From fcfbdb13abfb2fb29ced875c5bc729bf8bfd6c32 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 8 Mar 2018 18:10:28 -0500
Subject: [PATCH] provide new reference outputs for various reaxff examples
---
examples/reax/AB/log.5Oct16.AB.g++.4 | 70 -----------
...og.5Oct16.AB.g++.1 => log.8Mar18.AB.g++.1} | 47 ++++---
examples/reax/AB/log.8Mar18.AB.g++.4 | 81 ++++++++++++
....5Oct16.AuO.g++.1 => log.8Mar18.AuO.g++.1} | 41 ++++---
....5Oct16.AuO.g++.4 => log.8Mar18.AuO.g++.4} | 43 ++++---
....5Oct16.CHO.g++.1 => log.8Mar18.CHO.g++.1} | 43 ++++---
....5Oct16.CHO.g++.4 => log.8Mar18.CHO.g++.4} | 43 ++++---
...og.5Oct16.FC.g++.1 => log.8Mar18.FC.g++.1} | 59 +++++----
...og.5Oct16.FC.g++.4 => log.8Mar18.FC.g++.4} | 59 +++++----
examples/reax/HNS/in.reaxc.hns | 8 +-
examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1 | 115 ++++++++++++++++++
examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4 | 115 ++++++++++++++++++
....5Oct16.RDX.g++.1 => log.8Mar18.RDX.g++.1} | 47 ++++---
....5Oct16.RDX.g++.4 => log.8Mar18.RDX.g++.4} | 47 ++++---
examples/reax/VOH/log.5Oct16.VOH.g++.4 | 70 -----------
....5Oct16.VOH.g++.1 => log.8Mar18.VOH.g++.1} | 47 ++++---
examples/reax/VOH/log.8Mar18.VOH.g++.4 | 81 ++++++++++++
...t16.ZnOH2.g++.1 => log.8Mar18.ZnOH2.g++.1} | 47 ++++---
...t16.ZnOH2.g++.4 => log.8Mar18.ZnOH2.g++.4} | 45 ++++---
.../ci-reaxFF/{input.in => in.ci-reax.CH} | 0
...ct17.g++.1 => log.8Mar18.ci-reax.CH.g++.1} | 24 ++--
.../ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4 | 86 +++++++++++++
examples/reax/log.5Oct16.reax.rdx.g++.1 | 101 ---------------
examples/reax/log.5Oct16.reax.rdx.g++.4 | 101 ---------------
examples/reax/log.5Oct16.reaxc.rdx.g++.1 | 104 ----------------
examples/reax/log.5Oct16.reaxc.rdx.g++.4 | 104 ----------------
examples/reax/log.8March18.reax.rdx.g++.1 | 107 ++++++++++++++++
examples/reax/log.8March18.reax.rdx.g++.4 | 107 ++++++++++++++++
...atb.g++.1 => log.8March18.reax.tatb.g++.1} | 46 ++++---
...atb.g++.4 => log.8March18.reax.tatb.g++.4} | 44 ++++---
examples/reax/log.8March18.reaxc.rdx.g++.1 | 115 ++++++++++++++++++
examples/reax/log.8March18.reaxc.rdx.g++.4 | 115 ++++++++++++++++++
...tb.g++.1 => log.8March18.reaxc.tatb.g++.1} | 51 +++++---
...tb.g++.4 => log.8March18.reaxc.tatb.g++.4} | 51 +++++---
34 files changed, 1405 insertions(+), 859 deletions(-)
delete mode 100644 examples/reax/AB/log.5Oct16.AB.g++.4
rename examples/reax/AB/{log.5Oct16.AB.g++.1 => log.8Mar18.AB.g++.1} (50%)
create mode 100644 examples/reax/AB/log.8Mar18.AB.g++.4
rename examples/reax/AuO/{log.5Oct16.AuO.g++.1 => log.8Mar18.AuO.g++.1} (52%)
rename examples/reax/AuO/{log.5Oct16.AuO.g++.4 => log.8Mar18.AuO.g++.4} (51%)
rename examples/reax/CHO/{log.5Oct16.CHO.g++.1 => log.8Mar18.CHO.g++.1} (53%)
rename examples/reax/CHO/{log.5Oct16.CHO.g++.4 => log.8Mar18.CHO.g++.4} (51%)
rename examples/reax/FC/{log.5Oct16.FC.g++.1 => log.8Mar18.FC.g++.1} (67%)
rename examples/reax/FC/{log.5Oct16.FC.g++.4 => log.8Mar18.FC.g++.4} (67%)
create mode 100644 examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1
create mode 100644 examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4
rename examples/reax/RDX/{log.5Oct16.RDX.g++.1 => log.8Mar18.RDX.g++.1} (51%)
rename examples/reax/RDX/{log.5Oct16.RDX.g++.4 => log.8Mar18.RDX.g++.4} (50%)
delete mode 100644 examples/reax/VOH/log.5Oct16.VOH.g++.4
rename examples/reax/VOH/{log.5Oct16.VOH.g++.1 => log.8Mar18.VOH.g++.1} (50%)
create mode 100644 examples/reax/VOH/log.8Mar18.VOH.g++.4
rename examples/reax/ZnOH2/{log.5Oct16.ZnOH2.g++.1 => log.8Mar18.ZnOH2.g++.1} (50%)
rename examples/reax/ZnOH2/{log.5Oct16.ZnOH2.g++.4 => log.8Mar18.ZnOH2.g++.4} (51%)
rename examples/reax/ci-reaxFF/{input.in => in.ci-reax.CH} (100%)
rename examples/reax/ci-reaxFF/{log.23Oct17.g++.1 => log.8Mar18.ci-reax.CH.g++.1} (77%)
create mode 100644 examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4
delete mode 100644 examples/reax/log.5Oct16.reax.rdx.g++.1
delete mode 100644 examples/reax/log.5Oct16.reax.rdx.g++.4
delete mode 100644 examples/reax/log.5Oct16.reaxc.rdx.g++.1
delete mode 100644 examples/reax/log.5Oct16.reaxc.rdx.g++.4
create mode 100644 examples/reax/log.8March18.reax.rdx.g++.1
create mode 100644 examples/reax/log.8March18.reax.rdx.g++.4
rename examples/reax/{log.5Oct16.reax.tatb.g++.1 => log.8March18.reax.tatb.g++.1} (61%)
rename examples/reax/{log.5Oct16.reax.tatb.g++.4 => log.8March18.reax.tatb.g++.4} (61%)
create mode 100644 examples/reax/log.8March18.reaxc.rdx.g++.1
create mode 100644 examples/reax/log.8March18.reaxc.rdx.g++.4
rename examples/reax/{log.5Oct16.reaxc.tatb.g++.1 => log.8March18.reaxc.tatb.g++.1} (57%)
rename examples/reax/{log.5Oct16.reaxc.tatb.g++.4 => log.8March18.reaxc.tatb.g++.4} (57%)
diff --git a/examples/reax/AB/log.5Oct16.AB.g++.4 b/examples/reax/AB/log.5Oct16.AB.g++.4
deleted file mode 100644
index cfc4476ef5..0000000000
--- a/examples/reax/AB/log.5Oct16.AB.g++.4
+++ /dev/null
@@ -1,70 +0,0 @@
-LAMMPS (5 Oct 2016)
-# REAX potential for Nitroamines system
-# .....
-
-units real
-
-atom_style charge
-read_data data.AB
- orthogonal box = (0 0 0) to (25 25 25)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 104 atoms
-
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.AB H B N
-Reading potential file ffield.reax.AB with DATE: 2011-02-18
-
-neighbor 2 bin
-neigh_modify every 10 delay 0 check no
-
-fix 1 all nve
-fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
-fix 3 all temp/berendsen 500.0 500.0 100.0
-
-timestep 0.25
-
-#dump 1 all atom 30 dump.reax.ab
-
-run 3000
-Neighbor list info ...
- 2 neighbor list requests
- update every 10 steps, delay 0 steps, check no
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12
- ghost atom cutoff = 12
- binsize = 6 -> bins = 5 5 5
-Memory usage per processor = 12.622 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -8505.1816 0 -8505.1816 -673.36566
- 3000 496.56561 -8405.3755 0 -8252.9182 472.58916
-Loop time of 7.23109 on 4 procs for 3000 steps with 104 atoms
-
-Performance: 8.961 ns/day, 2.678 hours/ns, 414.875 timesteps/s
-99.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 5.705 | 5.7262 | 5.7504 | 0.7 | 79.19
-Neigh | 0.14367 | 0.15976 | 0.16805 | 2.4 | 2.21
-Comm | 0.053353 | 0.077311 | 0.097821 | 5.7 | 1.07
-Output | 1.812e-05 | 1.9848e-05 | 2.408e-05 | 0.1 | 0.00
-Modify | 1.2559 | 1.2647 | 1.2818 | 0.9 | 17.49
-Other | | 0.003126 | | | 0.04
-
-Nlocal: 26 ave 35 max 13 min
-Histogram: 1 0 0 0 0 1 0 0 1 1
-Nghost: 421 ave 450 max 377 min
-Histogram: 1 0 0 0 0 1 0 0 1 1
-Neighs: 847.25 ave 1149 max 444 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-
-Total # of neighbors = 3389
-Ave neighs/atom = 32.5865
-Neighbor list builds = 300
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:07
diff --git a/examples/reax/AB/log.5Oct16.AB.g++.1 b/examples/reax/AB/log.8Mar18.AB.g++.1
similarity index 50%
rename from examples/reax/AB/log.5Oct16.AB.g++.1
rename to examples/reax/AB/log.8Mar18.AB.g++.1
index df7d20d8bc..065b1a1e67 100644
--- a/examples/reax/AB/log.5Oct16.AB.g++.1
+++ b/examples/reax/AB/log.8Mar18.AB.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
@@ -28,43 +29,53 @@ timestep 0.25
run 3000
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 5 5 5
-Memory usage per processor = 18.4119 Mbytes
+ binsize = 6, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 19.3 | 19.3 | 19.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8505.1816 0 -8505.1816 -673.36566
- 3000 499.30579 -8405.1387 0 -8251.8401 -94.844317
-Loop time of 12.5114 on 1 procs for 3000 steps with 104 atoms
+ 3000 478.18595 -8398.4168 0 -8251.6025 1452.6935
+Loop time of 14.3573 on 1 procs for 3000 steps with 104 atoms
-Performance: 5.179 ns/day, 4.634 hours/ns, 239.782 timesteps/s
-99.3% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 4.513 ns/day, 5.318 hours/ns, 208.952 timesteps/s
+96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 11.137 | 11.137 | 11.137 | 0.0 | 89.01
-Neigh | 0.29816 | 0.29816 | 0.29816 | 0.0 | 2.38
-Comm | 0.016993 | 0.016993 | 0.016993 | 0.0 | 0.14
-Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00
-Modify | 1.0552 | 1.0552 | 1.0552 | 0.0 | 8.43
-Other | | 0.004142 | | | 0.03
+Pair | 12.709 | 12.709 | 12.709 | 0.0 | 88.52
+Neigh | 0.36804 | 0.36804 | 0.36804 | 0.0 | 2.56
+Comm | 0.022419 | 0.022419 | 0.022419 | 0.0 | 0.16
+Output | 2.8133e-05 | 2.8133e-05 | 2.8133e-05 | 0.0 | 0.00
+Modify | 1.2513 | 1.2513 | 1.2513 | 0.0 | 8.72
+Other | | 0.006263 | | | 0.04
Nlocal: 104 ave 104 max 104 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 694 ave 694 max 694 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 2927 ave 2927 max 2927 min
+Neighs: 2866 ave 2866 max 2866 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 2927
-Ave neighs/atom = 28.1442
+Total # of neighbors = 2866
+Ave neighs/atom = 27.5577
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:12
+Total wall time: 0:00:14
diff --git a/examples/reax/AB/log.8Mar18.AB.g++.4 b/examples/reax/AB/log.8Mar18.AB.g++.4
new file mode 100644
index 0000000000..1e02ec5725
--- /dev/null
+++ b/examples/reax/AB/log.8Mar18.AB.g++.4
@@ -0,0 +1,81 @@
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
+# REAX potential for Nitroamines system
+# .....
+
+units real
+
+atom_style charge
+read_data data.AB
+ orthogonal box = (0 0 0) to (25 25 25)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 104 atoms
+
+pair_style reax/c lmp_control
+pair_coeff * * ffield.reax.AB H B N
+Reading potential file ffield.reax.AB with DATE: 2011-02-18
+
+neighbor 2 bin
+neigh_modify every 10 delay 0 check no
+
+fix 1 all nve
+fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
+fix 3 all temp/berendsen 500.0 500.0 100.0
+
+timestep 0.25
+
+#dump 1 all atom 30 dump.reax.ab
+
+run 3000
+Neighbor list info ...
