diff --git a/doc/src/Eqs/fix_rhok.jpg b/doc/src/Eqs/fix_rhok.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..829a866be449ecb0f23dc77f547c5b7d053c0469
Binary files /dev/null and b/doc/src/Eqs/fix_rhok.jpg differ
diff --git a/doc/src/Eqs/fix_rhok.tex b/doc/src/Eqs/fix_rhok.tex
new file mode 100644
index 0000000000000000000000000000000000000000..a468dfedc963e5d5616ca9baae019145bc421e51
--- /dev/null
+++ b/doc/src/Eqs/fix_rhok.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ U &=& \frac{1}{2} K (|\rho_{\vec{k}}| - a)^2 \\
+ \rho_{\vec{k}} &=& \sum_j^N \exp(-i\vec{k} \cdot \vec{r}_j )/\sqrt{N} \\
+ \vec{k} &=& (2\pi n_x /L_x , 2\pi n_y /L_y , 2\pi n_z/L_z )
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 8eed777e49dd7dc511de2193169ae7dc7f849d77..40527dabbc947c49a3a106bcb7e3f2e4b2d58f04 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -728,6 +728,7 @@ package"_Section_start.html#start_3.
"qtb"_fix_qtb.html,
"reax/c/bonds"_fix_reax_bonds.html,
"reax/c/species"_fix_reaxc_species.html,
+"rhok"_fix_rhok.html,
"rx"_fix_rx.html,
"saed/vtk"_fix_saed_vtk.html,
"shardlow"_fix_shardlow.html,
diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5046303329256e0deda4d40f690211fd498ddaf2
--- /dev/null
+++ b/doc/src/fix_rhok.txt
@@ -0,0 +1,57 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix rhok command :h3
+
+fix ID group-ID rhok nx ny nz K a :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nx, ny, nz = k-vektor of collective density field
+K = spring constant of bias potential
+a = anchor point of bias potential :ul
+
+[Examples:]
+
+fix bias all rhok 16 0 0 4.0 16.0
+fix 1 all npt temp 0.8 0.8 4.0 z 2.2 2.2 8.0
+# output U_bias rho_k_RE rho_k_IM |rho_k|
+thermo_style custom step temp pzz lz f_bias f_bias\[1\] f_bias\[2\] f_bias\[3\] :pre
+
+[Description:]
+
+The fix applies an force to atoms given by the potential
+
+:c,image(Eqs/fix_rhok.jpg)
+
+as described in "(Pedersen)"_#Pedersen.
+
+This field, that bias configurations with long-range order,
+can be used to study crystal-liquid interfaces
+and determine melting temperatures "(Pedersen)"_#Pedersen.
+
+An example of using the interface pinning method
+is located in the folder
+{examples/USER/pinning} of the source code to LAMMPS.
+
+[Restrictions:]
+
+This fix is part of the MISC package. It is only enabled if LAMMPS
+was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"thermo_style"_thermo_style.html
+
+[Default:] none
+
+:line
+
+:link(Pedersen)
+[(Pedersen)] Pedersen, J. Chem. Phys., 139, 104102 (2013).
+
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index e363273a754a47e576f53eaaf5aaf2f3dd294c72..6d51151f31a7be6cafc688f58ca8b5311839c521 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -125,6 +125,7 @@ Fixes :h1
fix_reaxc_species
fix_recenter
fix_restrain
+ fix_rhok
fix_rigid
fix_rx
fix_saed_vtk
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 5ebf7466c8f41aa30fc9779e6e455485f2187dd2..9d1e920179de16b6fa4b52d50663e64d7517505e 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -254,6 +254,7 @@ fix_reaxc_species.html
fix_recenter.html
fix_restrain.html
fix_rigid.html
+fix_rhok.html
fix_rx.html
fix_saed_vtk.html
fix_setforce.html
diff --git a/examples/USER/misc/pinning/README.md b/examples/USER/misc/pinning/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..4e011255fcc8e7628379451a94ee30db8ec867a3
--- /dev/null
+++ b/examples/USER/misc/pinning/README.md
@@ -0,0 +1,74 @@
+# The Interface Pinning method for studying solid-liquid transitions
+
+In this example we will use the interface pinnig method to study a solid-liquid transition.
+This is done by adding a harmonic potential to the Hamiltonian
+that bias the system towards two-phase configurations:
+
+ U_bias = 0.5*K*(Q-a)^2
+
+The bias field couple to an order-parameter of crystallinity Q. The implementation use long-range order:
+
+ Q=|rho_k|,
+
+where rho_k is the collective density field of the wave-vector k.
+For future reference we note that the structure factor S(k) is given by the variance of the collective density field:
+
+ S(k)=|rho_k|^2.
+
+### About the method
+
+It is recommended to get familiar with the interface pinning method by reading:
+
+ [Ulf R. Pedersen, JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747)
+
+A detailed bibliography is provided at
+
+ <http://urp.dk/interface_pinning.htm>
+
+and a brief introduction can be found at YouTube:
+
+ [](http://www.youtube.com/watch?v=F_79JZNdyoQ)
+
+### Implimentation in LAMMPS
+
+For this example we will be using the rhok fix.
+
+ fix [name] [groupID] rhok [nx] [ny] [nz] [K] [a]
+
+This fix include a harmonic bias potential U_bias=0.5*K*(|rho_k|-a)^2 to the force calculation.
+The elements of the wave-vector k is given by the nx, ny and nz input:
+
+ k_x = (2 pi / L_x) * n_x, k_y = (2 pi / L_y) * n_y and k_z = (2 pi / L_z) * n_z.
+
+We will use a k vector that correspond to a Bragg peak.
+
+## Example: the Lennard-Jones (LJ) model
+
+We will use the interface pinning method to study melting of the LJ model
+at temperature 0.8 and pressure 2.185. This is a coexistence state-point, and the method
+can be used to show this. The present directory contains the input files that we will use:
+
+ in.crystal
+ in.setup
+ in.pinning
+
+1. First we will determine the density of the crystal with the LAMMPS input file in.crystal.
+ From the output we get that the average density after equilibration is 0.9731.
+ We need this density to ensure hydrostatic pressure when in a two-phase simulation.
+
+2. Next, we setup a two-phase configuration using in.setup.
+
+3. Finally, we run a two-phase simulation with the bias-field applied using in.pinning.
+ The last column in the output show |rho_k|. We note that after a equilibration period
+ the value fluctuates around the anchor point (a) -- showing that this is indeed a coexistence
+ state point.
+
+The reference [JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points,
+and the reference [JCP 142, 044104 (2015)](http://dx.doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations.
+That method have been experienced to be most effective in the slightly super-heated regime above the melting temperature.
+
+## Contact
+
+ Ulf R. Pedersen;
+ <http://www.urp.dk>;
+ ulf AT urp.dk
diff --git a/examples/USER/misc/pinning/in.crystal b/examples/USER/misc/pinning/in.crystal
new file mode 100644
index 0000000000000000000000000000000000000000..55e9e59a064ad93165d3a5f35ca5661b5e1be3c2
--- /dev/null
+++ b/examples/USER/misc/pinning/in.crystal
@@ -0,0 +1,36 @@
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+lattice fcc 0.9731
+region my_box block 0 8.0 0 8.0 0 20.0
+create_box 1 my_box
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify tail no
+pair_modify shift yes
+mass 1 1.0
+velocity all create 1.6 1 mom yes rot yes
+
+# simulation parameters
+neighbor 0.6 bin
+timestep 0.004
+run_style verlet
+fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32
+
+# computing long-range order (no bias is added since k=0)
+fix bias all rhok 16 0 0 0.0 0.0
+
+# output
+thermo 50
+thermo_style custom step temp press density f_bias[3]
+# dump dumpXYZ all xyz 2000 traj.xyz
+
+# NOTE: this is cut short to 5000 steps for demonstration purposes
+# run 100000
+run 5000
diff --git a/examples/USER/misc/pinning/in.pinning b/examples/USER/misc/pinning/in.pinning
new file mode 100644
index 0000000000000000000000000000000000000000..0c220f480b7ca8586c29b96b0455dd5002efda4d
--- /dev/null
+++ b/examples/USER/misc/pinning/in.pinning
@@ -0,0 +1,33 @@
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+read_data data.halfhalf
+pair_coeff 1 1 1.0 1.0 2.5
+mass 1 1.0
+
+# simulation parameters
+neighbor 0.6 bin
+timestep 0.004
+run_style verlet
+
+velocity all create 0.8 1 mom yes rot yes
+fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0
+fix 100 all momentum 100 linear 1 1 1
+
+# harmonic rho_k bias-field
+# nx ny nz K a
+fix bias all rhok 16 0 0 4.0 26.00
+
+# output U_bias rho_k_RE rho_k_IM |rho_k|
+thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]
