to new processors. Thus they will also
+discard unused "state" information from fixes. This means that, if
+desired, you must re-specify the relevant fixes and computes (which
+create fixes) before those commands are used.
+
Some pair styles, like the "granular pair styles"_pair_gran.html, also
use a fix to store "state" information that persists from timestep to
timestep. In the case of granular potentials, it is contact
diff --git a/examples/ASPHERE/box/log.box.1Feb14 b/examples/ASPHERE/box/log.1Feb14.box.g++.8
similarity index 100%
rename from examples/ASPHERE/box/log.box.1Feb14
rename to examples/ASPHERE/box/log.1Feb14.box.g++.8
diff --git a/examples/ASPHERE/box/log.box.mp.1Feb14 b/examples/ASPHERE/box/log.1Feb14.box.mp.g++.8
similarity index 100%
rename from examples/ASPHERE/box/log.box.mp.1Feb14
rename to examples/ASPHERE/box/log.1Feb14.box.mp.g++.8
diff --git a/examples/ASPHERE/dimer/log.dimer.1Feb14 b/examples/ASPHERE/dimer/log.1Feb14.dimer.g++.8
similarity index 100%
rename from examples/ASPHERE/dimer/log.dimer.1Feb14
rename to examples/ASPHERE/dimer/log.1Feb14.dimer.g++.8
diff --git a/examples/ASPHERE/dimer/log.dimer.mp.1Feb14 b/examples/ASPHERE/dimer/log.1Feb14.dimer.mp.g++.8
similarity index 100%
rename from examples/ASPHERE/dimer/log.dimer.mp.1Feb14
rename to examples/ASPHERE/dimer/log.1Feb14.dimer.mp.g++.8
diff --git a/examples/ASPHERE/ellipsoid/log.ellipsoid.1Feb14 b/examples/ASPHERE/ellipsoid/log.1Feb14.ellipsoid.g++.8
similarity index 100%
rename from examples/ASPHERE/ellipsoid/log.ellipsoid.1Feb14
rename to examples/ASPHERE/ellipsoid/log.1Feb14.ellipsoid.g++.8
diff --git a/examples/ASPHERE/ellipsoid/log.ellipsoid.mp.1Feb14 b/examples/ASPHERE/ellipsoid/log.1Feb14.ellipsoid.mp.g++.8
similarity index 100%
rename from examples/ASPHERE/ellipsoid/log.ellipsoid.mp.1Feb14
rename to examples/ASPHERE/ellipsoid/log.1Feb14.ellipsoid.mp.g++.8
diff --git a/examples/ASPHERE/line/log.line.1Feb14 b/examples/ASPHERE/line/log.1Feb14.line.g++.8
similarity index 100%
rename from examples/ASPHERE/line/log.line.1Feb14
rename to examples/ASPHERE/line/log.1Feb14.line.g++.8
diff --git a/examples/ASPHERE/line/log.line.srd.1Feb14 b/examples/ASPHERE/line/log.1Feb14.line.srd.g++.8
similarity index 100%
rename from examples/ASPHERE/line/log.line.srd.1Feb14
rename to examples/ASPHERE/line/log.1Feb14.line.srd.g++.8
diff --git a/examples/ASPHERE/poly/log.poly.1Feb14 b/examples/ASPHERE/poly/log.1Feb14.poly.g++.8
similarity index 100%
rename from examples/ASPHERE/poly/log.poly.1Feb14
rename to examples/ASPHERE/poly/log.1Feb14.poly.g++.8
diff --git a/examples/ASPHERE/poly/log.poly.mp.1Feb14 b/examples/ASPHERE/poly/log.1Feb14.poly.mp.g++.8
similarity index 100%
rename from examples/ASPHERE/poly/log.poly.mp.1Feb14
rename to examples/ASPHERE/poly/log.1Feb14.poly.mp.g++.8
diff --git a/examples/ASPHERE/star/log.star.1Feb14 b/examples/ASPHERE/star/log.1Feb14.star.g++.8
similarity index 100%
rename from examples/ASPHERE/star/log.star.1Feb14
rename to examples/ASPHERE/star/log.1Feb14.star.g++.8
diff --git a/examples/ASPHERE/star/log.star.mp.1Feb14 b/examples/ASPHERE/star/log.1Feb14.star.mp.g++.8
similarity index 100%
rename from examples/ASPHERE/star/log.star.mp.1Feb14
rename to examples/ASPHERE/star/log.1Feb14.star.mp.g++.8
diff --git a/examples/ASPHERE/tri/log.tri.srd.1Feb14 b/examples/ASPHERE/tri/log.1Feb14.tri.srd.g++.8
similarity index 100%
rename from examples/ASPHERE/tri/log.tri.srd.1Feb14
