diff --git a/examples/python/log.4May17.pair_python_coulomb.g++.1 b/examples/python/log.4May17.pair_python_coulomb.g++.1
index 67bb3b34965fbc85eeeb8fc405b71be4c9cd9ca7..b08d4b939c05e8ae379410e63202a87ac063ba31 100644
--- a/examples/python/log.4May17.pair_python_coulomb.g++.1
+++ b/examples/python/log.4May17.pair_python_coulomb.g++.1
@@ -21,14 +21,11 @@ read_data data.spce
1 = max # of 1-4 neighbors
2 = max # of special neighbors
-pair_style hybrid/overlay coul/long 12.0 python 12.0
-kspace_style pppm 1.0e-6
+pair_style hybrid/overlay coul/cut 12.0 python 12.0
-pair_coeff * * coul/long
+pair_coeff * * coul/cut
pair_coeff * * python py_pot.LJCutSPCE OW NULL
-pair_modify table 0
-
bond_style harmonic
angle_style harmonic
dihedral_style none
@@ -54,15 +51,6 @@ fix 2 all nvt temp 300.0 300.0 100.0
# create combined lj/coul table for all atom types
# generate tabulated potential from python variant
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
-PPPM initialization ...
-WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.279652
- grid = 40 40 40
- stencil order = 5
- estimated absolute RMS force accuracy = 0.000394206
- estimated relative force accuracy = 1.18714e-06
- using double precision FFTs
- 3d grid and FFT values/proc = 103823 64000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@@ -70,7 +58,7 @@ Neighbor list info ...
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
- (1) pair coul/long, perpetual
+ (1) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
@@ -81,25 +69,7 @@ Neighbor list info ...
stencil: none
bin: none
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
-PPPM initialization ...
-WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.279652
- grid = 40 40 40
- stencil order = 5
- estimated absolute RMS force accuracy = 0.000394206
- estimated relative force accuracy = 1.18714e-06
- using double precision FFTs
- 3d grid and FFT values/proc = 103823 64000
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
-PPPM initialization ...
-WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.279652
- grid = 40 40 40
- stencil order = 5
- estimated absolute RMS force accuracy = 0.000394206
- estimated relative force accuracy = 1.18714e-06
- using double precision FFTs
- 3d grid and FFT values/proc = 103823 64000
# switch to tabulated potential
pair_style table linear 2000 pppm
@@ -109,15 +79,6 @@ pair_coeff 2 2 spce.table HW-HW
thermo 10
run 100
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.279652
- grid = 40 40 40
- stencil order = 5
- estimated absolute RMS force accuracy = 0.000394674
- estimated relative force accuracy = 1.18855e-06
- using double precision FFTs
- 3d grid and FFT values/proc = 103823 64000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@@ -130,49 +91,48 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
-Per MPI rank memory allocation (min/avg/max) = 35.26 | 35.26 | 35.26 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 25.08 | 25.08 | 25.08 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 0 -100272.97 0 -100272.97 -1282.0708
- 10 120.61568 -101350.63 0 -100272.39 -4077.5051
- 20 136.11379 -101465.43 0 -100248.65 -5136.5677
- 30 137.01602 -101455.3 0 -100230.46 -5347.8311
- 40 153.424 -101582.46 0 -100210.93 -5223.1676
- 50 167.73654 -101686.24 0 -100186.77 -4468.6687
- 60 163.11642 -101618.16 0 -100159.99 -3291.7815
- 70 169.64512 -101647.89 0 -100131.35 -2611.638
- 80 182.9979 -101737.01 0 -100101.11 -2390.6293
- 90 191.33873 -101778.71 0 -100068.24 -2239.386
- 100 194.7458 -101775.84 0 -100034.92 -1951.9128
-Loop time of 7.63869 on 1 procs for 100 steps with 4500 atoms
-
-Performance: 1.131 ns/day, 21.219 hours/ns, 13.091 timesteps/s
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+ 0 0 -18284.922 0 -18284.922 -2080.7739
+ 10 146.83806 -19552.072 0 -18239.421 -4865.31
+ 20 183.15761 -18706.872 0 -17069.543 -4865.6695
+ 30 205.96203 -18901.541 0 -17060.354 -4454.8634
+ 40 241.62768 -18323.117 0 -16163.099 -3269.1475
+ 50 265.98384 -19883.562 0 -17505.813 -2788.5194
+ 60 274.01897 -21320.575 0 -18870.996 -2387.0708
+ 70 288.7601 -19849.269 0 -17267.913 -1235.818
+ 80 300.64724 -20958.602 0 -18270.981 -1714.7988
+ 90 304.19113 -21580.4 0 -18861.099 -2144.1614
+ 100 304.22027 -21239.014 0 -18519.452 -2092.6759
+Loop time of 6.01861 on 1 procs for 100 steps with 4500 atoms
+
+Performance: 1.436 ns/day, 16.718 hours/ns, 16.615 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 5.7777 | 5.7777 | 5.7777 | 0.0 | 75.64
-Bond | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.00
-Kspace | 1.5385 | 1.5385 | 1.5385 | 0.0 | 20.14
-Neigh | 0.22962 | 0.22962 | 0.22962 | 0.0 | 3.01
-Comm | 0.024123 | 0.024123 | 0.024123 | 0.0 | 0.32
-Output | 0.00061131 | 0.00061131 | 0.00061131 | 0.0 | 0.01
-Modify | 0.062444 | 0.062444 | 0.062444 | 0.0 | 0.82
-Other | | 0.005466 | | | 0.07
+Pair | 5.698 | 5.698 | 5.698 | 0.0 | 94.67
+Bond | 0.0001626 | 0.0001626 | 0.0001626 | 0.0 | 0.00
+Neigh | 0.23235 | 0.23235 | 0.23235 | 0.0 | 3.86
+Comm | 0.018961 | 0.018961 | 0.018961 | 0.0 | 0.32
+Output | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.01
+Modify | 0.063452 | 0.063452 | 0.063452 | 0.0 | 1.05
+Other | | 0.005146 | | | 0.09
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 21216 ave 21216 max 21216 min
+Nghost: 21285 ave 21285 max 21285 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
+Neighs: 2.59766e+06 ave 2.59766e+06 max 2.59766e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 2601766
-Ave neighs/atom = 578.17
+Total # of neighbors = 2597662
+Ave neighs/atom = 577.258
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
-Total wall time: 0:00:07
+Total wall time: 0:00:06
diff --git a/examples/python/log.4May17.pair_python_coulomb.g++.4 b/examples/python/log.4May17.pair_python_coulomb.g++.4
index d5fd15ccd348c8a60f370e9d6a97e2a8431cb703..b002d5c1abad878624327443357a18b129f420bf 100644
--- a/examples/python/log.4May17.pair_python_coulomb.g++.4
+++ b/examples/python/log.4May17.pair_python_coulomb.g++.4
@@ -21,14 +21,11 @@ read_data data.spce
1 = max # of 1-4 neighbors
2 = max # of special neighbors
-pair_style hybrid/overlay coul/long 12.0 python 12.0
-kspace_style pppm 1.0e-6
+pair_style hybrid/overlay coul/cut 12.0 python 12.0
-pair_coeff * * coul/long
+pair_coeff * * coul/cut
pair_coeff * * python py_pot.LJCutSPCE OW NULL
-pair_modify table 0
-
bond_style harmonic
angle_style harmonic
dihedral_style none
@@ -54,15 +51,6 @@ fix 2 all nvt temp 300.0 300.0 100.0
# create combined lj/coul table for all atom types
# generate tabulated potential from python variant
pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
-PPPM initialization ...
-WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.279652
- grid = 40 40 40
- stencil order = 5
- estimated absolute RMS force accuracy = 0.000394206
- estimated relative force accuracy = 1.18714e-06
- using double precision FFTs
- 3d grid and FFT values/proc = 34263 16000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@@ -70,7 +58,7 @@ Neighbor list info ...
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
- (1) pair coul/long, perpetual
+ (1) pair coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
@@ -81,25 +69,7 @@ Neighbor list info ...
stencil: none
bin: none
pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
-PPPM initialization ...
-WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.279652
- grid = 40 40 40
- stencil order = 5
- estimated absolute RMS force accuracy = 0.000394206
- estimated relative force accuracy = 1.18714e-06
- using double precision FFTs
- 3d grid and FFT values/proc = 34263 16000
pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
-PPPM initialization ...
-WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.279652
- grid = 40 40 40
- stencil order = 5
- estimated absolute RMS force accuracy = 0.000394206
- estimated relative force accuracy = 1.18714e-06
- using double precision FFTs
- 3d grid and FFT values/proc = 34263 16000
# switch to tabulated potential
pair_style table linear 2000 pppm
@@ -109,15 +79,6 @@ pair_coeff 2 2 spce.table HW-HW
thermo 10
run 100
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
- G vector (1/distance) = 0.279652
- grid = 40 40 40
- stencil order = 5
- estimated absolute RMS force accuracy = 0.000394674
- estimated relative force accuracy = 1.18855e-06
- using double precision FFTs
- 3d grid and FFT values/proc = 34263 16000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@@ -130,49 +91,48 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
-Per MPI rank memory allocation (min/avg/max) = 13.05 | 13.05 | 13.05 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 9.962 | 9.963 | 9.963 Mbytes
Step Temp E_pair E_mol TotEng Press
- 0 0 -100272.97 0 -100272.97 -1282.0708
- 10 120.61568 -101350.63 0 -100272.39 -4077.5051
- 20 136.11379 -101465.43 0 -100248.65 -5136.5677
- 30 137.01602 -101455.3 0 -100230.46 -5347.8311
- 40 153.424 -101582.46 0 -100210.93 -5223.1676
- 50 167.73654 -101686.24 0 -100186.77 -4468.6687
- 60 163.11642 -101618.16 0 -100159.99 -3291.7815
- 70 169.64512 -101647.89 0 -100131.35 -2611.638
- 80 182.9979 -101737.01 0 -100101.11 -2390.6293
- 90 191.33873 -101778.71 0 -100068.24 -2239.386
- 100 194.7458 -101775.84 0 -100034.92 -1951.9128
-Loop time of 2.35848 on 4 procs for 100 steps with 4500 atoms
-
-Performance: 3.663 ns/day, 6.551 hours/ns, 42.400 timesteps/s
-99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+ 0 0 -18284.922 0 -18284.922 -2080.7739
+ 10 146.83806 -19552.072 0 -18239.421 -4865.31
+ 20 183.15761 -18706.872 0 -17069.543 -4865.6695
+ 30 205.96203 -18901.541 0 -17060.354 -4454.8634
+ 40 241.62768 -18323.117 0 -16163.099 -3269.1475
+ 50 265.98384 -19883.562 0 -17505.813 -2788.5194
+ 60 274.01897 -21320.575 0 -18870.996 -2387.0708
+ 70 288.7601 -19849.269 0 -17267.913 -1235.818
+ 80 300.64724 -20958.602 0 -18270.981 -1714.7988
+ 90 304.19113 -21580.4 0 -18861.099 -2144.1614
+ 100 304.22027 -21239.014 0 -18519.452 -2092.6759
+Loop time of 1.7361 on 4 procs for 100 steps with 4500 atoms
+
+Performance: 4.977 ns/day, 4.823 hours/ns, 57.600 timesteps/s
+99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 1.5061 | 1.5612 | 1.6879 | 5.9 | 66.20
-Bond | 9.5129e-05 | 0.00012672 | 0.00014567 | 0.0 | 0.01
-Kspace | 0.52033 | 0.64456 | 0.69933 | 9.1 | 27.33
-Neigh | 0.066265 | 0.066342 | 0.06644 | 0.0 | 2.81
-Comm | 0.03394 | 0.036139 | 0.038043 | 0.8 | 1.53
-Output | 0.00040889 | 0.00044978 | 0.00056887 | 0.0 | 0.02
-Modify | 0.04557 | 0.045813 | 0.046082 | 0.1 | 1.94
-Other | | 0.003826 | | | 0.16
-
-Nlocal: 1125 ave 1154 max 1092 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-Nghost: 12256.2 ave 12296 max 12213 min
-Histogram: 1 0 1 0 0 0 0 0 1 1
-Neighs: 650442 ave 678824 max 626375 min
-Histogram: 1 0 0 0 2 0 0 0 0 1
-
-Total # of neighbors = 2601766
-Ave neighs/atom = 578.17
+Pair | 1.4424 | 1.5149 | 1.6066 | 5.3 | 87.26
+Bond | 8.9407e-05 | 0.00010258 | 0.00012374 | 0.0 | 0.01
+Neigh | 0.064205 | 0.064241 | 0.064295 | 0.0 | 3.70
+Comm | 0.023643 | 0.1155 | 0.18821 | 19.2 | 6.65
+Output | 0.00038004 | 0.00042355 | 0.00054145 | 0.0 | 0.02
+Modify | 0.037507 | 0.037787 | 0.038042 | 0.1 | 2.18
+Other | | 0.003148 | | | 0.18
+
+Nlocal: 1125 ave 1162 max 1098 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost: 12267.8 ave 12302 max 12238 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 649416 ave 681458 max 630541 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+
+Total # of neighbors = 2597662
+Ave neighs/atom = 577.258
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
shell rm spce.table
-Total wall time: 0:00:02
+Total wall time: 0:00:01
diff --git a/examples/python/log.4May17.pair_python_hybrid.g++.1 b/examples/python/log.4May17.pair_python_hybrid.g++.1
index 497943d4fd20d93ea75a6ee4b95ceae92dbef9da..718f794a578702b3027311b86ef62df3502b118a 100644
--- a/examples/python/log.4May17.pair_python_hybrid.g++.1
+++ b/examples/python/log.4May17.pair_python_hybrid.g++.1