+ update every 10 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 12.38 | 13.22 | 13.64 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -8505.1816 0 -8505.1816 -673.36566
+ 3000 555.17702 -8426.5541 0 -8256.1017 219.26856
+Loop time of 9.03521 on 4 procs for 3000 steps with 104 atoms
+
+Performance: 7.172 ns/day, 3.346 hours/ns, 332.034 timesteps/s
+94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 7.0347 | 7.0652 | 7.1049 | 1.0 | 78.20
+Neigh | 0.18481 | 0.20727 | 0.22108 | 3.0 | 2.29
+Comm | 0.075175 | 0.11496 | 0.14517 | 7.4 | 1.27
+Output | 2.2888e-05 | 2.569e-05 | 3.1948e-05 | 0.0 | 0.00
+Modify | 1.6286 | 1.6421 | 1.6649 | 1.1 | 18.17
+Other | | 0.005646 | | | 0.06
+
+Nlocal: 26 ave 35 max 13 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+Nghost: 420.25 ave 454 max 370 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+Neighs: 862.5 ave 1178 max 444 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 3450
+Ave neighs/atom = 33.1731
+Neighbor list builds = 300
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:09
diff --git a/examples/reax/AuO/log.5Oct16.AuO.g++.1 b/examples/reax/AuO/log.8Mar18.AuO.g++.1
similarity index 52%
rename from examples/reax/AuO/log.5Oct16.AuO.g++.1
rename to examples/reax/AuO/log.8Mar18.AuO.g++.1
index 7ae86b9d60..3c609ac023 100644
--- a/examples/reax/AuO/log.5Oct16.AuO.g++.1
+++ b/examples/reax/AuO/log.8Mar18.AuO.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for AuO system
# .....
@@ -28,30 +29,40 @@ timestep 0.25
run 100
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 5 4 5
-Memory usage per processor = 144.382 Mbytes
+ binsize = 6, bins = 5 4 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 157.6 | 157.6 | 157.6 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 0 -72201.743 0 -72201.743 -166.1947
- 100 69.043346 -72076.31 0 -71878.943 22702.308
-Loop time of 17.7559 on 1 procs for 100 steps with 960 atoms
+ 0 0 -72201.743 0 -72201.743 -166.19482
+ 100 69.043331 -72076.309 0 -71878.942 22702.89
+Loop time of 18.4369 on 1 procs for 100 steps with 960 atoms
-Performance: 0.122 ns/day, 197.288 hours/ns, 5.632 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.117 ns/day, 204.854 hours/ns, 5.424 timesteps/s
+98.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 15.102 | 15.102 | 15.102 | 0.0 | 85.05
-Neigh | 0.49358 | 0.49358 | 0.49358 | 0.0 | 2.78
-Comm | 0.0067561 | 0.0067561 | 0.0067561 | 0.0 | 0.04
-Output | 1.502e-05 | 1.502e-05 | 1.502e-05 | 0.0 | 0.00
-Modify | 2.1525 | 2.1525 | 2.1525 | 0.0 | 12.12
-Other | | 0.001267 | | | 0.01
+Pair | 15.373 | 15.373 | 15.373 | 0.0 | 83.38
+Neigh | 0.58774 | 0.58774 | 0.58774 | 0.0 | 3.19
+Comm | 0.0079026 | 0.0079026 | 0.0079026 | 0.0 | 0.04
+Output | 3.171e-05 | 3.171e-05 | 3.171e-05 | 0.0 | 0.00
+Modify | 2.4665 | 2.4665 | 2.4665 | 0.0 | 13.38
+Other | | 0.001366 | | | 0.01
Nlocal: 960 ave 960 max 960 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/reax/AuO/log.5Oct16.AuO.g++.4 b/examples/reax/AuO/log.8Mar18.AuO.g++.4
similarity index 51%
rename from examples/reax/AuO/log.5Oct16.AuO.g++.4
rename to examples/reax/AuO/log.8Mar18.AuO.g++.4
index 01f29738f2..ed98e1f2f4 100644
--- a/examples/reax/AuO/log.5Oct16.AuO.g++.4
+++ b/examples/reax/AuO/log.8Mar18.AuO.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for AuO system
# .....
@@ -28,30 +29,40 @@ timestep 0.25
run 100
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 5 4 5
-Memory usage per processor = 80.1039 Mbytes
+ binsize = 6, bins = 5 4 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 87.17 | 87.17 | 87.17 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 0 -72201.743 0 -72201.743 -166.20356
- 100 69.043372 -72076.31 0 -71878.943 22701.855
-Loop time of 7.66838 on 4 procs for 100 steps with 960 atoms
+ 0 0 -72201.743 0 -72201.743 -166.2027
+ 100 69.043379 -72076.31 0 -71878.943 22701.771
+Loop time of 8.44797 on 4 procs for 100 steps with 960 atoms
-Performance: 0.282 ns/day, 85.204 hours/ns, 13.041 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.256 ns/day, 93.866 hours/ns, 11.837 timesteps/s
+96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 6.7833 | 6.7864 | 6.7951 | 0.2 | 88.50
-Neigh | 0.2412 | 0.24206 | 0.24396 | 0.2 | 3.16
-Comm | 0.010402 | 0.019419 | 0.022561 | 3.7 | 0.25
-Output | 2.0981e-05 | 2.3007e-05 | 2.9087e-05 | 0.1 | 0.00
-Modify | 0.61733 | 0.61964 | 0.62064 | 0.2 | 8.08
-Other | | 0.0007888 | | | 0.01
+Pair | 7.3702 | 7.3757 | 7.3879 | 0.3 | 87.31
+Neigh | 0.28875 | 0.29449 | 0.29747 | 0.6 | 3.49
+Comm | 0.015008 | 0.027055 | 0.032681 | 4.3 | 0.32
+Output | 2.4319e-05 | 2.8551e-05 | 3.8624e-05 | 0.0 | 0.00
+Modify | 0.74721 | 0.74985 | 0.75539 | 0.4 | 8.88
+Other | | 0.0008975 | | | 0.01
Nlocal: 240 ave 240 max 240 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -67,4 +78,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:07
+Total wall time: 0:00:08
diff --git a/examples/reax/CHO/log.5Oct16.CHO.g++.1 b/examples/reax/CHO/log.8Mar18.CHO.g++.1
similarity index 53%
rename from examples/reax/CHO/log.5Oct16.CHO.g++.1
rename to examples/reax/CHO/log.8Mar18.CHO.g++.1
index 2e346f7585..305ccbf3a0 100644
--- a/examples/reax/CHO/log.5Oct16.CHO.g++.1
+++ b/examples/reax/CHO/log.8Mar18.CHO.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for CHO system
# .....
@@ -28,30 +29,40 @@ timestep 0.25
run 3000
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 5 5 5
-Memory usage per processor = 17.7936 Mbytes
+ binsize = 6, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 0 -10226.557 0 -10226.557 -106.09789
- 3000 548.72503 -10170.457 0 -10000.349 34.314945
-Loop time of 11.5678 on 1 procs for 3000 steps with 105 atoms
+ 0 0 -10226.557 0 -10226.557 -106.09755
+ 3000 548.5116 -10170.389 0 -10000.348 40.372297
+Loop time of 12.6046 on 1 procs for 3000 steps with 105 atoms
-Performance: 5.602 ns/day, 4.284 hours/ns, 259.340 timesteps/s
-99.3% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 5.141 ns/day, 4.668 hours/ns, 238.008 timesteps/s
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 10.111 | 10.111 | 10.111 | 0.0 | 87.41
-Neigh | 0.27992 | 0.27992 | 0.27992 | 0.0 | 2.42
-Comm | 0.01603 | 0.01603 | 0.01603 | 0.0 | 0.14
-Output | 1.2159e-05 | 1.2159e-05 | 1.2159e-05 | 0.0 | 0.00
-Modify | 1.1563 | 1.1563 | 1.1563 | 0.0 | 10.00
-Other | | 0.004084 | | | 0.04
+Pair | 10.931 | 10.931 | 10.931 | 0.0 | 86.72
+Neigh | 0.33107 | 0.33107 | 0.33107 | 0.0 | 2.63
+Comm | 0.017975 | 0.017975 | 0.017975 | 0.0 | 0.14
+Output | 2.0742e-05 | 2.0742e-05 | 2.0742e-05 | 0.0 | 0.00
+Modify | 1.3197 | 1.3197 | 1.3197 | 0.0 | 10.47
+Other | | 0.005059 | | | 0.04
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -67,4 +78,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:11
+Total wall time: 0:00:12
diff --git a/examples/reax/CHO/log.5Oct16.CHO.g++.4 b/examples/reax/CHO/log.8Mar18.CHO.g++.4
similarity index 51%
rename from examples/reax/CHO/log.5Oct16.CHO.g++.4
rename to examples/reax/CHO/log.8Mar18.CHO.g++.4
index 3536b91228..2bc19dc789 100644
--- a/examples/reax/CHO/log.5Oct16.CHO.g++.4
+++ b/examples/reax/CHO/log.8Mar18.CHO.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for CHO system
# .....
@@ -28,30 +29,40 @@ timestep 0.25
run 3000
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 5 5 5
-Memory usage per processor = 12.9938 Mbytes
+ binsize = 6, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 11.75 | 12.85 | 13.81 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 0 -10226.557 0 -10226.557 -106.0974
- 3000 547.91377 -10170.194 0 -10000.338 61.118402
-Loop time of 6.51546 on 4 procs for 3000 steps with 105 atoms
+ 0 0 -10226.557 0 -10226.557 -106.09745
+ 3000 548.30567 -10170.323 0 -10000.346 47.794514
+Loop time of 7.42367 on 4 procs for 3000 steps with 105 atoms
-Performance: 9.946 ns/day, 2.413 hours/ns, 460.443 timesteps/s
-99.1% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 8.729 ns/day, 2.750 hours/ns, 404.113 timesteps/s
+97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 4.9869 | 5.0615 | 5.1246 | 2.3 | 77.68
-Neigh | 0.12213 | 0.14723 | 0.17304 | 5.5 | 2.26
-Comm | 0.05189 | 0.11582 | 0.18932 | 15.4 | 1.78
-Output | 1.812e-05 | 2.0564e-05 | 2.5988e-05 | 0.1 | 0.00
-Modify | 1.1626 | 1.1878 | 1.2122 | 1.9 | 18.23
-Other | | 0.003059 | | | 0.05
+Pair | 5.3058 | 5.4086 | 5.4922 | 3.1 | 72.86
+Neigh | 0.14791 | 0.17866 | 0.2106 | 6.5 | 2.41
+Comm | 0.080185 | 0.16666 | 0.26933 | 17.7 | 2.24
+Output | 2.5988e-05 | 2.8491e-05 | 3.4571e-05 | 0.0 | 0.00
+Modify | 1.6364 | 1.6658 | 1.6941 | 2.0 | 22.44
+Other | | 0.003964 | | | 0.05
Nlocal: 26.25 ave 45 max 6 min
Histogram: 1 0 1 0 0 0 0 0 1 1
@@ -67,4 +78,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:06
+Total wall time: 0:00:07
diff --git a/examples/reax/FC/log.5Oct16.FC.g++.1 b/examples/reax/FC/log.8Mar18.FC.g++.1
similarity index 67%
rename from examples/reax/FC/log.5Oct16.FC.g++.1
rename to examples/reax/FC/log.8Mar18.FC.g++.1
index e669c39169..1e2f723966 100644
--- a/examples/reax/FC/log.5Oct16.FC.g++.1
+++ b/examples/reax/FC/log.8Mar18.FC.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
@@ -29,13 +30,23 @@ thermo 1
dump 4 all xyz 5000 dumpnpt.xyz
run 10
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 28 27 17
-Memory usage per processor = 440.212 Mbytes
+ binsize = 6, bins = 28 27 17
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes
Step Temp E_pair TotEng Press
0 0 -808525.04 -808525.04 58194.694
1 4.9935726 -808803.89 -808546.69 58205.825
@@ -48,20 +59,20 @@ Step Temp E_pair TotEng Press
8 320.17692 -826387.27 -809896.43 58886.877
9 404.17073 -831129.48 -810312.5 59064.551
10 497.02486 -836425.19 -810825.72 59260.714
-Loop time of 20.3094 on 1 procs for 10 steps with 17280 atoms
+Loop time of 21.5054 on 1 procs for 10 steps with 17280 atoms
-Performance: 0.009 ns/day, 2820.746 hours/ns, 0.492 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.008 ns/day, 2986.857 hours/ns, 0.465 timesteps/s
+98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 18.124 | 18.124 | 18.124 | 0.0 | 89.24
-Neigh | 0.072459 | 0.072459 | 0.072459 | 0.0 | 0.36
-Comm | 0.00077629 | 0.00077629 | 0.00077629 | 0.0 | 0.00
-Output | 0.00075412 | 0.00075412 | 0.00075412 | 0.0 | 0.00
-Modify | 2.1109 | 2.1109 | 2.1109 | 0.0 | 10.39
-Other | | 0.0005426 | | | 0.00
+Pair | 19.008 | 19.008 | 19.008 | 0.0 | 88.39
+Neigh | 0.084401 | 0.084401 | 0.084401 | 0.0 | 0.39
+Comm | 0.00080419 | 0.00080419 | 0.00080419 | 0.0 | 0.00
+Output | 0.00095367 | 0.00095367 | 0.00095367 | 0.0 | 0.00
+Modify | 2.4109 | 2.4109 | 2.4109 | 0.0 | 11.21
+Other | | 0.0004592 | | | 0.00
Nlocal: 17280 ave 17280 max 17280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -85,7 +96,7 @@ timestep 0.2
#dump 6 all custom 5000 dumpidtype.dat id type x y z
run 10
-Memory usage per processor = 440.212 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 470 | 470 | 470 Mbytes
Step Temp E_pair TotEng Press
10 497.02486 -836425.19 -810825.72 59260.714
11 601.65141 -841814.22 -810825.91 59489.422
@@ -98,20 +109,20 @@ Step Temp E_pair TotEng Press
18 1623.072 -894534.04 -810937.04 61739.541
19 1812.1865 -904337.99 -811000.57 62200.561
20 2011.5899 -915379.19 -811771.41 63361.151
-Loop time of 20.3051 on 1 procs for 10 steps with 17280 atoms
+Loop time of 21.362 on 1 procs for 10 steps with 17280 atoms
-Performance: 0.009 ns/day, 2820.155 hours/ns, 0.492 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.008 ns/day, 2966.945 hours/ns, 0.468 timesteps/s
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 18.008 | 18.008 | 18.008 | 0.0 | 88.69
-Neigh | 0.069963 | 0.069963 | 0.069963 | 0.0 | 0.34
-Comm | 0.00077033 | 0.00077033 | 0.00077033 | 0.0 | 0.00
-Output | 0.00077224 | 0.00077224 | 0.00077224 | 0.0 | 0.00
-Modify | 2.225 | 2.225 | 2.225 | 0.0 | 10.96
-Other | | 0.0005276 | | | 0.00
+Pair | 18.793 | 18.793 | 18.793 | 0.0 | 87.97
+Neigh | 0.077047 | 0.077047 | 0.077047 | 0.0 | 0.36
+Comm | 0.00080276 | 0.00080276 | 0.00080276 | 0.0 | 0.00
+Output | 0.0010097 | 0.0010097 | 0.0010097 | 0.0 | 0.00
+Modify | 2.4897 | 2.4897 | 2.4897 | 0.0 | 11.65
+Other | | 0.0004568 | | | 0.00
Nlocal: 17280 ave 17280 max 17280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -127,4 +138,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:45
+Total wall time: 0:00:47
diff --git a/examples/reax/FC/log.5Oct16.FC.g++.4 b/examples/reax/FC/log.8Mar18.FC.g++.4
similarity index 67%
rename from examples/reax/FC/log.5Oct16.FC.g++.4
rename to examples/reax/FC/log.8Mar18.FC.g++.4
index f231107270..76dcadfb0f 100644
--- a/examples/reax/FC/log.5Oct16.FC.g++.4
+++ b/examples/reax/FC/log.8Mar18.FC.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for Nitroamines system