rename to examples/ASPHERE/tri/log.1Feb14.tri.srd.g++.8
diff --git a/examples/DIFFUSE/log.msd.2d.1Feb14 b/examples/DIFFUSE/log.1Feb14.msd.2d.g++.8
similarity index 100%
rename from examples/DIFFUSE/log.msd.2d.1Feb14
rename to examples/DIFFUSE/log.1Feb14.msd.2d.g++.8
diff --git a/examples/DIFFUSE/log.vacf.2d.1Feb14 b/examples/DIFFUSE/log.1Feb14.vacf.2d.g++.8
similarity index 100%
rename from examples/DIFFUSE/log.vacf.2d.1Feb14
rename to examples/DIFFUSE/log.1Feb14.vacf.2d.g++.8
diff --git a/examples/HEAT/in.lj_ehex b/examples/HEAT/in.lj.ehex
similarity index 100%
rename from examples/HEAT/in.lj_ehex
rename to examples/HEAT/in.lj.ehex
diff --git a/examples/HEAT/in.lj_hex b/examples/HEAT/in.lj.hex
similarity index 100%
rename from examples/HEAT/in.lj_hex
rename to examples/HEAT/in.lj.hex
diff --git a/examples/HEAT/in.spce_ehex b/examples/HEAT/in.spce.ehex
similarity index 100%
rename from examples/HEAT/in.spce_ehex
rename to examples/HEAT/in.spce.ehex
diff --git a/examples/HEAT/in.spce_hex b/examples/HEAT/in.spce.hex
similarity index 100%
rename from examples/HEAT/in.spce_hex
rename to examples/HEAT/in.spce.hex
diff --git a/examples/HEAT/log.lj_ehex b/examples/HEAT/log.10May16.lj.ehex.g++.32
similarity index 100%
rename from examples/HEAT/log.lj_ehex
rename to examples/HEAT/log.10May16.lj.ehex.g++.32
diff --git a/examples/HEAT/log.lj_hex b/examples/HEAT/log.10May16.lj.hex.g++.32
similarity index 100%
rename from examples/HEAT/log.lj_hex
rename to examples/HEAT/log.10May16.lj.hex.g++.32
diff --git a/examples/HEAT/log.spce_ehex b/examples/HEAT/log.10May16.spce.ehex.g++.32
similarity index 100%
rename from examples/HEAT/log.spce_ehex
rename to examples/HEAT/log.10May16.spce.ehex.g++.32
diff --git a/examples/HEAT/log.spce_hex b/examples/HEAT/log.10May16.spce.hex.g++.32
similarity index 100%
rename from examples/HEAT/log.spce_hex
rename to examples/HEAT/log.10May16.spce.hex.g++.32
diff --git a/examples/HEAT/out.Elj_ehex b/examples/HEAT/out.10May16.Elj.ehex.g++.32
similarity index 100%
rename from examples/HEAT/out.Elj_ehex
rename to examples/HEAT/out.10May16.Elj.ehex.g++.32
diff --git a/examples/HEAT/out.Elj_hex b/examples/HEAT/out.10May16.Elj.hex.g++.32
similarity index 100%
rename from examples/HEAT/out.Elj_hex
rename to examples/HEAT/out.10May16.Elj.hex.g++.32
diff --git a/examples/HEAT/out.Espce_ehex b/examples/HEAT/out.10May16.Espce.ehex.g++.32
similarity index 100%
rename from examples/HEAT/out.Espce_ehex
rename to examples/HEAT/out.10May16.Espce.ehex.g++.32
diff --git a/examples/HEAT/out.Espce_hex b/examples/HEAT/out.10May16.Espce.hex.g++.32
similarity index 100%
rename from examples/HEAT/out.Espce_hex
rename to examples/HEAT/out.10May16.Espce.hex.g++.32
diff --git a/examples/HEAT/out.Tlj_ehex b/examples/HEAT/out.10May16.Tlj.ehex.g++.32
similarity index 100%
rename from examples/HEAT/out.Tlj_ehex
rename to examples/HEAT/out.10May16.Tlj.ehex.g++.32
diff --git a/examples/HEAT/out.Tlj_hex b/examples/HEAT/out.10May16.Tlj.hex.g++.32
similarity index 100%
rename from examples/HEAT/out.Tlj_hex
rename to examples/HEAT/out.10May16.Tlj.hex.g++.32
diff --git a/examples/HEAT/out.Tspce_ehex b/examples/HEAT/out.10May16.Tspce.ehex.g++.32
similarity index 100%
rename from examples/HEAT/out.Tspce_ehex
rename to examples/HEAT/out.10May16.Tspce.ehex.g++.32
diff --git a/examples/HEAT/out.Tspce_hex b/examples/HEAT/out.10May16.Tspce.hex.g++.32
similarity index 100%