+thermo 50
+# dump dumpXYZ all xyz 500 traj.xyz
+
+# NOTE: run reduced for demonstration purposes
+# run 50000
+run 5000
diff --git a/examples/USER/misc/pinning/in.setup b/examples/USER/misc/pinning/in.setup
new file mode 100644
index 0000000000000000000000000000000000000000..649b0f534c8fc8821ec301f2addac3568e3a120e
--- /dev/null
+++ b/examples/USER/misc/pinning/in.setup
@@ -0,0 +1,41 @@
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+
+# fcc lattice
+lattice fcc 0.9731
+region my_box block 0 8.0 0 8.0 0 20.0
+create_box 1 my_box
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+pair_coeff 1 1 1.0 1.0 2.5
+mass 1 1.0
+change_box all z final 0.0 34 remap units box
+
+# select particles in one side of the elongated box
+region left plane 0 0 10 0 0 1
+group left region left
+
+velocity left create 6.0 1 mom yes rot yes
+
+# simulation parameters
+neighbor 0.6 bin
+timestep 0.004
+run_style verlet
+fix ensemble left nve # Note: only move particle in left-hand side
+fix langevin left langevin 3.0 0.8 100.0 2017
+
+# outout
+thermo_style custom step temp pzz pe lz
+thermo 100
+# dump dumpXYZ all xyz 100 traj.xyz
+
+# run reduced for demonstration purposes
+# run 10000
+run 5000
+write_data data.halfhalf
diff --git a/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.1 b/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..05fadb5c032d51bca8064d40cb63a5948fa652ee
--- /dev/null
+++ b/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.1
@@ -0,0 +1,187 @@
+LAMMPS (22 Sep 2017)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+lattice fcc 0.9731
+Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
+region my_box block 0 8.0 0 8.0 0 20.0
+create_box 1 my_box
+Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
+ 1 by 1 by 1 MPI processor grid
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+Created 5120 atoms
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify tail no
+pair_modify shift yes
+mass 1 1.0
+velocity all create 1.6 1 mom yes rot yes
+
+# simulation parameters
+neighbor 0.6 bin
+timestep 0.004
+run_style verlet
+fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32
+
+# computing long-range order (no bias is added since k=0)
+fix bias all rhok 16 0 0 0.0 0.0
+
+# output
+thermo 50
+thermo_style custom step temp press density f_bias[3]
+# dump dumpXYZ all xyz 2000 traj.xyz
+
+# NOTE: this is cut short to 5000 steps for demonstration purposes
+# run 100000
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 3.1
+ ghost atom cutoff = 3.1
+ binsize = 1.55, bins = 9 9 21
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, 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) = 4.523 | 4.523 | 4.523 Mbytes
+Step Temp Press Density f_bias[3]
+ 0 1.6 -2.7568106 0.9731 71.554175
+ 50 0.78457786 3.1029192 0.97362639 54.327705
+ 100 0.85528971 2.4670259 0.97213457 55.189308
+ 150 0.85241818 2.3210306 0.9698027 56.138125
+ 200 0.82301385 2.3448692 0.96708227 55.735326
+ 250 0.83076383 2.0890816 0.96425763 55.320625
+ 300 0.81602823 2.0118796 0.96173925 54.095736
+ 350 0.81084006 1.9122192 0.95979392 54.526429
+ 400 0.80776593 1.8502174 0.95869117 54.434901
+ 450 0.80694697 1.8435873 0.95851085 53.20809
+ 500 0.81384248 1.8111331 0.95917305 53.419395
+ 550 0.81027072 1.9222272 0.96056019 54.36723
+ 600 0.81199582 2.0291945 0.96248486 54.888582
+ 650 0.82507964 2.0706462 0.96467227 55.807137
+ 700 0.832562 2.1471442 0.9668913 56.721267
+ 750 0.83358138 2.2674672 0.968984 56.723838
+ 800 0.83477542 2.3658275 0.97072603 56.234689
+ 850 0.84722921 2.3506233 0.97189674 56.262424
+ 900 0.83526965 2.4532068 0.97248856 56.219103
+ 950 0.83174583 2.4763958 0.97249527 56.409813
+ 1000 0.83022557 2.4334341 0.97194093 55.890858
+ 1050 0.83208978 2.3478416 0.97092452 54.934691
+ 1100 0.82789545 2.272404 0.9696152 54.90894
+ 1150 0.82678617 2.1798046 0.96819776 54.927782
+ 1200 0.8088841 2.1960256 0.96687735 54.914327
+ 1250 0.81512784 2.0736261 0.96579008 53.927291
+ 1300 0.81271067 2.0297138 0.96504188 54.289698
+ 1350 0.8201767 1.9493976 0.96464115 55.342131
+ 1400 0.80880489 2.0016987 0.96468463 55.757758
+ 1450 0.8114196 2.0282699 0.96514115 55.865676
+ 1500 0.81085664 2.0838361 0.96591869 56.553425
+ 1550 0.81257075 2.1283157 0.96694549 56.921544
+ 1600 0.82617645 2.1017986 0.96817075 56.858808
+ 1650 0.82616141 2.1885582 0.96941073 56.717917
+ 1700 0.81634174 2.2996967 0.97047447 56.453745
+ 1750 0.82447573 2.2924266 0.97128663 56.916813
+ 1800 0.83610432 2.236456 0.97178453 56.400752
+ 1850 0.82479203 2.3103493 0.97197318 55.891368
+ 1900 0.82298992 2.3059289 0.97181084 55.680563
+ 1950 0.82098556 2.2801003 0.97138609 55.754406
+ 2000 0.8181203 2.2480175 0.97078591 55.801363
+ 2050 0.82822293 2.1208884 0.97004107 55.687
+ 2100 0.7976818 2.2711199 0.96930169 55.459844
+ 2150 0.81817848 2.0680351 0.96860201 56.514731
+ 2200 0.80707457 2.1112141 0.96810519 55.504308
+ 2250 0.81651111 2.0077603 0.96781161 55.635702
+ 2300 0.80634534 2.0662241 0.96777177 56.051086
+ 2350 0.80892831 2.0619333 0.96799037 56.548711
+ 2400 0.82454203 1.9585394 0.9684672 56.695235
+ 2450 0.81517178 2.075283 0.96921622 56.613082
+ 2500 0.80969595 2.1624581 0.97010528 56.57516
+ 2550 0.80862964 2.2088622 0.97100774 57.072594
+ 2600 0.81468816 2.2293973 0.97192868 56.879212
+ 2650 0.82063107 2.2244887 0.97269715 55.454502
+ 2700 0.81691618 2.2789954 0.97319841 54.421943
+ 2750 0.8141787 2.2981247 0.97340453 54.469921
+ 2800 0.81973871 2.2422136 0.9733278 55.959235
+ 2850 0.82037399 2.201016 0.97302727 56.685826
+ 2900 0.80650164 2.2672955 0.9726128 56.574395
+ 2950 0.81752783 2.1317541 0.97207545 56.809412
+ 3000 0.80836945 2.1461483 0.97151192 57.205206
+ 3050 0.80785109 2.1189056 0.97103049 57.418763
+ 3100 0.79835058 2.146416 0.97069705 57.329383
+ 3150 0.79792089 2.1388267 0.97051679 57.279852
+ 3200 0.79934603 2.1049562 0.97046851 56.351494
+ 3250 0.79523232 2.1549779 0.97063956 56.00356
+ 3300 0.8004458 2.1145975 0.97096375 55.725509
+ 3350 0.79772742 2.166292 0.97143785 55.558075
+ 3400 0.80621087 2.1309217 0.97198456 55.816704
+ 3450 0.80540626 2.1727557 0.97263267 55.671283
+ 3500 0.80867606 2.1905129 0.97321538 55.390086
+ 3550 0.80917896 2.2144872 0.97370472 55.742085
+ 3600 0.80930722 2.2288938 0.974093 56.23064
+ 3650 0.80390523 2.2777327 0.97431886 56.084731
+ 3700 0.79620093 2.3143541 0.97435103 55.942797
+ 3750 0.80252393 2.2564638 0.9741875 56.042055
+ 3800 0.78981264 2.3156481 0.9739121 55.971352
+ 3850 0.80391951 2.1804938 0.97351088 55.855858
+ 3900 0.81268129 2.0855818 0.97308521 56.288315
+ 3950 0.7958182 2.175259 0.97273088 56.140141
+ 4000 0.80054484 2.1163279 0.97243129 56.366818
+ 4050 0.79760187 2.105362 0.97225308 56.684619
+ 4100 0.79283424 2.1357603 0.972206 56.203341
+ 4150 0.79543088 2.1036951 0.97227608 56.606315
+ 4200 0.79410999 2.1402049 0.97253758 56.277478
+ 4250 0.7985469 2.1285154 0.97293622 56.356076
+ 4300 0.79700387 2.1470614 0.97337091 56.722298
+ 4350 0.80479321 2.1403244 0.97384674 57.212574
+ 4400 0.79505512 2.224463 0.97434415 56.561877
+ 4450 0.78346648 2.3347865 0.97478611 56.681362
+ 4500 0.79811284 2.259123 0.97510069 57.365929
+ 4550 0.80015561 2.2345254 0.97523653 57.34799
+ 4600 0.79648318 2.2651869 0.97525975 57.502318
+ 4650 0.80524865 2.1943025 0.97507638 57.702488
+ 4700 0.80397778 2.1758629 0.97478268 57.162107
+ 4750 0.78914913 2.2470191 0.9744625 56.849565
+ 4800 0.79324889 2.2028993 0.97408817 57.572344
+ 4850 0.78993209 2.181763 0.97373372 57.683552
+ 4900 0.79041263 2.1604768 0.97348692 56.922312
+ 4950 0.79741332 2.1105901 0.97332545 57.488932
+ 5000 0.7891178 2.163416 0.97328963 57.365252
+Loop time of 33.6467 on 1 procs for 5000 steps with 5120 atoms
+
+Performance: 51357.258 tau/day, 148.603 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 | 24.699 | 24.699 | 24.699 | 0.0 | 73.41
+Neigh | 2.8894 | 2.8894 | 2.8894 | 0.0 | 8.59
+Comm | 0.34907 | 0.34907 | 0.34907 | 0.0 | 1.04
+Output | 0.0056 | 0.0056 | 0.0056 | 0.0 | 0.02
+Modify | 5.5718 | 5.5718 | 5.5718 | 0.0 | 16.56
+Other | | 0.1319 | | | 0.39
+