@@ -14,6 +14,9 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
create_atoms 1 box
Created 4000 atoms
mass * 1.0
+region half block -0.1 4.9 0 10 0 10
+set region half type 2
+ 2000 settings made for type
velocity all create 3.0 87287
@@ -50,7 +53,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.828 | 4.828 | 4.828 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
@@ -58,30 +61,30 @@ Step Temp E_pair E_mol TotEng Press
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
-Loop time of 21.9463 on 1 procs for 250 steps with 4000 atoms
+Loop time of 10.0384 on 1 procs for 250 steps with 4000 atoms
-Performance: 4921.114 tau/day, 11.391 timesteps/s
-98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 10758.705 tau/day, 24.904 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 | 21.819 | 21.819 | 21.819 | 0.0 | 99.42
-Neigh | 0.094718 | 0.094718 | 0.094718 | 0.0 | 0.43
-Comm | 0.01407 | 0.01407 | 0.01407 | 0.0 | 0.06
-Output | 0.00024915 | 0.00024915 | 0.00024915 | 0.0 | 0.00
-Modify | 0.015002 | 0.015002 | 0.015002 | 0.0 | 0.07
-Other | | 0.003232 | | | 0.01
+Pair | 9.913 | 9.913 | 9.913 | 0.0 | 98.75
+Neigh | 0.095569 | 0.095569 | 0.095569 | 0.0 | 0.95
+Comm | 0.012686 | 0.012686 | 0.012686 | 0.0 | 0.13
+Output | 0.00027537 | 0.00027537 | 0.00027537 | 0.0 | 0.00
+Modify | 0.01386 | 0.01386 | 0.01386 | 0.0 | 0.14
+Other | | 0.003027 | | | 0.03
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 0 ave 0 max 0 min
+Neighs: 85978 ave 85978 max 85978 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 0
-Ave neighs/atom = 0
+Total # of neighbors = 85978
+Ave neighs/atom = 21.4945
Neighbor list builds = 12
Dangerous builds not checked
@@ -126,7 +129,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.626 | 4.626 | 4.626 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 4.245 | 4.245 | 4.245 Mbytes
Step Temp E_pair E_mol TotEng Press
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
300 1.645592 -4.7496711 0 -2.2819002 5.8734193
@@ -134,30 +137,30 @@ Step Temp E_pair E_mol TotEng Press
400 1.6540555 -4.7622999 0 -2.281837 5.8200413
450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
-Loop time of 21.9098 on 1 procs for 250 steps with 4000 atoms
+Loop time of 10.0803 on 1 procs for 250 steps with 4000 atoms
-Performance: 4929.303 tau/day, 11.410 timesteps/s
-98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 10713.932 tau/day, 24.801 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 | 21.68 | 21.68 | 21.68 | 0.0 | 98.95
-Neigh | 0.19625 | 0.19625 | 0.19625 | 0.0 | 0.90
-Comm | 0.014877 | 0.014877 | 0.014877 | 0.0 | 0.07
-Output | 0.00027227 | 0.00027227 | 0.00027227 | 0.0 | 0.00
-Modify | 0.013663 | 0.013663 | 0.013663 | 0.0 | 0.06
-Other | | 0.004371 | | | 0.02
+Pair | 9.8479 | 9.8479 | 9.8479 | 0.0 | 97.69
+Neigh | 0.20002 | 0.20002 | 0.20002 | 0.0 | 1.98
+Comm | 0.01437 | 0.01437 | 0.01437 | 0.0 | 0.14
+Output | 0.00024033 | 0.00024033 | 0.00024033 | 0.0 | 0.00
+Modify | 0.013422 | 0.013422 | 0.013422 | 0.0 | 0.13
+Other | | 0.004348 | | | 0.04
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5472 ave 5472 max 5472 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 0 ave 0 max 0 min
+Neighs: 86930 ave 86930 max 86930 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 0
-Ave neighs/atom = 0
+Total # of neighbors = 86930
+Ave neighs/atom = 21.7325
Neighbor list builds = 25
Dangerous builds = 25
@@ -208,7 +211,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.126 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 3.745 | 3.745 | 3.745 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.6275257 -4.7224992 0 -2.281821 5.9567365
50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
@@ -216,32 +219,32 @@ Step Temp E_pair E_mol TotEng Press
150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
200 1.6258731 -4.7205017 0 -2.2823017 5.952511
250 1.6370862 -4.7373176 0 -2.2823022 5.925807
-Loop time of 22.091 on 1 procs for 250 steps with 4000 atoms
+Loop time of 9.93686 on 1 procs for 250 steps with 4000 atoms
-Performance: 4888.868 tau/day, 11.317 timesteps/s
+Performance: 10868.626 tau/day, 25.159 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 | 21.966 | 21.966 | 21.966 | 0.0 | 99.43
-Neigh | 0.094647 | 0.094647 | 0.094647 | 0.0 | 0.43
-Comm | 0.013071 | 0.013071 | 0.013071 | 0.0 | 0.06
-Output | 0.00027871 | 0.00027871 | 0.00027871 | 0.0 | 0.00
-Modify | 0.013882 | 0.013882 | 0.013882 | 0.0 | 0.06
-Other | | 0.003102 | | | 0.01
+Pair | 9.8119 | 9.8119 | 9.8119 | 0.0 | 98.74
+Neigh | 0.096041 | 0.096041 | 0.096041 | 0.0 | 0.97
+Comm | 0.01243 | 0.01243 | 0.01243 | 0.0 | 0.13
+Output | 0.00028133 | 0.00028133 | 0.00028133 | 0.0 | 0.00
+Modify | 0.013261 | 0.013261 | 0.013261 | 0.0 | 0.13
+Other | | 0.002994 | | | 0.03
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5487 ave 5487 max 5487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 0 ave 0 max 0 min
+Neighs: 86831 ave 86831 max 86831 min
Histogram: 1 0 0 0 0 0 0 0 0 0
-Total # of neighbors = 0
-Ave neighs/atom = 0
+Total # of neighbors = 86831
+Ave neighs/atom = 21.7078
Neighbor list builds = 12
Dangerous builds not checked
shell rm hybrid.data hybrid.restart
-Total wall time: 0:01:07
+Total wall time: 0:00:30
diff --git a/examples/python/log.4May17.pair_python_hybrid.g++.4 b/examples/python/log.4May17.pair_python_hybrid.g++.4