rename from examples/HEAT/out.Tspce_hex
rename to examples/HEAT/out.10May16.Tspce.hex.g++.32
diff --git a/examples/KAPPA/log.heatflux.1Feb14 b/examples/KAPPA/log.1Feb14.heatflux.g++.8
similarity index 100%
rename from examples/KAPPA/log.heatflux.1Feb14
rename to examples/KAPPA/log.1Feb14.heatflux.g++.8
diff --git a/examples/KAPPA/log.langevin.1Feb14 b/examples/KAPPA/log.1Feb14.langevin.g++.8
similarity index 100%
rename from examples/KAPPA/log.langevin.1Feb14
rename to examples/KAPPA/log.1Feb14.langevin.g++.8
diff --git a/examples/KAPPA/log.mp.1Feb14 b/examples/KAPPA/log.1Feb14.mp.g++.8
similarity index 100%
rename from examples/KAPPA/log.mp.1Feb14
rename to examples/KAPPA/log.1Feb14.mp.g++.8
diff --git a/examples/KAPPA/log.ehex.7Jun16 b/examples/KAPPA/log.7Jun16.ehex.g++.8
similarity index 100%
rename from examples/KAPPA/log.ehex.7Jun16
rename to examples/KAPPA/log.7Jun16.ehex.g++.8
diff --git a/examples/KAPPA/log.heat.7Jun16 b/examples/KAPPA/log.7Jun16.heat.g++.8
similarity index 100%
rename from examples/KAPPA/log.heat.7Jun16
rename to examples/KAPPA/log.7Jun16.heat.g++.8
diff --git a/examples/KAPPA/profile.heatflux.1Feb14 b/examples/KAPPA/profile.1Feb14.heatflux.g++.8
similarity index 100%
rename from examples/KAPPA/profile.heatflux.1Feb14
rename to examples/KAPPA/profile.1Feb14.heatflux.g++.8
diff --git a/examples/KAPPA/profile.langevin.1Feb14 b/examples/KAPPA/profile.1Feb14.langevin.g++.8
similarity index 100%
rename from examples/KAPPA/profile.langevin.1Feb14
rename to examples/KAPPA/profile.1Feb14.langevin.g++.8
diff --git a/examples/KAPPA/profile.mp.1Feb14 b/examples/KAPPA/profile.1Feb14.mp.g++.8
similarity index 100%
rename from examples/KAPPA/profile.mp.1Feb14
rename to examples/KAPPA/profile.1Feb14.mp.g++.8
diff --git a/examples/KAPPA/profile.ehex.7Jun16 b/examples/KAPPA/profile.7Jun16.ehex.g++.8
similarity index 100%
rename from examples/KAPPA/profile.ehex.7Jun16
rename to examples/KAPPA/profile.7Jun16.ehex.g++.8
diff --git a/examples/KAPPA/profile.heat.7Jun16 b/examples/KAPPA/profile.7Jun16.heat.g++.8
similarity index 100%
rename from examples/KAPPA/profile.heat.7Jun16
rename to examples/KAPPA/profile.7Jun16.heat.g++.8
diff --git a/examples/MC/log.mc.6Jun14 b/examples/MC/log.6Jun14.mc.g++.1
similarity index 100%
rename from examples/MC/log.mc.6Jun14
rename to examples/MC/log.6Jun14.mc.g++.1
diff --git a/examples/VISCOSITY/log.gk.2d.1Feb14 b/examples/VISCOSITY/log.1Feb14.gk.2d.g++.1
similarity index 100%
rename from examples/VISCOSITY/log.gk.2d.1Feb14
rename to examples/VISCOSITY/log.1Feb14.gk.2d.g++.1
diff --git a/examples/VISCOSITY/log.mp.2d.1Feb14 b/examples/VISCOSITY/log.1Feb14.mp.2d.g++.1
similarity index 100%
rename from examples/VISCOSITY/log.mp.2d.1Feb14
rename to examples/VISCOSITY/log.1Feb14.mp.2d.g++.1
diff --git a/examples/VISCOSITY/log.nemd.2d.1Feb14 b/examples/VISCOSITY/log.1Feb14.nemd.2d.g++.1
similarity index 100%
rename from examples/VISCOSITY/log.nemd.2d.1Feb14
rename to examples/VISCOSITY/log.1Feb14.nemd.2d.g++.1
diff --git a/examples/VISCOSITY/log.wall.2d.1Feb14 b/examples/VISCOSITY/log.1Feb14.wall.2d.g++.1
similarity index 100%
rename from examples/VISCOSITY/log.wall.2d.1Feb14
rename to examples/VISCOSITY/log.1Feb14.wall.2d.g++.1
diff --git a/examples/VISCOSITY/profile.gk.2d.1Feb14 b/examples/VISCOSITY/profile.1Feb14.gk.2d.g++.1
similarity index 100%
rename from examples/VISCOSITY/profile.gk.2d.1Feb14
