patch 23Oct17

Merge pull request #707 from akohlmey/granular-omp-refactor
Updated neighbor list history processing for USER-OMP
2017-10-23 16:07:21 -06:00 · 2017-10-23 13:35:43 -06:00 · 2017-10-23 14:12:19 -04:00 · 2017-10-21 16:12:23 -06:00 · 2017-10-21 15:50:27 -06:00 · 2017-10-20 17:01:50 -06:00
377 changed files with 21427 additions and 6136 deletions
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@ -37,6 +37,10 @@ enable_language(CXX)
 #####################################################################
 include(CheckCCompilerFlag)

+if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+endif()
+
 ########################################################################
 # User input options                                                   #
 ########################################################################
@ -76,7 +80,7 @@ add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
 if(LAMMPS_EXCEPTIONS)
  add_definitions(-DLAMMPS_EXCEPTIONS)
-  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES -DLAMMPS_EXCEPTIONS")
+  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS")
 endif()

 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically")
@ -101,7 +105,7 @@ set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
  USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
  USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
  USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
-  USER-SMTBQ USER-SPH USER-TALLY USER-VTK USER-QUIP USER-QMMM)
+  USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 foreach(PKG ${DEFAULT_PACKAGES})
  option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
@ -665,7 +669,9 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 ############################################
 add_library(lammps ${LIB_SOURCES})
 target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
-add_dependencies(lammps ${LAMMPS_DEPS})
+if(LAMMPS_DEPS)
+  add_dependencies(lammps ${LAMMPS_DEPS})
+endif()
 set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
 if(BUILD_SHARED_LIBS)
  set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
--- a/doc/src/Eqs/bond_gromos.jpg
+++ b/doc/src/Eqs/bond_gromos.jpg
--- a/doc/src/Eqs/bond_gromos.tex
+++ b/doc/src/Eqs/bond_gromos.tex
@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+$$
+   E = K (r^2 - r_0^2)^2
+$$
+
+\end{document}
--- a/doc/src/Eqs/fix_rhok.jpg
+++ b/doc/src/Eqs/fix_rhok.jpg
--- a/doc/src/Eqs/fix_rhok.tex
+++ 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}
--- a/doc/src/JPG/uef_frames.jpg
+++ b/doc/src/JPG/uef_frames.jpg
--- a/doc/src/JPG/user_intel.png
+++ b/doc/src/JPG/user_intel.png
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="22 Sep 2017 version">
+<META NAME="docnumber" CONTENT="23 Oct 2017 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>

 LAMMPS Documentation :c,h3
-22 Sep 2017 version :c,h4
+23 Oct 2017 version :c,h4

 Version info: :h4

--- a/doc/src/PDF/colvars-refman-lammps.pdf
+++ b/doc/src/PDF/colvars-refman-lammps.pdf
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -720,6 +720,8 @@ package"_Section_start.html#start_3.
 "nve/eff"_fix_nve_eff.html,
 "nvt/eff"_fix_nh_eff.html,
 "nvt/sllod/eff"_fix_nvt_sllod_eff.html,
+"npt/uef"_fix_nh_uef.html,
+"nvt/uef"_fix_nh_uef.html,
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "qbmsst"_fix_qbmsst.html,
@ -728,6 +730,7 @@ 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,
@ -856,6 +859,7 @@ package"_Section_start.html#start_3.
 "meso/t/atom"_compute_meso_t_atom.html,
 "pe/tally"_compute_tally.html,
 "pe/mol/tally"_compute_tally.html,
+"pressure/uef"_compute_pressure_uef.html,
 "saed"_compute_saed.html,
 "smd/contact/radius"_compute_smd_contact_radius.html,
 "smd/damage"_compute_smd_damage.html,
@ -884,6 +888,7 @@ package"_Section_start.html#start_3.
 "temp/deform/eff"_compute_temp_deform_eff.html,
 "temp/region/eff"_compute_temp_region_eff.html,
 "temp/rotate"_compute_temp_rotate.html,
+"temp/uef"_compute_temp_uef.html,
 "xrd"_compute_xrd.html :tb(c=6,ea=c)

 :line
@ -915,11 +920,12 @@ KOKKOS, o = USER-OMP, t = OPT.
 "born/coul/long/cs"_pair_born.html,
 "born/coul/msm (o)"_pair_born.html,
 "born/coul/wolf (go)"_pair_born.html,
+"born/coul/wolf/cs"_pair_born.html,
 "brownian (o)"_pair_brownian.html,
 "brownian/poly (o)"_pair_brownian.html,
-"buck (gkio)"_pair_buck.html,
-"buck/coul/cut (gkio)"_pair_buck.html,
-"buck/coul/long (gkio)"_pair_buck.html,
+"buck (giko)"_pair_buck.html,
+"buck/coul/cut (giko)"_pair_buck.html,
+"buck/coul/long (giko)"_pair_buck.html,
 "buck/coul/long/cs"_pair_buck.html,
 "buck/coul/msm (o)"_pair_buck.html,
 "buck/long/coul/long (o)"_pair_buck_long.html,
@ -934,12 +940,13 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (go)"_pair_dpd.html,
+"coul/wolf/cs"_pair_coul.html,
+"dpd (gio)"_pair_dpd.html,
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
-"eam (gkiot)"_pair_eam.html,
-"eam/alloy (gkiot)"_pair_eam.html,
-"eam/fs (gkiot)"_pair_eam.html,
+"eam (gikot)"_pair_eam.html,
+"eam/alloy (gikot)"_pair_eam.html,
+"eam/fs (gikot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
 "gauss (go)"_pair_gauss.html,
 "gayberne (gio)"_pair_gayberne.html,
@ -953,9 +960,9 @@ KOKKOS, o = USER-OMP, t = OPT.
 "kim"_pair_kim.html,
 "lcbop"_pair_lcbop.html,
 "line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (kio)"_pair_charmm.html,
+"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (gkio)"_pair_charmm.html,
+"lj/charmm/coul/long (giko)"_pair_charmm.html,
 "lj/charmm/coul/msm"_pair_charmm.html,
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
 "lj/charmmfsw/coul/long"_pair_charmm.html,
@ -1005,9 +1012,9 @@ KOKKOS, o = USER-OMP, t = OPT.
 "resquared (go)"_pair_resquared.html,
 "snap"_pair_snap.html,
 "soft (go)"_pair_soft.html,
-"sw (gkio)"_pair_sw.html,
+"sw (giko)"_pair_sw.html,
 "table (gko)"_pair_table.html,
-"tersoff (gkio)"_pair_tersoff.html,
+"tersoff (giko)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
 "tersoff/mod/c (o)"_pair_tersoff_mod.html,
 "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
@ -1111,6 +1118,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "class2 (ko)"_bond_class2.html,
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
+"gromos (o)"_bond_gromos.html,
 "harmonic (ko)"_bond_harmonic.html,
 "morse (o)"_bond_morse.html,
 "nonlinear (o)"_bond_nonlinear.html,
@ -1177,7 +1185,7 @@ USER-OMP, t = OPT.
 "none"_dihedral_none.html,
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
-"charmm (ko)"_dihedral_charmm.html,
+"charmm (iko)"_dihedral_charmm.html,
 "charmmfsw"_dihedral_charmm.html,
 "class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
@ -1190,7 +1198,7 @@ used if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.

 "cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (o)"_dihedral_fourier.html,
+"fourier (io)"_dihedral_fourier.html,
 "nharmonic (o)"_dihedral_nharmonic.html,
 "quadratic (o)"_dihedral_quadratic.html,
 "spherical (o)"_dihedral_spherical.html,
@ -1213,7 +1221,7 @@ USER-OMP, t = OPT.
 "hybrid"_improper_hybrid.html,
 "class2 (ko)"_improper_class2.html,
 "cvff (io)"_improper_cvff.html,
-"harmonic (ko)"_improper_harmonic.html,
+"harmonic (iko)"_improper_harmonic.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

 These are additional improper styles in USER packages, which can be
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -150,6 +150,7 @@ Package, Description, Doc page, Example, Library
 "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
 "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
 "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
+"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
 "USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)

 :line
@ -705,7 +706,7 @@ dynamics can be run with LAMMPS using density-functional tight-binding
 quantum forces calculated by LATTE.

 More information on LATTE can be found at this web site:
-"https://github.com/lanl/LATTE"_#latte_home.  A brief technical
+"https://github.com/lanl/LATTE"_latte_home.  A brief technical
 description is given with the "fix latte"_fix_latte.html command.

 :link(latte_home,https://github.com/lanl/LATTE)
@ -728,6 +729,7 @@ make lib-latte args="-b"                # download and build in lib/latte/LATTE-
 make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
 make lib-latte args="-b -m gfortran"    # download and build in lib/latte and 
                                        #   copy Makefile.lammps.gfortran to Makefile.lammps
+:pre

 Note that 3 symbolic (soft) links, "includelink" and "liblink" and
 "filelink", are created in lib/latte to point into the LATTE home dir.
@ -2770,13 +2772,44 @@ examples/USER/tally :ul

 :line

+USER-UEF package :link(USER-UEF),h4
+
+[Contents:]
+
+A fix style for the integration of the equations of motion under
+extensional flow with proper boundary conditions, as well as several
+supporting compute styles and an output option.
+
+[Author:] David Nicholson (MIT).
+
+[Install or un-install:]
+
+make yes-user-uef
+make machine :pre
+
+make no-user-uef
+make machine :pre
+
+[Supporting info:]
+
+src/USER-UEF: filenames -> commands
+src/USER-UEF/README
+"fix nvt/uef"_fix_nh_uef.html
+"fix npt/uef"_fix_nh_uef.html
+"compute pressure/uef"_compute_pressure_uef.html
+"compute temp/uef"_compute_temp_uef.html
+"dump cfg/uef"_dump_cfg_uef.html
+examples/uef :ul
+
+:line
+
 USER-VTK package :link(USER-VTK),h4

 [Contents:]

-A "dump vtk"_dump_vtk.html command which outputs
-snapshot info in the "VTK format"_vtk, enabling visualization by
-"Paraview"_paraview or other visuzlization packages.
+A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
+"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
+other visuzlization packages.

 :link(vtk,http://www.vtk.org)
 :link(paraview,http://www.paraview.org)
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -25,14 +25,14 @@ LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
 [Currently Available USER-INTEL Styles:]

 Angle Styles: charmm, harmonic :ulb,l
-Bond Styles: fene, harmonic :l
+Bond Styles: fene, fourier, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
-Fixes: nve, npt, nvt, nvt/sllod :l
+Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l
 Improper Styles: cvff, harmonic :l
 Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long, 
-buck, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, 
-lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, rebo,
-sw, tersoff :l
+buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, 
+lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, 
+rebo, sw, tersoff :l
 K-Space Styles: pppm, pppm/disp :l
 :ule

@ -54,11 +54,12 @@ warmup run (for use with offload benchmarks).
 :c,image(JPG/user_intel.png)

 Results are speedups obtained on Intel Xeon E5-2697v4 processors
-(code-named Broadwell) and Intel Xeon Phi 7250 processors
-(code-named Knights Landing) with "June 2017" LAMMPS built with
-Intel Parallel Studio 2017 update 2. Results are with 1 MPI task
-per physical core. See {src/USER-INTEL/TEST/README} for the raw
-simulation rates and instructions to reproduce.
+(code-named Broadwell), Intel Xeon Phi 7250 processors (code-named
+Knights Landing), and Intel Xeon Gold 6148 processors (code-named
+Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio
+2017 update 2. Results are with 1 MPI task per physical core. See
+{src/USER-INTEL/TEST/README} for the raw simulation rates and
+instructions to reproduce.

 :line

@ -82,6 +83,11 @@ this order :l
 The {newton} setting applies to all atoms, not just atoms shared
 between MPI tasks :l
 Vectorization can change the order for adding pairwise forces :l
+When using the -DLMP_USE_MKL_RNG define (all included intel optimized
+makefiles do) at build time, the random number generator for
+dissipative particle dynamics (pair style dpd/intel) uses the Mersenne
+Twister generator included in the Intel MKL library (that should be
+more robust than the default Masaglia random number generator) :l
 :ule

 The precision mode (described below) used with the USER-INTEL
@ -108,7 +114,7 @@ $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
 For some of the simple 2-body potentials without long-range
 electrostatics, performance and scalability can be better with
 the "newton off" setting added to the input script :l
-For simulations on higher node counts, add "processors * * * grid 
+For simulations on higher node counts, add "processors * * * grid
 numa" to the beginning of the input script for better scalability :l
 If using {kspace_style pppm} in the input script, add
 "kspace_modify diff ad" for better performance :l
@ -119,8 +125,8 @@ For Intel Xeon Phi CPUs:
 Runs should be performed using MCDRAM. :ulb,l
 :ule

-For simulations using {kspace_style pppm} on Intel CPUs
-supporting AVX-512:
+For simulations using {kspace_style pppm} on Intel CPUs supporting
+AVX-512:

 Add "kspace_modify diff ad" to the input script :ulb,l
 The command-line option should be changed to
@ -237,14 +243,17 @@ However, if you do not have coprocessors on your system, building
 without offload support will produce a smaller binary.

 The general requirements for Makefiles with the USER-INTEL package
-are as follows. "-DLAMMPS_MEMALIGN=64" is required for CCFLAGS. When
-using Intel compilers, "-restrict" is required and "-qopenmp" is
-highly recommended for CCFLAGS and LINKFLAGS. LIB should include
-"-ltbbmalloc". For builds supporting offload, "-DLMP_INTEL_OFFLOAD"
-is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.
-Other recommended CCFLAG options for best performance are
-"-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
-no-prec-div".
+are as follows. When using Intel compilers, "-restrict" is required 
+and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. 
+CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads
+are not supported in the build environment) and "-DLMP_USE_MKL_RNG"
+(unless Intel Math Kernel Library (MKL) is not available in the build
+environment). For Intel compilers, LIB should include "-ltbbmalloc" 
+or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added
+to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is
+required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other
+recommended CCFLAG options for best performance are "-O2 -fno-alias
+-ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div".

 NOTE: The vectorization and math capabilities can differ depending on
 the CPU. For Intel compilers, the "-x" flag specifies the type of
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@ -16,7 +16,7 @@ atom_modify keyword values ... :pre
 one or more keyword/value pairs may be appended :ulb,l
 keyword = {id} or {map} or {first} or {sort} :l
   {id} value = {yes} or {no}
-   {map} value = {array} or {hash}
+   {map} value = {yes} or {array} or {hash}
   {first} value = group-ID = group whose atoms will appear first in internal atom lists
   {sort} values = Nfreq binsize
     Nfreq = sort atoms spatially every this many time steps
@ -25,8 +25,8 @@ keyword = {id} or {map} or {first} or {sort} :l

 [Examples:]

-atom_modify map hash
-atom_modify map array sort 10000 2.0
+atom_modify map yes
+atom_modify map hash sort 10000 2.0
 atom_modify first colloid :pre

 [Description:]
@ -62,29 +62,33 @@ switch.  This is described in "Section 2.2"_Section_start.html#start_2
 of the manual.  If atom IDs are not used, they must be specified as 0
 for all atoms, e.g. in a data or restart file.

-The {map} keyword determines how atom ID lookup is done for molecular
-atom styles.  Lookups are performed by bond (angle, etc) routines in
-LAMMPS to find the local atom index associated with a global atom ID.
+The {map} keyword determines how atoms with specific IDs are found
+when required.  An example are the bond (angle, etc) methods which
+need to find the local index of an atom with a specific global ID
+which is a bond (angle, etc) partner.  LAMMPS performs this operation
+efficiently by creating a "map", which is either an {array} or {hash}
+table, as descibed below.

-When the {array} value is used, each processor stores a lookup table
-of length N, where N is the largest atom ID in the system.  This is a
+When the {map} keyword is not specified in your input script, LAMMPS
+only creates a map for "atom_styles"_atom_style.html for molecular
+systems which have permanent bonds (angles, etc).  No map is created
+for atomic systems, since it is normally not needed.  However some
+LAMMPS commands require a map, even for atomic systems, and will
+generate an error if one does not exist.  The {map} keyword thus
+allows you to force the creation of a map.  The {yes} value will
+create either an {array} or {hash} style map, as explained in the next
+paragraph.  The {array} and {hash} values create an atom-style or
+hash-style map respectively.
+
+For an {array}-style map, each processor stores a lookup table of
+length N, where N is the largest atom ID in the system.  This is a
 fast, simple method for many simulations, but requires too much memory
-for large simulations.  The {hash} value uses a hash table to perform
-the lookups.  This can be slightly slower than the {array} method, but
-its memory cost is proportional to the number of atoms owned by a
-processor, i.e. N/P when N is the total number of atoms in the system
-and P is the number of processors.
-
-When this setting is not specified in your input script, LAMMPS
-creates a map, if one is needed, as an array or hash.  See the
-discussion of default values below for how LAMMPS chooses which kind
-of map to build.  Note that atomic systems do not normally need to
-create a map.  However, even in this case some LAMMPS commands will
-create a map to find atoms (and then destroy it), or require a
-permanent map.  An example of the former is the "velocity loop
-all"_velocity.html command, which uses a map when looping over all
-atoms and insuring the same velocity values are assigned to an atom
-ID, no matter which processor owns it.
+for large simulations.  For a {hash}-style map, a hash table is
+created on each processor, which finds an atom ID in constant time
+(independent of the global number of atom IDs).  It can be slightly
+slower than the {array} map, but its memory cost is proportional to
+the number of atoms owned by a processor, i.e. N/P when N is the total
+number of atoms in the system and P is the number of processors.