# .....
@@ -29,13 +30,23 @@ thermo 1
dump 4 all xyz 5000 dumpnpt.xyz
run 10
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 28 27 17
-Memory usage per processor = 140.018 Mbytes
+ binsize = 6, bins = 28 27 17
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes
Step Temp E_pair TotEng Press
0 0 -808525.04 -808525.04 58194.694
1 4.9935726 -808803.89 -808546.69 58205.825
@@ -48,20 +59,20 @@ Step Temp E_pair TotEng Press
8 320.17692 -826387.27 -809896.43 58886.877
9 404.17073 -831129.48 -810312.5 59064.551
10 497.02486 -836425.19 -810825.72 59260.714
-Loop time of 5.47494 on 4 procs for 10 steps with 17280 atoms
+Loop time of 6.02109 on 4 procs for 10 steps with 17280 atoms
-Performance: 0.032 ns/day, 760.408 hours/ns, 1.827 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.029 ns/day, 836.262 hours/ns, 1.661 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 | 4.5958 | 4.7748 | 4.8852 | 5.4 | 87.21
-Neigh | 0.021961 | 0.022104 | 0.022431 | 0.1 | 0.40
-Comm | 0.0077388 | 0.11804 | 0.29694 | 34.2 | 2.16
-Output | 0.00047708 | 0.00051123 | 0.0005939 | 0.2 | 0.01
-Modify | 0.55906 | 0.55927 | 0.55946 | 0.0 | 10.22
-Other | | 0.0002034 | | | 0.00
+Pair | 4.9482 | 5.1186 | 5.3113 | 7.4 | 85.01
+Neigh | 0.024811 | 0.025702 | 0.027556 | 0.7 | 0.43
+Comm | 0.0027421 | 0.19541 | 0.36565 | 38.1 | 3.25
+Output | 0.00053239 | 0.00057119 | 0.00067186 | 0.0 | 0.01
+Modify | 0.67876 | 0.68059 | 0.68165 | 0.1 | 11.30
+Other | | 0.0001779 | | | 0.00
Nlocal: 4320 ave 4320 max 4320 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -85,7 +96,7 @@ timestep 0.2
#dump 6 all custom 5000 dumpidtype.dat id type x y z
run 10
-Memory usage per processor = 140.018 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 149.3 | 149.3 | 149.3 Mbytes
Step Temp E_pair TotEng Press
10 497.02486 -836425.19 -810825.72 59260.714
11 601.65141 -841814.22 -810825.91 59489.422
@@ -98,20 +109,20 @@ Step Temp E_pair TotEng Press
18 1623.072 -894534.04 -810937.04 61739.541
19 1812.1865 -904337.99 -811000.57 62200.561
20 2011.5899 -915379.19 -811771.41 63361.151
-Loop time of 5.49026 on 4 procs for 10 steps with 17280 atoms
+Loop time of 6.08805 on 4 procs for 10 steps with 17280 atoms
-Performance: 0.031 ns/day, 762.536 hours/ns, 1.821 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.028 ns/day, 845.563 hours/ns, 1.643 timesteps/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 4.5657 | 4.7603 | 4.8596 | 5.4 | 86.70
-Neigh | 0.021023 | 0.021468 | 0.022176 | 0.3 | 0.39
-Comm | 0.016467 | 0.1157 | 0.31031 | 34.7 | 2.11
-Output | 0.00047684 | 0.00050694 | 0.00059295 | 0.2 | 0.01
-Modify | 0.59135 | 0.59207 | 0.59251 | 0.1 | 10.78
-Other | | 0.0001938 | | | 0.00
+Pair | 4.9124 | 5.1008 | 5.3405 | 8.3 | 83.78
+Neigh | 0.023652 | 0.024473 | 0.025996 | 0.6 | 0.40
+Comm | 0.0020971 | 0.24171 | 0.43023 | 38.0 | 3.97
+Output | 0.00056076 | 0.00060701 | 0.00072312 | 0.0 | 0.01
+Modify | 0.71869 | 0.72023 | 0.72107 | 0.1 | 11.83
+Other | | 0.0001827 | | | 0.00
Nlocal: 4320 ave 4320 max 4320 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -127,4 +138,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:12
+Total wall time: 0:00:13
diff --git a/examples/reax/HNS/in.reaxc.hns b/examples/reax/HNS/in.reaxc.hns
index 51cec6afd2..775a389eca 100644
--- a/examples/reax/HNS/in.reaxc.hns
+++ b/examples/reax/HNS/in.reaxc.hns
@@ -1,6 +1,12 @@
# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
# See README for more info
+variable x index 2
+variable y index 2
+variable z index 2
+variable t index 100
+
+
units real
atom_style charge
atom_modify sort 100 0.0 # optional
@@ -24,7 +30,7 @@ timestep 0.1
thermo_style custom step temp pe press evdwl ecoul vol
thermo_modify norm yes
-thermo 100
+thermo 10
velocity all create 300.0 41279 loop geom
diff --git a/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1 b/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1
new file mode 100644
index 0000000000..d418d287b1
--- /dev/null
+++ b/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.1
@@ -0,0 +1,115 @@
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
+# See README for more info
+
+variable x index 2
+variable y index 2
+variable z index 2
+variable t index 100
+
+
+units real
+atom_style charge
+atom_modify sort 100 0.0 # optional
+dimension 3
+boundary p p p
+box tilt large
+
+read_data data.hns-equil
+ triclinic box = (0 0 0) to (22.326 11.1412 13.779) with tilt (0 -5.02603 0)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 304 atoms
+ reading velocities ...
+ 304 velocities
+replicate $x $y $z bbox
+replicate 2 $y $z bbox
+replicate 2 2 $z bbox
+replicate 2 2 2 bbox
+ triclinic box = (0 0 0) to (44.652 22.2824 27.5579) with tilt (0 -10.0521 0)
+ 1 by 1 by 1 MPI processor grid
+ 2432 atoms
+ Time spent = 0.000789404 secs
+
+
+pair_style reax/c NULL
+pair_coeff * * ffield.reax.hns C H O N
+
+compute reax all pair reax/c
+
+neighbor 1.0 bin
+neigh_modify every 20 delay 0 check no
+
+timestep 0.1
+
+thermo_style custom step temp pe press evdwl ecoul vol
+thermo_modify norm yes
+thermo 10
+
+velocity all create 300.0 41279 loop geom
+
+fix 1 all nve
+fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
+
+run 100
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11
+ ghost atom cutoff = 11
+ binsize = 5.5, bins = 10 5 6
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 262.4 | 262.4 | 262.4 Mbytes
+Step Temp PotEng Press E_vdwl E_coul Volume
+ 0 300 -113.27833 437.52103 -111.57687 -1.7014647 27418.867
+ 10 299.87174 -113.27778 2033.6337 -111.57645 -1.7013325 27418.867
+ 20 300.81718 -113.28046 4817.5889 -111.57931 -1.7011463 27418.867
+ 30 301.8622 -113.28323 8303.0039 -111.58237 -1.7008608 27418.867
+ 40 302.4646 -113.28493 10519.459 -111.58446 -1.700467 27418.867
+ 50 300.79064 -113.27989 10402.291 -111.57987 -1.7000218 27418.867
+ 60 296.11534 -113.26599 7929.1348 -111.5664 -1.6995929 27418.867
+ 70 291.73354 -113.25289 5071.5459 -111.5537 -1.6991916 27418.867
+ 80 292.189 -113.25399 5667.0962 -111.55519 -1.6987993 27418.867
+ 90 298.40792 -113.27253 7513.3806 -111.57409 -1.6984403 27418.867
+ 100 303.58246 -113.28809 10017.879 -111.58991 -1.698177 27418.867
+Loop time of 59.5461 on 1 procs for 100 steps with 2432 atoms
+
+Performance: 0.015 ns/day, 1654.060 hours/ns, 1.679 timesteps/s
+97.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 49.922 | 49.922 | 49.922 | 0.0 | 83.84
+Neigh | 0.53154 | 0.53154 | 0.53154 | 0.0 | 0.89
+Comm | 0.011399 | 0.011399 | 0.011399 | 0.0 | 0.02
+Output | 0.00064397 | 0.00064397 | 0.00064397 | 0.0 | 0.00
+Modify | 9.0782 | 9.0782 | 9.0782 | 0.0 | 15.25
+Other | | 0.002116 | | | 0.00
+
+Nlocal: 2432 ave 2432 max 2432 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 10687 ave 10687 max 10687 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 823977 ave 823977 max 823977 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 823977
+Ave neighs/atom = 338.806
+Neighbor list builds = 5
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:00
diff --git a/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4 b/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4
new file mode 100644
index 0000000000..aef07f80eb
--- /dev/null
+++ b/examples/reax/HNS/log.8Mar18.reaxc.hns.g++.4
@@ -0,0 +1,115 @@
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Pure HNS crystal, ReaxFF tests for benchmarking LAMMPS
+# See README for more info
+
+variable x index 2
+variable y index 2
+variable z index 2
+variable t index 100
+
+
+units real
+atom_style charge
+atom_modify sort 100 0.0 # optional
+dimension 3
+boundary p p p
+box tilt large
+
+read_data data.hns-equil
+ triclinic box = (0 0 0) to (22.326 11.1412 13.779) with tilt (0 -5.02603 0)
+ 2 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 304 atoms
+ reading velocities ...
+ 304 velocities
+replicate $x $y $z bbox
+replicate 2 $y $z bbox
+replicate 2 2 $z bbox
+replicate 2 2 2 bbox
+ triclinic box = (0 0 0) to (44.652 22.2824 27.5579) with tilt (0 -10.0521 0)
+ 2 by 1 by 2 MPI processor grid
+ 2432 atoms
+ Time spent = 0.000398397 secs
+
+
+pair_style reax/c NULL
+pair_coeff * * ffield.reax.hns C H O N
+
+compute reax all pair reax/c
+
+neighbor 1.0 bin
+neigh_modify every 20 delay 0 check no
+
+timestep 0.1
+
+thermo_style custom step temp pe press evdwl ecoul vol
+thermo_modify norm yes
+thermo 10
+
+velocity all create 300.0 41279 loop geom
+
+fix 1 all nve
+fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
+
+run 100
+Neighbor list info ...
+ update every 20 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 11
+ ghost atom cutoff = 11
+ binsize = 5.5, bins = 10 5 6
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 126.6 | 126.6 | 126.6 Mbytes
+Step Temp PotEng Press E_vdwl E_coul Volume
+ 0 300 -113.27833 437.52112 -111.57687 -1.7014647 27418.867
+ 10 299.87174 -113.27778 2033.632 -111.57645 -1.7013325 27418.867
+ 20 300.81719 -113.28046 4817.5761 -111.57931 -1.7011463 27418.867
+ 30 301.8622 -113.28323 8302.9767 -111.58237 -1.7008609 27418.867
+ 40 302.4646 -113.28493 10519.481 -111.58446 -1.700467 27418.867
+ 50 300.79064 -113.27989 10402.312 -111.57987 -1.7000217 27418.867
+ 60 296.11534 -113.26599 7929.1393 -111.5664 -1.6995929 27418.867
+ 70 291.73354 -113.25289 5071.5368 -111.5537 -1.6991916 27418.867
+ 80 292.18901 -113.25399 5667.1118 -111.55519 -1.6987993 27418.867
+ 90 298.40793 -113.27253 7513.4029 -111.57409 -1.6984403 27418.867
+ 100 303.58247 -113.28809 10017.892 -111.58991 -1.698177 27418.867
+Loop time of 21.3933 on 4 procs for 100 steps with 2432 atoms
+
+Performance: 0.040 ns/day, 594.257 hours/ns, 4.674 timesteps/s
+97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 14.863 | 16.367 | 18.027 | 28.6 | 76.51
+Neigh | 0.23943 | 0.2422 | 0.24658 | 0.6 | 1.13
+Comm | 0.024331 | 1.6845 | 3.189 | 89.2 | 7.87
+Output | 0.00051165 | 0.00056899 | 0.00068665 | 0.0 | 0.00
+Modify | 3.0933 | 3.0969 | 3.0999 | 0.1 | 14.48
+Other | | 0.001784 | | | 0.01
+
+Nlocal: 608 ave 608 max 608 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 5738.25 ave 5742 max 5734 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Neighs: 231544 ave 231625 max 231466 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 926176
+Ave neighs/atom = 380.829
+Neighbor list builds = 5
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:21
diff --git a/examples/reax/RDX/log.5Oct16.RDX.g++.1 b/examples/reax/RDX/log.8Mar18.RDX.g++.1
similarity index 51%
rename from examples/reax/RDX/log.5Oct16.RDX.g++.1
rename to examples/reax/RDX/log.8Mar18.RDX.g++.1
index 92bb048d43..d0765a97a5 100644
--- a/examples/reax/RDX/log.5Oct16.RDX.g++.1
+++ b/examples/reax/RDX/log.8Mar18.RDX.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems
# .....
@@ -28,43 +29,53 @@ timestep 0.25
run 3000
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 5 5 5
-Memory usage per processor = 18.1116 Mbytes
+ binsize = 6, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 19 | 19 | 19 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10197.932 0 -10197.932 38.347492
- 3000 510.85923 -10091.694 0 -9933.3253 1668.5084
-Loop time of 18.9088 on 1 procs for 3000 steps with 105 atoms
+ 3000 510.63767 -10091.537 0 -9933.2374 1144.545
+Loop time of 21.2931 on 1 procs for 3000 steps with 105 atoms
-Performance: 3.427 ns/day, 7.003 hours/ns, 158.657 timesteps/s
-99.5% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 3.043 ns/day, 7.886 hours/ns, 140.891 timesteps/s
+97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 17.724 | 17.724 | 17.724 | 0.0 | 93.73
-Neigh | 0.27457 | 0.27457 | 0.27457 | 0.0 | 1.45
-Comm | 0.015814 | 0.015814 | 0.015814 | 0.0 | 0.08
-Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00
-Modify | 0.89014 | 0.89014 | 0.89014 | 0.0 | 4.71
-Other | | 0.004246 | | | 0.02
+Pair | 19.887 | 19.887 | 19.887 | 0.0 | 93.40
+Neigh | 0.33143 | 0.33143 | 0.33143 | 0.0 | 1.56
+Comm | 0.02079 | 0.02079 | 0.02079 | 0.0 | 0.10
+Output | 2.5272e-05 | 2.5272e-05 | 2.5272e-05 | 0.0 | 0.00
+Modify | 1.0478 | 1.0478 | 1.0478 | 0.0 | 4.92
+Other | | 0.006125 | | | 0.03
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 645 ave 645 max 645 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3061 ave 3061 max 3061 min
+Neighs: 3063 ave 3063 max 3063 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 3061
-Ave neighs/atom = 29.1524
+Total # of neighbors = 3063
+Ave neighs/atom = 29.1714
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:19
+Total wall time: 0:00:21
diff --git a/examples/reax/RDX/log.5Oct16.RDX.g++.4 b/examples/reax/RDX/log.8Mar18.RDX.g++.4
similarity index 50%
rename from examples/reax/RDX/log.5Oct16.RDX.g++.4
rename to examples/reax/RDX/log.8Mar18.RDX.g++.4
index bcffe8f813..7082d30636 100644
--- a/examples/reax/RDX/log.5Oct16.RDX.g++.4
+++ b/examples/reax/RDX/log.8Mar18.RDX.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems
# .....
@@ -28,43 +29,53 @@ timestep 0.25
run 3000
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 5 5 5
-Memory usage per processor = 12.2102 Mbytes
+ binsize = 6, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 12.14 | 13.04 | 13.9 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10197.932 0 -10197.932 38.347492
- 3000 504.05354 -10089.494 0 -9933.2351 868.32505
-Loop time of 9.70759 on 4 procs for 3000 steps with 105 atoms
+ 3000 509.89257 -10091.36 0 -9933.2916 1406.1215
+Loop time of 10.8858 on 4 procs for 3000 steps with 105 atoms
-Performance: 6.675 ns/day, 3.595 hours/ns, 309.037 timesteps/s
-99.2% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 5.953 ns/day, 4.032 hours/ns, 275.588 timesteps/s
+98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 8.4621 | 8.5307 | 8.6001 | 1.9 | 87.88
-Neigh | 0.12583 | 0.14931 | 0.17341 | 4.5 | 1.54
-Comm | 0.053017 | 0.12311 | 0.19244 | 16.2 | 1.27
-Output | 1.9073e-05 | 2.0802e-05 | 2.408e-05 | 0.0 | 0.00
-Modify | 0.87638 | 0.9012 | 0.92557 | 1.9 | 9.28
-Other | | 0.003213 | | | 0.03
+Pair | 9.3081 | 9.4054 | 9.4994 | 2.6 | 86.40
+Neigh | 0.15541 | 0.18258 | 0.2099 | 4.7 | 1.68
+Comm | 0.070516 | 0.16621 | 0.26541 | 19.7 | 1.53
+Output | 2.2173e-05 | 2.5153e-05 | 3.3855e-05 | 0.0 | 0.00
+Modify | 1.0979 | 1.1272 | 1.1568 | 2.1 | 10.35
+Other | | 0.004379 | | | 0.04
Nlocal: 26.25 ave 46 max 8 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 399.5 ave 512 max 288 min
Histogram: 1 0 0 1 0 0 1 0 0 1
-Neighs: 1010.75 ave 1818 max 420 min
+Neighs: 1011.25 ave 1819 max 420 min
Histogram: 1 0 1 1 0 0 0 0 0 1
-Total # of neighbors = 4043
-Ave neighs/atom = 38.5048
+Total # of neighbors = 4045
+Ave neighs/atom = 38.5238
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:10
+Total wall time: 0:00:11
diff --git a/examples/reax/VOH/log.5Oct16.VOH.g++.4 b/examples/reax/VOH/log.5Oct16.VOH.g++.4
deleted file mode 100644
index 8afe957732..0000000000
--- a/examples/reax/VOH/log.5Oct16.VOH.g++.4
+++ /dev/null
@@ -1,70 +0,0 @@
-LAMMPS (5 Oct 2016)
-# REAX potential for VOH system
-# .....
-
-units real
-
-atom_style charge
-read_data data.VOH
- orthogonal box = (0 0 0) to (25 25 25)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 100 atoms
-
-pair_style reax/c lmp_control
-pair_coeff * * ffield.reax.V_O_C_H H C O V
-Reading potential file ffield.reax.V_O_C_H with DATE: 2011-02-18
-
-neighbor 2 bin
-neigh_modify every 10 delay 0 check no
-
-fix 1 all nve
-fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
-fix 3 all temp/berendsen 500.0 500.0 100.0
-
-timestep 0.25
-
-#dump 1 all atom 30 dump.reax.voh
-
-run 3000
-Neighbor list info ...
- 2 neighbor list requests
- update every 10 steps, delay 0 steps, check no
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12
- ghost atom cutoff = 12
- binsize = 6 -> bins = 5 5 5
-Memory usage per processor = 12.1769 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 0 -10246.825 0 -10246.825 42.256092
- 3000 518.1493 -10196.234 0 -10043.328 -334.5971
-Loop time of 5.59178 on 4 procs for 3000 steps with 100 atoms
-
-Performance: 11.588 ns/day, 2.071 hours/ns, 536.502 timesteps/s
-99.1% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 4.2807 | 4.3532 | 4.398 | 2.1 | 77.85
-Neigh | 0.12328 | 0.14561 | 0.16815 | 4.2 | 2.60
-Comm | 0.051619 | 0.097282 | 0.1697 | 14.1 | 1.74
-Output | 1.7881e-05 | 1.9372e-05 | 2.3842e-05 | 0.1 | 0.00
-Modify | 0.9701 | 0.99258 | 1.0148 | 1.6 | 17.75
-Other | | 0.003097 | | | 0.06
-
-Nlocal: 25 ave 38 max 11 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Nghost: 368.25 ave 449 max 283 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Neighs: 1084.5 ave 1793 max 418 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-
-Total # of neighbors = 4338
-Ave neighs/atom = 43.38
-Neighbor list builds = 300
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:05
diff --git a/examples/reax/VOH/log.5Oct16.VOH.g++.1 b/examples/reax/VOH/log.8Mar18.VOH.g++.1
similarity index 50%
rename from examples/reax/VOH/log.5Oct16.VOH.g++.1
rename to examples/reax/VOH/log.8Mar18.VOH.g++.1
index 9a7a6a59c7..924769e570 100644
--- a/examples/reax/VOH/log.5Oct16.VOH.g++.1
+++ b/examples/reax/VOH/log.8Mar18.VOH.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for VOH system
# .....
@@ -28,43 +29,53 @@ timestep 0.25
run 3000
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 5 5 5
-Memory usage per processor = 16.9211 Mbytes
+ binsize = 6, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 17.79 | 17.79 | 17.79 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10246.825 0 -10246.825 42.256089
- 3000 479.39686 -10186.225 0 -10044.755 -454.82798
-Loop time of 10.4348 on 1 procs for 3000 steps with 100 atoms
+ 3000 476.73301 -10185.256 0 -10044.572 -694.70737
+Loop time of 11.0577 on 1 procs for 3000 steps with 100 atoms
-Performance: 6.210 ns/day, 3.865 hours/ns, 287.499 timesteps/s
-99.2% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 5.860 ns/day, 4.095 hours/ns, 271.304 timesteps/s
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 9.2216 | 9.2216 | 9.2216 | 0.0 | 88.37
-Neigh | 0.2757 | 0.2757 | 0.2757 | 0.0 | 2.64
-Comm | 0.015626 | 0.015626 | 0.015626 | 0.0 | 0.15
-Output | 1.1921e-05 | 1.1921e-05 | 1.1921e-05 | 0.0 | 0.00
-Modify | 0.91782 | 0.91782 | 0.91782 | 0.0 | 8.80
-Other | | 0.004039 | | | 0.04
+Pair | 9.6785 | 9.6785 | 9.6785 | 0.0 | 87.53
+Neigh | 0.32599 | 0.32599 | 0.32599 | 0.0 | 2.95
+Comm | 0.017231 | 0.017231 | 0.017231 | 0.0 | 0.16
+Output | 2.5511e-05 | 2.5511e-05 | 2.5511e-05 | 0.0 | 0.00
+Modify | 1.0311 | 1.0311 | 1.0311 | 0.0 | 9.32
+Other | | 0.004857 | | | 0.04
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 598 ave 598 max 598 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3384 ave 3384 max 3384 min
+Neighs: 3390 ave 3390 max 3390 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 3384
-Ave neighs/atom = 33.84
+Total # of neighbors = 3390
+Ave neighs/atom = 33.9
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:10
+Total wall time: 0:00:11
diff --git a/examples/reax/VOH/log.8Mar18.VOH.g++.4 b/examples/reax/VOH/log.8Mar18.VOH.g++.4
new file mode 100644
index 0000000000..0395af6671
--- /dev/null
+++ b/examples/reax/VOH/log.8Mar18.VOH.g++.4
@@ -0,0 +1,81 @@
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
+# REAX potential for VOH system
+# .....
+
+units real
+
+atom_style charge
+read_data data.VOH
+ orthogonal box = (0 0 0) to (25 25 25)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 100 atoms
+
+pair_style reax/c lmp_control
+pair_coeff * * ffield.reax.V_O_C_H H C O V
+Reading potential file ffield.reax.V_O_C_H with DATE: 2011-02-18
+
+neighbor 2 bin
+neigh_modify every 10 delay 0 check no
+
+fix 1 all nve
+fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
+fix 3 all temp/berendsen 500.0 500.0 100.0
+
+timestep 0.25
+
+#dump 1 all atom 30 dump.reax.voh
+
+run 3000
+Neighbor list info ...
+ update every 10 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12
+ ghost atom cutoff = 12
+ binsize = 6, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 11.21 | 12.52 | 13.64 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -10246.825 0 -10246.825 42.256092
+ 3000 489.67803 -10188.866 0 -10044.362 -553.7513
+Loop time of 6.49847 on 4 procs for 3000 steps with 100 atoms
+
+Performance: 9.972 ns/day, 2.407 hours/ns, 461.647 timesteps/s
+97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 4.7412 | 4.8453 | 4.9104 | 2.9 | 74.56
+Neigh | 0.1468 | 0.17834 | 0.20151 | 4.7 | 2.74
+Comm | 0.071841 | 0.14037 | 0.24502 | 17.2 | 2.16
+Output | 2.1219e-05 | 2.408e-05 | 3.1948e-05 | 0.0 | 0.00
+Modify | 1.3072 | 1.3308 | 1.3627 | 1.7 | 20.48
+Other | | 0.003713 | | | 0.06
+
+Nlocal: 25 ave 38 max 11 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Nghost: 369.75 ave 453 max 283 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs: 1082.25 ave 1788 max 417 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 4329
+Ave neighs/atom = 43.29
+Neighbor list builds = 300
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:06
diff --git a/examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.1 b/examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.1
similarity index 50%
rename from examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.1
rename to examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.1
index 8fcc86dd17..58b1a36719 100644
--- a/examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.1
+++ b/examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for ZnOH2 system
# .....
@@ -28,43 +29,53 @@ timestep 0.25
run 3000
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 5 5 5
-Memory usage per processor = 17.485 Mbytes
+ binsize = 6, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 18.36 | 18.36 | 18.36 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -7900.2668 0 -7900.2668 60.076093
- 3000 522.42599 -7928.9641 0 -7767.0098 -755.28778
-Loop time of 6.38119 on 1 procs for 3000 steps with 105 atoms
+ 3000 535.58577 -7934.7287 0 -7768.6948 -475.46237
+Loop time of 7.29784 on 1 procs for 3000 steps with 105 atoms
-Performance: 10.155 ns/day, 2.363 hours/ns, 470.132 timesteps/s
-99.0% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 8.879 ns/day, 2.703 hours/ns, 411.081 timesteps/s
+97.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 5.2711 | 5.2711 | 5.2711 | 0.0 | 82.60
-Neigh | 0.30669 | 0.30669 | 0.30669 | 0.0 | 4.81
-Comm | 0.015599 | 0.015599 | 0.015599 | 0.0 | 0.24
-Output | 1.0967e-05 | 1.0967e-05 | 1.0967e-05 | 0.0 | 0.00
-Modify | 0.78376 | 0.78376 | 0.78376 | 0.0 | 12.28
-Other | | 0.004036 | | | 0.06
+Pair | 5.9988 | 5.9988 | 5.9988 | 0.0 | 82.20
+Neigh | 0.37455 | 0.37455 | 0.37455 | 0.0 | 5.13
+Comm | 0.019186 | 0.019186 | 0.019186 | 0.0 | 0.26
+Output | 2.4557e-05 | 2.4557e-05 | 2.4557e-05 | 0.0 | 0.00
+Modify | 0.89915 | 0.89915 | 0.89915 | 0.0 | 12.32
+Other | | 0.006108 | | | 0.08
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 649 ave 649 max 649 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 3956 ave 3956 max 3956 min
+Neighs: 3971 ave 3971 max 3971 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 3956
-Ave neighs/atom = 37.6762
+Total # of neighbors = 3971
+Ave neighs/atom = 37.819
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:06
+Total wall time: 0:00:07
diff --git a/examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.4 b/examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.4
similarity index 51%
rename from examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.4
rename to examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.4
index 104d806c33..77c5cbe1b7 100644
--- a/examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.4
+++ b/examples/reax/ZnOH2/log.8Mar18.ZnOH2.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# REAX potential for ZnOH2 system
# .....
@@ -28,40 +29,50 @@ timestep 0.25
run 3000
Neighbor list info ...