rename to examples/VISCOSITY/profile.1Feb14.gk.2d.g++.1
diff --git a/examples/VISCOSITY/profile.mp.2d.1Feb14 b/examples/VISCOSITY/profile.1Feb14.mp.2d.g++.1
similarity index 100%
rename from examples/VISCOSITY/profile.mp.2d.1Feb14
rename to examples/VISCOSITY/profile.1Feb14.mp.2d.g++.1
diff --git a/examples/VISCOSITY/profile.nemd.2d.1Feb14 b/examples/VISCOSITY/profile.1Feb14.nemd.2d.g++.1
similarity index 100%
rename from examples/VISCOSITY/profile.nemd.2d.1Feb14
rename to examples/VISCOSITY/profile.1Feb14.nemd.2d.g++.1
diff --git a/examples/VISCOSITY/profile.wall.2d.1Feb14 b/examples/VISCOSITY/profile.1Feb14.wall.2d.g++.1
similarity index 100%
rename from examples/VISCOSITY/profile.wall.2d.1Feb14
rename to examples/VISCOSITY/profile.1Feb14.wall.2d.g++.1
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index c10d6b1553..80fefe66ce 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -26,6 +26,7 @@
#include "modify.h"
#include "compute.h"
#include "fix.h"
+#include "fix_store.h"
#include "memory.h"
#include "error.h"
@@ -82,10 +83,17 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
buffer_flag = 1;
iregion = -1;
idregion = NULL;
+
nthresh = 0;
thresh_array = NULL;
thresh_op = NULL;
thresh_value = NULL;
+ thresh_last = NULL;
+
+ nthreshlast = 0;
+ thresh_fix = NULL;
+ thresh_fixID = NULL;
+ thresh_first = NULL;
// computes, fixes, variables which the dump accesses
@@ -193,6 +201,17 @@ DumpCustom::~DumpCustom()
memory->destroy(thresh_array);
memory->destroy(thresh_op);
memory->destroy(thresh_value);
+ memory->destroy(thresh_last);
+
+ // check nfix in case all fixes have already been deleted
+
+ for (int i = 0; i < nthreshlast; i++) {
+ if (modify->nfix) modify->delete_fix(thresh_fixID[i]);
+ delete [] thresh_fixID[i];
+ }
+ memory->sfree(thresh_fix);
+ memory->sfree(thresh_fixID);
+ memory->destroy(thresh_first);
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
memory->sfree(id_compute);
@@ -498,9 +517,10 @@ int DumpCustom::count()
// un-choose if any threshold criterion isn't met
if (nthresh) {
- double *ptr;
+ double *ptr,*ptrhold;
+ double *values;
double value;
- int nstride;
+ int nstride,lastflag;
int nlocal = atom->nlocal;
for (int ithresh = 0; ithresh < nthresh; ithresh++) {
@@ -926,32 +946,91 @@ int DumpCustom::count()
}
// unselect atoms that don't meet threshold criterion
+ // compare to single value or values stored in threshfix
+ // copy ptr attribute into thresh_fix if this is first comparison
- value = thresh_value[ithresh];
+ if (thresh_last[ithresh] < 0) {
+ lastflag = 0;
+ value = thresh_value[ithresh];
+ } else {
+ lastflag = 1;
+ int ilast = thresh_last[ithresh];
+ values = thresh_fix[ilast]->vstore;
+ ptrhold = ptr;
+ if (thresh_first[ilast]) {
+ thresh_first[ilast] = 0;
+ for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
+ ptr = ptrhold;
+ }
+ }
if (thresh_op[ithresh] == LT) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr >= value) choose[i] = 0;
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr >= values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr >= value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == LE) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr > value) choose[i] = 0;
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr > values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr > value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == GT) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr <= value) choose[i] = 0;
