diff --git a/examples/USER/misc/kolmogorov_crespi/data.bilayer-graphene b/examples/USER/misc/kolmogorov_crespi/data.bilayer-graphene
deleted file mode 100644
index 6c6ad3cb7cfe92179dd8ca009b95545816351f79..0000000000000000000000000000000000000000
--- a/examples/USER/misc/kolmogorov_crespi/data.bilayer-graphene
+++ /dev/null
@@ -1,266 +0,0 @@
-info: xyz2data 18:31, Mon 27-02-2017
-256 atoms
-2 atom types
-
- 0.00000000 17.04000000 xlo xhi
- 0.00000000 19.67609717 ylo yhi
- -20.00000000 40.00000000 zlo zhi
-
-Atoms
-
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- 6 1 3.55000000 1.22975607 0.00000000
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- 8 2 4.97000000 1.22975607 3.30000000
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- 12 2 2.84000000 2.45951215 3.30000000
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- 14 1 3.55000000 3.68926822 0.00000000
- 15 2 3.55000000 3.68926822 3.30000000
- 16 2 4.97000000 3.68926822 3.30000000
- 17 1 0.00000000 4.91902429 0.00000000
- 18 1 1.42000000 4.91902429 0.00000000
- 19 2 1.42000000 4.91902429 3.30000000
- 20 2 2.84000000 4.91902429 3.30000000
- 21 1 2.13000000 6.14878037 0.00000000
- 22 1 3.55000000 6.14878037 0.00000000
- 23 2 3.55000000 6.14878037 3.30000000
- 24 2 4.97000000 6.14878037 3.30000000
- 25 1 0.00000000 7.37853644 0.00000000
- 26 1 1.42000000 7.37853644 0.00000000
- 27 2 1.42000000 7.37853644 3.30000000
- 28 2 2.84000000 7.37853644 3.30000000
- 29 1 2.13000000 8.60829251 0.00000000
- 30 1 3.55000000 8.60829251 0.00000000
- 31 2 3.55000000 8.60829251 3.30000000
- 32 2 4.97000000 8.60829251 3.30000000
- 33 1 0.00000000 9.83804859 0.00000000
- 34 1 1.42000000 9.83804859 0.00000000
- 35 2 1.42000000 9.83804859 3.30000000
- 36 2 2.84000000 9.83804859 3.30000000
- 37 1 2.13000000 11.06780466 0.00000000
- 38 1 3.55000000 11.06780466 0.00000000
- 39 2 3.55000000 11.06780466 3.30000000
- 40 2 4.97000000 11.06780466 3.30000000
- 41 1 0.00000000 12.29756073 0.00000000
- 42 1 1.42000000 12.29756073 0.00000000
- 43 2 1.42000000 12.29756073 3.30000000
- 44 2 2.84000000 12.29756073 3.30000000
- 45 1 2.13000000 13.52731681 0.00000000
- 46 1 3.55000000 13.52731681 0.00000000
- 47 2 3.55000000 13.52731681 3.30000000
- 48 2 4.97000000 13.52731681 3.30000000
- 49 1 0.00000000 14.75707288 0.00000000
- 50 1 1.42000000 14.75707288 0.00000000
- 51 2 1.42000000 14.75707288 3.30000000
- 52 2 2.84000000 14.75707288 3.30000000
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- 55 2 3.55000000 15.98682895 3.30000000
- 56 2 4.97000000 15.98682895 3.30000000
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- 58 1 1.42000000 17.21658503 0.00000000
- 59 2 1.42000000 17.21658503 3.30000000
- 60 2 2.84000000 17.21658503 3.30000000
- 61 1 2.13000000 18.44634110 0.00000000
- 62 1 3.55000000 18.44634110 0.00000000
- 63 2 3.55000000 18.44634110 3.30000000
- 64 2 4.97000000 18.44634110 3.30000000
- 65 1 4.26000000 0.00000000 0.00000000
- 66 1 5.68000000 0.00000000 0.00000000
- 67 2 5.68000000 0.00000000 3.30000000
- 68 2 7.10000000 0.00000000 3.30000000
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- 79 2 7.81000000 3.68926822 3.30000000
- 80 2 9.23000000 3.68926822 3.30000000
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- 84 2 7.10000000 4.91902429 3.30000000
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- 86 1 7.81000000 6.14878037 0.00000000
- 87 2 7.81000000 6.14878037 3.30000000
- 88 2 9.23000000 6.14878037 3.30000000
- 89 1 4.26000000 7.37853644 0.00000000
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- 91 2 5.68000000 7.37853644 3.30000000
- 92 2 7.10000000 7.37853644 3.30000000
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- 96 2 9.23000000 8.60829251 3.30000000
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- 98 1 5.68000000 9.83804859 0.00000000
- 99 2 5.68000000 9.83804859 3.30000000
-100 2 7.10000000 9.83804859 3.30000000
-101 1 6.39000000 11.06780466 0.00000000
-102 1 7.81000000 11.06780466 0.00000000
-103 2 7.81000000 11.06780466 3.30000000
-104 2 9.23000000 11.06780466 3.30000000
-105 1 4.26000000 12.29756073 0.00000000
-106 1 5.68000000 12.29756073 0.00000000
-107 2 5.68000000 12.29756073 3.30000000
-108 2 7.10000000 12.29756073 3.30000000