index 0331f34a5e9f8b07514538b23810bcb25943f911..32d9fc174052c2a3c58f199b0a58a19689032e16 100644
--- a/examples/python/log.4May17.pair_python_hybrid.g++.4
+++ b/examples/python/log.4May17.pair_python_hybrid.g++.4
@@ -14,6 +14,9 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
create_atoms 1 box
Created 4000 atoms
mass * 1.0
+region half block -0.1 4.9 0 10 0 10
+set region half type 2
+ 2000 settings made for type
velocity all create 3.0 87287
@@ -58,30 +61,30 @@ Step Temp E_pair E_mol TotEng Press
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
-Loop time of 6.01723 on 4 procs for 250 steps with 4000 atoms
+Loop time of 2.71748 on 4 procs for 250 steps with 4000 atoms
-Performance: 17948.472 tau/day, 41.547 timesteps/s
-98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 39742.745 tau/day, 91.997 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 | 5.1507 | 5.4989 | 5.9629 | 13.1 | 91.39
-Neigh | 0.024123 | 0.024877 | 0.025959 | 0.5 | 0.41
-Comm | 0.02258 | 0.48785 | 0.83691 | 44.1 | 8.11
-Output | 0.00039768 | 0.00045246 | 0.00052929 | 0.0 | 0.01
-Modify | 0.0036325 | 0.0037773 | 0.0038905 | 0.2 | 0.06
-Other | | 0.001357 | | | 0.02
+Pair | 2.4777 | 2.5639 | 2.6253 | 3.9 | 94.35
+Neigh | 0.024626 | 0.025331 | 0.02598 | 0.3 | 0.93
+Comm | 0.061933 | 0.12297 | 0.20987 | 18.0 | 4.53
+Output | 0.00026131 | 0.00027591 | 0.00031352 | 0.0 | 0.01
+Modify | 0.0036087 | 0.0036573 | 0.0037553 | 0.1 | 0.13
+Other | | 0.001337 | | | 0.05
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
-Neighs: 0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 21469.8 ave 22167 max 20546 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
-Total # of neighbors = 0
-Ave neighs/atom = 0
+Total # of neighbors = 85879
+Ave neighs/atom = 21.4698
Neighbor list builds = 12
Dangerous builds not checked
@@ -134,30 +137,30 @@ Step Temp E_pair E_mol TotEng Press
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
500 1.643316 -4.7454222 0 -2.2810644 5.8454817
-Loop time of 6.09991 on 4 procs for 250 steps with 4000 atoms
+Loop time of 2.75827 on 4 procs for 250 steps with 4000 atoms
-Performance: 17705.179 tau/day, 40.984 timesteps/s
-98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 39155.038 tau/day, 90.637 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 5.2315 | 5.5179 | 6.0183 | 13.7 | 90.46
-Neigh | 0.049134 | 0.051424 | 0.053837 | 0.8 | 0.84
-Comm | 0.021671 | 0.52455 | 0.8132 | 44.5 | 8.60
-Output | 0.00019336 | 0.00026017 | 0.00032115 | 0.0 | 0.00
-Modify | 0.0036032 | 0.0036635 | 0.0038021 | 0.1 | 0.06
-Other | | 0.002068 | | | 0.03
+Pair | 2.3631 | 2.5412 | 2.6672 | 7.2 | 92.13
+Neigh | 0.050358 | 0.052316 | 0.053312 | 0.5 | 1.90
+Comm | 0.032793 | 0.15893 | 0.33904 | 29.1 | 5.76
+Output | 0.00018525 | 0.00020212 | 0.00024509 | 0.0 | 0.01
+Modify | 0.0034482 | 0.0035321 | 0.0036578 | 0.1 | 0.13
+Other | | 0.002039 | | | 0.07
Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 2699 ave 2706 max 2693 min
Histogram: 1 1 0 0 0 0 1 0 0 1
-Neighs: 0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 21802 ave 22700 max 21236 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
-Total # of neighbors = 0
-Ave neighs/atom = 0
+Total # of neighbors = 87208
+Ave neighs/atom = 21.802
Neighbor list builds = 25
Dangerous builds = 25
@@ -216,32 +219,32 @@ Step Temp E_pair E_mol TotEng Press
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
-Loop time of 6.04476 on 4 procs for 250 steps with 4000 atoms
+Loop time of 2.71936 on 4 procs for 250 steps with 4000 atoms
-Performance: 17866.705 tau/day, 41.358 timesteps/s
-98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 39715.257 tau/day, 91.933 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 | 5.2589 | 5.5841 | 5.9788 | 11.1 | 92.38
-Neigh | 0.023942 | 0.024705 | 0.025509 | 0.4 | 0.41
-Comm | 0.034946 | 0.43056 | 0.75671 | 40.0 | 7.12
-Output | 0.00022149 | 0.00029725 | 0.0003593 | 0.0 | 0.00
-Modify | 0.003613 | 0.0037647 | 0.003829 | 0.1 | 0.06
-Other | | 0.001313 | | | 0.02
+Pair | 2.3769 | 2.5432 | 2.6447 | 6.6 | 93.52
+Neigh | 0.024088 | 0.025093 | 0.025748 | 0.4 | 0.92
+Comm | 0.044614 | 0.14598 | 0.31339 | 27.5 | 5.37
+Output | 0.00026488 | 0.00028872 | 0.00034189 | 0.0 | 0.01
+Modify | 0.0034099 | 0.0035709 | 0.0036535 | 0.2 | 0.13
+Other | | 0.001215 | | | 0.04
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 2695.5 ave 2706 max 2682 min
Histogram: 1 0 0 0 0 0 2 0 0 1
-Neighs: 0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 21792 ave 22490 max 21457 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
-Total # of neighbors = 0
-Ave neighs/atom = 0
+Total # of neighbors = 87168
+Ave neighs/atom = 21.792
Neighbor list builds = 12
Dangerous builds not checked
shell rm hybrid.data hybrid.restart
-Total wall time: 0:00:18
+Total wall time: 0:00:08
diff --git a/examples/python/log.4May17.pair_python_long.g++.1 b/examples/python/log.4May17.pair_python_long.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..e2d7cf1bde85eec37f563dd5df29e12346a60fd0
--- /dev/null
+++ b/examples/python/log.4May17.pair_python_long.g++.1
@@ -0,0 +1,146 @@
+LAMMPS (4 May 2017)
+ using 1 OpenMP thread(s) per MPI task
+units real
+atom_style full
+
+read_data data.spce
+ orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 4500 atoms
+ scanning bonds ...
+ 2 = max bonds/atom
+ scanning angles ...