+Nlocal: 5120 ave 5120 max 5120 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 7594 ave 7594 max 7594 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 323081 ave 323081 max 323081 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 323081
+Ave neighs/atom = 63.1018
+Neighbor list builds = 248
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:33
diff --git a/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.4 b/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..cec9c69aff92e969c916400c4190e78160929e23
--- /dev/null
+++ b/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.4
@@ -0,0 +1,187 @@
+LAMMPS (22 Sep 2017)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+lattice fcc 0.9731
+Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
+region my_box block 0 8.0 0 8.0 0 20.0
+create_box 1 my_box
+Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
+ 1 by 1 by 4 MPI processor grid
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+Created 5120 atoms
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify tail no
+pair_modify shift yes
+mass 1 1.0
+velocity all create 1.6 1 mom yes rot yes
+
+# simulation parameters
+neighbor 0.6 bin
+timestep 0.004
+run_style verlet
+fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32
+
+# computing long-range order (no bias is added since k=0)
+fix bias all rhok 16 0 0 0.0 0.0
+
+# output
+thermo 50
+thermo_style custom step temp press density f_bias[3]
+# dump dumpXYZ all xyz 2000 traj.xyz
+
+# NOTE: this is cut short to 5000 steps for demonstration purposes
+# run 100000
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 3.1
+ ghost atom cutoff = 3.1
+ binsize = 1.55, bins = 9 9 21
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, 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) = 3.23 | 3.23 | 3.23 Mbytes
+Step Temp Press Density f_bias[3]
+ 0 1.6 -2.7568106 0.9731 71.554175
+ 50 0.78457786 3.1029192 0.97362639 54.327705
+ 100 0.85528971 2.4670259 0.97213457 55.189308
+ 150 0.85241818 2.3210306 0.9698027 56.138125
+ 200 0.82301385 2.3448692 0.96708227 55.735326
+ 250 0.83076383 2.0890816 0.96425763 55.320625
+ 300 0.81602823 2.0118796 0.96173925 54.095736
+ 350 0.81084006 1.9122192 0.95979392 54.526429
+ 400 0.80776593 1.8502174 0.95869117 54.434901
+ 450 0.80694697 1.8435873 0.95851085 53.20809
+ 500 0.81384248 1.8111331 0.95917305 53.419395
+ 550 0.81027072 1.9222272 0.96056019 54.36723
+ 600 0.81199582 2.0291945 0.96248486 54.888582
+ 650 0.82507964 2.0706462 0.96467227 55.807137
+ 700 0.832562 2.1471442 0.9668913 56.721267
+ 750 0.83358138 2.2674672 0.968984 56.723838
+ 800 0.83477542 2.3658275 0.97072603 56.234689
+ 850 0.84722921 2.3506233 0.97189674 56.262424
+ 900 0.83526965 2.4532068 0.97248856 56.219103
+ 950 0.83174583 2.4763958 0.97249527 56.409813
+ 1000 0.83022557 2.4334341 0.97194093 55.890858
+ 1050 0.83208978 2.3478416 0.97092452 54.934691
+ 1100 0.82789545 2.272404 0.9696152 54.90894
+ 1150 0.82678617 2.1798046 0.96819776 54.927782
+ 1200 0.8088841 2.1960256 0.96687735 54.914327
+ 1250 0.81512784 2.0736261 0.96579008 53.927291
+ 1300 0.81271067 2.0297138 0.96504188 54.289698
+ 1350 0.8201767 1.9493976 0.96464115 55.342131
+ 1400 0.80880489 2.0016987 0.96468463 55.757758
+ 1450 0.8114196 2.0282699 0.96514115 55.865676
+ 1500 0.81085664 2.0838361 0.96591869 56.553425
+ 1550 0.81257075 2.1283157 0.96694549 56.921544
+ 1600 0.82617645 2.1017986 0.96817075 56.858808
+ 1650 0.82616141 2.1885582 0.96941073 56.717917
+ 1700 0.81634174 2.2996967 0.97047447 56.453745
+ 1750 0.82447573 2.2924266 0.97128663 56.916813
+ 1800 0.83610432 2.236456 0.97178453 56.400752
+ 1850 0.824792 2.3103491 0.97197318 55.891368
+ 1900 0.82298989 2.3059287 0.97181084 55.680562
+ 1950 0.82098545 2.2801009 0.97138609 55.754404
+ 2000 0.81812031 2.2480166 0.97078591 55.801371
+ 2050 0.82822262 2.1208887 0.97004108 55.687001
+ 2100 0.79768162 2.2711186 0.9693017 55.459852
+ 2150 0.81817874 2.0680317 0.96860202 56.514744
+ 2200 0.80707412 2.1112032 0.96810521 55.504308
+ 2250 0.81650921 2.0077757 0.96781164 55.635717
+ 2300 0.80634656 2.066186 0.96777181 56.051088
+ 2350 0.80893174 2.0619084 0.96799042 56.548711
+ 2400 0.82453783 1.9585503 0.96846727 56.695111
+ 2450 0.81517275 2.0752617 0.96921631 56.614046
+ 2500 0.80969622 2.1624476 0.9701054 56.574846
+ 2550 0.80861922 2.2089505 0.97100787 57.072334
+ 2600 0.81468888 2.2293754 0.97192875 56.879416
+ 2650 0.82061239 2.2245462 0.97269723 55.442015
+ 2700 0.81687473 2.2792015 0.97319852 54.420301
+ 2750 0.81416567 2.2982988 0.97340467 54.469427
+ 2800 0.81978563 2.2418723 0.97332803 55.965451
+ 2850 0.82069759 2.1988948 0.97302752 56.686807
+ 2900 0.80631184 2.2684466 0.97261407 56.585682
+ 2950 0.81759744 2.1312328 0.97207888 56.812431
+ 3000 0.80748056 2.152676 0.97151807 57.178849
+ 3050 0.80789237 2.118162 0.97103728 57.433724
+ 3100 0.79882523 2.1414744 0.97070338 57.34686
+ 3150 0.79803949 2.1359043 0.97052875 57.382544
+ 3200 0.79170386 2.1548392 0.97049349 56.465806
+ 3250 0.78848813 2.1990144 0.97067557 55.929088
+ 3300 0.79820555 2.1304609 0.97101444 55.624487
+ 3350 0.79250565 2.1971235 0.97149233 55.933615
+ 3400 0.80584844 2.1417239 0.97206083 55.85922
+ 3450 0.80685744 2.1640501 0.97266047 55.135963
+ 3500 0.80751888 2.1858277 0.97318703 55.407581
+ 3550 0.79882754 2.2796452 0.97363149 55.392366
+ 3600 0.80219171 2.2715765 0.97392571 55.867887
+ 3650 0.79061794 2.3492866 0.97410985 56.0192
+ 3700 0.8058483 2.2327904 0.97411924 56.491303
+ 3750 0.79460746 2.2941868 0.97397764 55.929912
+ 3800 0.80447478 2.2018009 0.97367627 55.663208
+ 3850 0.80355335 2.17638 0.97333164 55.637261
+ 3900 0.80388417 2.1531434 0.9729647 56.03794
+ 3950 0.79557409 2.1853318 0.9726503 56.132348
+ 4000 0.79547396 2.1457051 0.97235244 55.552675
+ 4050 0.8058384 2.0637678 0.97213346 56.185416
+ 4100 0.7976931 2.1028246 0.97208255 56.050347
+ 4150 0.79555522 2.115473 0.97216375 56.868136
+ 4200 0.79324134 2.1510383 0.97246129 56.462635
+ 4250 0.80788167 2.0534887 0.97287821 55.650788
+ 4300 0.79389865 2.2019815 0.97337765 55.596846
+ 4350 0.79786309 2.1851119 0.97389825 57.000921
+ 4400 0.79986518 2.1997541 0.97443778 57.551564
+ 4450 0.8063901 2.1893874 0.97493151 57.236138
+ 4500 0.80005802 2.250364 0.97533075 57.341358
+ 4550 0.79707443 2.2995576 0.97557554 57.338713
+ 4600 0.79869949 2.2807889 0.97563277 57.084504
+ 4650 0.79694427 2.2673215 0.97544638 57.025663
+ 4700 0.79023986 2.2884131 0.97511483 57.131188
+ 4750 0.79566823 2.2215519 0.97464304 57.045676
+ 4800 0.78936986 2.2268037 0.97410626 57.384178
+ 4850 0.79025913 2.1836718 0.973616 57.78438
+ 4900 0.80138424 2.0657609 0.9732124 57.888266
+ 4950 0.77853735 2.207944 0.97296347 57.312213
+ 5000 0.79115984 2.1035893 0.97285578 57.109472
+Loop time of 9.53489 on 4 procs for 5000 steps with 5120 atoms
+
+Performance: 181229.223 tau/day, 524.390 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 6.312 | 6.4238 | 6.5139 | 3.1 | 67.37
+Neigh | 0.72062 | 0.73538 | 0.74531 | 1.1 | 7.71
+Comm | 0.52697 | 0.64152 | 0.78688 | 14.1 | 6.73
+Output | 0.0028393 | 0.0029888 | 0.0033851 | 0.4 | 0.03
+Modify | 1.6249 | 1.669 | 1.7253 | 2.9 | 17.50
+Other | | 0.06221 | | | 0.65
+
+Nlocal: 1280 ave 1289 max 1266 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Nghost: 3346.25 ave 3379 max 3331 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Neighs: 80701.8 ave 81534 max 79755 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+
+Total # of neighbors = 322807
+Ave neighs/atom = 63.0482
+Neighbor list builds = 248
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:09
diff --git a/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.1 b/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..c2aaa9a58118475f45c0c2887eec58ac8588a631
--- /dev/null
+++ b/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.1
@@ -0,0 +1,186 @@
+LAMMPS (22 Sep 2017)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+read_data data.halfhalf
+ orthogonal box = (0 0 0) to (12.8152 12.8152 34)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 5120 atoms
+ reading velocities ...