-109 1 6.39000000 13.52731681 0.00000000
-110 1 7.81000000 13.52731681 0.00000000
-111 2 7.81000000 13.52731681 3.30000000
-112 2 9.23000000 13.52731681 3.30000000
-113 1 4.26000000 14.75707288 0.00000000
-114 1 5.68000000 14.75707288 0.00000000
-115 2 5.68000000 14.75707288 3.30000000
-116 2 7.10000000 14.75707288 3.30000000
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-119 2 7.81000000 15.98682895 3.30000000
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-122 1 5.68000000 17.21658503 0.00000000
-123 2 5.68000000 17.21658503 3.30000000
-124 2 7.10000000 17.21658503 3.30000000
-125 1 6.39000000 18.44634110 0.00000000
-126 1 7.81000000 18.44634110 0.00000000
-127 2 7.81000000 18.44634110 3.30000000
-128 2 9.23000000 18.44634110 3.30000000
-129 1 8.52000000 0.00000000 0.00000000
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-151 2 12.07000000 6.14878037 3.30000000
-152 2 13.49000000 6.14878037 3.30000000
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-154 1 9.94000000 7.37853644 0.00000000
-155 2 9.94000000 7.37853644 3.30000000
-156 2 11.36000000 7.37853644 3.30000000
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-158 1 12.07000000 8.60829251 0.00000000
-159 2 12.07000000 8.60829251 3.30000000
-160 2 13.49000000 8.60829251 3.30000000
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-162 1 9.94000000 9.83804859 0.00000000
-163 2 9.94000000 9.83804859 3.30000000
-164 2 11.36000000 9.83804859 3.30000000
-165 1 10.65000000 11.06780466 0.00000000
-166 1 12.07000000 11.06780466 0.00000000
-167 2 12.07000000 11.06780466 3.30000000
-168 2 13.49000000 11.06780466 3.30000000
-169 1 8.52000000 12.29756073 0.00000000
-170 1 9.94000000 12.29756073 0.00000000
-171 2 9.94000000 12.29756073 3.30000000
-172 2 11.36000000 12.29756073 3.30000000
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-174 1 12.07000000 13.52731681 0.00000000
-175 2 12.07000000 13.52731681 3.30000000
-176 2 13.49000000 13.52731681 3.30000000
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-179 2 9.94000000 14.75707288 3.30000000
-180 2 11.36000000 14.75707288 3.30000000
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-182 1 12.07000000 15.98682895 0.00000000
-183 2 12.07000000 15.98682895 3.30000000
-184 2 13.49000000 15.98682895 3.30000000
-185 1 8.52000000 17.21658503 0.00000000
-186 1 9.94000000 17.21658503 0.00000000
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-188 2 11.36000000 17.21658503 3.30000000
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-190 1 12.07000000 18.44634110 0.00000000
-191 2 12.07000000 18.44634110 3.30000000
-192 2 13.49000000 18.44634110 3.30000000
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-194 1 14.20000000 0.00000000 0.00000000
-195 2 14.20000000 0.00000000 3.30000000
-196 2 15.62000000 0.00000000 3.30000000
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-199 2 16.33000000 1.22975607 3.30000000
-200 2 17.75000000 1.22975607 3.30000000
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-202 1 14.20000000 2.45951215 0.00000000
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-214 1 16.33000000 6.14878037 0.00000000
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-216 2 17.75000000 6.14878037 3.30000000
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-219 2 14.20000000 7.37853644 3.30000000
-220 2 15.62000000 7.37853644 3.30000000
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-222 1 16.33000000 8.60829251 0.00000000
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-224 2 17.75000000 8.60829251 3.30000000
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-227 2 14.20000000 9.83804859 3.30000000
-228 2 15.62000000 9.83804859 3.30000000
-229 1 14.91000000 11.06780466 0.00000000
-230 1 16.33000000 11.06780466 0.00000000
-231 2 16.33000000 11.06780466 3.30000000
-232 2 17.75000000 11.06780466 3.30000000
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-234 1 14.20000000 12.29756073 0.00000000
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-236 2 15.62000000 12.29756073 3.30000000
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-240 2 17.75000000 13.52731681 3.30000000
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-242 1 14.20000000 14.75707288 0.00000000