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr <= values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr <= value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == GE) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr < value) choose[i] = 0;
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr < values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr < value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == EQ) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr != value) choose[i] = 0;
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr != values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr != value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == NEQ) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && *ptr == value) choose[i] = 0;
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr == values[i]) choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && *ptr == value) choose[i] = 0;
+ }
} else if (thresh_op[ithresh] == XOR) {
- for (i = 0; i < nlocal; i++, ptr += nstride)
- if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
- (*ptr != 0.0 && value != 0.0))
- choose[i] = 0;
+ if (lastflag) {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && (*ptr == 0.0 && values[i] == 0.0) ||
+ (*ptr != 0.0 && values[i] != 0.0))
+ choose[i] = 0;
+ } else {
+ for (i = 0; i < nlocal; i++, ptr += nstride)
+ if (choose[i] && (*ptr == 0.0 && value == 0.0) ||
+ (*ptr != 0.0 && value != 0.0))
+ choose[i] = 0;
+ }
+ }
+
+ // update values stored in threshfix
+
+ if (lastflag) {
+ ptr = ptrhold;
+ for (i = 0; i < nlocal; i++, ptr += nstride) values[i] = *ptr;
}
}
}
@@ -1594,8 +1673,16 @@ int DumpCustom::modify_param(int narg, char **arg)
thresh_array = NULL;
thresh_op = NULL;
thresh_value = NULL;
+ thresh_last = NULL;
+ for (int i = 0; i < nthreshlast; i++) {
+ modify->delete_fix(thresh_fixID[i]);
+ delete [] thresh_fixID[i];
+ }
+ thresh_fix = NULL;
+ thresh_fixID = NULL;
+ thresh_first = NULL;
}
- nthresh = 0;
+ nthresh = nthreshlast = 0;
return 2;
}
@@ -1606,7 +1693,8 @@ int DumpCustom::modify_param(int narg, char **arg)
memory->grow(thresh_array,nthresh+1,"dump:thresh_array");
memory->grow(thresh_op,(nthresh+1),"dump:thresh_op");
memory->grow(thresh_value,(nthresh+1),"dump:thresh_value");
-
+ memory->grow(thresh_last,(nthresh+1),"dump:thresh_last");
+
// set attribute type of threshold
// customize by adding to if statement
@@ -1830,7 +1918,7 @@ int DumpCustom::modify_param(int narg, char **arg)
field2index[nfield+nthresh] = add_custom(suffix,0);
delete [] suffix;
- } else error->all(FLERR,"Invalid dump_modify threshhold operator");
+ } else error->all(FLERR,"Invalid dump_modify threshold operator");
// set operation type of threshold
@@ -1843,9 +1931,43 @@ int DumpCustom::modify_param(int narg, char **arg)
else if (strcmp(arg[2],"|^") == 0) thresh_op[nthresh] = XOR;
else error->all(FLERR,"Invalid dump_modify threshold operator");
- // set threshold value
+ // set threshold value as number or special LAST keyword
+ // create FixStore to hold LAST values, should work with restart
+ // id = dump-ID + nthreshlast + DUMP_STORE, fix group = dump group
- thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
+ if (strcmp(arg[3],"LAST") != 0) {
+ thresh_value[nthresh] = force->numeric(FLERR,arg[3]);
+ thresh_last[nthresh] = -1;
+ } else {
+ thresh_fix = (FixStore **)