+ 5120 velocities
+pair_coeff 1 1 1.0 1.0 2.5
+mass 1 1.0
+
+# simulation parameters
+neighbor 0.6 bin
+timestep 0.004
+run_style verlet
+
+velocity all create 0.8 1 mom yes rot yes
+fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0
+fix 100 all momentum 100 linear 1 1 1
+
+# harmonic rho_k bias-field
+# nx ny nz k a
+fix bias all rhok 16 0 0 4.0 26.00
+
+# output U_bias rho_k_RE rho_k_IM |rho_k|
+thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]
+thermo 50
+dump dumpXYZ all xyz 500 traj.xyz
+
+# NOTE: run reduced for demonstration purposes
+# run 50000
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 3.1
+ ghost atom cutoff = 3.1
+ binsize = 1.55, bins = 9 9 22
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, 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) = 5.723 | 5.723 | 5.723 Mbytes
+Step Temp Pzz PotEng Lz f_bias f_bias[1] f_bias[2] f_bias[3]
+ 0 0.8 5.1566801 -4.8556711 34 179.52419 35.473155 -0.2832763 35.474286
+ 50 1.072533 3.8158392 -5.2704532 34.024206 0.010596224 25.927135 -0.063106738 25.927212
+ 100 1.1093231 3.6703116 -5.3380965 34.094814 1.8552612 26.958236 -0.51403326 26.963136
+ 150 1.1080721 3.8202601 -5.3568368 34.207473 0.39188605 26.420755 -1.0759575 26.442655
+ 200 1.1435287 3.3445987 -5.4365298 34.354119 3.0758718 27.239465 -0.19115251 27.240135
+ 250 1.1203046 3.4669456 -5.4293867 34.511473 0.8543814 26.652785 -0.20818214 26.653598
+ 300 1.1012709 3.4583154 -5.4281803 34.664509 2.4837156 27.097674 0.9518628 27.114387
+ 350 1.0439632 3.8953869 -5.368619 34.810399 0.55385719 26.518391 0.64525272 26.52624
+ 400 1.0083878 4.0523864 -5.3418278 34.957669 0.34806057 26.404011 0.83368604 26.417169
+ 450 0.9675244 4.310087 -5.3089468 35.114208 0.7921285 26.607512 1.077889 26.629336
+ 500 0.94605476 4.1050097 -5.3062273 35.284018 0.87757754 26.639125 1.1140858 26.662411
+ 550 0.92662323 3.9299063 -5.3062927 35.458565 1.3746441 26.773494 1.7256603 26.829049
+ 600 0.89723165 3.7683555 -5.289725 35.629881 0.46692943 26.372973 2.4135502 26.483182
+ 650 0.90612566 3.1098837 -5.3267851 35.788537 0.032662126 25.918784 3.2982102 26.127793
+ 700 0.9152508 2.6527976 -5.3597799 35.923343 0.014621588 25.834591 3.6093492 26.085503
+ 750 0.90156356 2.3474851 -5.3545938 36.031813 0.75225637 26.307204 4.0247215 26.613293
+ 800 0.89748513 1.9825103 -5.3610202 36.113888 0.33402511 26.261326 2.7858039 26.408672
+ 850 0.89496343 1.8906342 -5.3673514 36.169424 0.85431557 26.534648 2.5150347 26.653573
+ 900 0.89463983 1.5654217 -5.3753283 36.20181 1.5689239 26.764737 2.5474794 26.885699
+ 950 0.88663832 1.4399476 -5.3703322 36.209971 0.044436903 25.818418 1.2963356 25.850941
+ 1000 0.87407208 1.485718 -5.3572665 36.195386 1.4405611 26.828072 1.0520795 26.848693
+ 1050 0.87580489 1.163155 -5.3647269 36.160279 0.15319559 26.234791 1.4845964 26.276763
+ 1100 0.86978111 1.3743181 -5.3594907 36.104958 1.1313537 25.19895 1.5711793 25.247885
+ 1150 0.86987861 1.3212927 -5.3628503 36.035486 0.039865678 25.841762 0.93898962 25.858816
+ 1200 0.87142486 1.3293818 -5.3676854 35.954411 0.16827389 25.70952 -0.14639427 25.709936
+ 1250 0.87582265 1.3203803 -5.3764058 35.86575 0.25946652 25.639682 0.082696867 25.639815
+ 1300 0.87371627 1.4680294 -5.375151 35.772824 0.17697069 25.701417 0.2397926 25.702535
+ 1350 0.88617453 1.5923057 -5.3954912 35.681046 0.00049155526 25.973634 -0.74521794 25.984323
+ 1400 0.87809636 1.5821707 -5.3850722 35.594706 0.024050814 26.107395 -0.34393685 26.10966
+ 1450 0.87912192 1.7820174 -5.3885842 35.514722 0.20999914 25.667238 -0.66933655 25.675964
+ 1500 0.88293618 2.0295275 -5.3963602 35.443445 0.60232374 25.376395 -1.9501461 25.451218
+ 1550 0.90012542 1.9476472 -5.4249456 35.382791 0.4488038 26.448928 -1.1452474 26.473711
+ 1600 0.89155063 2.2462603 -5.4153432 35.332095 0.039621687 26.138157 -0.36825239 26.140751
+ 1650 0.8942624 2.343747 -5.4233433 35.294954 0.0089980332 26.064277 0.38189192 26.067075
+ 1700 0.90047841 2.451289 -5.4376312 35.27234 0.86985171 26.646438 0.83408084 26.659489
+ 1750 0.87586052 2.6381221 -5.4067182 35.264564 6.346204 27.652722 2.6699692 27.78132
+ 1800 0.87392582 2.6338176 -5.4109056 35.270073 0.046414129 26.016188 2.6651053 26.152339
+ 1850 0.86540415 2.5434301 -5.4058587 35.285902 0.054615472 26.074279 2.1799787 26.165251
+ 1900 0.87043082 2.5776772 -5.4216997 35.309062 0.68978148 26.38648 3.2614091 26.587274
+ 1950 0.86281992 2.3107762 -5.4188978 35.338501 0.0072672577 25.736893 3.2375012 25.93972
+ 2000 0.85905576 2.2894047 -5.4215995 35.36787 0.095633435 26.072085 2.7685848 26.21867
+ 2050 0.85793751 2.2382039 -5.4279351 35.395213 0.13602344 25.598457 2.6881027 25.739209
+ 2100 0.85585253 2.0765811 -5.4324511 35.418877 0.0059888115 25.754128 3.1436222 25.945279
+ 2150 0.86701057 1.8449875 -5.4562208 35.436124 0.097328618 25.413697 4.3268293 25.7794
+ 2200 0.85168154 1.9024923 -5.4395776 35.44246 0.20764576 25.094788 5.4406104 25.677784
+ 2250 0.8429719 1.870335 -5.4320586 35.438363 0.34419961 24.998478 5.4475709 25.585151
+ 2300 0.84176891 1.7100228 -5.4351472 35.422863 0.76036958 24.697018 5.8629967 25.383409
+ 2350 0.84601588 1.8539039 -5.4456629 35.395979 0.38437531 25.647986 6.4163366 26.438392
+ 2400 0.84637647 1.6299091 -5.4498948 35.36125 0.074236719 24.995872 7.8269968 26.192661
+ 2450 0.85650449 1.6828907 -5.4683101 35.316669 0.3671827 25.280669 7.7040329 26.428476
+ 2500 0.84963707 1.7305222 -5.4605394 35.265508 0.1406965 25.236741 7.2780025 26.265232
+ 2550 0.84084365 1.8758368 -5.4497083 35.208725 0.33937687 24.544376 7.2334512 25.588067
+ 2600 0.85317342 1.7781674 -5.4702734 35.149747 0.60378248 24.046307 8.3370138 25.450554
+ 2650 0.85487644 2.0065374 -5.4747643 35.090431 0.22483651 24.937101 8.4669004 26.335288
+ 2700 0.84550083 1.9363031 -5.4628401 35.034349 0.43442577 24.250196 7.9943738 25.533939
+ 2750 0.85843419 2.0473138 -5.484528 34.980671 0.45959294 24.17438 8.179356 25.520629
+ 2800 0.86047607 2.0754522 -5.4899966 34.932466 0.00038123477 24.619856 8.3153434 25.986194
+ 2850 0.86375793 2.2751324 -5.4977459 34.892337 0.0016455263 24.927259 7.289789 25.971316
+ 2900 0.84438986 2.3790377 -5.4721407 34.863512 1.2372354 25.819445 7.132603 26.786523
+ 2950 0.8551438 2.2721926 -5.4925958 34.84473 1.5405388 25.956466 6.976385 26.87765
+ 3000 0.83737707 2.4009609 -5.4707188 34.834171 0.28507766 25.643879 6.1778846 26.377543
+ 3050 0.84923235 2.4187994 -5.4938573 34.830836 0.036512025 25.139252 7.1457857 26.135115
+ 3100 0.83872396 2.3811576 -5.4838787 34.833673 0.246984 24.21358 8.4588719 25.648586
+ 3150 0.83957817 2.3901421 -5.4913118 34.84163 0.20477984 24.309852 10.088243 26.319984
+ 3200 0.84283033 2.17292 -5.5025459 34.853975 1.3367154 24.581685 10.72011 26.817531
+ 3250 0.84002379 2.1247709 -5.5044955 34.866106 0.11434509 24.463842 9.4874246 26.239108
+ 3300 0.83311101 2.1492058 -5.5000847 34.875625 0.0053284993 23.815298 10.560222 26.051616
+ 3350 0.83216701 1.9587594 -5.5043446 34.881623 0.58985562 23.934253 11.475462 26.543073
+ 3400 0.82396039 2.1914951 -5.4971506 34.881199 0.098206955 23.393402 10.82936 25.778407
+ 3450 0.83483253 1.9783612 -5.5182844 34.877327 7.6571212e-05 23.675355 10.761012 26.006188
+ 3500 0.82712062 1.9718522 -5.5111818 34.869214 0.014836125 23.314122 11.312845 25.913872
+ 3550 0.8342927 1.9114357 -5.5259968 34.855179 1.4050442 22.442758 11.377192 25.161834
+ 3600 0.82631637 1.9836457 -5.5176244 34.835738 0.084637609 23.413286 10.824194 25.794285
+ 3650 0.82425697 1.9218541 -5.5178548 34.811901 0.11000071 22.788707 12.022258 25.765478
+ 3700 0.82491437 1.9624493 -5.521738 34.782417 0.034984027 23.011433 12.384217 26.132257
+ 3750 0.82758167 2.0856442 -5.5283493 34.748872 0.001362163 23.030662 12.122144 26.026098
+ 3800 0.81891108 1.9858824 -5.5177774 34.714618 0.17075993 23.21344 12.345683 26.292199
+ 3850 0.83392227 2.1631514 -5.5426333 34.681146 0.82106473 22.510204 11.678329 25.359272
+ 3900 0.82230654 2.0017132 -5.5276756 34.650221 0.48735732 23.444809 12.339117 26.493638
+ 3950 0.81929288 2.1749936 -5.5256673 34.61976 0.089219805 23.540062 11.527925 26.211211
+ 4000 0.83415169 2.0446791 -5.5506187 34.591266 0.15593937 23.742282 11.26508 26.279231
+ 4050 0.82362522 2.1998083 -5.5375157 34.563164 0.25405351 23.913834 11.081011 26.356408
+ 4100 0.82589505 2.3074345 -5.543718 34.537763 0.080213125 24.03253 10.435108 26.200266
+ 4150 0.83855297 2.2424199 -5.5658171 34.517758 0.62913338 23.974257 8.5079223 25.439138
+ 4200 0.82522111 2.2622619 -5.5493275 34.502472 1.8756517 25.754617 7.9996898 26.968414
+ 4250 0.82083124 2.4135193 -5.5464932 34.4919 1.1217436 25.8944 6.7070444 26.748914
+ 4300 0.83059704 2.1375109 -5.5653245 34.487366 0.53623038 26.05979 4.9072346 26.517798
+ 4350 0.82755047 2.1159821 -5.5650889 34.484506 0.10017723 25.405936 4.3532342 25.776195
+ 4400 0.83192877 2.180851 -5.5759565 34.480909 0.053664012 25.993034 2.9844338 26.163805
+ 4450 0.81860572 2.2333381 -5.5602138 34.477183 0.037864077 25.792233 1.9038859 25.862406
+ 4500 0.82821762 2.1142023 -5.5788682 34.474784 0.088221344 26.20329 0.59417897 26.210025
+ 4550 0.8205154 2.0896984 -5.5715531 34.472405 0.016076192 26.083166 -0.58187024 26.089655
+ 4600 0.81294948 2.2274108 -5.5642678 34.469014 0.033774986 25.869616 0.14951307 25.870048
+ 4650 0.80890532 2.1556346 -5.5622407 34.465277 0.67402048 25.413229 -0.56341819 25.419474
+ 4700 0.82070227 1.9852605 -5.583747 34.460206 0.052623237 26.158394 -0.44673492 26.162209
+ 4750 0.81451857 2.1097726 -5.5779782 34.451438 0.12221733 25.733718 -0.9911436 25.752798
+ 4800 0.81300453 2.0211325 -5.5790076 34.439504 0.34536082 26.358606 -1.7335167 26.415548
+ 4850 0.82035497 1.9489595 -5.5929886 34.424097 0.70899626 26.575865 -1.0191012 26.595397
+ 4900 0.8127066 2.1312269 -5.584271 34.405998 0.087959314 26.185217 -1.1329105 26.209713
+ 4950 0.81252621 2.1094866 -5.5866296 34.387869 0.79067667 26.564722 -1.8456354 26.628759
+ 5000 0.80575936 2.1875995 -5.579054 34.370679 0.031787364 26.027557 -2.2666774 26.12607
+Loop time of 32.2397 on 1 procs for 5000 steps with 5120 atoms
+
+Performance: 53598.557 tau/day, 155.088 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 | 22.967 | 22.967 | 22.967 | 0.0 | 71.24
+Neigh | 2.9914 | 2.9914 | 2.9914 | 0.0 | 9.28
+Comm | 0.37485 | 0.37485 | 0.37485 | 0.0 | 1.16
+Output | 0.064337 | 0.064337 | 0.064337 | 0.0 | 0.20
+Modify | 5.7143 | 5.7143 | 5.7143 | 0.0 | 17.72
+Other | | 0.1281 | | | 0.40
+
+Nlocal: 5120 ave 5120 max 5120 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 7962 ave 7962 max 7962 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 296101 ave 296101 max 296101 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 296101
+Ave neighs/atom = 57.8322
+Neighbor list builds = 283
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:32
diff --git a/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.4 b/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c7a77fb9cca5d5c9b190946d6a47459ffd048952
--- /dev/null
+++ b/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.4
@@ -0,0 +1,186 @@
+LAMMPS (22 Sep 2017)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+read_data data.halfhalf
+ orthogonal box = (0 0 0) to (12.8152 12.8152 34)
+ 1 by 1 by 4 MPI processor grid
+ reading atoms ...