-243 2 14.20000000 14.75707288 3.30000000
-244 2 15.62000000 14.75707288 3.30000000
-245 1 14.91000000 15.98682895 0.00000000
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-248 2 17.75000000 15.98682895 3.30000000
-249 1 12.78000000 17.21658503 0.00000000
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-251 2 14.20000000 17.21658503 3.30000000
-252 2 15.62000000 17.21658503 3.30000000
-253 1 14.91000000 18.44634110 0.00000000
-254 1 16.33000000 18.44634110 0.00000000
-255 2 16.33000000 18.44634110 3.30000000
-256 2 17.75000000 18.44634110 3.30000000
diff --git a/examples/USER/misc/kolmogorov_crespi/data.graphene-adsorbant b/examples/USER/misc/kolmogorov_crespi/data.graphene-adsorbant
deleted file mode 100644
index 35cd7c91f354335e4f0813606a36571b52e0d230..0000000000000000000000000000000000000000
--- a/examples/USER/misc/kolmogorov_crespi/data.graphene-adsorbant
+++ /dev/null
@@ -1,139 +0,0 @@
-info: xyz2data 11:52, Tue 28-02-2017
-129 atoms
-2 atom types
-
- 0.00000000 17.04000000 xlo xhi
- 0.00000000 19.67609717 ylo yhi
- -10.00000000 40.00000000 zlo zhi
-
-Atoms
-
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- 2 1 1.42000000 0.00000000 0.00000000
- 3 1 2.13000000 1.22975607 0.00000000
- 4 1 3.55000000 1.22975607 0.00000000
- 5 1 0.00000000 2.45951215 0.00000000
- 6 1 1.42000000 2.45951215 0.00000000
- 7 1 2.13000000 3.68926822 0.00000000
- 8 1 3.55000000 3.68926822 0.00000000
- 9 1 0.00000000 4.91902429 0.00000000
- 10 1 1.42000000 4.91902429 0.00000000
- 11 1 2.13000000 6.14878037 0.00000000
- 12 1 3.55000000 6.14878037 0.00000000
- 13 1 0.00000000 7.37853644 0.00000000
- 14 1 1.42000000 7.37853644 0.00000000
- 15 1 2.13000000 8.60829251 0.00000000
- 16 1 3.55000000 8.60829251 0.00000000
- 17 1 0.00000000 9.83804859 0.00000000
- 18 1 1.42000000 9.83804859 0.00000000
- 19 1 2.13000000 11.06780466 0.00000000
- 20 1 3.55000000 11.06780466 0.00000000
- 21 1 0.00000000 12.29756073 0.00000000
- 22 1 1.42000000 12.29756073 0.00000000
- 23 1 2.13000000 13.52731681 0.00000000
- 24 1 3.55000000 13.52731681 0.00000000
- 25 1 0.00000000 14.75707288 0.00000000
- 26 1 1.42000000 14.75707288 0.00000000
- 27 1 2.13000000 15.98682895 0.00000000
- 28 1 3.55000000 15.98682895 0.00000000
- 29 1 0.00000000 17.21658503 0.00000000
- 30 1 1.42000000 17.21658503 0.00000000
- 31 1 2.13000000 18.44634110 0.00000000
- 32 1 3.55000000 18.44634110 0.00000000
- 33 1 4.26000000 0.00000000 0.00000000
- 34 1 5.68000000 0.00000000 0.00000000
- 35 1 6.39000000 1.22975607 0.00000000
- 36 1 7.81000000 1.22975607 0.00000000
- 37 1 4.26000000 2.45951215 0.00000000
- 38 1 5.68000000 2.45951215 0.00000000
- 39 1 6.39000000 3.68926822 0.00000000
- 40 1 7.81000000 3.68926822 0.00000000
- 41 1 4.26000000 4.91902429 0.00000000
- 42 1 5.68000000 4.91902429 0.00000000
- 43 1 6.39000000 6.14878037 0.00000000
- 44 1 7.81000000 6.14878037 0.00000000
- 45 1 4.26000000 7.37853644 0.00000000
- 46 1 5.68000000 7.37853644 0.00000000
- 47 1 6.39000000 8.60829251 0.00000000
- 48 1 7.81000000 8.60829251 0.00000000
- 49 1 4.26000000 9.83804859 0.00000000
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- 51 1 6.39000000 11.06780466 0.00000000
- 52 1 7.81000000 11.06780466 0.00000000
- 53 1 4.26000000 12.29756073 0.00000000
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- 58 1 5.68000000 14.75707288 0.00000000
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- 84 1 12.07000000 11.06780466 0.00000000
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-103 1 14.91000000 3.68926822 0.00000000
-104 1 16.33000000 3.68926822 0.00000000
-105 1 12.78000000 4.91902429 0.00000000
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-107 1 14.91000000 6.14878037 0.00000000
-108 1 16.33000000 6.14878037 0.00000000
-109 1 12.78000000 7.37853644 0.00000000
-110 1 14.20000000 7.37853644 0.00000000
-111 1 14.91000000 8.60829251 0.00000000
-112 1 16.33000000 8.60829251 0.00000000
-113 1 12.78000000 9.83804859 0.00000000
-114 1 14.20000000 9.83804859 0.00000000
-115 1 14.91000000 11.06780466 0.00000000
-116 1 16.33000000 11.06780466 0.00000000
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-119 1 14.91000000 13.52731681 0.00000000
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-124 1 16.33000000 15.98682895 0.00000000