- 2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
- binsize = 6 -> bins = 5 5 5
-Memory usage per processor = 12.0066 Mbytes
+ binsize = 6, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 11.28 | 12.77 | 14.21 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -7900.2668 0 -7900.2668 60.076093
- 3000 536.8256 -7935.1437 0 -7768.7255 -479.27959
-Loop time of 3.77632 on 4 procs for 3000 steps with 105 atoms
+ 3000 538.25796 -7935.6159 0 -7768.7536 -525.47078
+Loop time of 4.48824 on 4 procs for 3000 steps with 105 atoms
-Performance: 17.160 ns/day, 1.399 hours/ns, 794.423 timesteps/s
-99.0% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 14.438 ns/day, 1.662 hours/ns, 668.414 timesteps/s
+97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 2.7337 | 2.7808 | 2.8316 | 2.5 | 73.64
-Neigh | 0.13455 | 0.16558 | 0.19493 | 5.3 | 4.38
-Comm | 0.046741 | 0.099375 | 0.14663 | 13.6 | 2.63
-Output | 1.7881e-05 | 2.0027e-05 | 2.408e-05 | 0.1 | 0.00
-Modify | 0.69792 | 0.7275 | 0.75887 | 2.5 | 19.26
-Other | | 0.003084 | | | 0.08
+Pair | 3.1031 | 3.1698 | 3.2378 | 3.3 | 70.62
+Neigh | 0.16642 | 0.20502 | 0.25003 | 6.6 | 4.57
+Comm | 0.074932 | 0.14224 | 0.21025 | 15.6 | 3.17
+Output | 0.00011349 | 0.00011736 | 0.00012231 | 0.0 | 0.00
+Modify | 0.92089 | 0.96736 | 1.0083 | 3.2 | 21.55
+Other | | 0.003731 | | | 0.08
Nlocal: 26.25 ave 45 max 15 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 399 ave 509 max 295 min
Histogram: 1 0 0 0 2 0 0 0 0 1
-Neighs: 1150 ave 2061 max 701 min
+Neighs: 1151.5 ave 2066 max 701 min
Histogram: 1 2 0 0 0 0 0 0 0 1
-Total # of neighbors = 4600
-Ave neighs/atom = 43.8095
+Total # of neighbors = 4606
+Ave neighs/atom = 43.8667
Neighbor list builds = 300
Dangerous builds not checked
diff --git a/examples/reax/ci-reaxFF/input.in b/examples/reax/ci-reaxFF/in.ci-reax.CH
similarity index 100%
rename from examples/reax/ci-reaxFF/input.in
rename to examples/reax/ci-reaxFF/in.ci-reax.CH
diff --git a/examples/reax/ci-reaxFF/log.23Oct17.g++.1 b/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1
similarity index 77%
rename from examples/reax/ci-reaxFF/log.23Oct17.g++.1
rename to examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1
index 1be46a9699..e966fd26b6 100644
--- a/examples/reax/ci-reaxFF/log.23Oct17.g++.1
+++ b/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (23 Oct 2017)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
#ci-reax potential for CH systems with tabulated ZBL correction
atom_style charge
units real
@@ -31,6 +32,7 @@ fix 2 all temp/berendsen 500.0 500.0 100.0
#dump 1 all atom 30 dump.ci-reax.lammpstrj
run 3000
+WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (../pair_reaxc.cpp:392)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@@ -52,20 +54,20 @@ Per MPI rank memory allocation (min/avg/max) = 43.46 | 43.46 | 43.46 Mbytes
Step Temp E_pair E_mol TotEng Press
0 508.42043 -28736.654 0 -28260.785 1678.3276
3000 480.41333 -28707.835 0 -28258.181 -3150.0762
-Loop time of 21.5509 on 1 procs for 3000 steps with 315 atoms
+Loop time of 45.3959 on 1 procs for 3000 steps with 315 atoms
-Performance: 3.007 ns/day, 7.982 hours/ns, 139.205 timesteps/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.427 ns/day, 16.813 hours/ns, 66.085 timesteps/s
+96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 21.315 | 21.315 | 21.315 | 0.0 | 98.91
-Neigh | 0.17846 | 0.17846 | 0.17846 | 0.0 | 0.83
-Comm | 0.028676 | 0.028676 | 0.028676 | 0.0 | 0.13
-Output | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.00
-Modify | 0.018969 | 0.018969 | 0.018969 | 0.0 | 0.09
-Other | | 0.009438 | | | 0.04
+Pair | 44.955 | 44.955 | 44.955 | 0.0 | 99.03
+Neigh | 0.29903 | 0.29903 | 0.29903 | 0.0 | 0.66
+Comm | 0.056547 | 0.056547 | 0.056547 | 0.0 | 0.12
+Output | 4.8399e-05 | 4.8399e-05 | 4.8399e-05 | 0.0 | 0.00
+Modify | 0.058722 | 0.058722 | 0.058722 | 0.0 | 0.13
+Other | | 0.02632 | | | 0.06
Nlocal: 315 ave 315 max 315 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -81,4 +83,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:21
+Total wall time: 0:00:45
diff --git a/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4 b/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4
new file mode 100644
index 0000000000..ccc87b3536
--- /dev/null
+++ b/examples/reax/ci-reaxFF/log.8Mar18.ci-reax.CH.g++.4
@@ -0,0 +1,86 @@
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
+#ci-reax potential for CH systems with tabulated ZBL correction
+atom_style charge
+units real
+
+read_data CH4.dat
+ orthogonal box = (0 0 0) to (20 20 20)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 315 atoms
+ reading velocities ...
+ 315 velocities
+
+pair_style hybrid/overlay reax/c control checkqeq no table linear 11000
+pair_coeff * * reax/c ffield.ci-reax.CH C H
+Reading potential file ffield.ci-reax.CH with DATE: 2017-11-20
+pair_coeff 1 1 table ci-reaxFF_ZBL.dat CC_cireaxFF
+WARNING: 2 of 10000 force values in table are inconsistent with -dE/dr.
+ Should only be flagged at inflection points (../pair_table.cpp:481)
+pair_coeff 1 2 table ci-reaxFF_ZBL.dat CH_cireaxFF
+WARNING: 2 of 11000 force values in table are inconsistent with -dE/dr.
+ Should only be flagged at inflection points (../pair_table.cpp:481)
+pair_coeff 2 2 table ci-reaxFF_ZBL.dat HH_cireaxFF
+WARNING: 2 of 6000 force values in table are inconsistent with -dE/dr.
+ Should only be flagged at inflection points (../pair_table.cpp:481)
+
+timestep 0.25
+fix 1 all nve
+fix 2 all temp/berendsen 500.0 500.0 100.0
+
+#dump 1 all atom 30 dump.ci-reax.lammpstrj
+
+run 3000
+WARNING: Total cutoff < 2*bond cutoff. May need to use an increased neighbor list skin. (../pair_reaxc.cpp:392)
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 9.5
+ ghost atom cutoff = 9.5
+ binsize = 4.75, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) pair table, 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) = 24.48 | 25.61 | 27.27 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 508.42043 -28736.654 0 -28260.785 1678.3276
+ 3000 480.41333 -28707.835 0 -28258.181 -3150.0762
+Loop time of 24.7034 on 4 procs for 3000 steps with 315 atoms
+
+Performance: 2.623 ns/day, 9.149 hours/ns, 121.441 timesteps/s
+95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 18.945 | 21.367 | 24.046 | 39.3 | 86.49
+Neigh | 0.1456 | 0.15254 | 0.16101 | 1.6 | 0.62
+Comm | 0.39168 | 3.0859 | 5.5185 | 103.9 | 12.49
+Output | 3.5763e-05 | 4.065e-05 | 5.2452e-05 | 0.0 | 0.00
+Modify | 0.05831 | 0.068811 | 0.077666 | 2.9 | 0.28
+Other | | 0.0292 | | | 0.12
+
+Nlocal: 78.75 ave 96 max 65 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 1233 ave 1348 max 1116 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Neighs: 9467.25 ave 12150 max 7160 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+
+Total # of neighbors = 37869
+Ave neighs/atom = 120.219
+Neighbor list builds = 37
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:24
diff --git a/examples/reax/log.5Oct16.reax.rdx.g++.1 b/examples/reax/log.5Oct16.reax.rdx.g++.1
deleted file mode 100644
index 08a24cf635..0000000000
--- a/examples/reax/log.5Oct16.reax.rdx.g++.1
+++ /dev/null
@@ -1,101 +0,0 @@
-LAMMPS (5 Oct 2016)
-# ReaxFF potential for RDX system
-
-units real
-
-atom_style charge
-read_data data.rdx
- orthogonal box = (35 35 35) to (48 48 48)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 21 atoms
-
-# reax args: hbcut hbnewflag tripflag precision
-
-pair_style reax 6.0 1 1 1.0e-6
-WARNING: The pair_style reax command will be deprecated soon - users should switch to pair_style reax/c (../pair_reax.cpp:49)
-pair_coeff * * ffield.reax 1 2 3 4
-
-compute reax all pair reax
-
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-variable elp equal c_reax[3]
-variable emol equal c_reax[4]
-variable ev equal c_reax[5]
-variable epen equal c_reax[6]
-variable ecoa equal c_reax[7]
-variable ehb equal c_reax[8]
-variable et equal c_reax[9]
-variable eco equal c_reax[10]
-variable ew equal c_reax[11]
-variable ep equal c_reax[12]
-variable efi equal c_reax[13]
-variable eqeq equal c_reax[14]
-
-neighbor 2.5 bin
-neigh_modify every 10 delay 0 check no
-
-fix 1 all nve
-
-thermo 10
-thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
-
-timestep 1.0
-
-#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
-
-#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3
-
-#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3
-
-run 100
-Neighbor list info ...
- 1 neighbor list requests
- update every 10 steps, delay 0 steps, check no
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12.5
- ghost atom cutoff = 12.5
- binsize = 6.25 -> bins = 3 3 3
-Memory usage per processor = 2.95105 Mbytes
-Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
- 0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79971 0 168.88435
- 10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070522 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17724 0 107.5115
- 20 516.83079 -1941.677 -1910.8655 -12525.41 -2801.8626 7.4107974 0.073134188 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574158
- 30 467.2641 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179959 0.049322439 0 78.853175 0.13604392 -51.653634 0 19.862872 -9.7098575 853.79334 -151.232 0 80.861768
- 40 647.45541 -1951.1994 -1912.6006 -5883.7147 -2798.3556 17.334807 0.15102863 0 63.23512 0.18070931 -54.598962 0 17.325008 -12.052277 883.01667 -164.21335 0 96.777422
- 50 716.38057 -1949.4749 -1906.767 5473.2085 -2800.931 9.2056917 0.15413274 0 85.371449 3.2986106 -78.253597 0 34.861773 -8.5531236 882.01435 -193.85275 0 117.2096
- 60 1175.2707 -1975.9611 -1905.8959 -1939.4971 -2726.5816 -11.651982 0.24296788 0 48.320663 7.1799636 -75.363641 0 16.520132 -4.8869463 844.754 -194.23296 0 119.73837
- 70 1156.7 -1975.3486 -1906.3905 24628.344 -2880.5223 25.652478 0.26894312 0 83.724884 7.1049303 -68.700942 0 24.750744 -8.6338218 911.20067 -183.4058 0 113.21158
- 80 840.23687 -1955.4768 -1905.3851 -17731.383 -2755.7295 -8.0168306 0.13867962 0 86.14748 2.2387306 -76.945841 0 23.595858 -7.2609645 853.6346 -167.88289 0 94.603895
- 90 365.79169 -1926.406 -1904.5989 898.37155 -2842.183 47.368211 0.23109 0 92.288131 0.38031313 -61.361483 0 18.476377 -12.255472 900.24202 -186.48056 0 116.88831
- 100 801.32078 -1953.4177 -1905.646 -2417.5518 -2802.7244 4.6676973 0.18046558 0 76.730114 5.4177372 -77.102556 0 24.997234 -7.7554179 898.67306 -196.8912 0 120.38952
-Loop time of 0.512828 on 1 procs for 100 steps with 21 atoms
-
-Performance: 16.848 ns/day, 1.425 hours/ns, 194.997 timesteps/s
-99.4% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.51126 | 0.51126 | 0.51126 | 0.0 | 99.69
-Neigh | 0.00071597 | 0.00071597 | 0.00071597 | 0.0 | 0.14
-Comm | 0.00040317 | 0.00040317 | 0.00040317 | 0.0 | 0.08
-Output | 0.00027037 | 0.00027037 | 0.00027037 | 0.0 | 0.05
-Modify | 7.2241e-05 | 7.2241e-05 | 7.2241e-05 | 0.0 | 0.01
-Other | | 0.000108 | | | 0.02
-
-Nlocal: 21 ave 21 max 21 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 546 ave 546 max 546 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 1106 ave 1106 max 1106 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1106
-Ave neighs/atom = 52.6667
-Neighbor list builds = 10
-Dangerous builds not checked
-Total wall time: 0:00:00
diff --git a/examples/reax/log.5Oct16.reax.rdx.g++.4 b/examples/reax/log.5Oct16.reax.rdx.g++.4
deleted file mode 100644
index 2f052fbf74..0000000000
--- a/examples/reax/log.5Oct16.reax.rdx.g++.4
+++ /dev/null
@@ -1,101 +0,0 @@
-LAMMPS (5 Oct 2016)
-# ReaxFF potential for RDX system
-
-units real
-
-atom_style charge
-read_data data.rdx
- orthogonal box = (35 35 35) to (48 48 48)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 21 atoms
-
-# reax args: hbcut hbnewflag tripflag precision
-
-pair_style reax 6.0 1 1 1.0e-6
-WARNING: The pair_style reax command will be deprecated soon - users should switch to pair_style reax/c (../pair_reax.cpp:49)
-pair_coeff * * ffield.reax 1 2 3 4
-
-compute reax all pair reax
-
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-variable elp equal c_reax[3]
-variable emol equal c_reax[4]
-variable ev equal c_reax[5]
-variable epen equal c_reax[6]
-variable ecoa equal c_reax[7]
-variable ehb equal c_reax[8]
-variable et equal c_reax[9]
-variable eco equal c_reax[10]
-variable ew equal c_reax[11]
-variable ep equal c_reax[12]
-variable efi equal c_reax[13]
-variable eqeq equal c_reax[14]
-
-neighbor 2.5 bin
-neigh_modify every 10 delay 0 check no
-
-fix 1 all nve
-
-thermo 10
-thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
-
-timestep 1.0
-
-#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
-
-#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3
-
-#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3
-
-run 100
-Neighbor list info ...