+ 1 = max angles/atom
+ reading bonds ...
+ 3000 bonds
+ reading angles ...
+ 1500 angles
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+
+pair_style python 12.0
+pair_coeff * * py_pot.LJCutSPCE OW HW
+
+bond_style harmonic
+angle_style harmonic
+dihedral_style none
+improper_style none
+
+bond_coeff 1 1000.00 1.000
+angle_coeff 1 100.0 109.47
+
+special_bonds lj/coul 0.0 0.0 1.0
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 2 = max # of special neighbors
+
+neighbor 2.0 bin
+
+fix 1 all shake 0.0001 20 0 b 1 a 1
+ 0 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 0 = # of size 4 clusters
+ 1500 = # of frozen angles
+fix 2 all nvt temp 300.0 300.0 100.0
+
+# create only lj/cut table for the oxygen atoms from python
+shell rm -f spce.table
+WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
+WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
+pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair python, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+
+# switch to tabulated potential with long-range coulomb as overlay
+pair_style hybrid/overlay coul/long 12.0 table linear 2000
+kspace_style pppm 1.0e-6
+pair_coeff * * coul/long
+pair_coeff 1 1 table spce.table OW-OW
+
+thermo 10
+run 100
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.279652
+ grid = 40 40 40
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.000394674
+ estimated relative force accuracy = 1.18855e-06
+ using double precision FFTs
+ 3d grid and FFT values/proc = 103823 64000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) pair table, perpetual, skip from (1)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 36.47 | 36.47 | 36.47 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -16690.032 0 -16690.032 -1268.9538
+ 10 120.58553 -17767.504 0 -16689.536 -4063.8589
+ 20 136.11736 -17882.557 0 -16665.742 -5124.6758
+ 30 137.00764 -17872.318 0 -16647.545 -5337.2022
+ 40 153.38868 -17999.269 0 -16628.059 -5213.6001
+ 50 167.70342 -18103.06 0 -16603.883 -4460.6632
+ 60 163.07134 -18034.856 0 -16577.088 -3285.0037
+ 70 169.59286 -18064.636 0 -16548.57 -2606.407
+ 80 182.92893 -18153.499 0 -16518.215 -2385.5152
+ 90 191.2793 -18195.356 0 -16485.425 -2235.3701
+ 100 194.68587 -18192.458 0 -16452.073 -1948.3746
+Loop time of 7.90705 on 1 procs for 100 steps with 4500 atoms
+
+Performance: 1.093 ns/day, 21.964 hours/ns, 12.647 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 | 6.0343 | 6.0343 | 6.0343 | 0.0 | 76.32
+Bond | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.00
+Kspace | 1.5311 | 1.5311 | 1.5311 | 0.0 | 19.36
+Neigh | 0.246 | 0.246 | 0.246 | 0.0 | 3.11
+Comm | 0.023937 | 0.023937 | 0.023937 | 0.0 | 0.30
+Output | 0.00060368 | 0.00060368 | 0.00060368 | 0.0 | 0.01
+Modify | 0.065543 | 0.065543 | 0.065543 | 0.0 | 0.83
+Other | | 0.005364 | | | 0.07
+
+Nlocal: 4500 ave 4500 max 4500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 21216 ave 21216 max 21216 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2601769
+Ave neighs/atom = 578.171
+Ave special neighs/atom = 2
+Neighbor list builds = 3
+Dangerous builds = 0
+
+shell rm spce.table
+
+Total wall time: 0:00:08
diff --git a/examples/python/log.4May17.pair_python_long.g++.4 b/examples/python/log.4May17.pair_python_long.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..35347da713711d85c11c8307d9074da48a444e1e
--- /dev/null
+++ b/examples/python/log.4May17.pair_python_long.g++.4
@@ -0,0 +1,146 @@
+LAMMPS (4 May 2017)
+ using 1 OpenMP thread(s) per MPI task
+units real
+atom_style full
+
+read_data data.spce
+ orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
+ 2 by 2 by 1 MPI processor grid
+ reading atoms ...
+ 4500 atoms
+ scanning bonds ...
+ 2 = max bonds/atom
+ scanning angles ...
+ 1 = max angles/atom
+ reading bonds ...
+ 3000 bonds
+ reading angles ...
+ 1500 angles
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+
+pair_style python 12.0
+pair_coeff * * py_pot.LJCutSPCE OW HW
+
+bond_style harmonic
+angle_style harmonic
+dihedral_style none
+improper_style none
+
+bond_coeff 1 1000.00 1.000
+angle_coeff 1 100.0 109.47
+
+special_bonds lj/coul 0.0 0.0 1.0
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 2 = max # of special neighbors
+
+neighbor 2.0 bin
+
+fix 1 all shake 0.0001 20 0 b 1 a 1
+ 0 = # of size 2 clusters
+ 0 = # of size 3 clusters
+ 0 = # of size 4 clusters
+ 1500 = # of frozen angles
+fix 2 all nvt temp 300.0 300.0 100.0
+
+# create only lj/cut table for the oxygen atoms from python
+shell rm -f spce.table
+WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
+WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
+pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair python, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+
+# switch to tabulated potential with long-range coulomb as overlay
+pair_style hybrid/overlay coul/long 12.0 table linear 2000
+kspace_style pppm 1.0e-6
+pair_coeff * * coul/long
+pair_coeff 1 1 table spce.table OW-OW
+
+thermo 10
+run 100
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.279652
+ grid = 40 40 40
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.000394674
+ estimated relative force accuracy = 1.18855e-06
+ using double precision FFTs