-125 1 12.78000000 17.21658503 0.00000000
-126 1 14.20000000 17.21658503 0.00000000
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diff --git a/examples/USER/misc/kolmogorov_crespi/in.atom-diffusion b/examples/USER/misc/kolmogorov_crespi/in.atom-diffusion
deleted file mode 100644
index 5e3135a8b418c18ee0ec37a61f58d39f436659e0..0000000000000000000000000000000000000000
--- a/examples/USER/misc/kolmogorov_crespi/in.atom-diffusion
+++ /dev/null
@@ -1,45 +0,0 @@
-# Initialization
-units metal
-boundary p p p
-atom_style atomic
-processors * * 1 # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data data.graphene-adsorbant # read lammps data file
-mass 1 12.0107 # carbon mass (g/mole) | membrane
-mass 2 12.0107 # carbon mass (g/mole) | adsorbate
-# Neighbor update settings
-neighbor 2.0 bin
-neigh_modify every 1
-neigh_modify delay 0
-neigh_modify check yes
-# Separate atom groups
-group membrane type 1
-group adsorbant type 2
-
-######################## Potential defition ########################
-pair_style hybrid/overlay kolmogorov/crespi/z 14.0
-####################################################################
-pair_coeff * * none
-pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
-####################################################################
-
-#### Simulation settings ####
-timestep 0.0001
-fix thermostat adsorbant nve
-fix rigid_membrane membrane setforce 0 0 0
-compute COM1 membrane com
-compute COM2 adsorbant com
-############################
-
-# Output
-#dump 1 all xyz 100 trajec.xyz
-#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
-thermo 100
-thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
-thermo_modify line one format float %14.8f
-
-###### Run molecular dynamics ######
-run 10000
diff --git a/examples/USER/misc/kolmogorov_crespi/in.bilayer-graphene b/examples/USER/misc/kolmogorov_crespi/in.bilayer-graphene
deleted file mode 100644
index 3d63fc09ed0683976fdf9391d68c51ef1e136488..0000000000000000000000000000000000000000
--- a/examples/USER/misc/kolmogorov_crespi/in.bilayer-graphene
+++ /dev/null
@@ -1,45 +0,0 @@
-# Initialization
-units metal
-boundary p p p
-atom_style atomic
-processors * * 1 # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data data.bilayer-graphene # read lammps data file
-mass 1 12.0107 # carbon mass (g/mole) | membrane
-mass 2 12.0107 # carbon mass (g/mole) | adsorbate
-# Neighbor update settings
-neighbor 2.0 bin
-neigh_modify every 1
-neigh_modify delay 0
-neigh_modify check yes
-# Separate atom groups
-group membrane type 1
-group adsorbant type 2
-
-######################## Potential defition ########################
-pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
-####################################################################
-pair_coeff * * rebo CH.airebo C C # chemical
-pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
-####################################################################
-
-#### Simulation settings ####
-timestep 0.0001
-velocity all create 300.0 12345
-fix thermostat all nve
-compute COM1 membrane com
-compute COM2 adsorbant com
-############################
-
-# Output
-#dump 1 all xyz 100 trajec.xyz
-#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
-thermo 10
-thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
-thermo_modify line one format float %14.8f
-
-###### Run molecular dynamics ######
-run 1000
diff --git a/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene b/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene
index d853b7208ae8fc7f10a8d727a3f14a2cf8ae769d..63ac92cb052040056eb5e6d38991abf738787056 100644
--- a/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene
+++ b/examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene
@@ -18,7 +18,7 @@ group adsorbate type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
####################################################################
-pair_coeff * * rebo CH.airebo NULL C # chemical
+pair_coeff * * rebo CH.airebo NULL C # chemical
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
####################################################################
# Neighbor update settings
@@ -49,12 +49,12 @@ variable KC equal c_1
