move examples away from USER-MISC now that the package folder is gone

examples/PACKAGES/entropy/in.entropy

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+echo both
+
+units		metal
+atom_style	full
+
+read_data	data.interface
+mass            1 22.98977
+
+neigh_modify    delay 10 every 1
+pair_style 	eam/fs
+pair_coeff 	* * Na_MendelevM_2014.eam.fs Na
+timestep	0.002
+thermo          500
+
+neighbor 	4. bin
+
+# Define computes
+# Global density, no average
+compute         1 all entropy/atom 0.25 7.75
+# Local density, no average
+compute         2 all entropy/atom 0.25 7.75 local yes
+# Global density, average over neighbors
+compute         3 all entropy/atom 0.25 7.75 avg yes 5.
+# Local density, average over neighbors
+compute         4 all entropy/atom 0.25 7.75 avg yes 5. local yes
+
+dump            myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4
+
+
+fix             1 all nph x 1. 1. 10.
+fix             2 all temp/csvr 350. 350. 0.1 64582
+
+run             1000
+

examples/PACKAGES/entropy/log.entropy

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+LAMMPS (18 Feb 2020)
+
+units		metal
+atom_style	full
+
+read_data	data.interface
+Reading data file ...
+  triclinic box = (0 0 0) to (138.4 34.57 34.57) with tilt (0 0 0)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4096 atoms
+  reading velocities ...
+  4096 velocities
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.00048995 secs
+  read_data CPU = 0.0104239 secs
+mass            1 22.98977
+
+neigh_modify    delay 10 every 1
+pair_style 	eam/fs
+pair_coeff 	* * Na_MendelevM_2014.eam.fs Na
+timestep	0.002
+thermo          500
+
+neighbor 	4. bin
+
+# Define computes
+# Global density, no average
+compute         1 all entropy/atom 0.25 7.75
+# Local density, no average
+compute         2 all entropy/atom 0.25 7.75 local yes
+# Global density, average over neighbors
+compute         3 all entropy/atom 0.25 7.75 avg yes 5.
+# Local density, average over neighbors
+compute         4 all entropy/atom 0.25 7.75 avg yes 5. local yes
+
+dump            myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4
+
+
+fix             1 all nph x 1. 1. 10.
+fix             2 all temp/csvr 350. 350. 0.1 64582
+
+run             1000
+WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
+WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
+WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
+WARNING: More than one compute entropy/atom (src/USER-MISC/compute_entropy_atom.cpp:136)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 13.2
+  ghost atom cutoff = 13.2
+  binsize = 6.6, bins = 21 6 6
+  5 neighbor lists, perpetual/occasional/extra = 3 2 0
+  (1) pair eam/fs, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton/tri
+      stencil: half/bin/3d/newton/tri
+      bin: standard
+  (2) compute entropy/atom, occasional, copy from (4)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) compute entropy/atom, occasional, copy from (4)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) compute entropy/atom, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (5) compute entropy/atom, perpetual, copy from (4)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.002
+Per MPI rank memory allocation (min/avg/max) = 58.81 | 58.81 | 58.81 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume 
+       0    346.29871    -4285.222            0   -4101.9191    594.65353    165399.75 
+     500    359.33769   -4285.2472            0   -4095.0424    472.02043    165847.09 
+    1000    348.99683   -4276.2282            0   -4091.4971    149.38771    166965.86 
+Loop time of 20.309 on 1 procs for 1000 steps with 4096 atoms
+
+Performance: 8.509 ns/day, 2.821 hours/ns, 49.239 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    | 17.851     | 17.851     | 17.851     |   0.0 | 87.89
+Bond    | 0.00029588 | 0.00029588 | 0.00029588 |   0.0 |  0.00
+Neigh   | 1.5377     | 1.5377     | 1.5377     |   0.0 |  7.57
+Comm    | 0.083142   | 0.083142   | 0.083142   |   0.0 |  0.41
+Output  | 0.59598    | 0.59598    | 0.59598    |   0.0 |  2.93
+Modify  | 0.20727    | 0.20727    | 0.20727    |   0.0 |  1.02
+Other   |            | 0.03411    |            |       |  0.17
+
+Nlocal:    4096 ave 4096 max 4096 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11116 ave 11116 max 11116 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    486987 ave 486987 max 486987 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  973974 ave 973974 max 973974 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 973974
+Ave neighs/atom = 237.787
+Ave special neighs/atom = 0
+Neighbor list builds = 13
+Dangerous builds = 0
+
+Total wall time: 0:00:20