 The {first} keyword allows a "group"_group.html to be specified whose
 atoms will be maintained as the first atoms in each processor's list
--- a/doc/src/bond_gromos.txt
+++ b/doc/src/bond_gromos.txt
@ -0,0 +1,73 @@
+"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
+
+bond_style gromos command :h3
+bond_style gromos/omp command :h3
+
+[Syntax:]
+
+bond_style gromos :pre
+
+[Examples:]
+
+bond_style gromos
+bond_coeff 5 80.0 1.2 :pre
+
+[Description:]
+
+The {gromos} bond style uses the potential
+
+:c,image(Eqs/bond_gromos.jpg)
+
+where r0 is the equilibrium bond distance.  Note that the usual 1/4
+factor is included in K.
+
+The following coefficients must be defined for each bond type via the
+"bond_coeff"_bond_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+K (energy/distance^4)
+r0 (distance) :ul
+
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+MOLECULE package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+[Related commands:]
+
+"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
+
+[Default:] none
--- a/doc/src/bonds.txt
+++ b/doc/src/bonds.txt
@ -8,6 +8,7 @@ Bond Styles :h1
   bond_class2
   bond_fene
   bond_fene_expand
+   bond_gromos
   bond_harmonic
   bond_harmonic_shift
   bond_harmonic_shift_cut
--- a/doc/src/commands.txt
+++ b/doc/src/commands.txt
@ -32,6 +32,7 @@ Commands :h1
   dimension
   displace_atoms
   dump
+   dump_cfg_uef
   dump_h5md
   dump_image
   dump_modify
--- a/doc/src/compute_pressure_uef.txt
+++ b/doc/src/compute_pressure_uef.txt
@ -0,0 +1,61 @@
+"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
+
+compute pressure/uef command :h3
+
+[Syntax:]
+
+compute ID group-ID pressure/uef temp-ID keyword ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+pressure/uef = style name of this compute command
+temp-ID = ID of compute that calculates temperature, can be NULL if not needed
+zero or more keywords may be appended
+keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
+
+[Examples:]
+
+compute 1 all pressure/uef my_temp_uef
+compute 2 all pressure/uef my_temp_uef virial :pre
+
+[Description:]
+
+This command is used to compute the pressure tensor in  
+the reference frame of the applied flow field when
+"fix nvt/uef"_fix_nh_uef.html" or 
+"fix npt/uef"_fix_nh_uef.html" is used. 
+It is not necessary to use this command to compute the scalar
+value of the pressure. A "compute pressure"_compute_pressure.html
+may be used for that purpose.
+
+The keywords and output information are documented in 
+"compute_pressure"_compute_pressure.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF 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.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+The kinetic contribution to the pressure tensor
+will be accurate only when 
+the compute specificed by {temp-ID} is a 
+"compute temp/uef"_compute_temp_uef.html.
+
+[Related commands:]
+
+"compute pressure"_compute_pressure.html,
+"fix nvt/uef"_fix_nh_uef.html,
+"compute temp/uef"_compute_temp_uef.html
+
+[Default:] none
+
+
--- a/doc/src/compute_temp_uef.txt
+++ b/doc/src/compute_temp_uef.txt
@ -0,0 +1,52 @@
+"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
+
+compute temp/uef command :h3
+
+[Syntax:]
+
+compute ID group-ID temp/uef :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+temp/uef = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all temp/uef 
+compute 2 sel temp/uef :pre
+
+[Description:]
+
+This command is used to compute the kinetic energy tensor in 
+the reference frame of the applied flow field when
+"fix nvt/uef"_fix_nh_uef.html" or
+"fix npt/uef"_fix_nh_uef.html" is used.
+It is not necessary to use this command to compute the scalar
+value of the temperature. A "compute temp"_compute_temp.html 
+may be used for that purpose.
+
+Output information for this command can be found in the
+documentation for "compute temp"_compute_temp.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF 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.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html 
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+[Related commands:]
+
+"compute temp"_compute_temp.html,
+"fix nvt/uef"_fix_nh_uef.html,
+"compute pressure/uef"_compute_pressure_uef.html
+
+
+[Default:] none
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@ -65,6 +65,7 @@ Computes :h1
   compute_pe_atom
   compute_plasticity_atom
   compute_pressure
+   compute_pressure_uef
   compute_property_atom
   compute_property_chunk
   compute_property_local
@ -114,6 +115,7 @@ Computes :h1
   compute_temp_region_eff
   compute_temp_rotate
   compute_temp_sphere
+   compute_temp_uef
   compute_ti
   compute_torque_chunk
   compute_vacf
--- a/doc/src/dihedral_fourier.txt
+++ b/doc/src/dihedral_fourier.txt
@ -7,6 +7,7 @@
 :line

 dihedral_style fourier command :h3
+dihedral_style fourier/intel command :h3
 dihedral_style fourier/omp command :h3

 [Syntax:]
--- a/doc/src/dump_cfg_uef.txt
+++ b/doc/src/dump_cfg_uef.txt
@ -0,0 +1,53 @@
+ "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
+
+dump cfg/uef command :h3
+
+[Syntax:]
+
+dump ID group-ID cfg/uef N file mass type xs ys zs args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be dumped :l
+N = dump every this many timesteps :l
+file = name of file to write dump info to :l
+args = same as args for "dump custom"_dump.html :pre
+
+:ule
+
+[Examples:]
+
+dump 1 all cfg/uef 10 dump.*.cfg mass type xs ys zs
+dump 2 all cfg/uef 100 dump.*.cfg mass type xs ys zs id c_stress :pre
+
+[Description:]
+
+This command is used to dump atomic coordinates in the
+reference frame of the applied flow field when 
+"fix nvt/uef"_fix_nh_uef.html or
+"fix npt/uef"_fix_nh_uef.html or is used. Only the atomic 
+coordinates and frame-invariant scalar quantities 
+will be in the flow frame. If velocities are selected
+as output, for example, they will not be in the same
+reference frame as the atomic positions.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF 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.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+[Related commands:]
+
+"dump"_dump.html,
+"fix nvt/uef"_fix_nh_uef.html
+
+[Default:] none
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@ -15,8 +15,9 @@ dump_modify dump-ID keyword values ... :pre
 dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
-keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
-  {append} arg = {yes} or {no} or {at} N
+keyword = {append} or {at} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+  {append} arg = {yes} or {no}
+  {at} arg = N
    N = index of frame written upon first dump
  {buffer} arg = {yes} or {no}
  {element} args = E1 E2 ... EN, where N = # of atom types
@ -141,13 +142,18 @@ and {dcd}.  It also applies only to text output files, not to binary
 or gzipped or image/movie files.  If specified as {yes}, then dump
 snapshots are appended to the end of an existing dump file.  If
 specified as {no}, then a new dump file will be created which will
-overwrite an existing file with the same name.  If the {at} option is present
-({netcdf} only), then the frame to append to can be specified.  Negative values
-are counted from the end of the file.  This keyword can only take effect if the
-dump_modify command is used after the "dump"_dump.html command, but before the
-first command that causes dump snapshots to be output, e.g. a "run"_run.html or
-"minimize"_minimize.html command.  Once the dump file has been opened, this
-keyword has no further effect.
+overwrite an existing file with the same name.
+
+:line
+
+The {at} keyword only applies to the {netcdf} dump style.  It can only
+be used if the {append yes} keyword is also used.  The {N} argument is
+the index of which frame to append to.  A negative value can be
+specified for {N}, which means a frame counted from the end of the
+file.  The {at} keyword can only be used if the dump_modify command is
+before the first command that causes dump snapshots to be output,
+e.g. a "run"_run.html or "minimize"_minimize.html command.  Once the
+dump file has been opened, this keyword has no further effect.

 :line

--- a/doc/src/dump_netcdf.txt
+++ b/doc/src/dump_netcdf.txt
@ -25,7 +25,8 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule

 dump 1 all netcdf 100 traj.nc type x y z vx vy vz
 dump_modify 1 append yes at -1 thermo yes
-dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre
+dump 1 all netcdf/mpiio 1000 traj.nc id type x y z
+dump 1 all netcdf 1000 traj.*.nc id type x y z :pre

 [Description:]

@ -73,4 +74,3 @@ section for more info.
 [Related commands:]

 "dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
-
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@ -86,11 +86,16 @@ Change the volume and/or shape of the simulation box during a dynamics
 run.  Orthogonal simulation boxes have 3 adjustable parameters
 (x,y,z).  Triclinic (non-orthogonal) simulation boxes have 6
 adjustable parameters (x,y,z,xy,xz,yz).  Any or all of them can be
-adjusted independently and simultaneously by this command.  This fix
-can be used to perform non-equilibrium MD (NEMD) simulations of a
-continuously strained system.  See the "fix
+adjusted independently and simultaneously by this command.  
+
+This fix can be used to perform non-equilibrium MD (NEMD) simulations
+of a continuously strained system.  See the "fix
 nvt/sllod"_fix_nvt_sllod.html and "compute
-temp/deform"_compute_temp_deform.html commands for more details.
+temp/deform"_compute_temp_deform.html commands for more details.  Note
+that simulation of a continuously extended system (extensional flow)
+can be modeled using the "USER-UEF
+package"_Section_packages.html#USER-UEF and its "fix
+commands"_fix_nh_uef.html.

 For the {x}, {y}, {z} parameters, the associated dimension cannot be
 shrink-wrapped.  For the {xy}, {yz}, {xz} parameters, the associated
--- a/doc/src/fix_latte.txt
+++ b/doc/src/fix_latte.txt
@ -66,7 +66,7 @@ reference charge of overlapping atom-centered densities and bond
 integrals are parameterized using a Slater-Koster tight-binding
 approach. This procedure, which usually is referred to as the DFTB
 method has been described in detail by ("Elstner"_#Elstner) and
-("Finnis"_#Finnis) and coworkers. 
+("Finnis"_#Finnis2) and coworkers. 

 The work of the LATTE developers follows that of Elstner closely with
 respect to the physical model.  However, the development of LATTE is
@ -173,7 +173,7 @@ M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
 M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
 7260 (1998).

-:link(Finnis)
+:link(Finnis2)
 [(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van
 Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).

@ -197,11 +197,11 @@ J. Sci. Comput. 36 (2), 147-170, (2014).
 [(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys.,
 141, 164123, (2014).

-:link(Niklasson2014)
+:link(Niklasson2017)
 [(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).

-:link(Niklasson2012)
-[(Niklasson2017)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
+:link(Cawkwell2012)
+[(Cawkwell2012)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
 (17), 174308 (2012).

 :link(Negre2016)
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@ -93,7 +93,7 @@ intermediate replica with the previous and the next image:

 Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre

-Note that in this case the specified {Kspring) is in force/distance
+Note that in this case the specified {Kspring} is in force/distance
 units.

 With a value of {ideal}, the spring force is computed as suggested in
@ -105,7 +105,7 @@ where RD is the "reaction coordinate" see "neb"_neb.html section, and
 RDideal is the ideal RD for which all the images are equally spaced.
 I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
 I is the replica number).  The meanDist is the average distance
-between replicas.  Note that in this case the specified {Kspring) is
+between replicas.  Note that in this case the specified {Kspring} is
 in force units.

 Note that the {ideal} form of nudging can often be more effective at
--- a/doc/src/fix_nh.txt
+++ b/doc/src/fix_nh.txt
@ -393,32 +393,36 @@ thermostatting and barostatting.
 :line

 These fixes compute a temperature and pressure each timestep.  To do
-this, the fix creates its own computes of style "temp" and "pressure",
-as if one of these two sets of commands had been issued:
+this, the thermostat and barostat fixes create their own computes of
+style "temp" and "pressure", as if one of these sets of commands had
+been issued:

+For fix nvt:
 compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp :pre

+For fix npt and fix nph:
 compute fix-ID_temp all temp
 compute fix-ID_press all pressure fix-ID_temp :pre

-See the "compute temp"_compute_temp.html and "compute
-pressure"_compute_pressure.html commands for details.  Note that the
-IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
-+ underscore + "press".  For fix nvt, the group for the new computes
-is the same as the fix group.  For fix nph and fix npt, the group for
-the new computes is "all" since pressure is computed for the entire
-system.
+For fix nvt, the group for the new temperature compute is the same as
+the fix group.  For fix npt and fix nph, the group for both the new
+temperature and pressure compute is "all" since pressure is computed
+for the entire system.  In the case of fix nph, the temperature
+compute is not used for thermostatting, but just for a kinetic-energy
+contribution to the pressure.  See the "compute
+temp"_compute_temp.html and "compute pressure"_compute_pressure.html
+commands for details.  Note that the IDs of the new computes are the
+fix-ID + underscore + "temp" or fix_ID + underscore + "press".

 Note that these are NOT the computes used by thermodynamic output (see
 the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
-and {thermo_press}.  This means you can change the attributes of this
+and {thermo_press}.  This means you can change the attributes of these
 fix's temperature or pressure via the
-"compute_modify"_compute_modify.html command or print this temperature
-or pressure during thermodynamic output via the "thermo_style
-custom"_thermo_style.html command using the appropriate compute-ID.
-It also means that changing attributes of {thermo_temp} or
-{thermo_press} will have no effect on this fix.
+"compute_modify"_compute_modify.html command.  Or you can print this
+temperature or pressure during thermodynamic output via the
+"thermo_style custom"_thermo_style.html command using the appropriate
+compute-ID.  It also means that changing attributes of {thermo_temp}
+or {thermo_press} will have no effect on this fix.

 Like other fixes that perform thermostatting, fix nvt and fix npt can
 be used with "compute commands"_compute.html that calculate a
--- a/doc/src/fix_nh_uef.txt
+++ b/doc/src/fix_nh_uef.txt
@ -0,0 +1,228 @@
+<"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 nvt/uef command :h3
+fix npt/uef command :h3
+
+[Syntax:]
+
+fix ID group-ID style_name erate edot_x edot_y temp Tstart Tstop Tdamp keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+style_name = {nvt/uef} or {npt/uef} :l
+{Tstart}, {Tstop}, and {Tdamp} are documented in the "fix npt"_fix_nh.html command :l
+{edot_x} and {edot_y} are the strain rates in the x and y directions (1/(time units)) :l
+one or more keyword/value pairs may be appended :l
+keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain} or {tloop} or {ploop} or {mtk}
+  {ext} value = {x} or {y} or {z} or {xy} or {yz} or {xz} = external dimensions
+    sets the external dimensions used to calculate the scalar pressure
+  {strain} values = e_x e_y = initial strain
+    usually not needed, but may be needed to resume a run with a data file.
+  {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, {mtk} keywords
+    documented by the "fix npt"_fix_nh.html command :pre
+:ule
+
+[Examples:]
+
+fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005
+fix biax_nvt all nvt/uef temp 400 400 100 erate 0.000005 0.000005
+fix uniax_npt all npt/uef temp 400 400 300 iso 1 1 3000 erate 0.00001 -0.000005 ext yz
+fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pre
+
+[Description:]
+
+This fix can be used to simulate non-equilibrium molecular dynamics
+(NEMD) under diagonal flow fields, including uniaxial and biaxial
+flow.  Simulations under continuous extensional flow may be carried
+out for an indefinite amount of time.  It is an implementation of the
+boundary conditions from "(Dobson)"_#Dobson, and also uses numerical
+lattice reduction as was proposed by "(Hunt)"_#Hunt. The lattice
+reduction algorithm is from "(Semaev)"_Semaev. The fix is intended for
+simulations of homogeneous flows, and integrates the SLLOD equations
+of motion, originally proposed by Hoover and Ladd (see "(Evans and
+Morriss)"_#Sllod).  Additional detail about this implementation can be
+found in "(Nicholson and Rutledge)"_#Nicholson.
+
+Note that NEMD simulations of a continuously strained system can be
+performed using the "fix deform"_fix_deform.html, "fix
+nvt/sllod"_fix_nvt_sllod.html, and "compute
+temp/deform"_compute_temp_deform.html commands.
+
+The applied flow field is set by the {eps} keyword. The values
+{edot_x} and {edot_y} correspond to the strain rates in the xx and yy
+directions.  It is implicitly assumed that the flow field is
+traceless, and therefore the strain rate in the zz direction is eqal
+to -({edot_x} + {edot_y}).
+
+NOTE: Due to an instability in the SLLOD equations under extension,
+"fix momentum"_fix_momentum.html should be used to regularly reset the
+linear momentum.
+
+The boundary conditions require a simulation box that does not have a
+consistent alignment relative to the applied flow field. Since LAMMPS
+utilizes an upper-triangular simulation box, it is not possible to
+express the evolving simulation box in the same coordinate system as
+the flow field.  This fix keeps track of two coordinate systems: the
+flow frame, and the upper triangular LAMMPS frame. The coordinate
+systems are related to each other through the QR decomposition, as is
+illustrated in the image below.
+
+:c,image(JPG/uef_frames.jpg)
+
+During most molecular dynamics operations, the system is represented
+in the LAMMPS frame. Only when the positions and velocities are
+updated is the system rotated to the flow frame, and it is rotated
+back to the LAMMPS frame immediately afterwards. For this reason, all
+vector-valued quantities (except for the tensors from
+"compute_pressure/uef"_compute_pressure_uef.html and
+"compute_temp/uef"_compute_temp_uef.html) will be computed in the
+LAMMPS frame. Rotationally invariant scalar quantities like the
+temperature and hydrostatic pressure are frame-invariant and will be
+computed correctly. Additionally, the system is in the LAMMPS frame
+during all of the output steps, and therefore trajectory files made
+using the dump command will be in the LAMMPS frame unless the
+"dump_cfg/uef"_dump_cfg_uef.html command is used.
+
+:line
+
+Temperature control is achieved with the default Nose-Hoover style
+thermostat documented in "fix npt"_fix_nh.html. When this fix is
+active, only the peculiar velocity of each atom is stored, defined as
+the velocity relative to the streaming velocity. This is in contrast
+to "fix nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame
+velocity, and removes the contribution from the streaming velocity in
+order to compute the temperature.
+
+Pressure control is achieved using the default Nose-Hoover barostat
+documented in "fix npt"_fix_nh.html. There are two ways to control the
+pressure using this fix. The first method involves using the {ext}
+keyword along with the {iso} pressure style. With this method, the
+pressure is controlled by scaling the simulation box isotropically to
+achieve the average pressure only in the directions specified by
+{ext}.  For example, if the {ext} value is set to {xy}, the average
+pressure (Pxx+Pyy)/2 will be controlled.
+
+This example command will control the total hydrostatic pressure under
+uniaxial tension:
+
+fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz :pre
+
+This example command will control the average stress in compression
+directions, which would typically correspond to free surfaces under
+drawing with uniaxial tension:
+
+fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy :pre
+
+The second method for pressure control involves setting the normal
+stresses using the {x}, {y} , and/or {z} keywords. When using this
+method, the same pressure must be specified via {Pstart} and {Pstop}
+for all dimensions controlled. Any choice of pressure conditions that
+would cause LAMMPS to compute a deviatoric stress are not permissible
+and will result in an error. Additionally, all dimensions with
+controlled stress must have the same applied strain rate. The {ext}
+keyword must be set to the default value ({xyz}) when using this
+method.
+
+For example, the following commands will work:
+
+fix f3 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 y 1 1 5 erate -0.5 -0.5
+fix f4 all npt/uef temp 0.7 0.7 0.5 z 1 1 5 erate 0.5 0.5 :pre
+
+The following commands will not work:
+
+fix f5 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 1 1 5 erate -0.5 -0.5
+fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5 :pre
+
+:line
+
+These fix computes a temperature and pressure each timestep.  To do
+this, it creates its own computes of style "temp/uef" and
+"pressure/uef", as if one of these two sets of commands had been
+issued:
+
+compute fix-ID_temp group-ID temp/uef
+compute fix-ID_press group-ID pressure/uef fix-ID_temp :pre
+
+compute fix-ID_temp all temp/uef
+compute fix-ID_press all pressure/uef fix-ID_temp :pre
+
+See the "compute temp/uef"_compute_temp_uef.html and "compute
+pressure/uef"_compute_pressure_uef.html commands for details.  Note
+that the IDs of the new computes are the fix-ID + underscore + "temp"
+or fix_ID + underscore + "press".
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+The fix writes the state of all the thermostat and barostat variables,
+as well as the cumulative strain applied, to "binary restart
+files"_restart.html.  See the "read_restart"_read_restart.html command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+NOTE: It is not necessary to set the {strain} keyword when resuming a
+run from a restart file. Only for resuming from data files, which do
+not contain the cumulative applied strain, will this keyword be
+necessary.
+
+This fix can be used with the "fix_modify"_fix_modify.html {temp} and
+{press} options. The temperature and pressure computes used must be of
+type {temp/uef} and {pressure/uef}.
+
+This fix computes the same global scalar and vecor quantities as "fix
+npt"_fix_nh.html.
+
+The fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF 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.
+
+Due to requirements of the boundary conditions, when the {strain}
+keyword is set to zero (or unset), the initial simulation box must be
+cubic and have style triclinic. If the box is initially of type ortho,
+use "change_box"_change_box.html before invoking the fix.
+
+NOTE: When resuming from restart files, you may need to use "box tilt
+large"_box.html since lammps has internal criteria from lattice
+reduction that are not the same as the criteria in the numerical
+lattice reduction algorithm.
+
+[Related commands:]
+
+"fix nvt"_fix_nh.html, "fix nvt/sllod"_fix_nvt_sllod.html, "compute
+temp/uef"_compute_temp_uef.html, "compute
+pressure/uef"_compute_pressure_uef.html, "dump
+cfg/uef"_dump_cfg_uef.html
+
+[Default:]
+
+The default keyword values specific to this fix are exy = xyz, strain
+= 0 0.  The remaining defaults are the same as for {fix
+npt}_fix_nh.html except tchain = 1.  The reason for this change is
+given in "fix nvt/sllod"_fix_nvt_sllod.html.
+
+:line
+
+:link(Dobson)
+[(Dobson)] Dobson, J Chem Phys, 141, 184103 (2014).
+
+:link(Hunt)
+[(Hunt)] Hunt, Mol Simul, 42, 347 (2016).
+
+:link(Semaev)
+[(Semaev)] Semaev, Cryptography and Lattices, 181 (2001).
+
+:link(Sllod)
+[(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984).
+
+:link(Nicholson)
+[(Nicholson and Rutledge)] Nicholson and Rutledge, J Chem Phys, 145,
+244903 (2016).
--- a/doc/src/fix_rhok.txt
+++ b/doc/src/fix_rhok.txt
@ -0,0 +1,56 @@
+"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 of 4 values from fix rhok: 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 a force to atoms given by the potential
+
+:c,image(Eqs/fix_rhok.jpg)
+
+as described in "(Pedersen)"_#Pedersen.
+
+This field, which biases 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
+{examples/USER/misc/rhok} directory.
+
+[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).
+
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@ -26,6 +26,9 @@ style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {
 bodystyle = {single} or {molecule} or {group} :l
  {single} args = none
  {molecule} args = none
+  {custom} args = {i_propname} or {v_varname}
+    i_propname = an integer property defined via fix property/atom
+    v_varname  = an atom-style or atomfile-style variable 
  {group} args = N groupID1 groupID2 ...
    N = # of groups
    groupID1, groupID2, ... = list of N group IDs :pre
@ -80,6 +83,16 @@ fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
 fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
 fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
 fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre
+
+variable bodyid atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)
+fix 1 clump rigid custom v_bodyid :pre
+
+variable bodyid atomfile bodies.txt
+fix 1 clump rigid custom v_bodyid :pre
+
+fix 0 all property/atom i_bodyid
+read_restart data.rigid fix 0 NULL Bodies
+fix 1 clump rigid/small custom i_bodyid :pre
 	