# Output
thermo 100
-thermo_style custom step cpu etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify line one format float %.16f
+thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
+thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
-dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
+#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
+#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
-run 10000
+run 1000
diff --git a/examples/USER/misc/kolmogorov_crespi_z/CC.KC b/examples/USER/misc/kolmogorov_crespi_z/CC.KC
new file mode 120000
index 0000000000000000000000000000000000000000..60708ac160a29aca54248370f656ab83e6e17d03
--- /dev/null
+++ b/examples/USER/misc/kolmogorov_crespi_z/CC.KC
@@ -0,0 +1 @@
+../../../../potentials/CC.KC
\ No newline at end of file
diff --git a/examples/USER/misc/kolmogorov_crespi_z/CH.airebo b/examples/USER/misc/kolmogorov_crespi_z/CH.airebo
new file mode 120000
index 0000000000000000000000000000000000000000..e43e44c133427fe8aa23a5592311e1a95dd30bd8
--- /dev/null
+++ b/examples/USER/misc/kolmogorov_crespi_z/CH.airebo
@@ -0,0 +1 @@
+../../../../potentials/CH.airebo
\ No newline at end of file
diff --git a/examples/USER/misc/kolmogorov_crespi/log.atom-diffusion b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.1
similarity index 91%
rename from examples/USER/misc/kolmogorov_crespi/log.atom-diffusion
rename to examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.1
index 5ed654221788e3dd5927a325df0e874f19f8fa47..a79617f7c4e9d1c79009ef60ea43e7c069a30fbf 100644
--- a/examples/USER/misc/kolmogorov_crespi/log.atom-diffusion
+++ b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (17 Nov 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
@@ -51,13 +52,23 @@ thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
- 2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
- binsize = 8 -> bins = 3 3 7
-Memory usage per processor = 2.48399 Mbytes
+ binsize = 8, bins = 3 3 7
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair kolmogorov/crespi/z, perpetual, skip from (2)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (2) neighbor class addition, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.206 | 3.206 | 3.206 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
@@ -160,20 +171,20 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
-Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms
+Loop time of 0.34689 on 1 procs for 10000 steps with 129 atoms
-Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s
-131.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 249.070 ns/day, 0.096 hours/ns, 28827.585 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 | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02
-Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04
-Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43
-Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47
-Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48
-Other | | 0.01361 | | | 3.56
+Pair | 0.2028 | 0.2028 | 0.2028 | 0.0 | 58.46
+Neigh | 0.00021529 | 0.00021529 | 0.00021529 | 0.0 | 0.06
+Comm | 0.10656 | 0.10656 | 0.10656 | 0.0 | 30.72
+Output | 0.0015109 | 0.0015109 | 0.0015109 | 0.0 | 0.44
+Modify | 0.011605 | 0.011605 | 0.011605 | 0.0 | 3.35
+Other | | 0.0242 | | | 6.98
Nlocal: 129 ave 129 max 129 min
Histogram: 1 0 0 0 0 0 0 0 0 0
diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.atom-diffusion b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.4
similarity index 90%
rename from examples/USER/misc/kolmogorov_crespi_z/log.atom-diffusion
rename to examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.4
index 5ed654221788e3dd5927a325df0e874f19f8fa47..6941777790712e40e02f11e2913f20fa5026c394 100644
--- a/examples/USER/misc/kolmogorov_crespi_z/log.atom-diffusion
+++ b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (17 Nov 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
@@ -10,7 +11,7 @@ processors * * 1 # domain decomposition over x and y
# interactions can be specified separately
read_data data.graphene-adsorbant # read lammps data file
orthogonal box = (0 0 -10) to (17.04 19.6761 40)
- 1 by 1 by 1 MPI processor grid
+ 2 by 2 by 1 MPI processor grid
reading atoms ...