- 1 neighbor list requests
- update every 10 steps, delay 0 steps, check no
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12.5
- ghost atom cutoff = 12.5
- binsize = 6.25 -> bins = 3 3 3
-Memory usage per processor = 3.0718 Mbytes
-Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
- 0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.8843
- 10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17725 0 107.51148
- 20 516.8308 -1941.677 -1910.8655 -12525.411 -2801.8626 7.4107973 0.07313419 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574155
- 30 467.26411 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179966 0.049322437 0 78.853175 0.13604391 -51.653634 0 19.862872 -9.7098574 853.79333 -151.232 0 80.861765
- 40 647.45584 -1951.1994 -1912.6006 -5883.7102 -2798.3557 17.334812 0.15102857 0 63.235124 0.18070914 -54.598951 0 17.325006 -12.052278 883.01674 -164.21335 0 96.777418
- 50 716.38108 -1949.4679 -1906.76 5473.1803 -2800.9311 9.2057064 0.15413272 0 85.371443 3.2986124 -78.253597 0 34.861778 -8.5531235 882.01441 -193.85213 0 117.21596
- 60 1175.2703 -1975.9632 -1905.898 -1939.6676 -2726.5815 -11.652032 0.24296779 0 48.320636 7.1799647 -75.363643 0 16.520124 -4.8869416 844.75396 -194.25563 0 119.75889
- 70 1156.7016 -1975.3469 -1906.3887 24628.125 -2880.5225 25.65252 0.26894309 0 83.724869 7.1048931 -68.700978 0 24.750754 -8.6338341 911.20067 -183.41947 0 113.22722
- 80 840.3323 -1955.4867 -1905.3893 -17732.956 -2755.7336 -8.0168615 0.13869303 0 86.143454 2.2388975 -76.946365 0 23.594977 -7.2608903 853.63682 -167.88599 0 94.604168
- 90 365.75853 -1926.4192 -1904.6141 902.29004 -2842.1715 47.360077 0.23110905 0 92.28805 0.38040356 -61.364192 0 18.473252 -12.253964 900.23128 -186.47889 0 116.88518
- 100 801.64661 -1953.4392 -1905.6481 -2464.5533 -2802.6922 4.6510183 0.18048786 0 76.715675 5.41849 -77.102069 0 24.987058 -7.7531389 898.65974 -196.87724 0 120.37303
-Loop time of 0.405054 on 4 procs for 100 steps with 21 atoms
-
-Performance: 21.331 ns/day, 1.125 hours/ns, 246.881 timesteps/s
-96.9% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.16194 | 0.24674 | 0.40012 | 18.4 | 60.92
-Neigh | 7.3671e-05 | 0.00024015 | 0.00053477 | 1.1 | 0.06
-Comm | 0.0037704 | 0.1575 | 0.24247 | 23.1 | 38.88
-Output | 0.00037122 | 0.00040913 | 0.0004406 | 0.1 | 0.10
-Modify | 4.22e-05 | 6.175e-05 | 8.3685e-05 | 0.2 | 0.02
-Other | | 0.0001087 | | | 0.03
-
-Nlocal: 5.25 ave 15 max 0 min
-Histogram: 1 0 2 0 0 0 0 0 0 1
-Nghost: 355.5 ave 432 max 282 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Neighs: 301.25 ave 827 max 0 min
-Histogram: 1 0 2 0 0 0 0 0 0 1
-
-Total # of neighbors = 1205
-Ave neighs/atom = 57.381
-Neighbor list builds = 10
-Dangerous builds not checked
-Total wall time: 0:00:00
diff --git a/examples/reax/log.5Oct16.reaxc.rdx.g++.1 b/examples/reax/log.5Oct16.reaxc.rdx.g++.1
deleted file mode 100644
index 5c8bb737b9..0000000000
--- a/examples/reax/log.5Oct16.reaxc.rdx.g++.1
+++ /dev/null
@@ -1,104 +0,0 @@
-LAMMPS (5 Oct 2016)
-# ReaxFF potential for RDX system
-# this run is equivalent to reax/in.reax.rdx
-
-units real
-
-atom_style charge
-read_data data.rdx
- orthogonal box = (35 35 35) to (48 48 48)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 21 atoms
-
-pair_style reax/c control.reax_c.rdx
-pair_coeff * * ffield.reax C H O N
-Reading potential file ffield.reax with DATE: 2010-02-19
-
-compute reax all pair reax/c
-
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-variable elp equal c_reax[3]
-variable emol equal c_reax[4]
-variable ev equal c_reax[5]
-variable epen equal c_reax[6]
-variable ecoa equal c_reax[7]
-variable ehb equal c_reax[8]
-variable et equal c_reax[9]
-variable eco equal c_reax[10]
-variable ew equal c_reax[11]
-variable ep equal c_reax[12]
-variable efi equal c_reax[13]
-variable eqeq equal c_reax[14]
-
-neighbor 2.5 bin
-neigh_modify every 10 delay 0 check no
-
-fix 1 all nve
-fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
-
-thermo 10
-thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
-
-timestep 1.0
-
-#dump 1 all atom 10 dump.reaxc.rdx
-
-#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3
-
-#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3
-
-run 100
-Neighbor list info ...
- 2 neighbor list requests
- update every 10 steps, delay 0 steps, check no
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12.5
- ghost atom cutoff = 12.5
- binsize = 6.25 -> bins = 3 3 3
-Memory usage per processor = 14.4462 Mbytes
-Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
- 0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396
- 10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935
- 20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379
- 30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727
- 40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096
- 50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995
- 60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413
- 70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648
- 80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398
- 90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068717 0.2433807 0 96.181613 0.96184887 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141
- 100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961
-Loop time of 0.362895 on 1 procs for 100 steps with 21 atoms
-
-Performance: 23.809 ns/day, 1.008 hours/ns, 275.562 timesteps/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.34367 | 0.34367 | 0.34367 | 0.0 | 94.70
-Neigh | 0.0078354 | 0.0078354 | 0.0078354 | 0.0 | 2.16
-Comm | 0.00043559 | 0.00043559 | 0.00043559 | 0.0 | 0.12
-Output | 0.00019908 | 0.00019908 | 0.00019908 | 0.0 | 0.05
-Modify | 0.010645 | 0.010645 | 0.010645 | 0.0 | 2.93
-Other | | 0.0001094 | | | 0.03
-
-Nlocal: 21 ave 21 max 21 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 546 ave 546 max 546 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 1096 ave 1096 max 1096 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1096
-Ave neighs/atom = 52.1905
-Neighbor list builds = 10
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:00
diff --git a/examples/reax/log.5Oct16.reaxc.rdx.g++.4 b/examples/reax/log.5Oct16.reaxc.rdx.g++.4
deleted file mode 100644
index 10f11811cf..0000000000
--- a/examples/reax/log.5Oct16.reaxc.rdx.g++.4
+++ /dev/null
@@ -1,104 +0,0 @@
-LAMMPS (5 Oct 2016)
-# ReaxFF potential for RDX system
-# this run is equivalent to reax/in.reax.rdx
-
-units real
-
-atom_style charge
-read_data data.rdx
- orthogonal box = (35 35 35) to (48 48 48)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 21 atoms
-
-pair_style reax/c control.reax_c.rdx
-pair_coeff * * ffield.reax C H O N
-Reading potential file ffield.reax with DATE: 2010-02-19
-
-compute reax all pair reax/c
-
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-variable elp equal c_reax[3]
-variable emol equal c_reax[4]
-variable ev equal c_reax[5]
-variable epen equal c_reax[6]
-variable ecoa equal c_reax[7]
-variable ehb equal c_reax[8]
-variable et equal c_reax[9]
-variable eco equal c_reax[10]
-variable ew equal c_reax[11]
-variable ep equal c_reax[12]
-variable efi equal c_reax[13]
-variable eqeq equal c_reax[14]
-
-neighbor 2.5 bin
-neigh_modify every 10 delay 0 check no
-
-fix 1 all nve
-fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
-
-thermo 10
-thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
-
-timestep 1.0
-
-#dump 1 all atom 10 dump.reaxc.rdx
-
-#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 3
-
-#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 3
-
-run 100
-Neighbor list info ...
- 2 neighbor list requests
- update every 10 steps, delay 0 steps, check no
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 12.5
- ghost atom cutoff = 12.5
- binsize = 6.25 -> bins = 3 3 3
-Memory usage per processor = 12.531 Mbytes
-Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
- 0 0 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418
- 10 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252288 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
- 20 538.95831 -1942.7037 -1910.5731 -10725.671 -2803.7395 7.9078306 0.077926651 0 81.610051 0.22951926 -57.557099 0 30.331204 -10.178049 878.99014 -159.69268 0 89.316921
- 30 463.09502 -1933.5765 -1905.9685 -33255.512 -2749.8591 -8.015455 0.027628766 0 81.6274 0.11972393 -50.262275 0 20.820315 -9.6327041 851.88722 -149.49498 0 79.205714
- 40 885.49378 -1958.9125 -1906.1228 -4814.644 -2795.644 9.1506485 0.13747497 0 70.948 0.24360511 -57.862677 0 19.076502 -11.141216 873.73898 -159.99393 0 92.43409
- 50 861.16297 -1954.4602 -1903.1209 -1896.8002 -2784.8451 3.8270162 0.157933 0 79.851673 3.3492148 -78.066132 0 32.628944 -7.9565368 872.81852 -190.98572 0 114.76001
- 60 1167.7835 -1971.8433 -1902.2245 -3482.8296 -2705.8635 -17.121613 0.2274909 0 44.507674 7.85602 -74.788998 0 16.256483 -4.6046575 835.83058 -188.33691 0 114.19414
- 70 1439.9939 -1989.3026 -1903.4556 23846.042 -2890.7893 31.958672 0.26671708 0 85.758381 3.1804035 -71.002944 0 24.357195 -10.311284 905.8679 -175.38487 0 106.79661
- 80 502.39535 -1930.7548 -1900.8039 -20356.194 -2703.8126 -18.662209 0.11286005 0 99.803849 2.0329206 -76.171278 0 19.23716 -6.2787147 826.47505 -166.03123 0 92.539386
- 90 749.07874 -1946.9841 -1902.3269 17798.394 -2863.7576 42.068612 0.24338059 0 96.181423 0.96185061 -69.95542 0 24.615344 -11.582758 903.68812 -190.13826 0 120.69124
- 100 1109.6904 -1968.5879 -1902.4323 -4490.0667 -2755.8991 -7.1224194 0.21757691 0 61.805857 7.0827218 -75.645383 0 20.115437 -6.23727 863.56487 -198.56975 0 122.09963
-Loop time of 0.293673 on 4 procs for 100 steps with 21 atoms
-
-Performance: 29.420 ns/day, 0.816 hours/ns, 340.514 timesteps/s
-99.1% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.24143 | 0.24223 | 0.24409 | 0.2 | 82.48
-Neigh | 0.003767 | 0.0049117 | 0.0061524 | 1.2 | 1.67
-Comm | 0.0030656 | 0.0048578 | 0.0057402 | 1.5 | 1.65
-Output | 0.00033545 | 0.00036347 | 0.00038052 | 0.1 | 0.12
-Modify | 0.039885 | 0.041207 | 0.042435 | 0.4 | 14.03
-Other | | 0.0001001 | | | 0.03
-
-Nlocal: 5.25 ave 15 max 0 min
-Histogram: 1 0 2 0 0 0 0 0 0 1
-Nghost: 355.5 ave 432 max 282 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Neighs: 298.75 ave 822 max 0 min
-Histogram: 1 0 2 0 0 0 0 0 0 1
-
-Total # of neighbors = 1195
-Ave neighs/atom = 56.9048
-Neighbor list builds = 10
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:00
diff --git a/examples/reax/log.8March18.reax.rdx.g++.1 b/examples/reax/log.8March18.reax.rdx.g++.1
new file mode 100644
index 0000000000..c2edc5d51f
--- /dev/null
+++ b/examples/reax/log.8March18.reax.rdx.g++.1
@@ -0,0 +1,107 @@
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
+# ReaxFF potential for RDX system
+
+units real
+
+atom_style charge
+read_data data.rdx
+ orthogonal box = (35 35 35) to (48 48 48)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 21 atoms
+
+# reax args: hbcut hbnewflag tripflag precision
+
+pair_style reax 6.0 1 1 1.0e-6
+WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
+pair_coeff * * ffield.reax 1 2 3 4
+
+compute reax all pair reax
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify every 10 delay 0 check no
+
+fix 1 all nve
+
+thermo 10
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 1.0
+
+#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+run 100
+Neighbor list info ...
+ update every 10 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25, bins = 3 3 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair reax, perpetual
+ attributes: half, newton off
+ pair build: half/bin/newtoff
+ stencil: half/bin/3d/newtoff
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.278 | 3.278 | 3.278 Mbytes
+Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+ 0 0 -1885.1269 -1885.1269 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79973 0 168.8842
+ 10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.02023 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.5115
+ 20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134186 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574159
+ 30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179958 0.049322453 0 78.853173 0.13604393 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.86177
+ 40 647.45528 -1951.1994 -1912.6006 -5883.713 -2798.3556 17.334814 0.15102862 0 63.235117 0.18070924 -54.598957 0 17.325007 -12.052278 883.0167 -164.21335 0 96.777424
+ 50 716.38088 -1949.4735 -1906.7656 5473.1969 -2800.9309 9.2056861 0.15413274 0 85.371466 3.2986127 -78.253597 0 34.861774 -8.553123 882.01431 -193.85254 0 117.21068
+ 60 1175.2705 -1975.961 -1905.8958 -1939.4966 -2726.5816 -11.651996 0.24296786 0 48.320654 7.1799691 -75.363638 0 16.520127 -4.8869441 844.75401 -194.23297 0 119.73841
+ 70 1156.701 -1975.3497 -1906.3916 24628.304 -2880.5225 25.652501 0.26894311 0 83.724852 7.1049152 -68.70096 0 24.750735 -8.6338267 911.20079 -183.40562 0 113.21047
+ 80 840.23677 -1955.4769 -1905.3851 -17731.334 -2755.7299 -8.0167723 0.1386797 0 86.147417 2.2387319 -76.945843 0 23.595869 -7.260968 853.63487 -167.88288 0 94.603961
+ 90 365.79122 -1926.4061 -1904.599 898.38479 -2842.1832 47.368107 0.23109002 0 92.288071 0.38031213 -61.361485 0 18.476336 -12.25546 900.24233 -186.48046 0 116.88827
+ 100 801.32158 -1953.418 -1905.6462 -2417.6887 -2802.7247 4.6676477 0.18046575 0 76.729987 5.4177322 -77.102566 0 24.997175 -7.7554074 898.67337 -196.89114 0 120.38946
+Loop time of 0.463306 on 1 procs for 100 steps with 21 atoms
+
+Performance: 18.649 ns/day, 1.287 hours/ns, 215.840 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.46143 | 0.46143 | 0.46143 | 0.0 | 99.60
+Neigh | 0.00087953 | 0.00087953 | 0.00087953 | 0.0 | 0.19
+Comm | 0.00042653 | 0.00042653 | 0.00042653 | 0.0 | 0.09
+Output | 0.00034237 | 0.00034237 | 0.00034237 | 0.0 | 0.07
+Modify | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.02
+Other | | 0.000124 | | | 0.03
+
+Nlocal: 21 ave 21 max 21 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 546 ave 546 max 546 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1106 ave 1106 max 1106 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1106
+Ave neighs/atom = 52.6667
+Neighbor list builds = 10
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/reax/log.8March18.reax.rdx.g++.4 b/examples/reax/log.8March18.reax.rdx.g++.4
new file mode 100644
index 0000000000..9526e25661
--- /dev/null
+++ b/examples/reax/log.8March18.reax.rdx.g++.4
@@ -0,0 +1,107 @@
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
+# ReaxFF potential for RDX system
+
+units real
+
+atom_style charge
+read_data data.rdx
+ orthogonal box = (35 35 35) to (48 48 48)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 21 atoms
+
+# reax args: hbcut hbnewflag tripflag precision
+
+pair_style reax 6.0 1 1 1.0e-6
+WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
+pair_coeff * * ffield.reax 1 2 3 4
+
+compute reax all pair reax
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify every 10 delay 0 check no
+
+fix 1 all nve
+
+thermo 10
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 1.0
+
+#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+run 100
+Neighbor list info ...