 [Description:]

@ -100,7 +113,7 @@ of a biomolecule such as a protein.

 Example of small rigid bodies are patchy nanoparticles, such as those
 modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of
-granular particles, lipid molecules consiting of one or more point
+granular particles, lipid molecules consisting of one or more point
 dipoles connected to other spheroids or ellipsoids, irregular
 particles built from line segments (2d) or triangles (3d), and
 coarse-grain models of nano or colloidal particles consisting of a
@ -203,11 +216,11 @@ most one rigid body.  Which atoms are in which bodies can be defined
 via several options.

 NOTE: With the {rigid/small} styles, which require that {bodystyle} be
-specified as {molecule}, you can define a system that has no rigid
-bodies initially.  This is useful when you are using the {mol} keyword
-in conjunction with another fix that is adding rigid bodies on-the-fly
-as molecules, such as "fix deposit"_fix_deposit.html or "fix
-pour"_fix_pour.html.
+specified as {molecule} or {custom}, you can define a system that has
+no rigid bodies initially.  This is useful when you are using the {mol}
+keyword in conjunction with another fix that is adding rigid bodies
+on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
+"fix pour"_fix_pour.html.

 For bodystyle {single} the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for the {rigid} styles.
@ -222,6 +235,15 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you
 want.  Thus you should be careful to use a fix group that only
 includes atoms you want to be part of rigid bodies.

+Bodystyle {custom} is similar to bodystyle {molecule}, however some
+custom properties are used to group atoms into rigid bodies. The
+special case for molecule/body ID = 0 is not available. Possible
+custom properties are an integer property associated with atoms through
+"fix property/atom"_fix_property_atom.html or an atom style variable
+or an atomfile style variable. For the latter two, the variable value
+will be rounded to an integer and then rigid bodies defined from
+those values.
+
 For bodystyle {group}, each of the listed groups is treated as a
 separate rigid body.  Only atoms that are also in the fix group are
 included in each rigid body.  This option is only allowed for the
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@ -59,6 +59,7 @@ Fixes :h1
   fix_langevin
   fix_langevin_drude
   fix_langevin_eff
+   fix_latte
   fix_lb_fluid
   fix_lb_momentum
   fix_lb_pc
@ -76,6 +77,7 @@ Fixes :h1
   fix_neb
   fix_nh
   fix_nh_eff
+   fix_nh_uef
   fix_nph_asphere
   fix_nph_body
   fix_nph_sphere
@ -124,6 +126,7 @@ Fixes :h1
   fix_reaxc_species
   fix_recenter
   fix_restrain
+   fix_rhok
   fix_rigid
   fix_rx
   fix_saed_vtk
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -62,6 +62,7 @@ dump_modify.html
 dump_molfile.html
 dump_netcdf.html
 dump_vtk.html
+dump_cfg_uef.html
 echo.html
 fix.html
 fix_modify.html
@ -187,6 +188,7 @@ fix_ipi.html
 fix_langevin.html
 fix_langevin_drude.html
 fix_langevin_eff.html
+fix_latte.html
 fix_lb_fluid.html
 fix_lb_momentum.html
 fix_lb_pc.html
@ -231,6 +233,7 @@ fix_nvt_manifold_rattle.html
 fix_nvt_sllod.html
 fix_nvt_sllod_eff.html
 fix_nvt_sphere.html
+fix_nh_uef.html
 fix_oneway.html
 fix_orient.html
 fix_phonon.html
@ -253,6 +256,7 @@ 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
@ -354,6 +358,7 @@ compute_pe.html
 compute_pe_atom.html
 compute_plasticity_atom.html
 compute_pressure.html
+compute_pressure_uef.html
 compute_property_atom.html
 compute_property_chunk.html
 compute_property_local.html
@ -403,6 +408,7 @@ compute_temp_region.html
 compute_temp_region_eff.html
 compute_temp_rotate.html
 compute_temp_sphere.html
+compute_temp_uef.html
 compute_ti.html
 compute_torque_chunk.html
 compute_vacf.html
@ -514,7 +520,7 @@ pair_zero.html
 bond_class2.html
 bond_fene.html
 bond_fene_expand.html
-bond_oxdna.html
+bond_gromos.html
 bond_harmonic.html
 bond_harmonic_shift.html
 bond_harmonic_shift_cut.html
@ -522,6 +528,7 @@ bond_hybrid.html
 bond_morse.html
 bond_none.html
 bond_nonlinear.html
+bond_oxdna.html
 bond_quartic.html
 bond_table.html
 bond_zero.html
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@ -62,7 +62,7 @@ args = arguments specific to the style :l
      {no_affinity} values = none
  {kokkos} args = keyword value ...
    zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward}
+    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse}
      {neigh} value = {full} or {half}
        full = full neighbor list
        half = half neighbor list built in thread-safe manner
@ -75,9 +75,10 @@ args = arguments specific to the style :l
      {binsize} value = size
        size = bin size for neighbor list construction (distance units)
      {comm} value = {no} or {host} or {device}
-        use value for both comm/exchange and comm/forward
+        use value for comm/exchange and comm/forward and comm/reverse
      {comm/exchange} value = {no} or {host} or {device}
      {comm/forward} value = {no} or {host} or {device}
+      {comm/reverse} value = {no} or {host} or {device}
        no = perform communication pack/unpack in non-KOKKOS mode
        host = perform pack/unpack on host (e.g. with OpenMP threading)
        device = perform pack/unpack on device (e.g. on GPU)
@ -429,17 +430,18 @@ Coulombic solver"_kspace_style.html because the GPU is faster at
 performing pairwise interactions, then this rule of thumb may give too
 large a binsize.

-The {comm} and {comm/exchange} and {comm/forward} keywords determine
+The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} keywords determine
 whether the host or device performs the packing and unpacking of data
 when communicating per-atom data between processors.  "Exchange"
 communication happens only on timesteps that neighbor lists are
 rebuilt.  The data is only for atoms that migrate to new processors.
-"Forward" communication happens every timestep.  The data is for atom
+"Forward" communication happens every timestep. "Reverse" communication
+happens every timestep if the {newton} option is on.  The data is for atom
 coordinates and any other atom properties that needs to be updated for
 ghost atoms owned by each processor.

 The {comm} keyword is simply a short-cut to set the same value
-for both the {comm/exchange} and {comm/forward} keywords.
+for both the {comm/exchange} and {comm/forward} and {comm/reverse} keywords.

 The value options for all 3 keywords are {no} or {host} or {device}.
 A value of {no} means to use the standard non-KOKKOS method of
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@ -17,6 +17,7 @@ pair_style born/coul/long/omp command :h3
 pair_style born/coul/msm command :h3
 pair_style born/coul/msm/omp command :h3
 pair_style born/coul/wolf command :h3
+pair_style born/coul/wolf/cs command :h3
 pair_style born/coul/wolf/gpu command :h3
 pair_style born/coul/wolf/omp command :h3
 pair_style born/coul/dsf command :h3
@ -36,7 +37,7 @@ args = list of arguments for a particular style :ul
  {born/coul/msm} args = cutoff (cutoff2)
    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  {born/coul/wolf} args = alpha cutoff (cutoff2)
+  {born/coul/wolf} or {born/coul/wolf/cs} args = alpha cutoff (cutoff2)
    alpha = damping parameter (inverse distance units)
    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
    cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -65,6 +66,7 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre

 pair_style born/coul/wolf 0.25 10.0
 pair_style born/coul/wolf 0.25 10.0 9.0
+pair_style born/coul/wolf/cs 0.25 10.0 9.0
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre

@ -106,8 +108,9 @@ damped shifted force model as in the "coul/dsf"_pair_coul.html style.
 Style {born/coul/long/cs} is identical to {born/coul/long} except that
 a term is added for the "core/shell model"_Section_howto.html#howto_25
 to allow charges on core and shell particles to be separated by r =
-0.0. The same correction is introduced for {born/coul/dsf/cs} style
-which is identical to {born/coul/dsf}.
+0.0.  The same correction is introduced for the {born/coul/dsf/cs}
+style which is identical to {born/coul/dsf}.  And likewise for
+{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.

 Note that these potentials are related to the "Buckingham
 potential"_pair_buck.html.
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@ -29,6 +29,7 @@ pair_style coul/streitz command :h3
 pair_style coul/wolf command :h3
 pair_style coul/wolf/kk command :h3
 pair_style coul/wolf/omp command :h3
+pair_style coul/wolf/cs command :h3
 pair_style tip4p/cut command :h3
 pair_style tip4p/long command :h3
 pair_style tip4p/cut/omp command :h3
@ -43,6 +44,7 @@ pair_style coul/long cutoff
 pair_style coul/long/cs cutoff
 pair_style coul/long/gpu cutoff
 pair_style coul/wolf alpha cutoff
+pair_style coul/wolf/cs alpha cutoff
 pair_style coul/streitz cutoff keyword alpha
 pair_style tip4p/cut otype htype btype atype qdist cutoff
 pair_style tip4p/long otype htype btype atype qdist cutoff :pre
@ -72,6 +74,7 @@ pair_style coul/msm 10.0
 pair_coeff * * :pre

 pair_style coul/wolf 0.2 9.0
+pair_style coul/wolf/cs 0.2 9.0
 pair_coeff * * :pre

 pair_style coul/streitz 12.0 ewald
@ -202,7 +205,9 @@ interactions outside that distance are computed in reciprocal space.

 Style {coul/long/cs} is identical to {coul/long} except that a term is
 added for the "core/shell model"_Section_howto.html#howto_25 to allow
-charges on core and shell particles to be separated by r = 0.0.
+charges on core and shell particles to be separated by r = 0.0.  The
+same correction is introduced for the {coul/wolf/cs} style which is
+identical to {coul/wolf}.

 Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of
 the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@ -9,12 +9,13 @@
 pair_style born/coul/long/cs command :h3
 pair_style buck/coul/long/cs command :h3
 pair_style born/coul/dsf/cs command :h3
+pair_style born/coul/wolf/cs command :h3

 [Syntax:]

 pair_style style args :pre

-style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs}
+style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} or {born/coul/wolf/cs}
 args = list of arguments for a particular style :ul
  {born/coul/long/cs} args = cutoff (cutoff2)
    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
@ -26,6 +27,10 @@ args = list of arguments for a particular style :ul
    alpha = damping parameter (inverse distance units)
    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
    cutoff2 = global cutoff for Coulombic (distance units) :pre
+  {born/coul/wolf/cs} args = alpha cutoff (cutoff2)
+    alpha = damping parameter (inverse distance units)
+    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)

 [Examples:]

@ -41,6 +46,10 @@ pair_style born/coul/dsf/cs 0.1 10.0 12.0
 pair_coeff * *   0.0 1.00 0.00 0.00 0.00
 pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre

+pair_style born/coul/wolf/cs 0.25 10.0 12.0
+pair_coeff * *   0.0 1.00 0.00 0.00 0.00
+pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
+
 [Description:]

 These pair styles are designed to be used with the adiabatic
@ -73,13 +82,21 @@ the core and shell, epsilon is the dielectric constant and r_min is the
 minimal distance.

 The pair style {born/coul/dsf/cs} is identical to the
-"pair_style born/coul/dsf"_pair_born.html style, which uses the
+"pair_style born/coul/dsf"_pair_born.html style, which uses
 the damped shifted force model as in "coul/dsf"_pair_coul.html
 to compute the Coulomb contribution. This approach does not require
 a long-range solver, thus the only correction is the addition of a
 minimal distance to avoid the possible r = 0.0 case for a
 core/shell pair.

+The pair style {born/coul/wolf/cs} is identical to the
+"pair_style born/coul/wolf"_pair_born.html style, which uses
+the Wolf summation as in "coul/wolf"_pair_coul.html to compute
+the Coulomb contribution. This approach does not require
+a long-range solver, thus the only correction is the addition of a
+minimal distance to avoid the possible r = 0.0 case for a
+core/shell pair.
+
 [Restrictions:]

 These pair styles are part of the CORESHELL package.  They are only
--- a/doc/src/pair_dpd.txt
+++ b/doc/src/pair_dpd.txt
@ -8,6 +8,7 @@

 pair_style dpd command :h3
 pair_style dpd/gpu command :h3
+pair_style dpd/intel command :h3
 pair_style dpd/omp command :h3
 pair_style dpd/tstat command :h3
 pair_style dpd/tstat/gpu command :h3
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@ -294,7 +294,7 @@ distribution have a ".cdeam" suffix.

 Style {eam/fs} computes pairwise interactions for metals and metal
 alloys using a generalized form of EAM potentials due to Finnis and
-Sinclair "(Finnis)"_#Finnis.  The total energy Ei of an atom I is
+Sinclair "(Finnis)"_#Finnis1.  The total energy Ei of an atom I is
 given by

 :c,image(Eqs/pair_eam_fs.jpg)
@ -442,7 +442,7 @@ of Physics: Condensed Matter, 16, S2629 (2004).
 [(Daw)] Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
 Daw, Baskes, Phys Rev B, 29, 6443 (1984).

-:link(Finnis)
+:link(Finnis1)
 [(Finnis)] Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).