129 atoms
mass 1 12.0107 # carbon mass (g/mole) | membrane
@@ -51,13 +52,23 @@ thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
- 2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
- binsize = 8 -> bins = 3 3 7
-Memory usage per processor = 2.48399 Mbytes
+ binsize = 8, bins = 3 3 7
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair kolmogorov/crespi/z, perpetual, skip from (2)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (2) neighbor class addition, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.167 | 3.167 | 3.168 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
@@ -160,27 +171,27 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
-Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms
+Loop time of 0.524797 on 4 procs for 10000 steps with 129 atoms
-Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s
-131.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 164.635 ns/day, 0.146 hours/ns, 19054.971 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 | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02
-Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04
-Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43
-Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47
-Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48
-Other | | 0.01361 | | | 3.56
+Pair | 0.043099 | 0.060851 | 0.10153 | 9.7 | 11.60
+Neigh | 6.2704e-05 | 6.628e-05 | 6.8188e-05 | 0.0 | 0.01
+Comm | 0.35059 | 0.39384 | 0.41232 | 4.0 | 75.05
+Output | 0.0028515 | 0.0031345 | 0.0037408 | 0.6 | 0.60
+Modify | 0.0063083 | 0.0065277 | 0.0066838 | 0.2 | 1.24
+Other | | 0.06038 | | | 11.50
-Nlocal: 129 ave 129 max 129 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1867 ave 1867 max 1867 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 290 ave 290 max 290 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
+Nlocal: 32.25 ave 33 max 32 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost: 1305.75 ave 1306 max 1305 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs: 72.5 ave 144 max 43 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 290
Ave neighs/atom = 2.24806
diff --git a/examples/USER/misc/kolmogorov_crespi/log.bilayer-graphene b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1
similarity index 89%
rename from examples/USER/misc/kolmogorov_crespi/log.bilayer-graphene
rename to examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1
index 3a5f1236339fb8be9978dd3391d57df776cb9e2b..3ba8bfd5df9445a332f24004793d37cde70edf3f 100644
--- a/examples/USER/misc/kolmogorov_crespi/log.bilayer-graphene
+++ b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (17 Nov 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
@@ -10,7 +11,7 @@ processors * * 1 # domain decomposition over x and y
# interactions can be specified separately
read_data data.bilayer-graphene # read lammps data file
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
- 2 by 2 by 1 MPI processor grid
+ 1 by 1 by 1 MPI processor grid
reading atoms ...