+ memory->srealloc(thresh_fix,(nthreshlast+1)*sizeof(FixStore *),
+ "dump:thresh_fix");
+ thresh_fixID = (char **)
+ memory->srealloc(thresh_fixID,(nthreshlast+1)*sizeof(char *),
+ "dump:thresh_fixID");
+ memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
+
+ int n = strlen(id) + strlen("_DUMP_STORE") + 8;
+ thresh_fixID[nthreshlast] = new char[n];
+ strcpy(thresh_fixID[nthreshlast],id);
+ sprintf(&thresh_fixID[nthreshlast][strlen(id)],"%d",nthreshlast);
+ strcat(thresh_fixID[nthreshlast],"_DUMP_STORE");
+
+ char **newarg = new char*[6];
+ newarg[0] = thresh_fixID[nthreshlast];
+ newarg[1] = group->names[igroup];
+ newarg[2] = (char *) "STORE";
+ newarg[3] = (char *) "peratom";
+ newarg[4] = (char *) "1";
+ newarg[5] = (char *) "1";
+ modify->add_fix(6,newarg);
+ thresh_fix[nthreshlast] = (FixStore *) modify->fix[modify->nfix-1];
+ delete [] newarg;
+
+ thresh_last[nthreshlast] = nthreshlast;
+ thresh_first[nthreshlast] = 1;
+ nthreshlast++;
+ }
nthresh++;
return 4;
diff --git a/src/dump_custom.h b/src/dump_custom.h
index 6caa70d1f7..38567b7523 100644
--- a/src/dump_custom.h
+++ b/src/dump_custom.h
@@ -33,10 +33,20 @@ class DumpCustom : public Dump {
int nevery; // dump frequency for output
int iregion; // -1 if no region, else which region
char *idregion; // region ID
- int nthresh; // # of defined threshholds
- int *thresh_array; // array to threshhhold on for each nthresh
- int *thresh_op; // threshhold operation for each nthresh
- double *thresh_value; // threshhold value for each nthresh
+
+ int nthresh; // # of defined thresholds
+ int nthreshlast; // # of defined thresholds with value = LAST
+
+ int *thresh_array; // array to threshold on for each nthresh
+ int *thresh_op; // threshold operation for each nthresh
+ double *thresh_value; // threshold value for each nthresh
+ int *thresh_last; // for threshold value = LAST,
+ // index into thresh_fix
+ // -1 if not LAST, value is numeric
+
+ class FixStore **thresh_fix; // stores values for each threshold LAST
+ char **thresh_fixID; // IDs of thresh_fixes
+ int *thresh_first; // 1 the first time a FixStore values accessed
int expand; // flag for whether field args were expanded
char **earg; // field names with wildcard expansion
@@ -50,7 +60,7 @@ class DumpCustom : public Dump {
int nchoose; // # of selected atoms
int maxlocal; // size of atom selection and variable arrays
int *choose; // local indices of selected atoms
- double *dchoose; // value for each atom to threshhold against
+ double *dchoose; // value for each atom to threshold against
int *clist; // compressed list of indices of selected atoms
int nfield; // # of keywords listed by user
@@ -233,9 +243,9 @@ E: Compute used in dump between runs is not current
The compute was not invoked on the current timestep, therefore it
cannot be used in a dump between runs.
-E: Threshhold for an atom property that isn't allocated
+E: Threshold for an atom property that isn't allocated
-A dump threshhold has been requested on a quantity that is
+A dump threshold has been requested on a quantity that is
not defined by the atom style used in this simulation.
E: Dumping an atom property that isn't allocated
@@ -362,7 +372,7 @@ E: Could not find dump modify custom atom integer property ID
Self-explanatory.
-E: Invalid dump_modify threshhold operator
+E: Invalid dump_modify threshold operator
Operator keyword used for threshold specification in not recognized.