+ 5120 atoms
+ reading velocities ...
+ 5120 velocities
+pair_coeff 1 1 1.0 1.0 2.5
+mass 1 1.0
+
+# simulation parameters
+neighbor 0.6 bin
+timestep 0.004
+run_style verlet
+
+velocity all create 0.8 1 mom yes rot yes
+fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0
+fix 100 all momentum 100 linear 1 1 1
+
+# harmonic rho_k bias-field
+# nx ny nz k a
+fix bias all rhok 16 0 0 4.0 26.00
+
+# output U_bias rho_k_RE rho_k_IM |rho_k|
+thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]
+thermo 50
+dump dumpXYZ all xyz 500 traj.xyz
+
+# NOTE: run reduced for demonstration purposes
+# run 50000
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 3.1
+ ghost atom cutoff = 3.1
+ binsize = 1.55, bins = 9 9 22
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, 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) = 4.023 | 4.027 | 4.03 Mbytes
+Step Temp Pzz PotEng Lz f_bias f_bias[1] f_bias[2] f_bias[3]
+ 0 0.8 5.1872229 -4.8361269 34 152.02869 34.711006 -0.72709593 34.71862
+ 50 1.0819371 3.9250728 -5.2655842 34.02563 0.51385908 26.505979 0.2187864 26.506882
+ 100 1.1182271 3.5397251 -5.3331401 34.100753 2.1059904 27.025883 -0.12127124 27.026156
+ 150 1.1121434 3.7845571 -5.3440494 34.213993 1.7206575 26.894862 -1.3261751 26.927539
+ 200 1.1446439 3.4114364 -5.4199119 34.358914 2.383615 27.054401 -1.4211151 27.091699
+ 250 1.1115073 3.5603047 -5.3988013 34.517397 0.60819391 26.51404 -1.4089688 26.55145
+ 300 1.0828478 3.7411116 -5.3842818 34.673948 0.73987465 26.528178 -2.062382 26.608225
+ 350 1.0342597 3.9206217 -5.3384367 34.825105 0.99965014 26.657737 -1.6211152 26.706983
+ 400 1.0064356 3.9929044 -5.324003 34.97579 0.41927007 26.402623 -1.7087432 26.457859
+ 450 0.96799277 4.2764255 -5.2947175 35.133839 0.77739461 26.503753 -2.5217998 26.623456
+ 500 0.94691076 4.1007962 -5.2922124 35.301893 0.17015805 26.212252 -2.0421698 26.291683
+ 550 0.93675297 3.7404088 -5.3056917 35.474301 0.56247039 26.335926 -3.205722 26.530316
+ 600 0.92707577 3.5439822 -5.3176094 35.641282 0.04054693 25.679461 -3.0301039 25.857615
+ 650 0.91828226 3.1833648 -5.3278237 35.794766 0.8427054 26.4003 -3.6331211 26.649117
+ 700 0.9084826 2.8374306 -5.3327944 35.928138 1.5635222 26.605971 -3.8575939 26.884173
+ 750 0.91219559 2.46172 -5.3548299 36.039156 6.3772911 27.350725 -4.8971146 27.785678
+ 800 0.90000337 2.2187716 -5.3499181 36.126451 4.9080838 27.085156 -5.1291678 27.566538
+ 850 0.9003432 1.8634244 -5.3614648 36.189019 0.0081092188 25.497333 -5.4038153 26.063676
+ 900 0.89741573 1.5697398 -5.3660799 36.226074 0.011155479 25.312724 -6.2574069 26.074684
+ 950 0.88871454 1.4427205 -5.3604669 36.237407 0.3287078 25.659237 -6.232896 26.405406
+ 1000 0.88606353 1.3088636 -5.3626576 36.226015 0.30068168 24.554896 -7.2832017 25.612262
+ 1050 0.88527541 1.3194263 -5.3666773 36.19311 0.10646314 24.514921 -7.9419424 25.76928
+ 1100 0.87522001 1.2852124 -5.3556811 36.143056 0.13675329 24.865981 -8.446822 26.261489
+ 1150 0.8805978 1.246973 -5.3671716 36.0781 0.00043275463 24.187039 -9.4985495 25.98529
+ 1200 0.85711495 1.376588 -5.3346243 36.002427 0.47623639 23.691349 -9.4648541 25.512026
+ 1250 0.88116805 1.3562001 -5.3731036 35.919289 0.32797055 23.322103 -10.54448 25.595049
+ 1300 0.87178482 1.5046564 -5.3610798 35.831278 0.17704849 24.190231 -10.314689 26.29753
+ 1350 0.87022621 1.6830825 -5.3603618 35.743318 0.0052854997 23.731157 -10.747465 26.051408
+ 1400 0.89019669 1.6144812 -5.3921986 35.659687 1.4152796 22.8393 -10.551347 25.158787
+ 1450 0.88852819 1.7587964 -5.3918592 35.580319 0.63560961 23.599033 -12.195 26.563742
+ 1500 0.89029085 1.8772498 -5.3966098 35.509232 0.20895386 23.055083 -12.703366 26.323229
+ 1550 0.88639722 2.2284824 -5.3933288 35.449043 0.44413965 22.448774 -12.156068 25.528757
+ 1600 0.88816451 2.2167704 -5.3994757 35.401661 0.12210235 23.108351 -12.44643 26.247085
+ 1650 0.89154791 2.3397824 -5.4086923 35.365815 0.4820208 23.090699 -12.984179 26.490928
+ 1700 0.88518032 2.5351236 -5.4041601 35.343757 0.080806002 22.749825 -12.99762 26.201005
+ 1750 0.86848721 2.5527491 -5.3851928 35.336433 0.045102165 22.357111 -13.564328 26.15017
+ 1800 0.88501061 2.5215825 -5.4169341 35.340849 0.27488483 22.086584 -14.408273 26.370732
+ 1850 0.8716061 2.5809558 -5.4045854 35.355038 0.042909785 21.270956 -14.695278 25.853525
+ 1900 0.85672517 2.4836326 -5.3902797 35.375469 0.72877764 21.639909 -15.474764 26.603646
+ 1950 0.85133731 2.3141629 -5.3902573 35.398523 0.0016908803 21.106617 -15.132733 25.970924
+ 2000 0.86152109 2.1562002 -5.4132601 35.419851 0.371016 21.325237 -15.614625 26.430706
+ 2050 0.86243551 2.019931 -5.4220349 35.436069 0.017935421 20.4131 -16.255418 26.094698
+ 2100 0.87417672 1.8083823 -5.4464117 35.445091 0.18429432 19.75625 -17.365705 26.303558
+ 2150 0.85872128 1.7608768 -5.4293103 35.44341 0.91209166 20.149648 -17.480387 26.675312
+ 2200 0.86615373 1.8372778 -5.4458315 35.430616 0.10151993 18.559234 -17.885469 25.7747
+ 2250 0.85053605 1.7198437 -5.4272104 35.408688 0.96154548 17.200861 -18.562206 25.306622
+ 2300 0.85400281 1.7939644 -5.4364682 35.377708 0.12283263 18.759325 -18.358539 26.247823
+ 2350 0.85495278 1.5856029 -5.4417321 35.337987 0.20564329 18.967923 -18.248149 26.320658
+ 2400 0.84606771 1.7782708 -5.4315646 35.287411 0.10063977 19.185527 -17.878215 26.224321
+ 2450 0.85210051 1.8190391 -5.4432116 35.232321 0.69988647 19.268861 -18.325448 26.59156
+ 2500 0.85304715 1.7466204 -5.4470889 35.175245 0.0048314937 18.09176 -18.74157 26.04915
+ 2550 0.85401123 1.8601945 -5.4509309 35.115748 0.99467901 17.170045 -18.574587 25.294777
+ 2600 0.85778606 1.974012 -5.4586742 35.058013 0.0026599702 17.438966 -19.333395 26.036469
+ 2650 0.8521239 2.0606329 -5.4526006 35.003616 0.091056354 17.16363 -19.244738 25.786627
+ 2700 0.85918482 2.0766792 -5.4658947 34.954171 0.89590606 15.77108 -19.822153 25.330707
+ 2750 0.85786577 2.225549 -5.4667773 34.911468 0.26577575 15.769018 -21.128817 26.364538
+ 2800 0.86764664 2.2325018 -5.4849414 34.877604 0.47167555 14.950515 -20.675229 25.514369
+ 2850 0.85209564 2.3434319 -5.465734 34.852715 2.7350296 13.51553 -20.829996 24.830592
+ 2900 0.85757283 2.3512971 -5.4786051 34.836138 0.14816492 14.06033 -21.545946 25.727819
+ 2950 0.86098926 2.3480431 -5.4890615 34.826408 0.26401534 13.381395 -22.714827 26.363329
+ 3000 0.85413421 2.3243973 -5.4844129 34.823242 0.024244334 12.739486 -22.538687 25.889899
+ 3050 0.85015323 2.5479266 -5.4844303 34.825228 0.4463147 12.990582 -21.975063 25.527605
+ 3100 0.8530523 2.3643505 -5.495343 34.834883 0.12144265 12.844293 -22.321989 25.753583
+ 3150 0.85098478 2.2521299 -5.4990526 34.848419 0.33194916 12.747856 -23.126671 26.4074
+ 3200 0.84391449 2.2650057 -5.495222 34.862626 0.031888328 12.788845 -22.782174 26.12627
+ 3250 0.84807155 2.1715388 -5.5080873 34.877548 0.082426694 13.316219 -22.09441 25.796989
+ 3300 0.83028242 2.242889 -5.4878846 34.89175 1.1334975 14.326678 -22.593363 26.752827
+ 3350 0.82924001 2.0324002 -5.4924558 34.903232 0.35473989 14.354166 -22.181868 26.421153
+ 3400 0.83032841 2.0003371 -5.4997142 34.908733 0.041677437 14.528378 -21.735998 26.144356
+ 3450 0.82908891 1.8683902 -5.5029185 34.907936 0.02365857 15.069507 -21.053887 25.891237
+ 3500 0.82842914 1.9165344 -5.5064218 34.898681 0.17663531 15.27043 -20.674834 25.702817
+ 3550 0.82735822 1.98221 -5.5088197 34.88272 1.5607134 14.915228 -20.208431 25.116622
+ 3600 0.82642915 1.8422766 -5.5110752 34.8611 1.1861112 15.312314 -20.051953 25.229899
+ 3650 0.82556781 1.9351408 -5.5130349 34.833406 1.018872 16.152478 -19.454871 25.286252