+ 3d grid and FFT values/proc = 34263 16000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 14
+ ghost atom cutoff = 14
+ binsize = 7, bins = 6 6 6
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) pair table, perpetual, skip from (1)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.45 | 13.45 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 0 -16690.032 0 -16690.032 -1268.9538
+ 10 120.58553 -17767.504 0 -16689.536 -4063.8589
+ 20 136.11736 -17882.557 0 -16665.742 -5124.6758
+ 30 137.00764 -17872.318 0 -16647.545 -5337.2022
+ 40 153.38868 -17999.269 0 -16628.059 -5213.6001
+ 50 167.70342 -18103.06 0 -16603.883 -4460.6632
+ 60 163.07134 -18034.856 0 -16577.088 -3285.0037
+ 70 169.59286 -18064.636 0 -16548.57 -2606.407
+ 80 182.92893 -18153.499 0 -16518.215 -2385.5152
+ 90 191.2793 -18195.356 0 -16485.425 -2235.3701
+ 100 194.68587 -18192.458 0 -16452.073 -1948.3746
+Loop time of 2.36748 on 4 procs for 100 steps with 4500 atoms
+
+Performance: 3.649 ns/day, 6.576 hours/ns, 42.239 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.5309 | 1.5977 | 1.6926 | 4.7 | 67.49
+Bond | 9.9182e-05 | 0.00012749 | 0.00016403 | 0.0 | 0.01
+Kspace | 0.52158 | 0.61232 | 0.67676 | 7.3 | 25.86
+Neigh | 0.066937 | 0.06702 | 0.067093 | 0.0 | 2.83
+Comm | 0.035882 | 0.039862 | 0.042244 | 1.2 | 1.68
+Output | 0.0004003 | 0.00044602 | 0.00057578 | 0.0 | 0.02
+Modify | 0.046088 | 0.046227 | 0.046315 | 0.0 | 1.95
+Other | | 0.003775 | | | 0.16
+
+Nlocal: 1125 ave 1154 max 1092 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Nghost: 12256.2 ave 12296 max 12213 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Neighs: 650442 ave 678831 max 626373 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+
+Total # of neighbors = 2601769
+Ave neighs/atom = 578.171
+Ave special neighs/atom = 2
+Neighbor list builds = 3
+Dangerous builds = 0
+
+shell rm spce.table
+
+Total wall time: 0:00:02
diff --git a/examples/python/log.4May17.pair_python_melt.g++.1 b/examples/python/log.4May17.pair_python_melt.g++.1
index fcb902fb3caa0cd7d97de032a9e08b8ab8e0d69b..d234ce93b59c9ae38ef519d119fa0a88e0e9cbd1 100644
--- a/examples/python/log.4May17.pair_python_melt.g++.1
+++ b/examples/python/log.4May17.pair_python_melt.g++.1
@@ -47,20 +47,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
-Loop time of 21.6481 on 1 procs for 250 steps with 4000 atoms
+Loop time of 20.9283 on 1 procs for 250 steps with 4000 atoms
-Performance: 4988.899 tau/day, 11.548 timesteps/s
-98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 5160.475 tau/day, 11.946 timesteps/s
+98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 21.529 | 21.529 | 21.529 | 0.0 | 99.45
-Neigh | 0.08819 | 0.08819 | 0.08819 | 0.0 | 0.41
-Comm | 0.013276 | 0.013276 | 0.013276 | 0.0 | 0.06
-Output | 0.00025654 | 0.00025654 | 0.00025654 | 0.0 | 0.00
-Modify | 0.014466 | 0.014466 | 0.014466 | 0.0 | 0.07
-Other | | 0.003143 | | | 0.01
+Pair | 20.809 | 20.809 | 20.809 | 0.0 | 99.43
+Neigh | 0.088638 | 0.088638 | 0.088638 | 0.0 | 0.42
+Comm | 0.013424 | 0.013424 | 0.013424 | 0.0 | 0.06
+Output | 0.0002737 | 0.0002737 | 0.0002737 | 0.0 | 0.00
+Modify | 0.014334 | 0.014334 | 0.014334 | 0.0 | 0.07
+Other | | 0.003089 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -112,20 +112,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6540555 -4.7622999 0 -2.281837 5.8200413
450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
-Loop time of 21.9592 on 1 procs for 250 steps with 4000 atoms
+Loop time of 21.1422 on 1 procs for 250 steps with 4000 atoms
-Performance: 4918.203 tau/day, 11.385 timesteps/s
+Performance: 5108.279 tau/day, 11.825 timesteps/s
98.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 21.74 | 21.74 | 21.74 | 0.0 | 99.00
-Neigh | 0.18588 | 0.18588 | 0.18588 | 0.0 | 0.85
-Comm | 0.01476 | 0.01476 | 0.01476 | 0.0 | 0.07
-Output | 0.00022244 | 0.00022244 | 0.00022244 | 0.0 | 0.00
-Modify | 0.01356 | 0.01356 | 0.01356 | 0.0 | 0.06
-Other | | 0.004382 | | | 0.02
+Pair | 20.925 | 20.925 | 20.925 | 0.0 | 98.97
+Neigh | 0.18452 | 0.18452 | 0.18452 | 0.0 | 0.87
+Comm | 0.014836 | 0.014836 | 0.014836 | 0.0 | 0.07
+Output | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.00
+Modify | 0.01366 | 0.01366 | 0.01366 | 0.0 | 0.06
+Other | | 0.004355 | | | 0.02
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -183,20 +183,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
200 1.6258731 -4.7205017 0 -2.2823017 5.952511
250 1.6370862 -4.7373176 0 -2.2823022 5.925807
-Loop time of 21.8255 on 1 procs for 250 steps with 4000 atoms
+Loop time of 21.1026 on 1 procs for 250 steps with 4000 atoms
-Performance: 4948.331 tau/day, 11.454 timesteps/s
-98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 5117.845 tau/day, 11.847 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 | 21.707 | 21.707 | 21.707 | 0.0 | 99.46
-Neigh | 0.088455 | 0.088455 | 0.088455 | 0.0 | 0.41
-Comm | 0.01311 | 0.01311 | 0.01311 | 0.0 | 0.06
-Output | 0.00025082 | 0.00025082 | 0.00025082 | 0.0 | 0.00
-Modify | 0.013836 | 0.013836 | 0.013836 | 0.0 | 0.06
-Other | | 0.003096 | | | 0.01
+Pair | 20.984 | 20.984 | 20.984 | 0.0 | 99.44
+Neigh | 0.088639 | 0.088639 | 0.088639 | 0.0 | 0.42
+Comm | 0.012881 | 0.012881 | 0.012881 | 0.0 | 0.06
+Output | 0.00028563 | 0.00028563 | 0.00028563 | 0.0 | 0.00