diff --git a/src/fix_store.cpp b/src/fix_store.cpp
index 19d2c72f9d..c856bb2db2 100644
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@@ -154,6 +154,9 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller)
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
else memory->create(astore,nrow,ncol,"fix/store:astore");
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
+
+
+ printf("AAA HOW GET HERE\n");
}
/* ----------------------------------------------------------------------
diff --git a/src/modify.cpp b/src/modify.cpp
index dea0d9dc08..6370998a23 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -68,10 +68,12 @@ Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
list_timeflag = NULL;
nfix_restart_global = 0;
- id_restart_global = style_restart_global = state_restart_global = NULL;
+ id_restart_global = style_restart_global = NULL;
+ state_restart_global = NULL;
+ used_restart_global = NULL;
nfix_restart_peratom = 0;
id_restart_peratom = style_restart_peratom = NULL;
- index_restart_peratom = NULL;
+ index_restart_peratom = used_restart_peratom = NULL;
ncompute = maxcompute = 0;
compute = NULL;
@@ -140,7 +142,7 @@ Modify::~Modify()
delete [] end_of_step_every;
delete [] list_timeflag;
- restart_deallocate();
+ restart_deallocate(0);
delete compute_map;
delete fix_map;
@@ -156,7 +158,7 @@ void Modify::init()
// delete storage of restart info since it is not valid after 1st run
- restart_deallocate();
+ restart_deallocate(1);
// create lists of fixes to call at each stage of run
@@ -819,11 +821,16 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
if (strcmp(id_restart_global[i],fix[ifix]->id) == 0 &&
strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
fix[ifix]->restart(state_restart_global[i]);
+ used_restart_global[i] = 1;
if (comm->me == 0) {
- const char *str = (const char *) ("Resetting global state of Fix %s "
- "Style %s from restart file info\n");
- if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
- if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
+ if (screen)
+ fprintf(screen,"Resetting global fix info from restart file:\n");
+ if (logfile)
+ fprintf(logfile,"Resetting global fix info from restart file:\n");
+ if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
+ fix[ifix]->style,fix[ifix]->id);
+ if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
+ fix[ifix]->style,fix[ifix]->id);
}
}
@@ -833,14 +840,19 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
for (int i = 0; i < nfix_restart_peratom; i++)
if (strcmp(id_restart_peratom[i],fix[ifix]->id) == 0 &&
strcmp(style_restart_peratom[i],fix[ifix]->style) == 0) {
+ used_restart_peratom[i] = 1;
for (int j = 0; j < atom->nlocal; j++)
fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
fix[ifix]->restart_reset = 1;
if (comm->me == 0) {
- char *str = (char *) ("Resetting per-atom state of Fix %s Style %s "
- "from restart file info\n");
- if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
- if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
+ if (screen)
+ fprintf(screen,"Resetting peratom fix info from restart file:\n");
+ if (logfile)
+ fprintf(logfile,"Resetting peratom fix info from restart file:\n");
+ if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
+ fix[ifix]->style,fix[ifix]->id);
+ if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
+ fix[ifix]->style,fix[ifix]->id);
}
}
@@ -1158,6 +1170,7 @@ int Modify::read_restart(FILE *fp)
id_restart_global = new char*[nfix_restart_global];
style_restart_global = new char*[nfix_restart_global];
state_restart_global = new char*[nfix_restart_global];
+ used_restart_global = new int[nfix_restart_global];
}
// read each entry and Bcast to all procs
@@ -1182,6 +1195,8 @@ int Modify::read_restart(FILE *fp)
state_restart_global[i] = new char[n];
if (me == 0) fread(state_restart_global[i],sizeof(char),n,fp);
MPI_Bcast(state_restart_global[i],n,MPI_CHAR,0,world);
+
+ used_restart_global[i] = 0;
}
// nfix_restart_peratom = # of restart entries with peratom info
@@ -1197,6 +1212,7 @@ int Modify::read_restart(FILE *fp)
id_restart_peratom = new char*[nfix_restart_peratom];
style_restart_peratom = new char*[nfix_restart_peratom];
index_restart_peratom = new int[nfix_restart_peratom];
+ used_restart_peratom = new int[nfix_restart_peratom];
}
// read each entry and Bcast to all procs
@@ -1221,6 +1237,7 @@ int Modify::read_restart(FILE *fp)
maxsize += n;
index_restart_peratom[i] = i;
+ used_restart_peratom[i] = 0;
}
return maxsize;
@@ -1228,11 +1245,36 @@ int Modify::read_restart(FILE *fp)