+ 3700 0.82360651 1.9791184 -5.5128431 34.802021 0.14080727 16.907104 -19.401616 25.734663
+ 3750 0.83017793 1.9855734 -5.5253254 34.768644 0.15311334 16.969506 -19.331958 25.723311
+ 3800 0.82362926 2.1029656 -5.5179624 34.734178 0.10807487 17.892584 -18.542426 25.76754
+ 3850 0.82313508 2.0781681 -5.5196175 34.70093 0.13343085 19.072706 -17.28778 25.741707
+ 3900 0.83643385 2.0570262 -5.5421224 34.669761 0.00022792038 19.551677 -17.1548 26.010675
+ 3950 0.82346174 2.0842322 -5.5252757 34.640849 0.0093759386 20.892792 -15.590263 26.068469
+ 4000 0.83485868 2.1196669 -5.5451736 34.612396 0.31198053 21.630258 -15.126984 26.394956
+ 4050 0.82729429 2.2033274 -5.5365945 34.585721 0.53752252 21.283533 -14.011497 25.481578
+ 4100 0.82040242 2.1757309 -5.5292269 34.562271 0.36031984 22.047609 -12.961927 25.575548
+ 4150 0.81932521 2.285666 -5.5307807 34.542102 0.84343149 22.486289 -11.70555 25.350604
+ 4200 0.83819319 2.231174 -5.5625532 34.526447 0.47190752 23.311855 -12.57189 26.485751
+ 4250 0.82542274 2.1874789 -5.5472057 34.513795 0.70518398 23.411553 -12.614639 26.593795
+ 4300 0.81971158 2.241167 -5.5424504 34.503969 0.26707612 23.089805 -12.727793 26.365429
+ 4350 0.83255377 2.1295532 -5.5657895 34.496326 0.072548591 23.003138 -12.52181 26.190458
+ 4400 0.8128474 2.3327845 -5.5402264 34.490126 0.0013023434 23.020811 -12.029795 25.974482
+ 4450 0.82013491 2.3069915 -5.5554953 34.488039 0.041123896 23.632908 -11.178674 26.143394
+ 4500 0.81411544 2.2247193 -5.5509183 34.488014 0.54440601 23.010678 -10.938506 25.478269
+ 4550 0.82814624 2.1142779 -5.5763482 34.487885 0.1518945 23.696817 -11.351972 26.275585
+ 4600 0.82929492 2.090881 -5.5823492 34.486698 0.0045520899 23.538527 -10.929741 25.952292
+ 4650 0.81061417 1.9818043 -5.5584018 34.484038 0.012526806 23.993543 -10.219174 26.079142
+ 4700 0.81816105 1.9605811 -5.5735005 34.476764 1.2079835 25.151166 -9.1888856 26.777169
+ 4750 0.81657042 2.0064313 -5.5744795 34.465784 1.2045017 25.487486 -8.2063886 26.776048
+ 4800 0.81789335 2.0838696 -5.5796632 34.451996 0.27642542 24.647157 -7.023095 25.62823
+ 4850 0.80649339 1.9892413 -5.5654796 34.436067 0.024697945 25.09823 -6.3492244 25.888874
+ 4900 0.81673441 2.0125635 -5.5835037 34.416236 0.0011188576 25.446818 -5.2182483 25.976348
+ 4950 0.82250033 1.9770391 -5.5946082 34.394723 0.72696707 26.37002 -3.5122842 26.602896
+ 5000 0.80762758 2.075517 -5.5746076 34.371696 0.12796344 26.102184 -2.8094827 26.252946
+Loop time of 10.3394 on 4 procs for 5000 steps with 5120 atoms
+
+Performance: 167127.370 tau/day, 483.586 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 | 5.029 | 6.0128 | 7.1918 | 35.0 | 58.15
+Neigh | 0.65673 | 0.75825 | 0.88597 | 10.3 | 7.33
+Comm | 0.43982 | 1.5284 | 2.4112 | 60.5 | 14.78
+Output | 0.022835 | 0.023039 | 0.023453 | 0.2 | 0.22
+Modify | 1.7294 | 1.9472 | 2.5687 | 25.7 | 18.83
+Other | | 0.06978 | | | 0.67
+
+Nlocal: 1280 ave 1404 max 1214 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost: 3521.25 ave 3581 max 3426 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+Neighs: 73872.2 ave 87973 max 64161 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 295489
+Ave neighs/atom = 57.7127
+Neighbor list builds = 278
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:10
diff --git a/examples/USER/misc/pinning/log.22Sep2017.setup.g++.1 b/examples/USER/misc/pinning/log.22Sep2017.setup.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..8606d4ed944137c289d272ad94a0eb47ad5bee86
--- /dev/null
+++ b/examples/USER/misc/pinning/log.22Sep2017.setup.g++.1
@@ -0,0 +1,141 @@
+LAMMPS (22 Sep 2017)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+
+# fcc lattice
+lattice fcc 0.9731
+Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
+region my_box block 0 8.0 0 8.0 0 20.0
+create_box 1 my_box
+Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
+ 1 by 1 by 1 MPI processor grid
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+Created 5120 atoms
+pair_coeff 1 1 1.0 1.0 2.5
+mass 1 1.0
+change_box all z final 0.0 34 remap units box
+ orthogonal box = (0 0 0) to (12.8152 12.8152 34)
+
+# select particles in one side of the elongated box
+region left plane 0 0 10 0 0 1
+group left region left
+2688 atoms in group left
+
+velocity left create 6.0 1 mom yes rot yes
+
+# simulation parameters
+neighbor 0.6 bin
+timestep 0.004
+run_style verlet
+fix ensemble left nve # Note: only move particle in left-hand side
+fix langevin left langevin 3.0 0.8 100.0 2017
+
+# outout
+thermo_style custom step temp pzz pe lz
+thermo 100
+# dump dumpXYZ all xyz 100 traj.xyz
+
+# run reduced for demonstration purposes
+# run 10000
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 3.1
+ ghost atom cutoff = 3.1
+ binsize = 1.55, bins = 9 9 22
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, 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) = 4.524 | 4.524 | 4.524 Mbytes
+Step Temp Pzz PotEng Lz
+ 0 3.1494433 -3.4735106 -6.8707307 34
+ 100 1.7727555 6.5330255 -4.8035477 34
+ 200 1.7462368 7.0070325 -4.7646426 34
+ 300 1.7564888 6.6190123 -4.7894637 34
+ 400 1.7641186 6.609684 -4.8064772 34
+ 500 1.7383511 6.7304936 -4.7708095 34
+ 600 1.731708 6.8574656 -4.7612918 34
+ 700 1.7332167 6.6530919 -4.7670014 34
+ 800 1.7487537 6.5644963 -4.7907458 34
+ 900 1.7353648 6.7115188 -4.7772149 34
+ 1000 1.728878 6.4175719 -4.7797216 34
+ 1100 1.7471488 6.5346083 -4.813376 34
+ 1200 1.7188149 6.2502104 -4.7822235 34
+ 1300 1.7151194 6.792534 -4.7781701 34
+ 1400 1.7406603 6.6639592 -4.8170174 34
+ 1500 1.7090537 6.4677579 -4.770701 34
+ 1600 1.7014954 6.2853535 -4.7679742 34
+ 1700 1.7064354 6.4352857 -4.7812978 34
+ 1800 1.7169971 6.5808758 -4.799426 34
+ 1900 1.6822712 6.3746758 -4.7522464 34
+ 2000 1.7126546 6.534969 -4.8091595 34
+ 2100 1.7086108 6.4679932 -4.8146664 34
+ 2200 1.6974952 6.3802129 -4.8052505 34
+ 2300 1.6868035 6.4009243 -4.7935769 34
+ 2400 1.7107125 6.2318869 -4.8358765 34
+ 2500 1.660241 6.4891487 -4.7661183 34
+ 2600 1.6801816 6.1988356 -4.8024291 34
+ 2700 1.6940298 6.1328187 -4.8290053 34
+ 2800 1.6755061 6.4150693 -4.8145473 34
+ 2900 1.6749928 6.4248792 -4.8213509 34
+ 3000 1.6310737 6.6491291 -4.7673027 34
+ 3100 1.6559915 6.2726719 -4.8109181 34
+ 3200 1.6574579 5.7132029 -4.8189484 34
+ 3300 1.6816136 5.7697439 -4.8652811 34
+ 3400 1.6489483 6.4463349 -4.8247812 34
+ 3500 1.6557974 5.9763333 -4.8383712 34
+ 3600 1.6215459 6.2806534 -4.7954657 34
+ 3700 1.6484987 6.0671609 -4.8470777 34
+ 3800 1.6473922 5.8688108 -4.8555351 34
+ 3900 1.6435957 5.930425 -4.8562076 34
+ 4000 1.6514434 6.1962122 -4.872998 34
+ 4100 1.6138337 6.4808124 -4.8219373 34
+ 4200 1.6215239 5.9467966 -4.8412146 34
+ 4300 1.6129295 5.9377323 -4.8414596 34
+ 4400 1.6020549 6.1104301 -4.8395939 34
+ 4500 1.6047738 6.0816222 -4.8538151 34
+ 4600 1.6053565 6.183466 -4.8686817 34
+ 4700 1.6088152 5.7416542 -4.894114 34
+ 4800 1.5954309 5.694319 -4.8840198 34
+ 4900 1.5582564 6.1199614 -4.8429998 34
+ 5000 1.5786672 5.8813574 -4.8907344 34
+Loop time of 28.3867 on 1 procs for 5000 steps with 5120 atoms
+
+Performance: 60873.483 tau/day, 176.139 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 | 22.269 | 22.269 | 22.269 | 0.0 | 78.45
+Neigh | 4.7222 | 4.7222 | 4.7222 | 0.0 | 16.64
+Comm | 0.40821 | 0.40821 | 0.40821 | 0.0 | 1.44
+Output | 0.0042329 | 0.0042329 | 0.0042329 | 0.0 | 0.01
+Modify | 0.88231 | 0.88231 | 0.88231 | 0.0 | 3.11
+Other | | 0.1005 | | | 0.35
+