+Modify | 0.013523 | 0.013523 | 0.013523 | 0.0 | 0.06
+Other | | 0.003033 | | | 0.01
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -211,4 +211,4 @@ Neighbor list builds = 12
Dangerous builds not checked
shell rm melt.data melt.restart
-Total wall time: 0:01:07
+Total wall time: 0:01:05
diff --git a/examples/python/log.4May17.pair_python_melt.g++.4 b/examples/python/log.4May17.pair_python_melt.g++.4
index d504efc4ac766837ca67cc75656d939e77358c36..58dae340bdd2cba7e8282c14f9f1e87db2379065 100644
--- a/examples/python/log.4May17.pair_python_melt.g++.4
+++ b/examples/python/log.4May17.pair_python_melt.g++.4
@@ -47,20 +47,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
-Loop time of 5.83903 on 4 procs for 250 steps with 4000 atoms
+Loop time of 5.65922 on 4 procs for 250 steps with 4000 atoms
-Performance: 18496.226 tau/day, 42.815 timesteps/s
-98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 19083.895 tau/day, 44.176 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 5.152 | 5.5209 | 5.7679 | 9.6 | 94.55
-Neigh | 0.022809 | 0.023364 | 0.023891 | 0.3 | 0.40
-Comm | 0.041927 | 0.28952 | 0.65893 | 42.2 | 4.96
-Output | 0.0002389 | 0.00024772 | 0.00026727 | 0.0 | 0.00
-Modify | 0.0036368 | 0.0036796 | 0.0037563 | 0.1 | 0.06
-Other | | 0.001328 | | | 0.02
+Pair | 5.4529 | 5.5207 | 5.5575 | 1.7 | 97.55
+Neigh | 0.023164 | 0.023376 | 0.023883 | 0.2 | 0.41
+Comm | 0.073318 | 0.1099 | 0.17804 | 12.2 | 1.94
+Output | 0.00023365 | 0.00026143 | 0.00030684 | 0.0 | 0.00
+Modify | 0.0036483 | 0.0037143 | 0.003896 | 0.2 | 0.07
+Other | | 0.001274 | | | 0.02
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
@@ -112,20 +112,20 @@ Step Temp E_pair E_mol TotEng Press
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
500 1.643316 -4.7454222 0 -2.2810644 5.8454817
-Loop time of 5.85683 on 4 procs for 250 steps with 4000 atoms
+Loop time of 5.70169 on 4 procs for 250 steps with 4000 atoms
-Performance: 18440.001 tau/day, 42.685 timesteps/s
-98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 18941.760 tau/day, 43.847 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 5.2483 | 5.5095 | 5.7744 | 8.0 | 94.07
-Neigh | 0.047228 | 0.047998 | 0.049293 | 0.4 | 0.82
-Comm | 0.027134 | 0.29341 | 0.55554 | 34.6 | 5.01
-Output | 0.00020003 | 0.00021219 | 0.0002358 | 0.0 | 0.00
-Modify | 0.0035472 | 0.0036988 | 0.0038681 | 0.2 | 0.06
-Other | | 0.001984 | | | 0.03
+Pair | 5.3919 | 5.4905 | 5.6136 | 3.7 | 96.30
+Neigh | 0.046791 | 0.047817 | 0.048795 | 0.3 | 0.84
+Comm | 0.034221 | 0.1575 | 0.25635 | 22.1 | 2.76
+Output | 0.00020409 | 0.00023448 | 0.00026131 | 0.0 | 0.00
+Modify | 0.0035028 | 0.0035674 | 0.0036926 | 0.1 | 0.06
+Other | | 0.002079 | | | 0.04
Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1
@@ -183,20 +183,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
-Loop time of 5.86684 on 4 procs for 250 steps with 4000 atoms
+Loop time of 5.69568 on 4 procs for 250 steps with 4000 atoms
-Performance: 18408.545 tau/day, 42.612 timesteps/s
-98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 18961.751 tau/day, 43.893 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 5.3207 | 5.5695 | 5.8071 | 7.6 | 94.93
-Neigh | 0.023073 | 0.023405 | 0.023834 | 0.2 | 0.40
-Comm | 0.030558 | 0.2686 | 0.51789 | 34.7 | 4.58
-Output | 0.00028825 | 0.00036758 | 0.00042987 | 0.0 | 0.01
-Modify | 0.0034878 | 0.0036733 | 0.0039375 | 0.3 | 0.06
-Other | | 0.001259 | | | 0.02
+Pair | 5.4041 | 5.5245 | 5.6139 | 3.2 | 96.99
+Neigh | 0.022658 | 0.022986 | 0.023398 | 0.2 | 0.40
+Comm | 0.053521 | 0.14309 | 0.26385 | 20.2 | 2.51
+Output | 0.00027037 | 0.00029504 | 0.00033665 | 0.0 | 0.01
+Modify | 0.0035288 | 0.0035585 | 0.0035827 | 0.0 | 0.06
+Other | | 0.001275 | | | 0.02
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1
@@ -211,4 +211,4 @@ Neighbor list builds = 12
Dangerous builds not checked
shell rm melt.data melt.restart
-Total wall time: 0:00:18
+Total wall time: 0:00:17
diff --git a/examples/python/log.4May17.pair_python_spce.g++.1 b/examples/python/log.4May17.pair_python_spce.g++.1
index 1a535df0e94940a54d036a51b1d426fa1e1e3bb9..540c06853f2aedcc4870fdd9bf5a0c3bf2973b53 100644
--- a/examples/python/log.4May17.pair_python_spce.g++.1
+++ b/examples/python/log.4May17.pair_python_spce.g++.1
@@ -90,22 +90,22 @@ Step Temp E_pair E_mol TotEng Press
80 182.94811 -18155.978 0 -16520.523 -2393.3156
90 191.29902 -18197.887 0 -16487.779 -2242.7104
100 194.70949 -18195.021 0 -16454.425 -1955.2916
-Loop time of 23.0818 on 1 procs for 100 steps with 4500 atoms
+Loop time of 23.5385 on 1 procs for 100 steps with 4500 atoms
-Performance: 0.374 ns/day, 64.116 hours/ns, 4.332 timesteps/s
+Performance: 0.367 ns/day, 65.385 hours/ns, 4.248 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 | 21.186 | 21.186 | 21.186 | 0.0 | 91.79
-Bond | 0.00022054 | 0.00022054 | 0.00022054 | 0.0 | 0.00
-Kspace | 1.5442 | 1.5442 | 1.5442 | 0.0 | 6.69
-Neigh | 0.25672 | 0.25672 | 0.25672 | 0.0 | 1.11
-Comm | 0.023787 | 0.023787 | 0.023787 | 0.0 | 0.10
-Output | 0.00060248 | 0.00060248 | 0.00060248 | 0.0 | 0.00
-Modify | 0.064809 | 0.064809 | 0.064809 | 0.0 | 0.28
-Other | | 0.005301 | | | 0.02
+Pair | 21.642 | 21.642 | 21.642 | 0.0 | 91.94