 :link(Stukowski)
--- a/examples/USER/misc/rhok/README.md
+++ b/examples/USER/misc/rhok/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:
+
+  [![Interface Pinning](http://img.youtube.com/vi/F_79JZNdyoQ/0.jpg)](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
--- a/examples/USER/misc/rhok/in.crystal
+++ b/examples/USER/misc/rhok/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
--- a/examples/USER/misc/rhok/in.pinning
+++ b/examples/USER/misc/rhok/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
--- a/examples/USER/misc/rhok/in.setup
+++ b/examples/USER/misc/rhok/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
--- a/examples/USER/misc/rhok/log.22Sep2017.crystal.g++.1
+++ b/examples/USER/misc/rhok/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
--- a/examples/USER/misc/rhok/log.22Sep2017.crystal.g++.4
+++ b/examples/USER/misc/rhok/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
--- a/examples/USER/misc/rhok/log.22Sep2017.pinning.g++.1
+++ b/examples/USER/misc/rhok/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
--- a/examples/USER/misc/rhok/log.22Sep2017.pinning.g++.4
+++ b/examples/USER/misc/rhok/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
--- a/examples/USER/misc/rhok/log.22Sep2017.setup.g++.1
+++ b/examples/USER/misc/rhok/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
--- a/examples/USER/misc/rhok/log.22Sep2017.setup.g++.4
+++ b/examples/USER/misc/rhok/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
--- a/examples/USER/uef/README
+++ b/examples/USER/uef/README
@ -0,0 +1,19 @@
+This directory contains two short example scripts for the USER-UEF
+package.
+
+
+nvt_uniaxial:
+  A simulation of a WCA fluid under constant volume uniaxial strain
+  with stretching in the z direction, compression in the x and y
+  directions.The xx, yy and zz components of the pressure tensor are 
+  written to the log file. The simulation conditions are the same 
+  used in the paper by Thomas Hunt [http://arxiv.org/abs/1310.3905]
+  and should yield an zz pressure near 5 and xx/yy pressures near 10.
+
+npt_biaxial:
+  A simulation of a WCA fluid under stress-controlled biaxial strain 
+  with stretching in the x and y directions, compression in the z 
+  direction. The zz stress is controlled using the ext keyword in fix
+  npt/uef. The xx yy and zz components of the pressure tensor are 
+  written to the log file. The simulations conditions should yield 
+  xx/yy pressures near 5 and zz pressure near 10
--- a/examples/USER/uef/npt_biaxial/data.wca
+++ b/examples/USER/uef/npt_biaxial/data.wca
--- a/examples/USER/uef/npt_biaxial/in.npt_biaxial
+++ b/examples/USER/uef/npt_biaxial/in.npt_biaxial
@ -0,0 +1,31 @@
+# biaxial NPT deformation of WCA fluid
+
+units		lj
+atom_style	atomic
+
+
+pair_style	lj/cut 1.122562
+read_data       data.wca
+pair_coeff	1 1 1.0 1.0
+pair_modify     shift yes
+
+neighbor	0.5 bin
+neigh_modify	delay 0
+
+change_box      all triclinic
+
+# these commads show the different methods that may be used to impose
+# a constant stress through isotropic or anisotropic coupling
+fix		1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z
+#fix		1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5  erate 0.5 0.5 ext xyz
+
+fix             2 all momentum 100 linear 1 1 1
+
+#dump		1 all atom 25 dump.lammpstrj
+
+#dump		2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
+
+thermo_style    custom step c_1_press[1] c_1_press[2] c_1_press[3]
+
+thermo		50
+run		10000
--- a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1
+++ b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1
@ -0,0 +1,284 @@
+LAMMPS (22 Sep 2017)
+# biaxial NPT deformation of WCA fluid
+
+units		lj
+atom_style	atomic
+
+
+pair_style	lj/cut 1.122562
+read_data       data.wca
+  orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  500 atoms
+  reading velocities ...
+  500 velocities
+pair_coeff	1 1 1.0 1.0
+pair_modify     shift yes
+
+neighbor	0.5 bin
+neigh_modify	delay 0
+
+change_box      all triclinic
+  triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0)
+
+# these commads show the different methods that may be used to impose
+# a constant stress through isotropic or anisotropic coupling
+fix		1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z
+#fix		1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5  erate 0.5 0.5 ext xyz
+
+fix             2 all momentum 100 linear 1 1 1
+
+#dump		1 all atom 25 dump.lammpstrj
+
+#dump		2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
+
+thermo_style    custom step c_1_press[1] c_1_press[2] c_1_press[3]
+
+thermo		50
+run		10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.62256
+  ghost atom cutoff = 1.62256
+  binsize = 0.811281, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton/tri
+      stencil: half/bin/3d/newton/tri
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes
+Step c_1_press[1] c_1_press[2] c_1_press[3] 
+       0    6.3937851    7.0436438    6.4461087 
+      50    7.9020345     7.303289    14.733929 
+     100    8.3214325     8.385843    13.166247 
+     150    5.7168419    5.6083988    9.7224198 
+     200    3.8875348    4.0840705    7.9912973 
+     250    4.2933724    4.2410519    7.7200953 
+     300    4.5452314    4.2434949    8.6709832 
+     350     5.446489    5.6166962    11.300536 
+     400    6.0682558    5.7787878    12.106852 
+     450    5.3884296    5.5066688    9.9100012 
+     500    4.8046418    4.7115986    9.9769201 
+     550    4.9043933    4.6240966     9.319336 
+     600    4.6843238    4.9571246    9.5325487 
+     650    5.1952989     5.195648    9.6187047 
+     700    5.4163364    5.2938289    10.136655 
+     750    5.6723178    5.0670261    11.415221 
+     800    5.9379901    5.6402916    10.815209 
+     850    5.0695389    5.3021432    10.742859 
+     900    4.6498962    4.7111912    9.8453523 
+     950    4.4811641     5.170132     9.421765 
+    1000    4.7501483    4.2420772    9.3510803 
+    1050    4.5973379    5.2046799    9.8632975 
+    1100    4.7879562    4.9051316    9.8658626 
+    1150    5.0528771    5.5048545    10.110913 
+    1200    4.9926563    5.2482081    9.9610863 
+    1250    4.8476232    4.8498859    9.5752989 
+    1300    5.2932038    5.0594534    10.869545 
+    1350    5.4720421    5.0830442     10.69386 
+    1400    4.8175566    4.9863651    10.041898 
+    1450    4.6307145    4.5615459     9.231299 
+    1500    5.0296259    4.5433558    8.7180513 
+    1550    4.8708444    5.1601014    10.256791 
+    1600    5.5098593     5.316773    10.224386 
+    1650    5.5055907    5.0516814    10.272037 
+    1700    4.6965552    5.2436628    9.8272905 
+    1750    5.0212307     4.740601    8.9738802 
+    1800    4.7756351     5.199734    9.9929449 
+    1850    4.7107092     5.177203    10.580427 
+    1900    5.0935608    4.5286844    9.3036832 
+    1950    4.8035855     4.894359    9.4423987 
+    2000    4.5643937    4.7480477    9.4384251 
+    2050    4.9314701     4.990414    10.151815 
+    2100    5.9828824    5.8188026    12.262691 
+    2150    5.5337303    5.4598468    10.136112 
+    2200     4.892172    4.8699674    9.1629905 
+    2250    4.5680591    4.5740533    9.5633545 
+    2300    5.0023535    4.3948659    8.9645774 
+    2350    5.2533056    4.9803884    10.255653 
+    2400    5.3330196    5.3888322    10.021617 
+    2450    5.2095527    4.8765336    10.135381 
+    2500     5.221153    5.2974568      10.2493 
+    2550     5.385331    5.0801192    10.490479 
+    2600    5.3274988    5.0253548    10.147587 
+    2650     4.718677    5.2710337    9.7549521 
+    2700    4.5811521    4.6083971    8.1923164 
+    2750    4.4743752    4.3319737    8.8690805 
+    2800    5.0215013    5.2262961    9.8627954 
+    2850    6.1005107    5.5994942    11.170661 
+    2900    5.9673524     5.362124    10.401699 
+    2950    5.5400849    5.7523993    10.292536 
+    3000    4.9202636    5.1210431    10.125839 
+    3050    4.5286487    5.3586164    9.8634322 
+    3100    4.5719961    5.1615414    9.8027972 
+    3150    5.4091919    4.8581943      9.96938 
+    3200     5.522125    5.3564838    9.7638407 
+    3250    4.9019062    5.2514758    9.2993079 
+    3300    5.2375918    5.1439012    9.4313575 
+    3350     4.750235    4.8692016     10.54193 
+    3400    5.5793211    5.4184157    11.021389 
+    3450    4.9022614    5.3166498    9.4629659 
+    3500    4.6348617    4.4650979    9.0665548 
+    3550    4.7922405    4.8961269    10.255446 
+    3600    4.8914457    5.1158894    9.4736084 
+    3650     5.062771    4.6725475    10.263484 
+    3700    5.4842823    5.7793971    10.342915 
+    3750    5.3136012     5.063065    10.398307 
+    3800    4.9372149    4.9270414    9.5304748 
+    3850    5.2144752    5.1716455    9.7575725 
+    3900    5.0892665    5.1697057     9.918052 
+    3950    5.1124507     5.354702     9.791366 
+    4000    5.1255084    5.1143653    10.913101 
+    4050    5.1891698    4.9913681    9.6871728 
+    4100    4.7663368    4.2435014    8.3815668 
+    4150    4.8060033    4.3415868    9.6553386 
+    4200    4.8548303    4.8006768    9.5995801 
+    4250    5.0976366    5.2683175    10.386444 
+    4300    5.8921937    5.5134696    10.788143 
+    4350    5.8323871    5.5255869    11.199128 
+    4400    5.2464655    5.0005905    10.311055 
+    4450    4.9264849    5.2499854     10.26702 
+    4500    4.4431895     4.536981    8.7489096 
+    4550    4.5180914    4.2080277    8.6525529 
+    4600    5.1782188    5.1224059    10.683341 
+    4650    5.4156233    4.8714464    10.473939 
+    4700    5.3107669     5.224614    10.569391 
+    4750    4.9538022    5.2509475    10.288918 
+    4800    4.6976945    4.8107142    9.8299772 
+    4850    5.1227936    5.0737571    10.440452 
+    4900    4.7580514    4.6375995    9.1971008 
+    4950    5.0647601    4.6470735     9.583131 
+    5000     5.196231    5.7531491    10.409807 
+    5050    5.6691323    5.7163652    12.335701 
+    5100    5.3603738    5.4887106    10.961712 
+    5150     4.455028    4.6494465    9.8096968 
+    5200    4.7596912    4.4804896    9.3762885 
+    5250    5.3144927    5.0113772     9.553101 
+    5300    5.3445266    4.8262035    9.1220802 
+    5350    5.1540657    5.5982676    10.765178 
+    5400    5.1773418    5.2684381    10.452351 
+    5450    4.8946859    5.3283747    9.8015564 
+    5500    5.2009608    4.7183522    9.4558009 
+    5550    5.4158589    5.5005458    10.539505 
+    5600    4.7196831    5.4181991    9.6439249 
+    5650    4.8333571    4.8601728    8.9350189 
+    5700    5.4395698    4.9730096    10.669681 
+    5750    5.2947443    5.6973259    10.020539 
+    5800    5.4391993    5.5255143    10.264969 
+    5850    4.9921388    5.2643827    10.217028 
+    5900    5.0048643    4.7952641    8.9718929 
+    5950    5.1843818    4.5987295    9.6858944 
+    6000    5.0343993     4.946933    9.7436708 
+    6050    4.6202714    5.3502658    10.752915 
+    6100    5.6914422    5.3621964    10.281827 
+    6150    5.1928763    5.9652686    10.923881 
+    6200    5.0030409    5.2013891    10.056308 
+    6250    4.9699876    5.2363753    9.9964211 
+    6300    4.9129606    4.4558458    9.0419952 
+    6350    4.6623958    4.4078264     8.528649 
+    6400    4.9811441    5.1183207    10.261751 
+    6450    5.3644017    5.5153937    10.401295 
+    6500    5.6674981    5.7427566    11.928777 
+    6550    5.1622364    5.3212928    10.067198 
+    6600    4.5954278    5.1645397     10.16724 
+    6650    4.9192712    5.0413326      9.95656 
+    6700    4.6179845    4.5656214    9.3798952 
+    6750    4.7287495    4.5071148    8.7890116 
+    6800    4.8600442    4.8083512    10.245595 
+    6850    5.0515531    5.1609272    10.553855 
+    6900    5.1159742    5.1359869    10.594699 
+    6950    4.8908884    5.0592418    9.5698704 
+    7000    4.7654136    4.7530776    8.9439321 
+    7050     4.779293    4.7534957    9.7244349 
+    7100    5.2265831    5.6869073     10.32717 
+    7150    5.4019177      5.15174    10.457567 
+    7200    4.9817102    5.0596098    10.337574 
+    7250    5.1836654    5.6065238    10.723108 
+    7300    4.2916569     4.457143    8.5419099 
+    7350    4.3906104    4.5439294    9.0805415 
+    7400     4.998572    5.3386063    10.491418 
+    7450    5.1109022    5.0506801    10.636116 
+    7500    5.0248381     5.019932    10.217023 
+    7550    5.0109265    5.1438717    9.9032426 
+    7600    4.6628614    4.6204146    8.9459669 
+    7650    4.8930717    5.0650009    10.049331 
+    7700    4.9373454    5.6265835    10.210644 
+    7750    5.5001067    5.3133253    10.667995 
+    7800    5.0816102    5.0125753    10.591986 
+    7850    4.9638046    5.1969015    9.9728333 
+    7900    4.8438207    4.9217213    8.9978809 
+    7950    4.7318805    4.6248537    8.6806596 
+    8000    5.2808543    5.2892613    10.932535 
+    8050    5.9609722      5.87087     10.47602 
+    8100    5.2190231    5.6693244    11.244536 
+    8150    5.3481127    5.2849903    10.222845 
+    8200    4.7833053    4.7404657    9.2034474 
+    8250    4.5461994     4.510467    10.294452 
+    8300    4.6025175    4.8332817    8.7967546 
+    8350    5.0389897    5.6642908    10.243402 
+    8400    4.8414338    4.8925143    9.3653631 
+    8450    5.5087429    4.7830361    10.831666 
+    8500    5.2678146    5.1697789    9.9105782 
+    8550    5.1211843    4.9097801    9.4165956 
+    8600    5.8239149    5.0821022    10.803261 
+    8650    5.3620154    5.5831747     11.16202 
+    8700    5.1625813    4.8791404    10.537681 
+    8750    4.5622461    5.0157549    10.013227 
+    8800    4.4051517    5.0224553    9.6364273 
+    8850    4.1711629     4.635617    8.5470244 
+    8900    4.7049907    5.2458435    10.100728 
+    8950    4.8568883    5.2360772    9.2306469 
+    9000    5.0091899    5.2203574    10.718541 
+    9050    5.1037824    4.9022451     10.24271 
+    9100    5.0789015    4.9331454     9.173614 
+    9150    5.3865455    5.3427553     11.40199 
+    9200    5.5089482    5.9423232    10.976063 
+    9250    5.1353552    5.0650262    10.040607 
+    9300    4.6761948    4.9155175    9.6413722 
+    9350    4.4780834    4.3934708    8.7049819 
+    9400    4.2561799    4.7906324     9.046134 
+    9450    5.6162819    5.2881846    9.9040868 
+    9500    5.7554547    5.6111262     10.23849 
+    9550    5.4230462    5.5656045    10.908006 
+    9600    5.5045685    4.9818892    9.8929535 
+    9650    5.0541481    5.0183351    9.5226021 
+    9700    4.9712829    5.2395398    9.9996693 
+    9750    5.0960017    5.4419775    10.914719 
+    9800    5.0790688    5.6378474     10.00789 
+    9850    4.9661747     5.114502    9.4585052 
+    9900    5.0133498    4.7456254    9.4572653 
+    9950    5.3318846    4.6643122    10.096292 
+   10000    5.2227687    4.8924305    9.5894615 
+Loop time of 4.78247 on 1 procs for 10000 steps with 500 atoms
+
+Performance: 903298.340 tau/day, 2090.968 timesteps/s
+99.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.73894    | 0.73894    | 0.73894    |   0.0 | 15.45
+Neigh   | 2.9092     | 2.9092     | 2.9092     |   0.0 | 60.83
+Comm    | 0.32306    | 0.32306    | 0.32306    |   0.0 |  6.76
+Output  | 0.003392   | 0.003392   | 0.003392   |   0.0 |  0.07
+Modify  | 0.6959     | 0.6959     | 0.6959     |   0.0 | 14.55
+Other   |            | 0.112      |            |       |  2.34
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    905 ave 905 max 905 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3340 ave 3340 max 3340 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3340
+Ave neighs/atom = 6.68
+Neighbor list builds = 4580
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04
--- a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4
+++ b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4
@ -0,0 +1,284 @@
+LAMMPS (22 Sep 2017)
+# biaxial NPT deformation of WCA fluid
+
+units		lj
+atom_style	atomic
+
+
+pair_style	lj/cut 1.122562
+read_data       data.wca
+  orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  500 atoms
+  reading velocities ...
+  500 velocities
+pair_coeff	1 1 1.0 1.0
+pair_modify     shift yes
+
+neighbor	0.5 bin
+neigh_modify	delay 0
+
+change_box      all triclinic
+  triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0)
+
+# these commads show the different methods that may be used to impose
+# a constant stress through isotropic or anisotropic coupling
+fix		1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z
+#fix		1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5  erate 0.5 0.5 ext xyz
+
+fix             2 all momentum 100 linear 1 1 1
+
+#dump		1 all atom 25 dump.lammpstrj
+
+#dump		2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
+
+thermo_style    custom step c_1_press[1] c_1_press[2] c_1_press[3]
+
+thermo		50
+run		10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.62256
+  ghost atom cutoff = 1.62256
+  binsize = 0.811281, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton/tri
+      stencil: half/bin/3d/newton/tri
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.71 | 2.71 | 2.71 Mbytes
+Step c_1_press[1] c_1_press[2] c_1_press[3] 
+       0    6.3937851    7.0436438    6.4461087 
+      50    7.9020345     7.303289    14.733929 
+     100    8.3214325     8.385843    13.166247 
+     150    5.7168419    5.6083988    9.7224198 
+     200    3.8875348    4.0840705    7.9912973 
+     250    4.2933724    4.2410519    7.7200953 
+     300    4.5452314    4.2434949    8.6709832 
+     350     5.446489    5.6166962    11.300536 
+     400    6.0682558    5.7787878    12.106852 
+     450    5.3884296    5.5066688    9.9100012 
+     500    4.8046418    4.7115986    9.9769201 
+     550    4.9043933    4.6240966     9.319336 
+     600    4.6843238    4.9571246    9.5325487 
+     650    5.1952989     5.195648    9.6187047 
+     700    5.4163364    5.2938289    10.136655 
+     750    5.6723178    5.0670261    11.415221 
+     800    5.9379901    5.6402916    10.815209 
+     850    5.0695389    5.3021432    10.742859 
+     900    4.6498961    4.7111912    9.8453524 
+     950    4.4811637    5.1701321    9.4217645 
+    1000     4.750149    4.2420768    9.3510788 
+    1050    4.5973376    5.2046787    9.8633025 
+    1100    4.7879517    4.9051339    9.8658578 
+    1150    5.0528775    5.5048671    10.110905 
+    1200    4.9926841    5.2482049    9.9610519 
+    1250    4.8475836    4.8499116    9.5753651 
+    1300    5.2930219    5.0593566    10.869335 
+    1350    5.4722342    5.0830411    10.693439 
+    1400    4.8165803    4.9851498     10.04213 
+    1450    4.6276458    4.5642988    9.2306141 
+    1500    5.0196773    4.5470773    8.7204145 
+    1550     4.878246    5.1583406    10.263895 
+    1600    5.4921049    5.3126759    10.274755 
+    1650    5.4363266    5.1708866    9.9880665 
+    1700    4.9186005    5.2841155    9.5911223 
+    1750    4.9105668    4.7112031    8.9221295 
+    1800    4.9833291     4.886821    9.6573393 
+    1850    5.0729703    4.8331712    10.094971 
+    1900    5.7220173    5.9330299    10.580261 
+    1950    5.3176022    5.7140521     11.11604 
+    2000    5.3247727    5.5172893    10.622834 
+    2050    5.2055235    4.8768078    9.9819356 
+    2100    4.4604981    4.1427844    7.8106592 
+    2150    4.4406592    4.8264893    9.6662695 
+    2200    5.2350836    5.1039145     10.36006 
+    2250    5.3777857    5.3274609    11.357157 
+    2300    5.4888334    5.9555482     10.76346 
+    2350    4.6122564    4.7356468    9.0833059 
+    2400    4.6670237    4.4895588    9.0619648 
+    2450    4.2201177    4.2558397    9.4898835 
+    2500     5.452448    5.4336384     10.50224 
+    2550     5.012581     5.316158    10.324517 
+    2600    5.0880279    5.1264772    10.085103 
+    2650    4.8885834    5.2368982    9.6002032 
+    2700    5.1549266    5.3419678    11.335447 
+    2750     5.497105    5.3643445    9.9990393 
+    2800    4.8826744    4.9875712    10.125435 
+    2850    4.8617121    5.1282348    9.5629401 
+    2900    4.7883446    4.6187804    9.0562496 
+    2950    4.7656266    5.1293592    10.693811 
+    3000    5.2676745     5.110172    9.3512146 
+    3050    4.5749222    4.8413907    10.311305 
+    3100    5.0794819     5.265009    9.1598496 
+    3150    5.2078869    5.1879882    10.412548 
+    3200    5.0187616    4.6226213    9.7266174 
+    3250    5.1541897    4.5157063    9.8355764 
+    3300    5.0721396    5.3545282    10.174356 
+    3350    5.3984495    5.3222207    10.008886 
+    3400    5.1263226    5.1189192    10.361534 
+    3450    5.1251845    4.8312752    9.6546597 
+    3500    5.1133696    5.2646289    10.320765 
+    3550    4.9884235    5.3861707    9.1944042 
+    3600     5.196909     5.203186    10.085965 
+    3650    5.4717592    5.2205442    10.251283 
+    3700    5.4429771    5.3027898    11.385714 
+    3750    5.5688484    5.5980199    10.558193 
+    3800    4.5239453    4.7021545     8.952588 
+    3850    4.6438079    4.6409958    9.3890154 
+    3900    5.1108473    4.8787691    10.665694 