+Nlocal: 5120 ave 5120 max 5120 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 7768 ave 7768 max 7768 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 297167 ave 297167 max 297167 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 297167
+Ave neighs/atom = 58.0404
+Neighbor list builds = 474
+Dangerous builds = 246
+write_data data.halfhalf
+Total wall time: 0:00:28
diff --git a/examples/USER/misc/pinning/log.22Sep2017.setup.g++.4 b/examples/USER/misc/pinning/log.22Sep2017.setup.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..14088f7c95cfd220b3895a8d3861a70ec093c849
--- /dev/null
+++ b/examples/USER/misc/pinning/log.22Sep2017.setup.g++.4
@@ -0,0 +1,141 @@
+LAMMPS (22 Sep 2017)
+ using 1 OpenMP thread(s) per MPI task
+units lj
+dimension 3
+boundary p p p
+atom_style atomic
+
+# truncated and shifted LJ potential
+pair_style lj/cut 2.5
+pair_modify shift yes
+
+# fcc lattice
+lattice fcc 0.9731
+Lattice spacing in x,y,z = 1.6019 1.6019 1.6019
+region my_box block 0 8.0 0 8.0 0 20.0
+create_box 1 my_box
+Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)
+ 1 by 1 by 4 MPI processor grid
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+Created 5120 atoms
+pair_coeff 1 1 1.0 1.0 2.5
+mass 1 1.0
+change_box all z final 0.0 34 remap units box
+ orthogonal box = (0 0 0) to (12.8152 12.8152 34)
+
+# select particles in one side of the elongated box
+region left plane 0 0 10 0 0 1
+group left region left
+2688 atoms in group left
+
+velocity left create 6.0 1 mom yes rot yes
+
+# simulation parameters
+neighbor 0.6 bin
+timestep 0.004
+run_style verlet
+fix ensemble left nve # Note: only move particle in left-hand side
+fix langevin left langevin 3.0 0.8 100.0 2017
+
+# outout
+thermo_style custom step temp pzz pe lz
+thermo 100
+# dump dumpXYZ all xyz 100 traj.xyz
+
+# run reduced for demonstration purposes
+# run 10000
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 3.1
+ ghost atom cutoff = 3.1
+ binsize = 1.55, bins = 9 9 22
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, 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) = 3.23 | 3.23 | 3.23 Mbytes
+Step Temp Pzz PotEng Lz
+ 0 3.1494433 -3.4735106 -6.8707307 34
+ 100 1.7914373 6.4805818 -4.8420353 34
+ 200 1.740256 6.6108149 -4.7672571 34
+ 300 1.7663827 6.5188941 -4.8103672 34
+ 400 1.7440644 6.5156543 -4.7769467 34
+ 500 1.7471724 6.5208992 -4.7843928 34
+ 600 1.7320106 6.6557835 -4.7654637 34
+ 700 1.6839043 6.7689759 -4.7045352 34
+ 800 1.7216746 6.66436 -4.7601673 34
+ 900 1.7342542 6.3242367 -4.7790803 34
+ 1000 1.7338566 6.5803438 -4.7854529 34
+ 1100 1.7328856 6.3846366 -4.7902625 34
+ 1200 1.7546906 6.5048137 -4.8213443 34
+ 1300 1.7163891 6.3903221 -4.7665145 34
+ 1400 1.7011627 6.5782672 -4.7517875 34
+ 1500 1.7105234 6.5811813 -4.7677748 34
+ 1600 1.7334403 6.5032837 -4.8067749 34
+ 1700 1.7252102 6.5443871 -4.8058994 34
+ 1800 1.721958 6.3378188 -4.8150073 34
+ 1900 1.6797892 6.6780506 -4.7538618 34
+ 2000 1.7001774 6.3578192 -4.7894018 34
+ 2100 1.7127784 6.3219105 -4.8161059 34
+ 2200 1.696825 6.536793 -4.7946902 34
+ 2300 1.6704578 6.7186933 -4.7609628 34
+ 2400 1.6772498 6.3432817 -4.7778471 34
+ 2500 1.7073862 6.2153226 -4.8299181 34
+ 2600 1.6951557 6.4397257 -4.8156787 34
+ 2700 1.6845984 6.0123544 -4.8136864 34
+ 2800 1.6550565 6.2489392 -4.7829639 34
+ 2900 1.6892315 6.158499 -4.8423004 34
+ 3000 1.6814436 6.07976 -4.8400696 34
+ 3100 1.6387025 6.330166 -4.7878978 34
+ 3200 1.6747855 6.0767043 -4.8481995 34
+ 3300 1.6508768 6.2749233 -4.8181888 34
+ 3400 1.6426364 6.3934935 -4.8223824 34
+ 3500 1.6576512 6.0638185 -4.8559078 34
+ 3600 1.6444173 6.1376573 -4.8463113 34
+ 3700 1.6480039 5.9943705 -4.8601776 34
+ 3800 1.6467212 6.0556591 -4.8722719 34
+ 3900 1.6271804 6.116738 -4.8547278 34
+ 4000 1.6158134 5.9089534 -4.8477829 34
+ 4100 1.6388157 5.9890465 -4.8920284 34
+ 4200 1.6182368 6.0639887 -4.8724963 34
+ 4300 1.647633 5.6333906 -4.9267536 34
+ 4400 1.5856411 6.2675475 -4.8471239 34
+ 4500 1.5773417 6.1789163 -4.8469057 34
+ 4600 1.6181445 5.7988068 -4.922419 34
+ 4700 1.5876712 5.7398111 -4.8853849 34
+ 4800 1.5708353 6.2204997 -4.8718872 34
+ 4900 1.5514708 5.9782256 -4.8523812 34
+ 5000 1.553347 5.9286523 -4.86582 34
+Loop time of 8.10259 on 4 procs for 5000 steps with 5120 atoms
+
+Performance: 213265.164 tau/day, 617.087 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 | 5.2964 | 5.6236 | 5.8982 | 9.0 | 69.40
+Neigh | 1.0562 | 1.1907 | 1.3257 | 8.7 | 14.70
+Comm | 0.43963 | 0.98786 | 1.5968 | 42.5 | 12.19
+Output | 0.0023124 | 0.004741 | 0.0090873 | 4.0 | 0.06
+Modify | 0.018652 | 0.22213 | 0.39884 | 36.4 | 2.74
+Other | | 0.07357 | | | 0.91
+
+Nlocal: 1280 ave 1337 max 1211 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Nghost: 3416.25 ave 3549 max 3297 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 74269.8 ave 77932 max 69612 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+
+Total # of neighbors = 297079
+Ave neighs/atom = 58.0232
+Neighbor list builds = 474
+Dangerous builds = 247
+write_data data.halfhalf
+Total wall time: 0:00:08
diff --git a/src/.gitignore b/src/.gitignore
index af973a3aa1970b97c11c3f2ed3476c71b2adb60f..0d85b637e5dbfd9ab23d525ef8d6d0f2c6490d13 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -507,6 +507,8 @@
/fix_reaxc_bonds.h
/fix_reaxc_species.cpp
/fix_reaxc_species.h
+/fix_rhok.cpp
+/fix_rhok.h
/fix_rigid.cpp
/fix_rigid.h
/fix_rigid_nh.cpp
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 65146abd5436cd2b0e7ddc2afc66ebfdfa36d463..8f37825867b908473aa7b3d748f44f2ca9a93e20 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -47,6 +47,7 @@ fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009
fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
fix nvk, Efrem Braun (UC Berkeley), efrem.braun at gmail.com, https://github.com/lammps/lammps/pull/310
fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014
+fix rhok, Ulf Pedersen (Roskilde U), ulf AT urp.dk, 25 Sep 2017
fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
fix ttm/mod, Sergey Starikov and Vasily Pisarev (JIHT), pisarevvv at gmail.com, 2 Feb 2015
diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..58b0e95a97e0abe10ac7d48e1e93807a0c5a16ab
--- /dev/null
+++ b/src/USER-MISC/fix_rhok.cpp
@@ -0,0 +1,245 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Ulf R. Pedersen, ulf@urp.dk
+------------------------------------------------------------------------- */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+
+#include "fix_rhok.h"
+#include "atom.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "respa.h"
+#include "update.h"
+#include "citeme.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+static const char cite_fix_rhok[] =
+ "Bias on the collective density field (fix rhok):\n\n"
+ "@Article{pedersen_jcp139_104102_2013,\n"
+ "title = {Direct calculation of the solid-liquid Gibbs free energy difference in a single equilibrium simulation},\n"
+ "volume = {139},\n"
+ "number = {10},\n"
+ "url = {http://aip.scitation.org/doi/10.1063/1.4818747},\n"
+ "doi = {10.1063/1.4818747},\n"
+ "urldate = {2017-10-03},\n"
+ "journal = {J. Chem. Phys.},\n"
+ "author = {Pedersen, Ulf R.},\n"
+ "year = {2013},\n"
+ "pages = {104102}\n"
+ "}\n\n";
+
+FixRhok::FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv )
+ : Fix( inLMP, inArgc, inArgv )
+{
+
+ if (lmp->citeme) lmp->citeme->add(cite_fix_rhok);
+
+ // Check arguments
+ if( inArgc != 8 )
+ error->all(FLERR,"Illegal fix rhoKUmbrella command" );
+
+ // Set up fix flags
+ scalar_flag = 1; // have compute_scalar
+ vector_flag = 1; // have compute_vector...