+ update every 10 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25, bins = 3 3 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair reax, perpetual
+ attributes: half, newton off
+ pair build: half/bin/newtoff
+ stencil: half/bin/3d/newtoff
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.262 | 3.36 | 3.647 Mbytes
+Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+ 0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.88428
+ 10 1281.7558 -1989.1322 -1912.7187 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.51152
+ 20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134187 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574168
+ 30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179959 0.049322449 0 78.853173 0.13604392 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.861765
+ 40 647.45479 -1951.1995 -1912.6007 -5883.7199 -2798.3556 17.334805 0.15102868 0 63.235116 0.18070946 -54.59897 0 17.32501 -12.052277 883.0166 -164.21339 0 96.777473
+ 50 716.37927 -1949.466 -1906.7582 5473.2486 -2800.9309 9.2056758 0.15413278 0 85.37143 3.2986099 -78.253596 0 34.861773 -8.5531243 882.01424 -193.85223 0 117.21791
+ 60 1175.2698 -1975.9612 -1905.896 -1939.5206 -2726.5818 -11.651942 0.24296793 0 48.320679 7.1799538 -75.36365 0 16.520134 -4.8869515 844.75405 -194.23289 0 119.7383
+ 70 1156.6963 -1975.3494 -1906.3915 24628.423 -2880.5221 25.65242 0.26894312 0 83.724787 7.1049615 -68.700925 0 24.750729 -8.6338123 911.2006 -183.40591 0 113.21091
+ 80 840.238 -1955.4788 -1905.387 -17731.371 -2755.7301 -8.0167357 0.13868007 0 86.147246 2.2387405 -76.945868 0 23.595868 -7.2609697 853.6349 -167.88312 0 94.602512
+ 90 365.78645 -1926.4072 -1904.6004 898.36945 -2842.1831 47.368307 0.23108998 0 92.288039 0.38031101 -61.361464 0 18.476388 -12.255481 900.24216 -186.48066 0 116.88716
+ 100 801.31322 -1953.4165 -1905.6452 -2417.2041 -2802.7247 4.6678077 0.18046498 0 76.730367 5.4176812 -77.102592 0 24.9973 -7.7554425 898.6732 -196.89097 0 120.39043
+Loop time of 0.404551 on 4 procs for 100 steps with 21 atoms
+
+Performance: 21.357 ns/day, 1.124 hours/ns, 247.188 timesteps/s
+97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.2191 | 0.28038 | 0.39839 | 13.2 | 69.31
+Neigh | 5.8651e-05 | 0.00025928 | 0.00062203 | 0.0 | 0.06
+Comm | 0.0046599 | 0.12307 | 0.1845 | 19.9 | 30.42
+Output | 0.00055337 | 0.00062728 | 0.00071192 | 0.0 | 0.16
+Modify | 5.3167e-05 | 7.844e-05 | 0.00010109 | 0.0 | 0.02
+Other | | 0.0001363 | | | 0.03
+
+Nlocal: 5.25 ave 15 max 0 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Nghost: 355.5 ave 432 max 282 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs: 301.25 ave 827 max 0 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+
+Total # of neighbors = 1205
+Ave neighs/atom = 57.381
+Neighbor list builds = 10
+Dangerous builds not checked
+Total wall time: 0:00:00
diff --git a/examples/reax/log.5Oct16.reax.tatb.g++.1 b/examples/reax/log.8March18.reax.tatb.g++.1
similarity index 61%
rename from examples/reax/log.5Oct16.reax.tatb.g++.1
rename to examples/reax/log.8March18.reax.tatb.g++.1
index cc8d42a583..53d77cd1da 100644
--- a/examples/reax/log.5Oct16.reax.tatb.g++.1
+++ b/examples/reax/log.8March18.reax.tatb.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
@@ -12,7 +13,7 @@ read_data data.tatb
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
-WARNING: The pair_style reax command will be deprecated soon - users should switch to pair_style reax/c (../pair_reax.cpp:49)
+WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
@@ -54,34 +55,39 @@ fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Neighbor list info ...
- 1 neighbor list requests
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
- binsize = 6.25 -> bins = 5 4 3
-Memory usage per processor = 6.61277 Mbytes
+ binsize = 6.25, bins = 5 4 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair reax, perpetual
+ attributes: half, newton off
+ pair build: half/bin/newtoff
+ stencil: half/bin/3d/newtoff
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.764 | 7.764 | 7.764 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
- 5 0.63682807 -44767.737 -44767.01 8391.5966 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2727 0 6388.8127
- 10 2.4306957 -44769.41 -44766.635 11717.369 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0713 0 6381.7946
- 15 5.0590478 -44772.63 -44766.854 17125.033 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3112 0 6370.4665
- 20 8.0678579 -44775.923 -44766.713 24620.824 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3104 0 6355.1097
- 25 10.975539 -44777.231 -44764.701 34381.278 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.2311 -1582.8552 253.88696 -653.46042 18790.855 -8683.8362 0 6336.3099
-Loop time of 7.48375 on 1 procs for 25 steps with 384 atoms
+ 5 0.63682806 -44767.737 -44767.01 8391.5964 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2728 0 6388.8127
+ 10 2.4306958 -44769.409 -44766.634 11717.376 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0693 0 6381.7942
+ 15 5.0590493 -44772.631 -44766.855 17125.067 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28962 -1566.5961 252.97781 -654.93836 18835.335 -8719.3013 0 6370.4551
+ 20 8.067859 -44775.936 -44766.725 24620.627 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3748 0 6355.1614
+ 25 10.975538 -44777.233 -44764.702 34381.173 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.23109 -1582.8552 253.88696 -653.46042 18790.855 -8683.8691 0 6336.3409
+Loop time of 7.80129 on 1 procs for 25 steps with 384 atoms
-Performance: 0.018 ns/day, 1330.444 hours/ns, 3.341 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.017 ns/day, 1386.896 hours/ns, 3.205 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 7.4284 | 7.4284 | 7.4284 | 0.0 | 99.26
-Neigh | 0.051549 | 0.051549 | 0.051549 | 0.0 | 0.69
-Comm | 0.0021887 | 0.0021887 | 0.0021887 | 0.0 | 0.03
-Output | 0.00025821 | 0.00025821 | 0.00025821 | 0.0 | 0.00
-Modify | 0.00099206 | 0.00099206 | 0.00099206 | 0.0 | 0.01
-Other | | 0.0003154 | | | 0.00
+Pair | 7.7384 | 7.7384 | 7.7384 | 0.0 | 99.19
+Neigh | 0.058615 | 0.058615 | 0.058615 | 0.0 | 0.75
+Comm | 0.0022428 | 0.0022428 | 0.0022428 | 0.0 | 0.03
+Output | 0.00033212 | 0.00033212 | 0.00033212 | 0.0 | 0.00
+Modify | 0.0013618 | 0.0013618 | 0.0013618 | 0.0 | 0.02
+Other | | 0.0003309 | | | 0.00
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -94,4 +100,4 @@ Total # of neighbors = 286828
Ave neighs/atom = 746.948
Neighbor list builds = 5
Dangerous builds not checked
-Total wall time: 0:00:07
+Total wall time: 0:00:08
diff --git a/examples/reax/log.5Oct16.reax.tatb.g++.4 b/examples/reax/log.8March18.reax.tatb.g++.4
similarity index 61%
rename from examples/reax/log.5Oct16.reax.tatb.g++.4
rename to examples/reax/log.8March18.reax.tatb.g++.4
index 8fa9a608cf..e3acac9d0e 100644
--- a/examples/reax/log.5Oct16.reax.tatb.g++.4
+++ b/examples/reax/log.8March18.reax.tatb.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
@@ -12,7 +13,7 @@ read_data data.tatb
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
-WARNING: The pair_style reax command will be deprecated soon - users should switch to pair_style reax/c (../pair_reax.cpp:49)
+WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
@@ -54,34 +55,39 @@ fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Neighbor list info ...
- 1 neighbor list requests
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
- binsize = 6.25 -> bins = 5 4 3
-Memory usage per processor = 4.03843 Mbytes
+ binsize = 6.25, bins = 5 4 3
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair reax, perpetual
+ attributes: half, newton off
+ pair build: half/bin/newtoff
+ stencil: half/bin/3d/newtoff
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
- 5 0.63682726 -44767.816 -44767.089 8391.165 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3995 0 6388.86
- 10 2.4306905 -44769.408 -44766.633 11717.247 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.0965 0 6381.8216
- 15 5.0590422 -44772.626 -44766.85 17124.943 -61103.34 489.2801 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3383 0 6370.4973
- 20 8.0678512 -44775.934 -44766.723 24620.531 -61088.791 490.42349 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.4033 0 6355.1921
- 25 10.97553 -44777.231 -44764.701 34381.242 -61068.889 490.53154 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.8451 0 6336.3185
-Loop time of 3.27945 on 4 procs for 25 steps with 384 atoms
+ 5 0.63682727 -44767.816 -44767.089 8391.1708 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3973 0 6388.8581
+ 10 2.4306941 -44769.405 -44766.63 11717.306 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.08 0 6381.8083
+ 15 5.0590444 -44772.6 -44766.824 17125.207 -61103.34 489.28008 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.2653 0 6370.4505
+ 20 8.0678523 -44775.983 -44766.772 24620.114 -61088.791 490.42348 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.5228 0 6355.2629
+ 25 10.975532 -44777.234 -44764.704 34381.065 -61068.889 490.53151 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.898 0 6336.3682
+Loop time of 3.74388 on 4 procs for 25 steps with 384 atoms
-Performance: 0.041 ns/day, 583.013 hours/ns, 7.623 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.036 ns/day, 665.579 hours/ns, 6.678 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 3.0329 | 3.1456 | 3.2612 | 5.2 | 95.92
-Neigh | 0.011087 | 0.011261 | 0.011608 | 0.2 | 0.34
-Comm | 0.0057111 | 0.12121 | 0.23398 | 26.2 | 3.70
-Output | 0.00039172 | 0.0005855 | 0.00080633 | 0.6 | 0.02
-Modify | 0.00035787 | 0.00059456 | 0.00082469 | 0.7 | 0.02
-Other | | 0.0002265 | | | 0.01
+Pair | 3.478 | 3.6025 | 3.7215 | 4.8 | 96.22
+Neigh | 0.012731 | 0.01299 | 0.013174 | 0.2 | 0.35
+Comm | 0.0073411 | 0.12653 | 0.25119 | 25.4 | 3.38
+Output | 0.00050354 | 0.00081849 | 0.0011628 | 0.0 | 0.02
+Modify | 0.00049281 | 0.00082356 | 0.001157 | 0.0 | 0.02
+Other | | 0.0002663 | | | 0.01
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
diff --git a/examples/reax/log.8March18.reaxc.rdx.g++.1 b/examples/reax/log.8March18.reaxc.rdx.g++.1
new file mode 100644
index 0000000000..4ae10e3f52
--- /dev/null
+++ b/examples/reax/log.8March18.reaxc.rdx.g++.1
@@ -0,0 +1,115 @@
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
+# ReaxFF potential for RDX system
+# this run is equivalent to reax/in.reax.rdx
+
+units real
+
+atom_style charge
+read_data data.rdx
+ orthogonal box = (35 35 35) to (48 48 48)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 21 atoms
+
+pair_style reax/c control.reax_c.rdx
+pair_coeff * * ffield.reax C H O N
+Reading potential file ffield.reax with DATE: 2010-02-19
+
+compute reax all pair reax/c
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify every 10 delay 0 check no
+
+fix 1 all nve
+fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+
+thermo 10
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 1.0
+
+#dump 1 all atom 10 dump.reaxc.rdx
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+run 100
+Neighbor list info ...