+    3950    5.6398426    5.4386578    10.668189 
+    4000     5.063697    4.9663173    10.513266 
+    4050    4.8770847    4.4603573    9.8101845 
+    4100    4.3950768    4.3579384    8.3402845 
+    4150    4.3355402    5.0429352    10.323111 
+    4200    4.7688478     5.051487    9.0632339 
+    4250    4.9879366    5.3367146    10.409554 
+    4300    5.4578199    5.4889206    10.418789 
+    4350    5.6598068    5.4538572    10.842349 
+    4400    5.3705312    5.3796871    10.430547 
+    4450     4.663804     5.058851    9.2705923 
+    4500    4.3439039    4.3523422    8.1747925 
+    4550    4.5414802    4.3750772    9.2702452 
+    4600    4.9216199    5.2897069    10.747727 
+    4650    5.5154852    5.9628437      10.5168 
+    4700      5.45199     5.382787    10.654544 
+    4750    4.7525419    5.4701385    9.3189378 
+    4800    5.3696365    4.6134207    9.4455676 
+    4850    5.2444123     5.035993    9.4148435 
+    4900    5.6006507    4.8536828    10.283579 
+    4950     5.155711     4.978634     10.58973 
+    5000    5.0854607    4.9853307    9.2414296 
+    5050    5.1098462    4.7349164    9.8739001 
+    5100    5.1989395    5.0217416    9.8780949 
+    5150     5.612116    5.2165007    10.338464 
+    5200    5.0571356    5.3109846    10.685262 
+    5250    5.4832657    5.0371665    8.9420853 
+    5300    4.5312549    4.9629392    8.2478064 
+    5350    5.1617038    5.0533699    10.452218 
+    5400    5.7873394    5.6776926    11.926526 
+    5450    5.7002516     5.243239    10.940265 
+    5500    4.7896799     4.898544    10.163856 
+    5550    4.9155627    4.9567495    9.4445476 
+    5600    4.2447343    4.5045912    8.7732992 
+    5650     5.070197    4.7343938    9.9908239 
+    5700    4.9609446    5.0901934    10.812786 
+    5750    5.4001631    5.5552888    10.085896 
+    5800    5.4209837    4.7153245    9.6865245 
+    5850    4.9801041     5.180338    9.8930439 
+    5900    5.3423595    5.2341361    10.294159 
+    5950     5.683047    5.6830131     10.24313 
+    6000    5.0618789    5.4533644    10.713412 
+    6050    5.4034888    4.6341621    10.031976 
+    6100    5.1934299    4.7525347    9.1287151 
+    6150    5.0092398     4.806931    10.024305 
+    6200    5.3046516    5.3083532    9.6396223 
+    6250    5.2824046    4.7957557    10.305279 
+    6300    5.3007029    5.0071874    11.175322 
+    6350    5.1128883     4.990408    9.3439118 
+    6400    5.0543602    4.9971378    9.8259954 
+    6450    4.8843692    4.9116343     10.08132 
+    6500    4.5966453    4.8042861     9.160272 
+    6550    4.8510961    4.7096646    9.8009968 
+    6600     5.658307    5.2330511    10.739519 
+    6650    5.2374409    5.3241249    10.291779 
+    6700    4.9006975    5.0036186    9.9872029 
+    6750    5.2209104    5.1826025    9.5671875 
+    6800    4.5238727    4.3070529    8.6072303 
+    6850    4.2617247    4.7551571    9.7302077 
+    6900    5.6499354    4.8714257    10.723511 
+    6950    5.6881769    5.1800721     10.18134 
+    7000     5.588834    5.0104896    10.304105 
+    7050    4.9404045    4.8589121    9.7096741 
+    7100    5.2208179    4.9339808    9.7737491 
+    7150    5.4507842     5.046485    10.734783 
+    7200    4.9737171    5.5760486    9.1627431 
+    7250    4.5967409     4.750471     9.315832 
+    7300    5.5147308    5.3202861    10.542679 
+    7350    5.7730418    5.5363574    10.384376 
+    7400    4.9879586    5.2837443    9.4485798 
+    7450    5.1862431    4.8357842    10.017598 
+    7500    5.4528245    5.1864957    10.941774 
+    7550    5.4202434    5.1089468    10.128264 
+    7600    4.8063537    4.8723653    9.0364984 
+    7650    4.3144701    4.6148377    9.4939315 
+    7700    4.9033831    5.5327473    9.9054613 
+    7750    5.0693093    5.0768222    10.473081 
+    7800    5.0591805    5.6009473    10.006225 
+    7850      5.15269     5.468248    10.404619 
+    7900    5.1971759    5.0615117    9.9614488 
+    7950    4.9771238     4.886213    9.4730722 
+    8000    4.7731123    5.1111433    9.9550597 
+    8050    5.1655183    5.4432364    9.6649669 
+    8100    5.4597006    5.4026039    11.631184 
+    8150    5.3229643    5.4394219    9.9830611 
+    8200    4.5420712    4.9359646    9.0121988 
+    8250    4.5455108    4.3883996    10.304568 
+    8300     5.219721    5.1571958    10.305462 
+    8350    4.7291561    4.7391636    9.0768372 
+    8400    5.3262934    5.8221591    11.065466 
+    8450    4.7583026    5.2282086    10.291955 
+    8500    4.9174536    4.5701979    10.140444 
+    8550     4.459922    4.8293188    9.4438719 
+    8600    4.7962584    4.5811071    9.5158666 
+    8650    4.6097275     4.431952    9.4350505 
+    8700     5.166554    5.2000584    11.162202 
+    8750    5.2353596    5.1668944    10.829751 
+    8800    5.3150111    4.9983333    9.8402224 
+    8850    4.9571197    4.9196589    9.4880549 
+    8900     4.902223    4.7539187    10.002425 
+    8950    4.9531983    5.0517321    9.7838444 
+    9000    5.4003802    4.9900303    10.550808 
+    9050    4.9254643    5.0678701     10.24321 
+    9100    4.9902263    4.9056928    9.0326566 
+    9150    5.1003677    5.1555374    10.049056 
+    9200    5.2358131    5.5834504    10.354698 
+    9250    5.5781649    5.1188429    10.361369 
+    9300    5.2100192    5.0737267    10.074694 
+    9350    5.1462976    4.8010759    9.0279769 
+    9400    5.0177693    5.4890092     10.03612 
+    9450    5.2507957     5.541141    10.639854 
+    9500     5.836784    4.9498236    10.288015 
+    9550    5.4698183    5.8761209    10.979924 
+    9600    5.0534023    5.0043428    10.436057 
+    9650    4.3619773    4.5413125     9.047513 
+    9700    4.3777508    4.7902251    8.9501908 
+    9750    4.6851974    4.3152085     8.825764 
+    9800    5.7312665     4.850913    10.247637 
+    9850    6.2290614    5.5480801    10.934907 
+    9900    6.0316892    6.1098926    11.562223 
+    9950    5.6370814    5.3933342    11.148805 
+   10000    4.6429923    5.0853156    9.4267693 
+Loop time of 3.06414 on 4 procs for 10000 steps with 500 atoms
+
+Performance: 1409858.531 tau/day, 3263.561 timesteps/s
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.27954    | 0.30916    | 0.3866     |   8.1 | 10.09
+Neigh   | 1.0657     | 1.129      | 1.2853     |   8.5 | 36.85
+Comm    | 0.56334    | 0.80526    | 0.89816    |  15.6 | 26.28
+Output  | 0.0032749  | 0.0041527  | 0.006541   |   2.1 |  0.14
+Modify  | 0.6522     | 0.67016    | 0.69843    |   2.1 | 21.87
+Other   |            | 0.1464     |            |       |  4.78
+
+Nlocal:    125 ave 130 max 122 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Nghost:    459.75 ave 470 max 448 min
+Histogram: 1 0 0 0 0 1 1 0 0 1
+Neighs:    837 ave 867 max 811 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 3348
+Ave neighs/atom = 6.696
+Neighbor list builds = 4589
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
--- a/examples/USER/uef/nvt_uniaxial/data.wca
+++ b/examples/USER/uef/nvt_uniaxial/data.wca
--- a/examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial
+++ b/examples/USER/uef/nvt_uniaxial/in.nvt_uniaxial
@ -0,0 +1,28 @@
+# uniaxial NVT deformation of WCA fluid
+
+units		lj
+atom_style	atomic
+
+
+pair_style	lj/cut 1.122562
+read_data       data.wca
+pair_coeff	1 1 1.0 1.0
+pair_modify     shift yes
+
+neighbor	0.5 bin
+neigh_modify	delay 0
+
+change_box      all triclinic
+
+fix		1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5
+
+fix             2 all momentum 100 linear 1 1 1
+
+#dump		1 all atom 25 dump.lammpstrj
+
+#dump		2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
+
+thermo_style    custom step c_1_press[1] c_1_press[2] c_1_press[3]
+
+thermo		50
+run		10000
--- a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1
+++ b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1
@ -0,0 +1,281 @@
+LAMMPS (22 Sep 2017)
+# uniaxial NVT deformation of WCA fluid
+
+units		lj
+atom_style	atomic
+
+
+pair_style	lj/cut 1.122562
+read_data       data.wca
+  orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  500 atoms
+  reading velocities ...
+  500 velocities
+pair_coeff	1 1 1.0 1.0
+pair_modify     shift yes
+
+neighbor	0.5 bin
+neigh_modify	delay 0
+
+change_box      all triclinic
+  triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0)
+
+fix		1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5
+
+fix             2 all momentum 100 linear 1 1 1
+
+#dump		1 all atom 25 dump.lammpstrj
+
+#dump		2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
+
+thermo_style    custom step c_1_press[1] c_1_press[2] c_1_press[3]
+
+thermo		50
+run		10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.62256
+  ghost atom cutoff = 1.62256
+  binsize = 0.811281, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton/tri
+      stencil: half/bin/3d/newton/tri
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes
+Step c_1_press[1] c_1_press[2] c_1_press[3] 
+       0    6.3937851    7.0436438    6.4461087 
+      50    10.369902    10.999889    6.5437384 
+     100    12.411384    13.145871    7.8892802 
+     150     12.88182    12.114068    7.5155182 
+     200    10.375571    10.979773    6.5624056 
+     250    10.158901    10.251273    5.4525068 
+     300    10.011314    9.8371382    5.4031393 
+     350    9.4890008    9.7992108     5.054963 
+     400    9.1715116    9.2647886    4.9600208 
+     450    9.8495961    9.3353483     4.986786 
+     500    9.5903809     8.576173    4.8252116 
+     550    8.8057509    9.7152078    4.9089022 
+     600    8.9743682    10.031277    4.8924072 
+     650    10.233852    9.3059527    5.1977058 
+     700    9.2361906    9.6439971    5.0923763 
+     750    10.449751    9.5911465    5.2548714 
+     800    9.8366857    9.9873885    4.9456956 
+     850    10.266351    9.9620134    5.0602713 
+     900    9.6325813    9.3910946    5.1466624 
+     950    9.1911919    9.1519006    4.8275345 
+    1000    9.2871712    9.8508501    5.2674099 
+    1050    9.7052035    10.291793     5.160359 
+    1100    9.9425552    10.361827    5.5520484 
+    1150    10.377563     10.26588    5.5997436 
+    1200    9.6368269    10.354413    5.4137873 
+    1250    9.2071055    9.1706334    4.9800411 
+    1300    9.7140516    8.7257777    4.8536943 
+    1350    10.145983    9.8247797    4.8921813 
+    1400    9.1998975    9.6935675    5.2269871 
+    1450    9.4838136    8.9035726    4.6867121 
+    1500     9.066389     9.811658    4.8875316 
+    1550    10.007083    9.8946118     5.204609 
+    1600     9.722137    9.9291588     5.326712 
+    1650    9.7424614    9.6995966    5.3577819 
+    1700    9.7185135    9.5922931     5.385856 
+    1750    9.6368481    8.1414594    5.0046079 
+    1800    9.8065782    9.6798036      4.92473 
+    1850    9.0463737    10.024205    5.6495695 
+    1900    9.0774484    10.527582    5.0363426 
+    1950    9.1691461    10.049703    4.8517514 
+    2000    9.7619602    10.049532    5.2088038 
+    2050    9.9203348    9.8056395    5.7699852 
+    2100    9.1455665    9.5864018    5.1410542 
+    2150    8.8501135    9.7917307     5.141824 
+    2200    9.1433685    9.8168548    5.1742441 
+    2250    9.3248968    10.454532    5.5456356 
+    2300    10.210505     9.361499    5.0935226 
+    2350    9.5041186     9.598986    5.2451005 
+    2400     8.968896    9.2811921    4.7799868 
+    2450    9.8201159    10.133892    4.9981817 
+    2500    9.4421084    9.7875766    5.4124809 
+    2550    9.6410643    9.9148309    5.0603288 
+    2600    9.3810676    9.5346849    5.3233836 
+    2650    9.2340337    8.7233538    5.0361302 
+    2700     9.405597    9.7848488    4.7537042 
+    2750    9.9447412    9.2366502    4.9736459 
+    2800    10.189443     9.452684     5.624362 
+    2850    9.6680124    9.0941543    5.0101469 
+    2900    8.4350889    9.1595018    4.7706866 
+    2950    9.0056117    9.3498593    4.7655963 
+    3000    9.4795416    9.7400747    5.4705868 
+    3050    9.6605264    9.4558374    5.1240166 
+    3100     9.681451    9.7966554    5.3174458 
+    3150    9.7887528    9.7371194    4.9349103 
+    3200    9.9720054    9.5592538    5.2306417 
+    3250    10.185023    9.9436037    5.4127312 
+    3300    9.9670676    9.6069307     5.026261 
+    3350    9.0090411    9.5975249    4.8881019 
+    3400    9.6535707     9.748683    4.9933873 
+    3450    9.7774977    9.7570511    4.8512619 
+    3500    9.7250053     10.36386    5.4057249 
+    3550     9.567788     9.773413    5.3936671 
+    3600    9.2094148    9.0211247    5.2328675 
+    3650    9.3512098      9.73407     4.576624 
+    3700     9.159074    9.2611591    5.2996448 
+    3750    9.4772798    8.9792211    5.1007079 
+    3800    9.3898357    9.1150609    5.2126508 
+    3850    9.2466312    9.1460651     4.867472 
+    3900    9.9316993    9.3061137    5.1219265 
+    3950    9.2550913     9.780254     5.371885 
+    4000    10.005356    9.7328972    5.2535791 
+    4050    9.5228242    9.5134113    5.4181393 
+    4100     9.576808    10.082425    5.1272491 
+    4150     10.20265    9.6667058     5.529118 
+    4200    9.9443671     10.09427    5.6163734 
+    4250    9.4956875    9.9462818    5.0820085 
+    4300    10.350144    10.003702    5.1621505 
+    4350    10.119486    9.8691507    5.4913457 
+    4400    9.4991604    10.516185    5.2512264 
+    4450    9.0812854    9.2835603    5.1695714 
+    4500    9.7538478    8.5298834    4.5954607 
+    4550    9.8920394    9.3581299     5.202587 
+    4600    9.2694921    9.3338291     5.201958 
+    4650    10.925818    9.5062049    4.8694531 
+    4700    11.020014    10.130224     5.582409 
+    4750    9.5005142    9.3571561     5.456739 
+    4800    9.6670147    9.6628702    5.0451252 
+    4850     9.134147    9.1308788    4.7950594 
+    4900    9.7466206    8.6171443    4.8716275 
+    4950    9.0397505    9.1996036    5.2010502 
+    5000    9.6898652    9.8914655    5.3959279 
+    5050     10.06771    9.7523891    5.3690408 
+    5100    10.000963    9.6279379    5.4077384 
+    5150    9.8686159    10.179702    5.0686824 
+    5200    9.8866247     9.725152    5.4350049 
+    5250    9.2068346    10.214424    5.3187713 
+    5300     9.713992    9.8069045     5.496359 
+    5350     9.423852     9.364085    5.2144606 
+    5400    9.4350241    9.5584633    5.0339001 
+    5450    10.555124    10.784922    5.1938072 
+    5500    9.4147344     10.33187    5.4360602 
+    5550    9.8514653    9.6575827    5.4959779 
+    5600    9.3138107    9.6592624     4.941387 
+    5650    9.1224809    8.7112257    5.0435936 
+    5700    8.8289158    10.749686    4.8916132 
+    5750    9.7200279    10.030606    5.2033161 
+    5800    9.8439873    9.6289015    5.5131934 
+    5850    9.6257294    9.4128988    4.9196038 
+    5900    9.7490214    9.5776313    5.0301815 
+    5950    9.1430855    10.108944    5.1406243 
+    6000    9.3358644    9.5633737    4.9787073 
+    6050    9.4432774    8.9464304    5.1466052 
+    6100    8.8878373    9.5048946    4.9190238 
+    6150    9.6451898    9.2419823    5.0159841 
+    6200    9.5042173    8.9414307    5.2634247 
+    6250    9.0896505    9.7230651    5.3340322 
+    6300    8.8100599    8.8781352    5.4117914 
+    6350    9.3104601    9.0233294    5.3136432 
+    6400     9.368101    9.6387362    4.7833216 
+    6450    10.334343    9.8384149    5.3606204 
+    6500    9.8824036    10.022627    6.0857086 
+    6550    9.7034443    10.026765      5.17604 
+    6600    9.3757845     9.899268    5.2301359 
+    6650    10.540821      10.4343    5.5287065 
+    6700    9.6317649    9.8923579    5.6045768 
+    6750    9.5982772     10.07897    5.1221451 
+    6800    10.239883    10.189967    5.3167447 
+    6850    10.017271    9.7680902     5.229621 
+    6900    9.6200416    10.129301    5.1998759 
+    6950    9.0361417     8.923798    5.1652612 
+    7000    9.3153521     9.063054    4.6860773 
+    7050    8.6434091    9.0363436    4.7811975 
+    7100    9.4955395    9.3830541     5.022538 
+    7150    9.3392402    9.1847119    5.1544622 
+    7200    9.4676321    9.8370036    4.8854442 
+    7250    9.5115882    10.350324    4.9780525 
+    7300    9.6025583    9.6247917     5.473794 
+    7350    9.8919524    10.049446    4.9816931 
+    7400    9.6814319    9.9410894     5.265078 
+    7450    9.4130955    10.191436    5.2531256 
+    7500    9.8114668    8.8461635    5.0562894 
+    7550    10.321567    9.4730124    5.2043655 
+    7600    9.5059024    9.8330367    5.0749721 
+    7650    10.067084    10.606423    5.5598818 
+    7700    10.896159    10.084281    5.5159718 
+    7750     9.754306    10.162301    5.2475876 
+    7800    9.7278145     9.801009    5.0685504 
+    7850    9.8639905    10.323104    5.2458864 
+    7900    9.7246799    9.1377357    5.1841319 
+    7950    10.381792    9.6977533    5.0977386 
+    8000    9.7265224    9.2999829    4.7925571 
+    8050    9.5203288    9.3144956    4.7539211 
+    8100    9.6900973    9.6614063     5.304712 
+    8150     9.713677    9.9154149    4.8178575 
+    8200    9.4733597    9.8948632     5.036112 
+    8250    9.7783036    9.9554334    5.3355682 
+    8300    9.4034783    9.9156801    5.5539279 
+    8350    9.2984025    9.2013949    5.0753991 
+    8400    9.9299078    9.6166801     5.115776 
+    8450     9.526737    9.3312125    4.7800587 
+    8500     9.581956    10.065906    4.9756092 
+    8550    9.2767953     9.326006    5.3024978 
+    8600     9.799968    8.4660845    5.0199109 
+    8650    9.8985354    10.127852    4.9098064 
+    8700    8.7952691    10.521133    5.6840528 
+    8750    9.8299997    9.5588553    5.3085734 
+    8800    9.0811776    9.5704532    5.1684993 
+    8850    9.8303571    9.7618932    5.1251259 
+    8900    9.9238794    9.9654863    5.2999683 
+    8950    10.851304    9.9682289    5.4133763 
+    9000    9.5523794    9.1890766    5.1469144 
+    9050    9.7461948    8.9611236    4.9490826 
+    9100    10.138917    9.6757567    5.0473544 
+    9150    9.4869835    9.4786575    5.0142464 
+    9200    10.263518    10.079135    5.1493398 
+    9250    9.8691684    9.0908275    5.3221203 
+    9300    9.8586707    9.4177643    5.1525265 
+    9350    9.3375816    9.9167208    5.4846207 
+    9400    9.5603903    9.4813199    4.6237495 
+    9450     10.30892    9.5217736    5.6163214 
+    9500     9.327949    9.9831649    4.8923915 
+    9550    9.8421656    9.3202702    5.3352046 
+    9600    8.8543704    9.4556702    4.6430041 
+    9650    10.103399    9.2161072    4.8658062 
+    9700     9.507811    9.9647378     5.227369 
+    9750    9.4988096    8.9942893    5.2491418 
+    9800    9.8007958     9.234452    5.1740203 
+    9850    9.6029685    10.076042     5.023107 
+    9900    9.4035691     10.13782    5.2775777 
+    9950    9.6517135    10.355994    5.3035779 
+   10000    9.9157616    9.7741952    5.5269431 
+Loop time of 3.47119 on 1 procs for 10000 steps with 500 atoms
+
+Performance: 1244529.812 tau/day, 2880.856 timesteps/s
+99.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.53077    | 0.53077    | 0.53077    |   0.0 | 15.29
+Neigh   | 2.219      | 2.219      | 2.219      |   0.0 | 63.93
+Comm    | 0.21866    | 0.21866    | 0.21866    |   0.0 |  6.30
+Output  | 0.0027909  | 0.0027909  | 0.0027909  |   0.0 |  0.08
+Modify  | 0.41956    | 0.41956    | 0.41956    |   0.0 | 12.09
+Other   |            | 0.08042    |            |       |  2.32
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    908 ave 908 max 908 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3489 ave 3489 max 3489 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3489
+Ave neighs/atom = 6.978
+Neighbor list builds = 4567
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
--- a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4
+++ b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4
@ -0,0 +1,281 @@
+LAMMPS (22 Sep 2017)
+# uniaxial NVT deformation of WCA fluid
+
+units		lj
+atom_style	atomic
+
+
+pair_style	lj/cut 1.122562
+read_data       data.wca
+  orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  500 atoms
+  reading velocities ...
+  500 velocities
+pair_coeff	1 1 1.0 1.0
+pair_modify     shift yes
+
+neighbor	0.5 bin
+neigh_modify	delay 0
+
+change_box      all triclinic
+  triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0)
+
+fix		1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5
+
+fix             2 all momentum 100 linear 1 1 1
+
+#dump		1 all atom 25 dump.lammpstrj
+
+#dump		2 all cfg/uef 25 dump.*.cfg mass type xs ys zs
+
+thermo_style    custom step c_1_press[1] c_1_press[2] c_1_press[3]
+
+thermo		50
+run		10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.62256
+  ghost atom cutoff = 1.62256
+  binsize = 0.811281, bins = 11 11 11
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton/tri
+      stencil: half/bin/3d/newton/tri
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.71 | 2.71 | 2.71 Mbytes
+Step c_1_press[1] c_1_press[2] c_1_press[3] 
+       0    6.3937851    7.0436438    6.4461087 