+ size_vector = 3; // ...with this many components
+ global_freq = 1; // whose value can be computed at every timestep
+ thermo_energy = 1; // this fix changes system's potential energy
+ extscalar = 0; // but the deltaPE might not scale with # of atoms
+ extvector = 0; // neither do the components of the vector
+
+ // Parse fix options
+ int n[3];
+
+ n[0] = force->inumeric(FLERR,inArgv[3]);
+ n[1] = force->inumeric(FLERR,inArgv[4]);
+ n[2] = force->inumeric(FLERR,inArgv[5]);
+
+ mK[0] = n[0]*(2*M_PI / (domain->boxhi[0] - domain->boxlo[0]));
+ mK[1] = n[1]*(2*M_PI / (domain->boxhi[1] - domain->boxlo[1]));
+ mK[2] = n[2]*(2*M_PI / (domain->boxhi[2] - domain->boxlo[2]));
+
+ mKappa = force->numeric(FLERR,inArgv[6]);
+ mRhoK0 = force->numeric(FLERR,inArgv[7]);
+}
+
+// Methods that this fix implements
+// --------------------------------
+
+// Tells LAMMPS where this fix should act
+int
+FixRhok::setmask()
+{
+ int mask = 0;
+
+ // This fix modifies forces...
+ mask |= POST_FORCE;
+ mask |= POST_FORCE_RESPA;
+ mask |= MIN_POST_FORCE;
+
+ // ...and potential energies
+ mask |= THERMO_ENERGY;
+
+ return mask;
+}
+
+// Initializes the fix at the beginning of a run
+void
+FixRhok::init()
+{
+ // RESPA boilerplate
+ if( strcmp( update->integrate_style, "respa" ) == 0 )
+ mNLevelsRESPA = ((Respa *) update->integrate)->nlevels;
+
+ // Count the number of affected particles
+ int nThisLocal = 0;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU
+ if( mask[i] & groupbit ) { // ...only those affected by this fix
+ nThisLocal++;
+ }
+ }
+ MPI_Allreduce( &nThisLocal, &mNThis,
+ 1, MPI_INT, MPI_SUM, world );
+ mSqrtNThis = sqrt( mNThis );
+}
+
+// Initial application of the fix to a system (when doing MD)
+void
+FixRhok::setup( int inVFlag )
+{
+ if( strcmp( update->integrate_style, "verlet" ) == 0 )
+ post_force( inVFlag );
+ else
+ {
+ ((Respa *) update->integrate)->copy_flevel_f( mNLevelsRESPA - 1 );
+ post_force_respa( inVFlag, mNLevelsRESPA - 1,0 );
+ ((Respa *) update->integrate)->copy_f_flevel( mNLevelsRESPA - 1 );
+ }
+}
+
+// Initial application of the fix to a system (when doing minimization)
+void
+FixRhok::min_setup( int inVFlag )
+{
+ post_force( inVFlag );
+}
+
+// Modify the forces calculated in the main force loop of ordinary MD
+void
+FixRhok::post_force( int inVFlag )
+{
+ double **x = atom->x;
+ double **f = atom->f;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ // Loop over locally-owned atoms affected by this fix and calculate the
+ // partial rhoK's
+ mRhoKLocal[0] = 0.0;
+ mRhoKLocal[1] = 0.0;
+
+ for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU
+ if( mask[i] & groupbit ) { // ...only those affected by this fix
+
+ // rho_k = sum_i exp( - i k.r_i )
+ mRhoKLocal[0] += cos( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
+ mRhoKLocal[1] -= sin( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
+ }
+ }
+
+ // Now calculate mRhoKGlobal
+ MPI_Allreduce( mRhoKLocal, mRhoKGlobal,
+ 2, MPI_DOUBLE, MPI_SUM, world );
+
+ // Info: < \sum_{i,j} e^{-ik.(r_i - r_j)} > ~ N, so
+ // we define rho_k as (1 / sqrt(N)) \sum_i e^{-i k.r_i}, so that
+ // <rho_k^2> is intensive.
+ mRhoKGlobal[0] /= mSqrtNThis;
+ mRhoKGlobal[1] /= mSqrtNThis;
+
+ // We'll need magnitude of rho_k
+ double rhoK = sqrt( mRhoKGlobal[0]*mRhoKGlobal[0]
+ + mRhoKGlobal[1]*mRhoKGlobal[1] );
+
+ for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU
+ if( mask[i] & groupbit ) { // ...only those affected by this fix
+
+ // Calculate forces
+ // U = kappa/2 ( |rho_k| - rho_k^0 )^2
+ // f_i = -grad_i U = -kappa ( |rho_k| - rho_k^0 ) grad_i |rho_k|
+ // grad_i |rho_k| = Re( rho_k* (-i k e^{-i k . r_i} / sqrt(N)) ) / |rho_k|
+ //
+ // In terms of real and imag parts of rho_k,
+ //
+ // Re( rho_k* (-i k e^{-i k . r_i}) ) =
+ // (- Re[rho_k] * sin( k . r_i ) - Im[rho_k] * cos( k . r_i )) * k
+
+ double sinKRi = sin( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
+ double cosKRi = cos( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] );
+
+ double prefactor = mKappa * ( rhoK - mRhoK0 ) / rhoK
+ * (-mRhoKGlobal[0]*sinKRi - mRhoKGlobal[1]*cosKRi) / mSqrtNThis;
+ f[i][0] -= prefactor * mK[0];
+ f[i][1] -= prefactor * mK[1];
+ f[i][2] -= prefactor * mK[2];
+ }
+ }
+}
+
+// Forces in RESPA loop
+void
+FixRhok::post_force_respa( int inVFlag, int inILevel, int inILoop )
+{
+ if( inILevel == mNLevelsRESPA - 1 )
+ post_force( inVFlag );
+}
+
+// Forces in minimization loop
+void
+FixRhok::min_post_force( int inVFlag )
+{
+ post_force( inVFlag );
+}
+
+// Compute the change in the potential energy induced by this fix
+double
+FixRhok::compute_scalar()
+{
+ double rhoK = sqrt( mRhoKGlobal[0]*mRhoKGlobal[0]
+ + mRhoKGlobal[1]*mRhoKGlobal[1] );
+
+ return 0.5 * mKappa * (rhoK - mRhoK0) * (rhoK - mRhoK0);
+}
+
+// Compute the ith component of the vector
+double
+FixRhok::compute_vector( int inI )
+{
+ if( inI == 0 )
+ return mRhoKGlobal[0]; // Real part
+ else if( inI == 1 )
+ return mRhoKGlobal[1]; // Imagniary part
+ else if( inI == 2 )
+ return sqrt( mRhoKGlobal[0]*mRhoKGlobal[0]
+ + mRhoKGlobal[1]*mRhoKGlobal[1] );
+ else
+ return 12345.0;
+}
diff --git a/src/USER-MISC/fix_rhok.h b/src/USER-MISC/fix_rhok.h
new file mode 100644
index 0000000000000000000000000000000000000000..c950c08b1d14aa3b22f14ce98e9b5c65eb513750
--- /dev/null
+++ b/src/USER-MISC/fix_rhok.h
@@ -0,0 +1,77 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(rhok,FixRhok)
+
+#else
+
+#ifndef LMP_FIX_RHOK_H
+#define LMP_FIX_RHOK_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixRhok : public Fix
+{
+public:
+ // Constructor: all the parameters to this fix specified in
+ // the LAMMPS input get passed in
+ FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv );
+ virtual ~FixRhok() {};
+
+ // Methods that this fix implements
+ // --------------------------------
+
+ // Tells LAMMPS where this fix should act
+ int setmask();
+
+ // Initializes the fix at the beginning of a run
+ void init();
+
+ // Initial application of the fix to a system (when doing MD / minimization)
+ void setup( int inVFlag );
+ void min_setup( int inVFlag );
+
+ // Modify the forces calculated in the main force loop, either when
+ // doing usual MD, RESPA MD or minimization
+ void post_force( int inVFlag );
+ void post_force_respa( int inVFlag, int inILevel, int inILoop );
+ void min_post_force( int inVFlag );
+
+ // Compute the change in the potential energy induced by this fix
+ double compute_scalar();
+
+ // Compute the ith component of the vector associated with this fix
+ double compute_vector( int inI );
+
+private:
+ // RESPA boilerplate
+ int mNLevelsRESPA;
+
+ // Defining parameters for this umbrella
+ double mK[3], mKappa, mRhoK0;
+
+ // Number of particles affected by the fix
+ int mNThis;
+ double mSqrtNThis;
+
+ // Real and imaginary parts of rho_k := sum_i exp( - i k . r_i )
+ double mRhoKLocal[2], mRhoKGlobal[2];
+};
+
+} // namespace LAMMPS_NS
+
+#endif // __FIX_RHOK__
+#endif // FIX_CLASS
+