/* ----------------------------------------------------------------------
delete all lists of restart file Fix info
+ if flag set, print list of restart file info not assigned to new fixes
------------------------------------------------------------------------- */
-void Modify::restart_deallocate()
+void Modify::restart_deallocate(int flag)
{
if (nfix_restart_global) {
+ if (flag && comm->me == 0) {
+ int i;
+ for (i = 0; i < nfix_restart_global; i++)
+ if (used_restart_global[i] == 0) break;
+ if (i == nfix_restart_global) {
+ if (screen)
+ fprintf(screen,"All restart file global fix info "
+ "was re-assigned\n");
+ if (logfile)
+ fprintf(logfile,"All restart file global fix info "
+ "was re-assigned\n");
+ } else {
+ if (screen) fprintf(screen,"Unused restart file global fix info:\n");
+ if (logfile) fprintf(logfile,"Unused restart file global fix info:\n");
+ for (i = 0; i < nfix_restart_global; i++) {
+ if (used_restart_global[i]) continue;
+ if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
+ style_restart_global[i],id_restart_global[i]);
+ if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
+ style_restart_global[i],id_restart_global[i]);
+ }
+ }
+ }
+
for (int i = 0; i < nfix_restart_global; i++) {
delete [] id_restart_global[i];
delete [] style_restart_global[i];
@@ -1241,9 +1283,34 @@ void Modify::restart_deallocate()
delete [] id_restart_global;
delete [] style_restart_global;
delete [] state_restart_global;
+ delete [] used_restart_global;
}
if (nfix_restart_peratom) {
+ if (flag && comm->me == 0) {
+ int i;
+ for (i = 0; i < nfix_restart_peratom; i++)
+ if (used_restart_peratom[i] == 0) break;
+ if (i == nfix_restart_peratom) {
+ if (screen)
+ fprintf(screen,"All restart file peratom fix info "
+ "was re-assigned\n");
+ if (logfile)
+ fprintf(logfile,"All restart file peratom fix info "
+ "was re-assigned\n");
+ } else {
+ if (screen) fprintf(screen,"Unused restart file peratom fix info:\n");
+ if (logfile) fprintf(logfile,"Unused restart file peratom fix info:\n");
+ for (i = 0; i < nfix_restart_peratom; i++) {
+ if (used_restart_peratom[i]) continue;
+ if (screen) fprintf(screen," fix style: %s, fix ID: %s\n",
+ style_restart_peratom[i],id_restart_peratom[i]);
+ if (logfile) fprintf(logfile," fix style: %s, fix ID: %s\n",
+ style_restart_peratom[i],id_restart_peratom[i]);
+ }
+ }
+ }
+
for (int i = 0; i < nfix_restart_peratom; i++) {
delete [] id_restart_peratom[i];
delete [] style_restart_peratom[i];
@@ -1251,6 +1318,7 @@ void Modify::restart_deallocate()
delete [] id_restart_peratom;
delete [] style_restart_peratom;
delete [] index_restart_peratom;
+ delete [] used_restart_peratom;
}
nfix_restart_global = nfix_restart_peratom = 0;
diff --git a/src/modify.h b/src/modify.h
index 6472c9bf6a..f6f59a6a9c 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -107,7 +107,7 @@ class Modify : protected Pointers {
void write_restart(FILE *);
int read_restart(FILE *);
- void restart_deallocate();
+ void restart_deallocate(int);
bigint memory_usage();
@@ -135,10 +135,12 @@ class Modify : protected Pointers {
char **id_restart_global; // stored fix global info
char **style_restart_global; // from read-in restart file
char **state_restart_global;
+ int *used_restart_global;
char **id_restart_peratom; // stored fix peratom info
char **style_restart_peratom; // from read-in restart file
int *index_restart_peratom;
+ int *used_restart_peratom;
int index_permanent; // fix/compute index returned to library call
diff --git a/src/region.h b/src/region.h
index 4b53c4e23b..2b920de496 100644
--- a/src/region.h
+++ b/src/region.h
@@ -106,11 +106,12 @@ class Region : protected Pointers {
void options(int, char **);
void point_on_line_segment(double *, double *, double *, double *);
void forward_transform(double &, double &, double &);
+ double point[3],runit[3];
private:
char *xstr,*ystr,*zstr,*tstr;
int xvar,yvar,zvar,tvar;
- double axis[3],point[3],runit[3];
+ double axis[3];
void inverse_transform(double &, double &, double &);
void rotate(double &, double &, double &, double);
diff --git a/src/version.h b/src/version.h
index e24bd29bf3..a2b011376f 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "6 Oct 2016"
+#define LAMMPS_VERSION "11 Oct 2016"
diff --git a/src/write_dump.cpp b/src/write_dump.cpp
index a8ad5419ac..31fca773eb 100644
--- a/src/write_dump.cpp
+++ b/src/write_dump.cpp
@@ -32,7 +32,6 @@ using namespace LAMMPS_NS;
void WriteDump::command(int narg, char **arg)
{
-
if (narg < 3) error->all(FLERR,"Illegal write_dump command");
// modindex = index in args of "modify" keyword