+ update every 10 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25, bins = 3 3 3
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 15.28 | 15.28 | 15.28 Mbytes
+Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+ 0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79937 0 168.88402
+ 10 1288.6114 -1989.6644 -1912.8422 -19456.35 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252294 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43322 0 107.75935
+ 20 538.95849 -1942.7037 -1910.5731 -10725.658 -2803.7395 7.9078331 0.077926702 0 81.610043 0.22951937 -57.557104 0 30.331203 -10.178049 878.99015 -159.69092 0 89.315159
+ 30 463.09542 -1933.5765 -1905.9685 -33255.507 -2749.8591 -8.0154628 0.027628767 0 81.627403 0.11972403 -50.262284 0 20.82032 -9.6327022 851.88722 -149.495 0 79.205731
+ 40 885.49449 -1958.9126 -1906.1228 -4814.7123 -2795.644 9.1506221 0.1374749 0 70.948046 0.24360579 -57.8627 0 19.076515 -11.141211 873.73892 -159.9939 0 92.434059
+ 50 861.1646 -1954.4599 -1903.1206 -1896.7387 -2784.8446 3.8269113 0.1579328 0 79.851775 3.3492107 -78.066127 0 32.628975 -7.9565255 872.81826 -190.98565 0 114.75994
+ 60 1167.785 -1971.8432 -1902.2243 -3482.6975 -2705.8638 -17.121582 0.22749067 0 44.507705 7.856069 -74.788959 0 16.256519 -4.6046602 835.8308 -188.33691 0 114.19414
+ 70 1439.9947 -1989.3024 -1903.4554 23845.067 -2890.7896 31.958874 0.26671735 0 85.758608 3.1803486 -71.002907 0 24.357106 -10.311315 905.86799 -175.38482 0 106.79659
+ 80 502.40024 -1930.7547 -1900.8035 -20356.557 -2703.8096 -18.663105 0.11286226 0 99.803799 2.0329394 -76.171387 0 19.236609 -6.2786041 826.47358 -166.03157 0 92.539694
+ 90 749.09267 -1946.9834 -1902.3254 17798.812 -2863.7586 42.068927 0.24338042 0 96.18195 0.96181754 -69.955528 0 24.61541 -11.58277 903.68895 -190.13838 0 120.69139
+ 100 1109.7046 -1968.5875 -1902.4311 -4490.6736 -2755.8953 -7.1235173 0.21757663 0 61.806405 7.0825933 -75.645487 0 20.114745 -6.2371664 863.56285 -198.56939 0 122.09923
+Loop time of 0.395195 on 1 procs for 100 steps with 21 atoms
+
+Performance: 21.863 ns/day, 1.098 hours/ns, 253.039 timesteps/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.3722 | 0.3722 | 0.3722 | 0.0 | 94.18
+Neigh | 0.0098455 | 0.0098455 | 0.0098455 | 0.0 | 2.49
+Comm | 0.00047445 | 0.00047445 | 0.00047445 | 0.0 | 0.12
+Output | 0.00034022 | 0.00034022 | 0.00034022 | 0.0 | 0.09
+Modify | 0.012187 | 0.012187 | 0.012187 | 0.0 | 3.08
+Other | | 0.0001521 | | | 0.04
+
+Nlocal: 21 ave 21 max 21 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 546 ave 546 max 546 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 1096 ave 1096 max 1096 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1096
+Ave neighs/atom = 52.1905
+Neighbor list builds = 10
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/reax/log.8March18.reaxc.rdx.g++.4 b/examples/reax/log.8March18.reaxc.rdx.g++.4
new file mode 100644
index 0000000000..6ea4835402
--- /dev/null
+++ b/examples/reax/log.8March18.reaxc.rdx.g++.4
@@ -0,0 +1,115 @@
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
+# ReaxFF potential for RDX system
+# this run is equivalent to reax/in.reax.rdx
+
+units real
+
+atom_style charge
+read_data data.rdx
+ orthogonal box = (35 35 35) to (48 48 48)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 21 atoms
+
+pair_style reax/c control.reax_c.rdx
+pair_coeff * * ffield.reax C H O N
+Reading potential file ffield.reax with DATE: 2010-02-19
+
+compute reax all pair reax/c
+
+variable eb equal c_reax[1]
+variable ea equal c_reax[2]
+variable elp equal c_reax[3]
+variable emol equal c_reax[4]
+variable ev equal c_reax[5]
+variable epen equal c_reax[6]
+variable ecoa equal c_reax[7]
+variable ehb equal c_reax[8]
+variable et equal c_reax[9]
+variable eco equal c_reax[10]
+variable ew equal c_reax[11]
+variable ep equal c_reax[12]
+variable efi equal c_reax[13]
+variable eqeq equal c_reax[14]
+
+neighbor 2.5 bin
+neigh_modify every 10 delay 0 check no
+
+fix 1 all nve
+fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+
+thermo 10
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep 1.0
+
+#dump 1 all atom 10 dump.reaxc.rdx
+
+#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 3
+
+#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 3
+
+run 100
+Neighbor list info ...
+ update every 10 steps, delay 0 steps, check no
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 12.5
+ ghost atom cutoff = 12.5
+ binsize = 6.25, bins = 3 3 3
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 10.37 | 11.76 | 13.34 Mbytes
+Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+ 0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79988 0 168.88453
+ 10 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252286 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934
+ 20 538.95818 -1942.7037 -1910.5731 -10725.623 -2803.7394 7.9078307 0.077926702 0 81.61005 0.22951942 -57.557107 0 30.331206 -10.178049 878.9901 -159.68951 0 89.313749
+ 30 463.09514 -1933.5765 -1905.9685 -33255.525 -2749.859 -8.0154737 0.027628797 0 81.627408 0.11972402 -50.262283 0 20.82031 -9.6327021 851.88715 -149.49499 0 79.205724
+ 40 885.49412 -1958.9125 -1906.1227 -4814.6606 -2795.6439 9.150622 0.13747487 0 70.948029 0.24360517 -57.862679 0 19.076509 -11.141214 873.7389 -159.99392 0 92.434078
+ 50 861.16393 -1954.46 -1903.1207 -1896.7323 -2784.8449 3.8270197 0.1579328 0 79.851743 3.3492115 -78.066132 0 32.628992 -7.9565379 872.81841 -190.98568 0 114.75996
+ 60 1167.7846 -1971.8432 -1902.2243 -3482.8111 -2705.8633 -17.121657 0.2274907 0 44.507681 7.8560366 -74.788989 0 16.256493 -4.6046537 835.8305 -188.33687 0 114.1941
+ 70 1439.9942 -1989.3023 -1903.4554 23845.444 -2890.7894 31.958784 0.26671721 0 85.758586 3.1803655 -71.002918 0 24.357158 -10.311304 905.86792 -175.38481 0 106.79657
+ 80 502.3975 -1930.7546 -1900.8036 -20356.439 -2703.8105 -18.662812 0.11286123 0 99.80391 2.0329293 -76.171334 0 19.236803 -6.2786439 826.47397 -166.03141 0 92.539551
+ 90 749.09048 -1946.9837 -1902.3258 17798.718 -2863.7582 42.068719 0.24338057 0 96.181773 0.96183581 -69.955529 0 24.615414 -11.582758 903.68862 -190.1384 0 120.69139
+ 100 1109.6999 -1968.5875 -1902.4314 -4490.3728 -2755.8964 -7.1231468 0.21757685 0 61.806149 7.0826648 -75.645428 0 20.115002 -6.2371958 863.56343 -198.56957 0 122.09942
+Loop time of 0.329552 on 4 procs for 100 steps with 21 atoms
+
+Performance: 26.217 ns/day, 0.915 hours/ns, 303.443 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 | 0.26372 | 0.26499 | 0.26754 | 0.3 | 80.41
+Neigh | 0.0045478 | 0.0062494 | 0.0076699 | 1.5 | 1.90
+Comm | 0.0041637 | 0.0064691 | 0.0080271 | 1.8 | 1.96
+Output | 0.00054169 | 0.00056636 | 0.00060368 | 0.0 | 0.17
+Modify | 0.049433 | 0.051134 | 0.05311 | 0.6 | 15.52
+Other | | 0.000141 | | | 0.04
+
+Nlocal: 5.25 ave 15 max 0 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Nghost: 355.5 ave 432 max 282 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs: 298.75 ave 822 max 0 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+
+Total # of neighbors = 1195
+Ave neighs/atom = 56.9048
+Neighbor list builds = 10
+Dangerous builds not checked
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00
diff --git a/examples/reax/log.5Oct16.reaxc.tatb.g++.1 b/examples/reax/log.8March18.reaxc.tatb.g++.1
similarity index 57%
rename from examples/reax/log.5Oct16.reaxc.tatb.g++.1
rename to examples/reax/log.8March18.reaxc.tatb.g++.1
index deb1c5f1d7..ac5537bba4 100644
--- a/examples/reax/log.5Oct16.reaxc.tatb.g++.1
+++ b/examples/reax/log.8March18.reaxc.tatb.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
@@ -56,34 +57,44 @@ fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
- 2 neighbor list requests
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
- binsize = 6.25 -> bins = 5 4 3
-Memory usage per processor = 155.82 Mbytes
+ binsize = 6.25, bins = 5 4 3
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 176.7 | 176.7 | 176.7 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
- 0 0 -44760.998 -44760.998 7827.7879 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274
- 5 0.61603942 -44761.698 -44760.994 8934.6281 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691
- 10 2.3525551 -44763.227 -44760.541 12288.607 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9688 0 6381.7066
- 15 4.9013326 -44766.36 -44760.764 17717.015 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.237 0 6370.4033
- 20 7.829471 -44769.686 -44760.747 25205.558 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5091 0 6355.2604
- 25 10.697926 -44772.904 -44760.691 34232.793 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3608 0 6336.8416
-Loop time of 4.34725 on 1 procs for 25 steps with 384 atoms
+ 0 0 -44760.998 -44760.998 7827.7874 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6395 0 6391.0275
+ 5 0.61603968 -44761.698 -44760.994 8934.6347 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671
+ 10 2.3525551 -44763.227 -44760.541 12288.583 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9768 0 6381.7146
+ 15 4.9013279 -44766.36 -44760.764 17717.01 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2375 0 6370.4038
+ 20 7.8294645 -44769.686 -44760.747 25205.624 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4889 0 6355.2402
+ 25 10.697904 -44772.904 -44760.691 34232.965 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3125 0 6336.7934
+Loop time of 4.72562 on 1 procs for 25 steps with 384 atoms
-Performance: 0.031 ns/day, 772.845 hours/ns, 5.751 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.029 ns/day, 840.110 hours/ns, 5.290 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 3.5264 | 3.5264 | 3.5264 | 0.0 | 81.12
-Neigh | 0.40335 | 0.40335 | 0.40335 | 0.0 | 9.28
-Comm | 0.0021031 | 0.0021031 | 0.0021031 | 0.0 | 0.05
-Output | 0.00019765 | 0.00019765 | 0.00019765 | 0.0 | 0.00
-Modify | 0.41479 | 0.41479 | 0.41479 | 0.0 | 9.54
-Other | | 0.0004084 | | | 0.01
+Pair | 3.775 | 3.775 | 3.775 | 0.0 | 79.88
+Neigh | 0.47047 | 0.47047 | 0.47047 | 0.0 | 9.96
+Comm | 0.0025151 | 0.0025151 | 0.0025151 | 0.0 | 0.05
+Output | 0.0003159 | 0.0003159 | 0.0003159 | 0.0 | 0.01
+Modify | 0.47676 | 0.47676 | 0.47676 | 0.0 | 10.09
+Other | | 0.0005293 | | | 0.01
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -99,4 +110,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:04
+Total wall time: 0:00:05
diff --git a/examples/reax/log.5Oct16.reaxc.tatb.g++.4 b/examples/reax/log.8March18.reaxc.tatb.g++.4
similarity index 57%
rename from examples/reax/log.5Oct16.reaxc.tatb.g++.4
rename to examples/reax/log.8March18.reaxc.tatb.g++.4
index 064a4da54c..12558be68a 100644
--- a/examples/reax/log.5Oct16.reaxc.tatb.g++.4
+++ b/examples/reax/log.8March18.reaxc.tatb.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
@@ -56,34 +57,44 @@ fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
- 2 neighbor list requests
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
- binsize = 6.25 -> bins = 5 4 3
-Memory usage per processor = 105.386 Mbytes
+ binsize = 6.25, bins = 5 4 3
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair reax/c, perpetual
+ attributes: half, newton off, ghost
+ pair build: half/bin/newtoff/ghost
+ stencil: half/ghost/bin/3d/newtoff
+ bin: standard
+ (2) fix qeq/reax, perpetual, copy from (1)
+ attributes: half, newton off, ghost
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 118 | 118 | 118 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
- 0 0 -44760.998 -44760.998 7827.7867 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277
- 5 0.61603967 -44761.698 -44760.994 8934.6339 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1905 0 6388.6665
- 10 2.3525545 -44763.227 -44760.541 12288.586 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.714
- 15 4.9013281 -44766.36 -44760.764 17716.982 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2476 0 6370.4138
- 20 7.8294637 -44769.686 -44760.747 25205.512 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.518 0 6355.2692
- 25 10.697905 -44772.904 -44760.691 34232.815 -61069.308 490.25887 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3481 0 6336.829
-Loop time of 2.60733 on 4 procs for 25 steps with 384 atoms
+ 0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277
+ 5 0.61603968 -44761.698 -44760.994 8934.6335 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666
+ 10 2.3525544 -44763.227 -44760.541 12288.587 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9764 0 6381.7141
+ 15 4.9013311 -44766.36 -44760.764 17716.955 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2558 0 6370.4221
+ 20 7.8294715 -44769.686 -44760.747 25205.613 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.4906 0 6355.2419
+ 25 10.697924 -44772.904 -44760.691 34232.794 -61069.308 490.25886 4.7163736 0 1570.7397 20.181347 -251.91376 -1582.3261 253.82253 -653.53183 18791.975 -8684.3641 0 6336.8449
+Loop time of 2.84068 on 4 procs for 25 steps with 384 atoms
-Performance: 0.052 ns/day, 463.526 hours/ns, 9.588 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.048 ns/day, 505.009 hours/ns, 8.801 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 2.1835 | 2.1843 | 2.1854 | 0.0 | 83.77
-Neigh | 0.22091 | 0.22364 | 0.22821 | 0.6 | 8.58
-Comm | 0.005677 | 0.0069622 | 0.0078082 | 1.0 | 0.27
-Output | 0.00036621 | 0.0028675 | 0.0037034 | 2.7 | 0.11
-Modify | 0.18736 | 0.18921 | 0.19102 | 0.4 | 7.26
-Other | | 0.0003636 | | | 0.01
+Pair | 2.3253 | 2.328 | 2.3305 | 0.2 | 81.95
+Neigh | 0.2589 | 0.26458 | 0.26897 | 0.7 | 9.31
+Comm | 0.0094428 | 0.012062 | 0.014872 | 2.3 | 0.42
+Output | 0.00043392 | 0.0042209 | 0.0054941 | 3.4 | 0.15
+Modify | 0.22563 | 0.23134 | 0.23579 | 0.8 | 8.14
+Other | | 0.0005122 | | | 0.02
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -99,4 +110,4 @@ Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:02
+Total wall time: 0:00:03
--
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