+      50    10.369902    10.999889    6.5437384 
+     100    12.411384    13.145871    7.8892802 
+     150     12.88182    12.114068    7.5155182 
+     200    10.375571    10.979773    6.5624056 
+     250    10.158901    10.251273    5.4525068 
+     300    10.011314    9.8371382    5.4031393 
+     350    9.4890008    9.7992108     5.054963 
+     400    9.1715116    9.2647886    4.9600208 
+     450    9.8495961    9.3353483     4.986786 
+     500    9.5903809     8.576173    4.8252116 
+     550    8.8057509    9.7152078    4.9089022 
+     600    8.9743682    10.031277    4.8924072 
+     650    10.233852    9.3059527    5.1977058 
+     700    9.2361906    9.6439971    5.0923762 
+     750    10.449751    9.5911465    5.2548714 
+     800    9.8366858    9.9873885    4.9456956 
+     850    10.266351    9.9620134    5.0602713 
+     900    9.6325811    9.3910947    5.1466627 
+     950    9.1911906    9.1518996    4.8275336 
+    1000    9.2871726    9.8508561    5.2674079 
+    1050    9.7052019    10.291782    5.1603609 
+    1100    9.9425827    10.361848    5.5520588 
+    1150     10.37757    10.265891    5.5997246 
+    1200    9.6367069    10.354451    5.4138749 
+    1250    9.2075006    9.1705136    4.9806417 
+    1300    9.7126123    8.7247301    4.8528533 
+    1350    10.146034    9.8319205    4.8958266 
+    1400      9.19638    9.7052094    5.2332913 
+    1450    9.4667073    8.9014702    4.7073387 
+    1500    9.0949401    9.8381729    4.8904182 
+    1550    10.068959    9.8096692    5.1613658 
+    1600    10.131443    9.7086921    5.0913546 
+    1650    9.9557572    9.9183989    5.2635245 
+    1700    9.3820418    8.6135867    4.9395498 
+    1750    8.9486365    9.3433293    5.2674469 
+    1800    10.352322    10.354432    5.3335153 
+    1850    8.9629784    9.6172224    5.0824828 
+    1900    8.5429652     9.749815    5.1577895 
+    1950    8.9828002    8.9631646    5.0948426 
+    2000    9.4171989    9.7122117    5.1386251 
+    2050     9.767299    9.6146113    4.8965319 
+    2100    10.049399     10.02243    5.3856622 
+    2150    9.2639644     10.09669    5.3020322 
+    2200    9.1916162    10.841127    5.0271109 
+    2250    9.9859708     8.519568      5.24568 
+    2300    9.9462279    9.5850706    5.0632906 
+    2350    9.8043011    9.7605126    5.3148323 
+    2400     9.089818    9.6474522    5.0012486 
+    2450     9.655874    9.3255636    4.8291262 
+    2500    9.0259445    9.3074827    5.1593031 
+    2550    9.1610478    9.7356492    5.0741161 
+    2600    9.3153881    9.3936949    5.4830363 
+    2650    9.6212696     9.598252    4.7172875 
+    2700     9.318906     9.665656    5.1917527 
+    2750    9.6613838    9.7106796    5.1843146 
+    2800    10.231844    9.9407641    4.6940455 
+    2850    10.008093    9.2781076    5.2624957 
+    2900    10.464168     9.808666    5.1457978 
+    2950    9.7080601    9.6972304     5.406456 
+    3000    9.6851209    10.050737    5.1198394 
+    3050    8.9093581     9.213428     5.233108 
+    3100    8.8098921    9.6607476    4.9625331 
+    3150    8.6608386    9.7503441    5.0737533 
+    3200    9.7004403    9.6748778    5.0734462 
+    3250    10.077054    10.318711    5.3233841 
+    3300     10.63887    9.4901739     5.516542 
+    3350    10.232909    9.3407073    5.4989967 
+    3400    9.8854134    9.9542625    5.1982468 
+    3450    9.9388203    9.3394716    4.8135833 
+    3500    9.2514026    9.5857527    5.4605449 
+    3550    8.3940282    9.0549836    4.6951548 
+    3600    8.7696659    9.6262816    4.6302087 
+    3650    9.0695173    8.8520895    5.0814723 
+    3700    9.4700744    9.2777557    4.6825004 
+    3750    9.0221844    9.3407486    5.3984156 
+    3800    9.1478369    9.1420043    5.3024474 
+    3850    9.2652818     9.700053    5.3355364 
+    3900    10.248456    9.2480211    5.2375956 
+    3950    9.8259922    9.6130415    5.5978761 
+    4000     9.404877    9.7931698    5.3767927 
+    4050    10.131713    9.7047295    5.2964594 
+    4100    9.8128638    9.4253237    5.5308166 
+    4150     10.25183    9.1333595    5.1957555 
+    4200    10.449736     9.295762    4.7863033 
+    4250    9.7304858    9.4482515     5.356439 
+    4300    9.2773777    9.4110855    4.9879246 
+    4350    8.9325082    9.3429549    5.0410132 
+    4400    9.2603855    9.7905381    4.7436126 
+    4450    8.7600443    9.9160722     5.196316 
+    4500    9.0824514    10.036035     4.873051 
+    4550    9.3884333    9.6644343    5.1154951 
+    4600    9.8181676    9.6385118    5.3639835 
+    4650    9.1574799    9.5386974    4.7487094 
+    4700    10.275911    9.5383553    5.1084297 
+    4750    9.2476854    9.3353591    5.4773008 
+    4800    9.3422407    9.1931821    4.9210291 
+    4850    9.9033126    9.6443642    5.1334553 
+    4900    9.8469467    9.6836455    5.5101146 
+    4950    10.211229     9.760253    5.0151668 
+    5000    9.3256273    10.109873    5.4129479 
+    5050    9.9704879    9.8504809    5.2191163 
+    5100    9.4820718     9.711504    4.9633504 
+    5150    9.2952171    9.6955742    5.3214246 
+    5200    9.8400791    9.4763906    4.9149518 
+    5250    10.080112    9.5634741    5.1701348 
+    5300    9.4221014    9.8149742    5.3605931 
+    5350    8.8228402    10.121343    5.3192212 
+    5400    9.7318719    10.508763    5.0044083 
+    5450    8.7429847    9.6583774     5.033313 
+    5500    9.9243256    10.239521    5.2956506 
+    5550    9.6088558    9.8555986     5.359257 
+    5600    10.904352     10.72033    5.7874034 
+    5650    9.4774477    9.7246962     5.596949 
+    5700    9.8527139    9.2188245    4.6518586 
+    5750    9.7932375    9.2763721    4.6663307 
+    5800    9.5630073    9.1704583    5.4784197 
+    5850    10.159996    9.5206168    5.0012706 
+    5900    9.1667978    9.6891715    5.1959301 
+    5950    9.2194131    9.2170699    5.1653264 
+    6000    9.5917124    9.2038051    5.1004966 
+    6050    9.4141124    9.9166471    5.0535712 
+    6100    10.231166    9.7746591    5.2399634 
+    6150    9.6054192      9.34446    5.0711646 
+    6200    9.9279645    8.9546561    5.4698039 
+    6250    9.1581437      8.95439    4.9336111 
+    6300    8.9257232    9.0665473     5.188718 
+    6350    9.7685695    9.0822789    4.8454457 
+    6400    9.5140226    9.5073414    5.3420644 
+    6450    9.5379198    9.3316002    5.1940338 
+    6500    10.216584    9.8982859    5.2790157 
+    6550    10.221286    10.913585    5.4521496 
+    6600    10.925166    10.088055    5.2079758 
+    6650    10.012501    9.3870455    5.1740433 
+    6700    10.176139    9.4869588    5.3783369 
+    6750    9.2819415    8.1431975    4.8256476 
+    6800     9.790723    9.7932943    5.3602927 
+    6850    9.1327199    9.8354267    5.1356642 
+    6900     9.240909    9.3854618    5.1767268 
+    6950    10.652806    9.4355671    5.1314851 
+    7000    9.1676917    10.055501    5.2824651 
+    7050    9.6486488    9.1063089    4.9596976 
+    7100    9.3733678    9.5875095    5.0882285 
+    7150     9.282243     9.354934    4.6752644 
+    7200    8.7370777      10.1445    5.0217245 
+    7250     9.563419     9.929442    5.1720916 
+    7300    9.9128346    9.2426863    5.3595023 
+    7350    9.9319949    9.9479477    5.4844629 
+    7400    9.4671739    9.2380048    5.3274217 
+    7450    9.7531193    9.4075641    4.9426738 
+    7500    10.331422    9.4704554    5.3036636 
+    7550    8.7724434     9.663179    4.9492563 
+    7600    10.222748    9.1674852    4.8135992 
+    7650    9.5288583    8.5866929    5.0342955 
+    7700    8.8832847    8.8035037    4.6184473 
+    7750    9.4847076    9.7969656    5.0035855 
+    7800    9.2782486    9.1283641    5.3151299 
+    7850     8.962989    8.7729872    5.0374817 
+    7900    9.6336556    9.4975426    4.9832641 
+    7950    10.125279    10.044247    5.2740873 
+    8000    9.9705097    9.6925988    5.2344188 
+    8050    9.7836318    9.5794261    4.9174534 
+    8100     10.79561     10.04809    5.1604639 
+    8150    9.7261726    10.372878    5.3083843 
+    8200    10.338569     10.08189    5.6555172 
+    8250    9.7833315    9.9834209    5.3790753 
+    8300    9.5857944    9.6052323    5.0689289 
+    8350    9.6706688    9.6189242    4.7725678 
+    8400    10.570423    9.5786093    5.1894242 
+    8450    9.6514599    10.168359    5.0733592 
+    8500    10.273682    9.9179284    5.4014563 
+    8550    9.3120287    10.146837    4.9895115 
+    8600     9.511943     9.644112     5.462624 
+    8650    10.380674    9.1117114     5.156727 
+    8700    10.068596    8.7687113    5.1440814 
+    8750    9.2484971    9.2477678    4.9318794 
+    8800    9.7298469    8.9480303    5.1151321 
+    8850    9.7299502    10.415138    4.7902908 
+    8900    10.966912    10.732962    5.4793574 
+    8950    10.328384    9.9501313    5.6238396 
+    9000    9.7385041    9.8319224    5.1926497 
+    9050    9.7971055    9.5740203    5.1111302 
+    9100    9.7789727    9.9281901    5.1786549 
+    9150    9.9306964    9.3360599    4.9524547 
+    9200    9.8798841    10.240752    5.1691344 
+    9250    10.185445    9.4934917    4.9188964 
+    9300    8.9184663    8.9349408    4.8079511 
+    9350    9.6552187    9.9846949    4.9619969 
+    9400    10.304306    9.2298208    5.2822855 
+    9450    9.8379613    10.041703    5.4186514 
+    9500    10.221443    9.5342818    4.8929802 
+    9550    9.9723047    10.072856    5.4169676 
+    9600    9.3923879    9.2984387    5.4452785 
+    9650    8.9072589    9.7482374    4.7835208 
+    9700    9.8370121    10.205922    5.0385145 
+    9750    9.4274542    9.4653248    5.6340681 
+    9800    9.7668106    9.3265705    5.3154126 
+    9850    10.422549    10.362922     5.361592 
+    9900    9.6264407    9.9790162    5.6381052 
+    9950     10.35018    9.8853593    5.2639184 
+   10000    9.6190853    9.7903758    5.1583115 
+Loop time of 1.32471 on 4 procs for 10000 steps with 500 atoms
+
+Performance: 3261084.476 tau/day, 7548.807 timesteps/s
+98.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.1301     | 0.13489    | 0.13886    |   0.9 | 10.18
+Neigh   | 0.5654     | 0.575      | 0.5883     |   1.3 | 43.41
+Comm    | 0.35135    | 0.37147    | 0.38856    |   2.4 | 28.04
+Output  | 0.0028336  | 0.0032777  | 0.004292   |   1.0 |  0.25
+Modify  | 0.16328    | 0.16711    | 0.17231    |   0.8 | 12.61
+Other   |            | 0.07297    |            |       |  5.51
+
+Nlocal:    125 ave 128 max 122 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    477 ave 489 max 469 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Neighs:    861 ave 877 max 848 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+
+Total # of neighbors = 3444
+Ave neighs/atom = 6.888
+Neighbor list builds = 4560
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01
--- a/examples/coreshell/in.coreshell.wolf
+++ b/examples/coreshell/in.coreshell.wolf
@ -0,0 +1,71 @@
+# Testsystem for core-shell model compared to Mitchel and Finchham
+# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.
+
+# ------------------------ INITIALIZATION ----------------------------
+
+units 		metal
+dimension	3
+boundary	p	p	p
+atom_style	full
+
+# ----------------------- ATOM DEFINITION ----------------------------
+
+fix csinfo all property/atom i_CSID
+read_data data.coreshell fix csinfo NULL CS-Info
+
+group cores type 1 2
+group shells type 3 4
+
+neighbor 2.0 bin
+comm_modify vel yes
+
+# ------------------------ FORCE FIELDS ------------------------------
+
+pair_style   born/coul/wolf/cs 0.1 20.0 20.0    # A, rho, sigma=0, C, D 
+pair_coeff   * *      0.0 1.000   0.00  0.00   0.00
+pair_coeff   3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+pair_coeff   3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+pair_coeff   4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+
+bond_style harmonic
+bond_coeff 1 63.014 0.0
+bond_coeff 2 25.724 0.0
+
+# ------------------------ Equilibration Run -------------------------------
+
+reset_timestep 0
+
+thermo 50
+thermo_style custom step etotal pe ke temp press &
+             epair evdwl ecoul elong ebond fnorm fmax vol
+
+compute CSequ all temp/cs cores shells 
+
+# output via chunk method
+
+#compute prop all property/atom i_CSID
+#compute cs_chunk all chunk/atom c_prop
+#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
+#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector 
+
+thermo_modify temp CSequ
+
+# velocity bias option
+
+velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
+velocity all scale 1427 temp CSequ
+
+fix thermoberendsen all temp/berendsen 1427 1427 0.4
+fix nve all nve
+fix_modify thermoberendsen temp CSequ
+
+# 2 fmsec timestep
+
+timestep 0.002
+run 500
+
+unfix thermoberendsen
+
+# ------------------------ Dynamic Run -------------------------------
+
+run 1000
--- a/examples/coreshell/log.22Sep17.coreshell.wolf.g++.1
+++ b/examples/coreshell/log.22Sep17.coreshell.wolf.g++.1
@ -0,0 +1,190 @@
+LAMMPS (22 Sep 2017)
+# Testsystem for core-shell model compared to Mitchel and Finchham
+# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.
+
+# ------------------------ INITIALIZATION ----------------------------
+
+units 		metal
+dimension	3
+boundary	p	p	p
+atom_style	full
+
+# ----------------------- ATOM DEFINITION ----------------------------
+
+fix csinfo all property/atom i_CSID
+read_data data.coreshell fix csinfo NULL CS-Info
+  orthogonal box = (0 0 0) to (24.096 24.096 24.096)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  432 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  216 bonds
+  1 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+group cores type 1 2
+216 atoms in group cores
+group shells type 3 4
+216 atoms in group shells
+
+neighbor 2.0 bin
+comm_modify vel yes
+
+# ------------------------ FORCE FIELDS ------------------------------
+
+pair_style   born/coul/wolf/cs 0.1 20.0 20.0    # A, rho, sigma=0, C, D
+pair_coeff   * *      0.0 1.000   0.00  0.00   0.00
+pair_coeff   3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+pair_coeff   3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+pair_coeff   4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+
+bond_style harmonic
+bond_coeff 1 63.014 0.0
+bond_coeff 2 25.724 0.0
+
+# ------------------------ Equilibration Run -------------------------------
+
+reset_timestep 0
+
+thermo 50
+thermo_style custom step etotal pe ke temp press              epair evdwl ecoul elong ebond fnorm fmax vol
+
+compute CSequ all temp/cs cores shells
+
+# output via chunk method
+
+#compute prop all property/atom i_CSID
+#compute cs_chunk all chunk/atom c_prop
+#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
+#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
+
+thermo_modify temp CSequ
+
+# velocity bias option
+
+velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 22
+  ghost atom cutoff = 22
+  binsize = 11, bins = 3 3 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair born/coul/wolf/cs, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+velocity all scale 1427 temp CSequ
+
+fix thermoberendsen all temp/berendsen 1427 1427 0.4
+fix nve all nve
+fix_modify thermoberendsen temp CSequ
+
+# 2 fmsec timestep
+
+timestep 0.002
+run 500
+Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes
+Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 
+       0   -637.41039   -677.06805    39.657659         1427   -21302.622   -677.06805    1.6320365   -678.70009            0            0 1.2935454e-14 3.3306691e-15      13990.5 
+      50   -635.62711   -667.67134    32.044236    1153.0465   -4533.0717   -669.45724     37.76997   -707.22721            0    1.7858939    9.6844521    2.2001656      13990.5 
+     100   -632.76337   -662.83035    30.066977    1081.8989   -3492.8736   -664.98454    39.197093   -704.18164            0    2.1541967    11.063962    2.1543406      13990.5 
+     150   -630.82538   -663.70056    32.875182    1182.9464   -74.330324   -666.12202    46.263665   -712.38569            0    2.4214607    11.739683    2.7558416      13990.5 
+     200    -629.1541   -664.54637     35.39227    1273.5187   -1707.5508   -666.87772    41.796197   -708.67391            0    2.3313445    10.594804    3.0025376      13990.5 
+     250   -627.86587   -662.60879    34.742918    1250.1531   -1258.7537   -665.21416    43.017024   -708.23118            0    2.6053655    10.576999    1.8400986      13990.5 
+     300   -627.10755   -664.12897    37.021419    1332.1403   -1891.3466   -666.39618    40.769593   -707.16577            0    2.2672094     9.412943    1.2434258      13990.5 
+     350   -626.27558   -665.04303    38.767448    1394.9676   -1436.8514   -667.47081    41.854746   -709.32556            0    2.4277827    10.304721     1.977594      13990.5 
+     400   -625.55098   -661.86388    36.312896    1306.6455   -331.92076    -664.4632    44.426542   -708.88975            0     2.599325    11.081635    2.1734468      13990.5 
+     450   -624.88626   -661.07359    36.187328    1302.1272    -2325.834    -663.6031    39.662697   -703.26579            0    2.5295037    9.9810051    1.3068929      13990.5 
+     500   -623.87093   -660.24145    36.370525    1308.7192    410.85324   -662.86944    45.869201   -708.73864            0    2.6279856    10.592785    1.8162326      13990.5 
+Loop time of 11.7065 on 1 procs for 500 steps with 432 atoms
+
+Performance: 7.381 ns/day, 3.252 hours/ns, 42.711 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.535     | 11.535     | 11.535     |   0.0 | 98.54
+Bond    | 0.001443   | 0.001443   | 0.001443   |   0.0 |  0.01
+Neigh   | 0.10952    | 0.10952    | 0.10952    |   0.0 |  0.94
+Comm    | 0.048796   | 0.048796   | 0.048796   |   0.0 |  0.42
+Output  | 0.00038695 | 0.00038695 | 0.00038695 |   0.0 |  0.00
+Modify  | 0.0067511  | 0.0067511  | 0.0067511  |   0.0 |  0.06
+Other   |            | 0.004243   |            |       |  0.04
+
+Nlocal:    432 ave 432 max 432 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    9328 ave 9328 max 9328 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    297280 ave 297280 max 297280 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 297280
+Ave neighs/atom = 688.148
+Ave special neighs/atom = 1
+Neighbor list builds = 21
+Dangerous builds = 0
+
+unfix thermoberendsen
+
+# ------------------------ Dynamic Run -------------------------------
+
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes
+Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 
+     500   -623.87093   -660.24145    36.370525    1308.7192    410.85324   -662.86944    45.869201   -708.73864            0    2.6279856    10.592785    1.8162326      13990.5 
+     550   -623.95762   -659.99899    36.041371    1296.8752   -442.62446   -662.68699    44.004419   -706.69141            0    2.6879934    10.936057    1.7358509      13990.5 
+     600   -624.04214   -661.21748    37.175332    1337.6785    47.615854   -663.76133    45.009742   -708.77107            0    2.5438549    11.431366    2.1185464      13990.5 
+     650   -623.98279   -661.85255     37.86976    1362.6661   -1708.3823   -664.31138    40.933446   -705.24482            0    2.4588298    9.7960191    1.4159904      13990.5 
+     700   -624.02941   -661.57484     37.54543    1350.9958   -124.09512   -663.95322    44.666402   -708.61962            0    2.3783801    10.518712    2.0854584      13990.5 
+     750   -624.03935   -661.11619    37.076837    1334.1344   -1163.2721   -663.82553      42.1219   -705.94743            0    2.7093404    10.634859    1.9381654      13990.5 
+     800   -623.98709   -659.43647     35.44938    1275.5737   -285.65702   -662.23782    44.650233   -706.88805            0    2.8013482     11.83459    3.4506407      13990.5 
+     850   -623.96081   -661.77923    37.818422    1360.8188   -814.33212   -664.38161    42.860208   -707.24181            0    2.6023728    10.766451    2.9211132      13990.5 
+     900   -623.96136   -662.98419    39.022831     1404.157    308.13105   -665.65877    45.053188   -710.71195            0    2.6745786    11.028799    1.8494322      13990.5 
+     950   -623.91048   -660.63828      36.7278     1321.575   -445.31526   -663.79806     43.94833   -707.74639            0    3.1597729    11.852051    1.8238458      13990.5 
+    1000   -623.90541   -661.03474    37.129332    1336.0233    522.57958   -663.50212    45.863261   -709.36538            0    2.4673781    10.949291    1.8614095      13990.5 
+    1050   -624.01134   -660.99076    36.979422    1330.6291   -1710.2829   -663.67762    41.056102   -704.73372            0    2.6868521     10.86533    2.2154165      13990.5 
+    1100   -624.02639   -660.86661    36.840225    1325.6204    1151.0236    -663.5066    47.207185   -710.71378            0    2.6399847    11.298044    1.8900703      13990.5 
+    1150   -624.04418   -661.29819    37.254006    1340.5094    161.09847   -663.73735    45.222561   -708.95991            0    2.4391651    11.261119    2.2245673      13990.5 