256 atoms
mass 1 12.0107 # carbon mass (g/mole) | membrane
@@ -52,13 +53,28 @@ thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
- 3 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
- binsize = 8 -> bins = 3 3 8
-Memory usage per processor = 3.22197 Mbytes
+ binsize = 8, bins = 3 3 8
+ 3 neighbor lists, perpetual/occasional/extra = 3 0 0
+ (1) pair rebo, perpetual
+ attributes: full, newton on, ghost
+ pair build: full/bin/ghost
+ stencil: full/ghost/bin/3d
+ bin: standard
+ (2) pair kolmogorov/crespi/z, perpetual, skip from (3)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (3) neighbor class addition, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
@@ -161,32 +177,32 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
-Loop time of 2.21183 on 4 procs for 1000 steps with 256 atoms
+Loop time of 3.90147 on 1 procs for 1000 steps with 256 atoms
-Performance: 3.906 ns/day, 6.144 hours/ns, 452.115 timesteps/s
-120.2% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 2.215 ns/day, 10.837 hours/ns, 256.314 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 | 1.9363 | 1.9928 | 2.0303 | 2.5 | 90.10
+Pair | 3.8786 | 3.8786 | 3.8786 | 0.0 | 99.41
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.16714 | 0.20465 | 0.26123 | 7.8 | 9.25
-Output | 0.002469 | 0.0028505 | 0.003949 | 1.2 | 0.13
-Modify | 0.002423 | 0.0026275 | 0.002853 | 0.4 | 0.12
-Other | | 0.008904 | | | 0.40
+Comm | 0.010816 | 0.010816 | 0.010816 | 0.0 | 0.28
+Output | 0.002461 | 0.002461 | 0.002461 | 0.0 | 0.06
+Modify | 0.0051703 | 0.0051703 | 0.0051703 | 0.0 | 0.13
+Other | | 0.004447 | | | 0.11
-Nlocal: 64 ave 64 max 64 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost: 1265 ave 1265 max 1265 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs: 11824 ave 11824 max 11824 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs: 23648 ave 23648 max 23648 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
+Nlocal: 256 ave 256 max 256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1721 ave 1721 max 1721 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 37312 ave 37312 max 37312 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 94592 ave 94592 max 94592 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 94592
Ave neighs/atom = 369.5
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:02
+Total wall time: 0:00:03
diff --git a/examples/USER/misc/kolmogorov_crespi_z/log.bilayer-graphene b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4
similarity index 91%
rename from examples/USER/misc/kolmogorov_crespi_z/log.bilayer-graphene
rename to examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4
index 3a5f1236339fb8be9978dd3391d57df776cb9e2b..b2dd5516540eb7b2eeb4d2c4eb28811d5241713b 100644
--- a/examples/USER/misc/kolmogorov_crespi_z/log.bilayer-graphene
+++ b/examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (17 Nov 2016)
+LAMMPS (8 Mar 2018)
+ using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
@@ -52,13 +53,28 @@ thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
- 3 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
- binsize = 8 -> bins = 3 3 8
-Memory usage per processor = 3.22197 Mbytes
+ binsize = 8, bins = 3 3 8
+ 3 neighbor lists, perpetual/occasional/extra = 3 0 0
+ (1) pair rebo, perpetual
+ attributes: full, newton on, ghost
+ pair build: full/bin/ghost
+ stencil: full/ghost/bin/3d
+ bin: standard
+ (2) pair kolmogorov/crespi/z, perpetual, skip from (3)
+ attributes: half, newton on
+ pair build: skip
+ stencil: none
+ bin: none
+ (3) neighbor class addition, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
@@ -161,26 +177,26 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
-Loop time of 2.21183 on 4 procs for 1000 steps with 256 atoms
+Loop time of 1.32192 on 4 procs for 1000 steps with 256 atoms
-Performance: 3.906 ns/day, 6.144 hours/ns, 452.115 timesteps/s
-120.2% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 6.536 ns/day, 3.672 hours/ns, 756.476 timesteps/s
+98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 1.9363 | 1.9928 | 2.0303 | 2.5 | 90.10
+Pair | 1.1157 | 1.172 | 1.2369 | 4.0 | 88.66
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.16714 | 0.20465 | 0.26123 | 7.8 | 9.25
-Output | 0.002469 | 0.0028505 | 0.003949 | 1.2 | 0.13
-Modify | 0.002423 | 0.0026275 | 0.002853 | 0.4 | 0.12
-Other | | 0.008904 | | | 0.40
+Comm | 0.071678 | 0.13667 | 0.19304 | 11.8 | 10.34
+Output | 0.0029244 | 0.0031272 | 0.0035112 | 0.4 | 0.24
+Modify | 0.0016961 | 0.0017477 | 0.0017846 | 0.1 | 0.13
+Other | | 0.008334 | | | 0.63
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1265 ave 1265 max 1265 min
Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs: 11824 ave 11824 max 11824 min
+Neighs: 9328 ave 9328 max 9328 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 23648 ave 23648 max 23648 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -189,4 +205,4 @@ Total # of neighbors = 94592
Ave neighs/atom = 369.5
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:02
+Total wall time: 0:00:01