+Bond | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.00
+Kspace | 1.5436 | 1.5436 | 1.5436 | 0.0 | 6.56
+Neigh | 0.25623 | 0.25623 | 0.25623 | 0.0 | 1.09
+Comm | 0.024325 | 0.024325 | 0.024325 | 0.0 | 0.10
+Output | 0.00064301 | 0.00064301 | 0.00064301 | 0.0 | 0.00
+Modify | 0.065919 | 0.065919 | 0.065919 | 0.0 | 0.28
+Other | | 0.005401 | | | 0.02
Nlocal: 4500 ave 4500 max 4500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -119,4 +119,4 @@ Ave neighs/atom = 578.169
Ave special neighs/atom = 2
Neighbor list builds = 3
Dangerous builds = 0
-Total wall time: 0:00:23
+Total wall time: 0:00:24
diff --git a/examples/python/log.4May17.pair_python_spce.g++.4 b/examples/python/log.4May17.pair_python_spce.g++.4
index c2776632871cbab7ad711c5db4d56c8a7e73379c..332c079ec1fca8b35ce874133ebf728b219ba727 100644
--- a/examples/python/log.4May17.pair_python_spce.g++.4
+++ b/examples/python/log.4May17.pair_python_spce.g++.4
@@ -90,22 +90,22 @@ Step Temp E_pair E_mol TotEng Press
80 182.94811 -18155.978 0 -16520.523 -2393.3156
90 191.29902 -18197.887 0 -16487.779 -2242.7104
100 194.70949 -18195.021 0 -16454.425 -1955.2916
-Loop time of 6.588 on 4 procs for 100 steps with 4500 atoms
+Loop time of 6.4942 on 4 procs for 100 steps with 4500 atoms
-Performance: 1.311 ns/day, 18.300 hours/ns, 15.179 timesteps/s
-98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 1.330 ns/day, 18.039 hours/ns, 15.398 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 | 5.3756 | 5.5417 | 5.8745 | 8.3 | 84.12
-Bond | 0.0001049 | 0.00013965 | 0.0001812 | 0.0 | 0.00
-Kspace | 0.54765 | 0.87786 | 1.042 | 20.8 | 13.33
-Neigh | 0.072695 | 0.072884 | 0.072973 | 0.0 | 1.11
-Comm | 0.04138 | 0.043576 | 0.045475 | 0.7 | 0.66
-Output | 0.00041032 | 0.00043947 | 0.00052142 | 0.0 | 0.01
-Modify | 0.047381 | 0.047567 | 0.047745 | 0.1 | 0.72
-Other | | 0.003845 | | | 0.06
+Pair | 5.4084 | 5.572 | 5.8013 | 7.2 | 85.80
+Bond | 0.00012994 | 0.0001421 | 0.00016356 | 0.0 | 0.00
+Kspace | 0.52942 | 0.75773 | 0.92078 | 19.5 | 11.67
+Neigh | 0.071055 | 0.07116 | 0.071278 | 0.0 | 1.10
+Comm | 0.040311 | 0.041255 | 0.041817 | 0.3 | 0.64
+Output | 0.00040603 | 0.00048071 | 0.00058675 | 0.0 | 0.01
+Modify | 0.047507 | 0.047629 | 0.047772 | 0.1 | 0.73
+Other | | 0.003771 | | | 0.06
Nlocal: 1125 ave 1154 max 1092 min
Histogram: 1 0 0 0 1 0 0 1 0 1
diff --git a/examples/python/log.4May17.pair_python_table.g++.1 b/examples/python/log.4May17.pair_python_table.g++.1
index bd3e86501b8dca72e522ee4451a6f50770b698c5..c594a8e90ae1024e6bdfee98b1d336734bd0e4b4 100644
--- a/examples/python/log.4May17.pair_python_table.g++.1
+++ b/examples/python/log.4May17.pair_python_table.g++.1
@@ -67,20 +67,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.632425 -4.7284533 0 -2.2804279 5.9595684
200 1.6631578 -4.7749889 0 -2.2808759 5.7365839
250 1.6277062 -4.7224727 0 -2.2815238 5.9572913
-Loop time of 0.996652 on 1 procs for 250 steps with 4000 atoms
+Loop time of 0.996739 on 1 procs for 250 steps with 4000 atoms
-Performance: 108362.785 tau/day, 250.840 timesteps/s
+Performance: 108353.298 tau/day, 250.818 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.87999 | 0.87999 | 0.87999 | 0.0 | 88.29
-Neigh | 0.087921 | 0.087921 | 0.087921 | 0.0 | 8.82
-Comm | 0.012098 | 0.012098 | 0.012098 | 0.0 | 1.21
-Output | 0.00013614 | 0.00013614 | 0.00013614 | 0.0 | 0.01
-Modify | 0.01363 | 0.01363 | 0.01363 | 0.0 | 1.37
-Other | | 0.002882 | | | 0.29
+Pair | 0.87985 | 0.87985 | 0.87985 | 0.0 | 88.27
+Neigh | 0.08799 | 0.08799 | 0.08799 | 0.0 | 8.83
+Comm | 0.012301 | 0.012301 | 0.012301 | 0.0 | 1.23
+Output | 0.00013161 | 0.00013161 | 0.00013161 | 0.0 | 0.01
+Modify | 0.013656 | 0.013656 | 0.013656 | 0.0 | 1.37
+Other | | 0.002808 | | | 0.28
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/python/log.4May17.pair_python_table.g++.4 b/examples/python/log.4May17.pair_python_table.g++.4
index 8dfe82097ec0317cb1456708c202d57a7c859cc8..e509fc7f6adb9568ffb525c3d8a836c319f21011 100644
--- a/examples/python/log.4May17.pair_python_table.g++.4
+++ b/examples/python/log.4May17.pair_python_table.g++.4
@@ -67,20 +67,20 @@ Step Temp E_pair E_mol TotEng Press
150 1.6595852 -4.7697199 0 -2.2809644 5.7837898
200 1.6371471 -4.7363942 0 -2.2812874 5.924977
250 1.6315623 -4.7278268 0 -2.2810951 5.9807196
-Loop time of 0.300176 on 4 procs for 250 steps with 4000 atoms
+Loop time of 0.291846 on 4 procs for 250 steps with 4000 atoms
-Performance: 359789.395 tau/day, 832.846 timesteps/s
-99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 370058.286 tau/day, 856.616 timesteps/s
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.23104 | 0.23876 | 0.2451 | 1.2 | 79.54
-Neigh | 0.022763 | 0.023687 | 0.024305 | 0.4 | 7.89
-Comm | 0.025416 | 0.032499 | 0.041304 | 3.7 | 10.83
-Output | 0.00015378 | 0.00016057 | 0.00017667 | 0.0 | 0.05
-Modify | 0.0035894 | 0.0036637 | 0.0037456 | 0.1 | 1.22
-Other | | 0.001409 | | | 0.47
+Pair | 0.22586 | 0.23364 | 0.24085 | 1.3 | 80.06
+Neigh | 0.022808 | 0.023235 | 0.023602 | 0.2 | 7.96
+Comm | 0.022573 | 0.030065 | 0.038092 | 3.9 | 10.30
+Output | 0.00013423 | 0.00014067 | 0.00015759 | 0.0 | 0.05
+Modify | 0.0035079 | 0.0035501 | 0.0036008 | 0.1 | 1.22
+Other | | 0.001211 | | | 0.42
Nlocal: 1000 ave 1010 max 981 min
Histogram: 1 0 0 0 0 0 1 0 0 2