+    1200   -624.08628   -662.39932    38.313043    1378.6168   -1405.0927   -664.93121    41.728112   -706.65933            0    2.5318927    10.458041    2.1153159      13990.5 
+    1250   -624.03036   -661.25661    37.226248    1339.5106    63.407721   -663.72719    45.086961   -708.81415            0    2.4705832    11.766021    2.2297809      13990.5 
+    1300   -623.97475   -661.55998    37.585229    1352.4278   -763.66781   -663.80645    42.870244    -706.6767            0    2.2464703    10.098322    1.7614596      13990.5 
+    1350   -623.93123   -660.30786    36.376631    1308.9389   -2389.8052   -663.04725    39.749029   -702.79628            0    2.7393936    10.879364    2.6622521      13990.5 
+    1400   -623.86468   -658.44644    34.581765    1244.3543    2262.7586   -660.95368     50.10608   -711.05976            0    2.5072434    11.528291    1.7861906      13990.5 
+    1450   -623.85494   -661.47216    37.617217    1353.5789   -1435.0174   -664.13587    41.701767   -705.83764            0    2.6637191    11.297444    2.0038345      13990.5 
+    1500   -623.79928   -659.70124    35.901959    1291.8588   -198.39562   -662.57415    44.358482   -706.93263            0     2.872907    11.075746    2.2821286      13990.5 
+Loop time of 23.4119 on 1 procs for 1000 steps with 432 atoms
+
+Performance: 7.381 ns/day, 3.252 hours/ns, 42.713 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 23.069     | 23.069     | 23.069     |   0.0 | 98.54
+Bond    | 0.0029275  | 0.0029275  | 0.0029275  |   0.0 |  0.01
+Neigh   | 0.22821    | 0.22821    | 0.22821    |   0.0 |  0.97
+Comm    | 0.097941   | 0.097941   | 0.097941   |   0.0 |  0.42
+Output  | 0.00074033 | 0.00074033 | 0.00074033 |   0.0 |  0.00
+Modify  | 0.0042015  | 0.0042015  | 0.0042015  |   0.0 |  0.02
+Other   |            | 0.00865    |            |       |  0.04
+
+Nlocal:    432 ave 432 max 432 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    9388 ave 9388 max 9388 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    297212 ave 297212 max 297212 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 297212
+Ave neighs/atom = 687.991
+Ave special neighs/atom = 1
+Neighbor list builds = 45
+Dangerous builds = 0
+Total wall time: 0:00:35
--- a/examples/coreshell/log.22Sep17.coreshell.wolf.g++.4
+++ b/examples/coreshell/log.22Sep17.coreshell.wolf.g++.4
@ -0,0 +1,190 @@
+LAMMPS (22 Sep 2017)
+# Testsystem for core-shell model compared to Mitchel and Finchham
+# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.
+
+# ------------------------ INITIALIZATION ----------------------------
+
+units 		metal
+dimension	3
+boundary	p	p	p
+atom_style	full
+
+# ----------------------- ATOM DEFINITION ----------------------------
+
+fix csinfo all property/atom i_CSID
+read_data data.coreshell fix csinfo NULL CS-Info
+  orthogonal box = (0 0 0) to (24.096 24.096 24.096)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  432 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  216 bonds
+  1 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+group cores type 1 2
+216 atoms in group cores
+group shells type 3 4
+216 atoms in group shells
+
+neighbor 2.0 bin
+comm_modify vel yes
+
+# ------------------------ FORCE FIELDS ------------------------------
+
+pair_style   born/coul/wolf/cs 0.1 20.0 20.0    # A, rho, sigma=0, C, D
+pair_coeff   * *      0.0 1.000   0.00  0.00   0.00
+pair_coeff   3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+pair_coeff   3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+pair_coeff   4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+
+bond_style harmonic
+bond_coeff 1 63.014 0.0
+bond_coeff 2 25.724 0.0
+
+# ------------------------ Equilibration Run -------------------------------
+
+reset_timestep 0
+
+thermo 50
+thermo_style custom step etotal pe ke temp press              epair evdwl ecoul elong ebond fnorm fmax vol
+
+compute CSequ all temp/cs cores shells
+
+# output via chunk method
+
+#compute prop all property/atom i_CSID
+#compute cs_chunk all chunk/atom c_prop
+#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
+#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
+
+thermo_modify temp CSequ
+
+# velocity bias option
+
+velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 22
+  ghost atom cutoff = 22
+  binsize = 11, bins = 3 3 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair born/coul/wolf/cs, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+velocity all scale 1427 temp CSequ
+
+fix thermoberendsen all temp/berendsen 1427 1427 0.4
+fix nve all nve
+fix_modify thermoberendsen temp CSequ
+
+# 2 fmsec timestep
+
+timestep 0.002
+run 500
+Per MPI rank memory allocation (min/avg/max) = 6.881 | 6.881 | 6.881 Mbytes
+Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 
+       0   -637.41039   -677.06805    39.657659         1427   -21302.622   -677.06805    1.6320365   -678.70009            0            0 1.3530839e-14 3.6429193e-15      13990.5 
+      50   -635.62704   -667.67108    32.044047    1153.0397   -4532.6842   -669.45828    37.771018    -707.2293            0     1.787201    9.6848095    2.2028349      13990.5 
+     100   -632.76343   -662.83014    30.066711    1081.8893   -3493.0827   -664.98212    39.195967   -704.17809            0     2.151977    11.060773    2.1578583      13990.5 
+     150   -630.82533   -663.70172    32.876385    1182.9897   -75.706974   -666.12608    46.261038   -712.38712            0    2.4243598    11.746728    2.7663319      13990.5 
+     200   -629.15463   -664.55009    35.395466    1273.6337   -1707.9185   -666.88117    41.794868   -708.67604            0     2.331082    10.596229    3.0031523      13990.5 
+     250   -627.86625   -662.60876    34.742511    1250.1384   -1263.5726     -665.214    43.005742   -708.21974            0    2.6052329    10.572641     1.841604      13990.5 
+     300   -627.10829   -664.12159    37.013298    1331.8481   -1884.8587   -666.39136    40.786141    -707.1775            0    2.2697693    9.4160685    1.2472271      13990.5 
+     350    -626.2729   -665.01858    38.745682    1394.1844   -1433.1302   -667.44315    41.864785   -709.30793            0    2.4245625    10.312641    1.9815612      13990.5 
+     400   -625.54274   -661.84438    36.301638    1306.2404   -355.45544    -664.4483    44.370671   -708.81897            0    2.6039276    11.076154    2.1819703      13990.5 
+     450   -624.88802   -661.12299    36.234964    1303.8413   -2356.6101    -663.6463     39.57847   -703.22477            0     2.523314    9.8995886    1.3113549      13990.5 
+     500   -623.86344   -660.20235    36.338906    1307.5814    462.72862    -662.8515    45.983055   -708.83455            0    2.6491489    10.523732    1.6709561      13990.5 
+Loop time of 4.63313 on 4 procs for 500 steps with 432 atoms
+
+Performance: 18.648 ns/day, 1.287 hours/ns, 107.919 timesteps/s
+99.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.8133     | 3.5934     | 4.4255     |  36.3 | 77.56
+Bond    | 0.00042245 | 0.00050305 | 0.00059825 |   0.0 |  0.01
+Neigh   | 0.0411     | 0.041561   | 0.04202    |   0.2 |  0.90
+Comm    | 0.15622    | 0.9884     | 1.7686     |  69.2 | 21.33
+Output  | 0.00028311 | 0.00031345 | 0.00040011 |   0.0 |  0.01
+Modify  | 0.0039899  | 0.00403    | 0.0040654  |   0.0 |  0.09
+Other   |            | 0.004911   |            |       |  0.11
+
+Nlocal:    108 ave 112 max 106 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+Nghost:    6531.75 ave 6611 max 6460 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs:    74316.2 ave 75641 max 72780 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 297265
+Ave neighs/atom = 688.113
+Ave special neighs/atom = 1
+Neighbor list builds = 21
+Dangerous builds = 0
+
+unfix thermoberendsen
+
+# ------------------------ Dynamic Run -------------------------------
+
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 6.884 | 7.01 | 7.138 Mbytes
+Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 
+     500   -623.86344   -660.20235    36.338906    1307.5814    462.72862    -662.8515    45.983055   -708.83455            0    2.6491489    10.523732    1.6709561      13990.5 
+     550   -623.95339   -660.07946    36.126069    1299.9229   -362.67288    -662.8047    44.180832   -706.98553            0     2.725239     11.07199    2.0461377      13990.5 
+     600   -624.04508   -661.27298    37.227902    1339.5701    110.39823   -663.90927    45.166569   -709.07584            0    2.6362911    11.747923    2.1846828      13990.5 
+     650    -623.9608   -661.50573    37.544934    1350.9779   -1594.4701   -663.91531    41.226571   -705.14188            0    2.4095736    10.022027    1.6264014      13990.5 
+     700   -624.00658   -663.55636    39.549777    1423.1181    -588.9804   -665.88666    43.124023   -709.01068            0    2.3302979     9.924587    2.1027837      13990.5 
+     750   -623.99813   -659.97695    35.978816    1294.6243    -364.1415   -662.75959    43.973556   -706.73315            0     2.782646    11.487832    1.8799695      13990.5 
+     800   -624.01235   -661.04908    37.036728    1332.6911   -85.655852   -663.49204    44.570117   -708.06215            0    2.4429547    11.213149    1.6792926      13990.5 
+     850   -624.02581   -659.39933    35.373519     1272.844   -1090.9179   -662.11969    42.375064   -704.49476            0    2.7203673    11.214629    2.2907474      13990.5 
+     900   -624.09244   -663.33386    39.241421    1412.0225    303.76207   -666.00593    45.332458   -711.33839            0    2.6720667    11.897188    2.0599033      13990.5 
+     950   -624.04544   -661.11578    37.070341    1333.9007    1637.6438   -663.61305     48.65892   -712.27197            0      2.49727    12.343774     2.429225      13990.5 
+    1000   -623.95457   -661.51816    37.563586    1351.6491   -851.77182   -663.83594    42.813468   -706.64941            0     2.317782    10.251422    1.6922864      13990.5 
+    1050   -623.98731   -662.01988    38.032562    1368.5242   -2123.9075   -664.72609    39.917382   -704.64348            0     2.706218     9.600838    1.7365559      13990.5 
+    1100    -623.9653   -659.32023    35.354929    1272.1751   -436.90576   -662.14454    44.057776   -706.20232            0    2.8243167    11.267546    2.6807602      13990.5 
+    1150   -624.02273   -665.13902    41.116293     1479.486   -128.13268    -667.4769    44.013761   -711.49066            0    2.3378768    10.406604    1.5102324      13990.5 
+    1200   -623.97328   -663.08042    39.107135    1407.1905   -539.63284   -665.67946    43.319308   -708.99877            0     2.599042    10.632657    1.4608707      13990.5 
+    1250   -623.92529   -661.81902    37.893723    1363.5284    1708.0621   -664.63624    48.396874   -713.03311            0    2.8172251    11.369352    1.8836979      13990.5 
+    1300   -623.99283   -662.19734    38.204509    1374.7114   -820.77291   -664.34556    42.656202   -707.00176            0    2.1482151    10.186898    1.7081329      13990.5 
+    1350   -623.99798   -658.70752    34.709535    1248.9519    776.28486   -662.01647    46.925412   -708.94188            0    3.3089536    12.457581    2.5027978      13990.5 
+    1400   -623.96941   -662.15959    38.190183    1374.1959    880.21756   -664.90452    46.628183    -711.5327            0    2.7449282    11.918894    3.0466188      13990.5 
+    1450   -623.95068   -662.25435    38.303671    1378.2795   -391.56711    -664.7631    43.644066   -708.40716            0    2.5087493    10.465803    1.8744864      13990.5 
+    1500   -624.00637   -661.48756    37.481185     1348.684    430.69453   -664.32151    45.704366   -710.02587            0    2.8339501    11.650821    2.0752813      13990.5 
+Loop time of 6.7003 on 4 procs for 1000 steps with 432 atoms
+
+Performance: 25.790 ns/day, 0.931 hours/ns, 149.247 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.9613     | 6.0752     | 6.2064     |   4.1 | 90.67
+Bond    | 0.00087095 | 0.00088993 | 0.00091671 |   0.0 |  0.01
+Neigh   | 0.06494    | 0.064964   | 0.064987   |   0.0 |  0.97
+Comm    | 0.41743    | 0.54863    | 0.6626     |  13.8 |  8.19
+Output  | 0.00053867 | 0.00059268 | 0.00074867 |   0.0 |  0.01
+Modify  | 0.0013288  | 0.0013592  | 0.0013841  |   0.1 |  0.02
+Other   |            | 0.008613   |            |       |  0.13
+
+Nlocal:    108 ave 116 max 102 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost:    6504.5 ave 6624 max 6380 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:    74267 ave 79230 max 70993 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 297068
+Ave neighs/atom = 687.657
+Ave special neighs/atom = 1
+Neighbor list builds = 45
+Dangerous builds = 0
+Total wall time: 0:00:11
--- a/examples/rigid/bodies.txt
+++ b/examples/rigid/bodies.txt
@ -0,0 +1,83 @@
+81
+1 1
+2 1
+3 1
+4 1
+5 1
+6 1
+7 1
+8 1
+9 1
+10 2
+11 2
+12 2
+13 2
+14 2
+15 2
+16 2
+17 2
+18 2
+19 3
+20 3
+21 3
+22 3
+23 3
+24 3
+25 3
+26 3
+27 3
+28 4
+29 4
+30 4
+31 4
+32 4
+33 4
+34 4
+35 4
+36 4
+37 5
+38 5
+39 5
+40 5
+41 5
+42 5
+43 5
+44 5
+45 5
+46 6
+47 6
+48 6
+49 6
+50 6
+51 6
+52 6
+53 6
+54 6
+55 7
+56 7
+57 7
+58 7
+59 7
+60 7
+61 7
+62 7
+63 7
+64 8
+65 8
+66 8
+67 8
+68 8
+69 8
+70 8
+71 8
+72 8
+73 9
+74 9
+75 9
+76 9
+77 9
+78 9
+79 9
+80 9
+81 9
+
--- a/examples/rigid/data.rigid-property
+++ b/examples/rigid/data.rigid-property
@ -0,0 +1,185 @@
+# LAMMPS data file for rigid bodies
+
+81	atoms		
+1	atom types	
+
+-12 12 xlo xhi
+-12 12 ylo yhi
+-12 12 zlo zhi
+
+Masses			
+
+1 1		
+
+Pair Coeffs			
+
+1 1 1		
+
+Atoms				
+
+1	1	0	0	0
+2	1	0	1	0
+3	1	0	0.5	0
+4	1	0.5	0	0
+5	1	0.5	0.5	1
+6	1	1	0.5	0
+7	1	0.5	1	0
+8	1	1	0	0
+9	1	1	1	0
+10	1	2	1	0
+11	1	1	2	0
+12	1	1.5	2	0
+13	1	1.5	1	0
+14	1	1	1.5	0
+15	1	1.5	1.5	1
+16	1	2	1.5	0
+17	1	2	2	0
+18	1	2	3	0
+19	1	2	2.5	0
+20	1	2.5	2	0
+21	1	2.5	2.5	1
+22	1	3	2.5	0
+23	1	2.5	3	0
+24	1	3	2	0
+25	1	3	3	0
+26	1	4	3	0
+27	1	3	4	0
+28	1	3.5	4	0
+29	1	3.5	3	0
+30	1	3	3.5	0
+31	1	3.5	3.5	1
+32	1	4	3.5	0
+33	1	4	4	0
+34	1	4	5	0
+35	1	4	4.5	0
+36	1	4.5	4	0
+37	1	4.5	4.5	1
+38	1	5	4.5	0
+39	1	4.5	5	0
+40	1	5	4	0
+41	1	5	5	0
+42	1	6	5	0
+43	1	5	6	0
+44	1	5.5	6	0
+45	1	5.5	5	0
+46	1	5	5.5	0
+47	1	5.5	5.5	1
+48	1	6	5.5	0
+49	1	6	6	0
+50	1	6	7	0
+51	1	6	6.5	0
+52	1	6.5	6	0
+53	1	6.5	6.5	1
+54	1	7	6.5	0
+55	1	6.5	7	0
+56	1	7	6	0
+57	1	7	7	0
+58	1	8	7	0
+59	1	7	8	0
+60	1	7.5	8	0
+61	1	7.5	7	0
+62	1	7	7.5	0
+63	1	7.5	7.5	1
+64	1	8	7.5	0
+65	1	8	8	0
+66	1	8	9	0
+67	1	8	8.5	0
+68	1	8.5	8	0
+69	1	8.5	8.5	1
+70	1	9	8.5	0
+71	1	8.5	9	0
+72	1	9	8	0
+73	1	9	9	0
+74	1	10	9	0
+75	1	9	10	0
+76	1	9.5	10	0
+77	1	9.5	9	0
+78	1	9	9.5	0
+79	1	9.5	9.5	1
+80	1	10	9.5	0
+81	1	10	10	0
+
+Bodies
+
+1 1
+2 1
+3 1
+4 1
+5 1
+6 1
+7 1
+8 1
+9 1
+10 2
+11 2
+12 2
+13 2
+14 2
+15 2
+16 2
+17 2
+18 2
+19 3
+20 3
+21 3
+22 3
+23 3
+24 3
+25 3
+26 3
+27 3
+28 4
+29 4
+30 4
+31 4
+32 4
+33 4
+34 4
+35 4
+36 4
+37 5
+38 5
+39 5
+40 5
+41 5
+42 5
+43 5
+44 5
+45 5
+46 6
+47 6
+48 6
+49 6
+50 6
+51 6
+52 6
+53 6
+54 6
+55 7
+56 7
+57 7
+58 7
+59 7
+60 7
+61 7
+62 7
+63 7
+64 8
+65 8
+66 8
+67 8
+68 8
+69 8
+70 8
+71 8
+72 8
+73 9
+74 9
+75 9
+76 9
+77 9
+78 9
+79 9
+80 9
+81 9
+
--- a/examples/rigid/in.rigid-atomfile
+++ b/examples/rigid/in.rigid-atomfile
@ -0,0 +1,83 @@
+# Simple rigid body system
+
+units		lj
+atom_style	atomic
+atom_modify  map array
+
+pair_style	lj/cut 2.5
+
+read_data	data.rigid
+
+velocity 	all create 100.0 4928459
+
+
+# unconnected bodies
+
+group		clump1 id <> 1 9
+group		clump2 id <> 10 18
+group		clump3 id <> 19 27
+group		clump4 id <> 28 36
+group		clump5 id <> 37 45
+group		clump6 id <> 46 54
+group		clump7 id <> 55 63
+group		clump8 id <> 64 72
+group		clump9 id <> 73 81
+
+variable bodies atomfile bodies.txt
+fix 1 all rigid custom v_bodies
+
+# 1 chain of connected bodies
+
+#group		clump1 id <> 1 9
+#group		clump2 id <> 9 18
+#group		clump3 id <> 18 27
+#group		clump4 id <> 27 36
+#group		clump5 id <> 36 45
+#group		clump6 id <> 45 54
+#group		clump7 id <> 54 63
+#group		clump8 id <> 63 72
+#group		clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+#	  	      clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group		clump1 id <> 1 9
+#group		clump2 id <> 9 18
+#group		clump3 id <> 18 27
+#group		clump4 id <> 27 36
+#group		clump5 id <> 37 45
+#group		clump6 id <> 45 54
+#group		clump7 id <> 54 63
+#group		clump8 id <> 63 72
+#group		clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify	exclude group clump1 clump1
+neigh_modify	exclude group clump2 clump2
+neigh_modify	exclude group clump3 clump3
+neigh_modify	exclude group clump4 clump4
+neigh_modify	exclude group clump5 clump5
+neigh_modify	exclude group clump6 clump6
+neigh_modify	exclude group clump7 clump7
+neigh_modify	exclude group clump8 clump8
+neigh_modify	exclude group clump9 clump9
+
+thermo		100
+
+#dump		1 all atom 50 dump.rigid
+
+#dump		2 all image 100 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 5
+
+#dump		3 all movie 100 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 5
+
+timestep 	0.0001
+thermo		50
+run		10000
--- a/examples/rigid/in.rigid-atomvar
+++ b/examples/rigid/in.rigid-atomvar
@ -0,0 +1,83 @@
+# Simple rigid body system
+
+units		lj
+atom_style	atomic
+atom_modify  map array
+
+pair_style	lj/cut 2.5
+
+read_data	data.rigid
+
+velocity 	all create 100.0 4928459
+
+
+# unconnected bodies
+
+group		clump1 id <> 1 9
+group		clump2 id <> 10 18
+group		clump3 id <> 19 27
+group		clump4 id <> 28 36
+group		clump5 id <> 37 45
+group		clump6 id <> 46 54
+group		clump7 id <> 55 63
+group		clump8 id <> 64 72
+group		clump9 id <> 73 81
+
+variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
+fix 1 all rigid custom v_bodies
+
+# 1 chain of connected bodies
+
+#group		clump1 id <> 1 9
+#group		clump2 id <> 9 18
+#group		clump3 id <> 18 27
+#group		clump4 id <> 27 36
+#group		clump5 id <> 36 45
+#group		clump6 id <> 45 54
+#group		clump7 id <> 54 63
+#group		clump8 id <> 63 72
+#group		clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+#	  	      clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group		clump1 id <> 1 9
+#group		clump2 id <> 9 18
+#group		clump3 id <> 18 27
+#group		clump4 id <> 27 36
+#group		clump5 id <> 37 45
+#group		clump6 id <> 45 54
+#group		clump7 id <> 54 63
+#group		clump8 id <> 63 72
+#group		clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify	exclude group clump1 clump1
+neigh_modify	exclude group clump2 clump2
+neigh_modify	exclude group clump3 clump3
+neigh_modify	exclude group clump4 clump4
+neigh_modify	exclude group clump5 clump5
+neigh_modify	exclude group clump6 clump6
+neigh_modify	exclude group clump7 clump7
+neigh_modify	exclude group clump8 clump8
+neigh_modify	exclude group clump9 clump9
+
+thermo		100
+
+#dump		1 all atom 50 dump.rigid
+
+#dump		2 all image 100 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 5
+
+#dump		3 all movie 100 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 5
+
+timestep 	0.0001
+thermo		50
+run		10000
--- a/examples/rigid/in.rigid-property
+++ b/examples/rigid/in.rigid-property
@ -0,0 +1,85 @@
+# Simple rigid body system
+
+units		lj
+atom_style	atomic
+atom_modify  map array
+
+pair_style	lj/cut 2.5
+
+fix 0 all property/atom i_bodies
+
+read_data	data.rigid-property fix 0 NULL Bodies
+
+velocity 	all create 100.0 4928459
+
+
+# unconnected bodies
+
+group		clump1 id <> 1 9
+group		clump2 id <> 10 18
+group		clump3 id <> 19 27
+group		clump4 id <> 28 36
+group		clump5 id <> 37 45
+group		clump6 id <> 46 54
+group		clump7 id <> 55 63
+group		clump8 id <> 64 72
+group		clump9 id <> 73 81
+
+# assemble bodies from per-atom custom integer property bodies
+fix 1 all rigid custom i_bodies
+
+# 1 chain of connected bodies
+
+#group		clump1 id <> 1 9
+#group		clump2 id <> 9 18
+#group		clump3 id <> 18 27
+#group		clump4 id <> 27 36
+#group		clump5 id <> 36 45
+#group		clump6 id <> 45 54
+#group		clump7 id <> 54 63
+#group		clump8 id <> 63 72
+#group		clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+#	  	      clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group		clump1 id <> 1 9
+#group		clump2 id <> 9 18
+#group		clump3 id <> 18 27
+#group		clump4 id <> 27 36
+#group		clump5 id <> 37 45
+#group		clump6 id <> 45 54
+#group		clump7 id <> 54 63
+#group		clump8 id <> 63 72
+#group		clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify	exclude group clump1 clump1
+neigh_modify	exclude group clump2 clump2
+neigh_modify	exclude group clump3 clump3
+neigh_modify	exclude group clump4 clump4
+neigh_modify	exclude group clump5 clump5
+neigh_modify	exclude group clump6 clump6
+neigh_modify	exclude group clump7 clump7
+neigh_modify	exclude group clump8 clump8
+neigh_modify	exclude group clump9 clump9
+
+thermo		100
+
+#dump		1 all atom 50 dump.rigid
+
+#dump		2 all image 100 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 5
+
+#dump		3 all movie 100 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 5
+
+timestep 	0.0001
+thermo		50
+run		10000
--- a/lib/colvars/Makefile.common
+++ b/lib/colvars/Makefile.common
@ -12,7 +12,7 @@
 ifeq ($(COLVARS_DEBUG),)
 COLVARS_DEBUG_INCFLAGS =
 else
-COLVARS_DEBUG_INCFLAGS= -DCOLVARS_DEBUG
+COLVARS_DEBUG_INCFLAGS = -DCOLVARS_DEBUG
 endif

 COLVARS_INCFLAGS = $(COLVARS_DEBUG_INCFLAGS) $(COLVARS_PYTHON_INCFLAGS)
@ -21,6 +21,7 @@ COLVARS_INCFLAGS = $(COLVARS_DEBUG_INCFLAGS) $(COLVARS_PYTHON_INCFLAGS)
 .SUFFIXES:
 .SUFFIXES: .cpp .o

+
 COLVARS_SRCS = \
        colvaratoms.cpp \
        colvarbias_abf.cpp \
@ -45,21 +46,32 @@ COLVARS_SRCS = \
        colvartypes.cpp \
        colvarvalue.cpp

-COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o)
+LEPTON_SRCS = \
+	lepton/src/CompiledExpression.cpp lepton/src/ExpressionTreeNode.cpp \
+	lepton/src/ParsedExpression.cpp lepton/src/ExpressionProgram.cpp    \
+	lepton/src/Operation.cpp lepton/src/Parser.cpp

-.cpp.o:
-	$(CXX) $(CXXFLAGS) $(COLVARS_INCFLAGS) -c $<
+LEPTON_OBJS = \
+	lepton/src/CompiledExpression.o lepton/src/ExpressionTreeNode.o \
+	lepton/src/ParsedExpression.o lepton/src/ExpressionProgram.o    \
+	lepton/src/Operation.o lepton/src/Parser.o
+
+COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) $(LEPTON_OBJS)
+
+%.o: %.cpp
+	$(CXX) $(CXXFLAGS) $(COLVARS_INCFLAGS) -Ilepton/include -DLEPTON -c -o $@ $<

 $(COLVARS_LIB):	Makefile.deps $(COLVARS_OBJS)
-	$(AR) $(ARFLAGS) $(COLVARS_LIB) $(COLVARS_OBJS)
+	$(AR) $(ARFLAGS) $(COLVARS_LIB) $(COLVARS_OBJS) $(LEPTON_OBJS)


 Makefile.deps: $(COLVARS_SRCS)
 	@echo > $@
 	@for src in $^ ; do \
 	  obj=`basename $$src .cpp`.o ; \
-	  $(CXX) -MM $(COLVARS_INCFLAGS) \
+	  $(CXX) -MM $(COLVARS_INCFLAGS)  -Ilepton/include -DLEPTON \
 	    -MT '$$(COLVARS_OBJ_DIR)'$$obj $$src >> $@ ; \
 	  done

 include Makefile.deps
+include Makefile.lepton.deps # Hand-generated
--- a/lib/colvars/Makefile.deps
+++ b/lib/colvars/Makefile.deps
@ -4,73 +4,232 @@ $(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
 colvarparse.h colvaratoms.h colvardeps.h
 $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvar.h \
- colvarparse.h colvardeps.h colvarbias_abf.h colvarbias.h colvargrid.h
+ colvarparse.h colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarbias_abf.h colvarbias.h colvargrid.h colvar_UIestimator.h
 $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \
- colvarbias_alb.h colvar.h colvarparse.h colvardeps.h colvarbias.h
+ colvarbias_alb.h colvar.h colvarparse.h colvardeps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarbias.h
 $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h \
- colvar.h colvarparse.h colvardeps.h
+ colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvargrid.h
 $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarbias_histogram.h \
- colvarbias.h colvargrid.h
+ colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarbias_histogram.h colvarbias.h colvargrid.h
 $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h \
 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvardeps.h colvarbias_meta.h colvarbias.h \
- colvargrid.h
+ colvarvalue.h colvarparse.h colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarbias_meta.h colvarbias.h colvargrid.h
 $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
 colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
- colvardeps.h
+ colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h
 $(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarcomp.h \
- colvaratoms.h
+ colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h
 $(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
 colvarvalue.h colvarparse.h colvaratoms.h colvardeps.h colvar.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
 colvarcomp.h
 $(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvar.h \
- colvarparse.h colvardeps.h colvarcomp.h colvaratoms.h
+ colvarparse.h colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h
 $(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvardeps.h colvarcomp.h \
- colvaratoms.h
+ colvarvalue.h colvarparse.h colvar.h colvardeps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h
 $(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvardeps.h colvarcomp.h \
- colvaratoms.h
+ colvarvalue.h colvarparse.h colvar.h colvardeps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h
 $(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarparse.h colvar.h colvardeps.h colvarcomp.h \
- colvaratoms.h
+ colvarvalue.h colvarparse.h colvar.h colvardeps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h
 $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
- colvardeps.h colvarcomp.h colvaratoms.h colvarscript.h colvarbias.h
+ colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvarscript.h colvarbias.h
 $(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvardeps.h \
 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
 colvarvalue.h colvarparse.h
 $(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \
- colvarparse.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
- colvargrid.h
+ colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarcomp.h colvaratoms.h colvargrid.h
 $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \
- colvarparse.h colvar.h colvardeps.h colvarbias.h colvarbias_abf.h \
- colvargrid.h colvarbias_alb.h colvarbias_histogram.h colvarbias_meta.h \
- colvarbias_restraint.h colvarscript.h colvaratoms.h
+ colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
+ colvarbias.h colvarbias_abf.h colvargrid.h colvar_UIestimator.h \
+ colvarbias_alb.h colvarbias_histogram.h colvarbias_meta.h \
+ colvarbias_restraint.h colvarscript.h colvaratoms.h colvarcomp.h
 $(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \
 colvarparse.h
 $(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \
 colvarscript.h colvarbias.h colvar.h colvarparse.h colvardeps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
 colvaratoms.h
 $(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarscript.h \
 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \
- colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h
+ colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h \
+ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h
 $(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \
 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \
 colvarparse.h
--- a/lib/colvars/Makefile.lepton.deps
+++ b/lib/colvars/Makefile.lepton.deps
@ -0,0 +1,40 @@
+lepton/src/CompiledExpression.o: lepton/src/CompiledExpression.cpp \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h
+lepton/src/ExpressionProgram.o: lepton/src/ExpressionProgram.cpp \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h
+lepton/src/ExpressionTreeNode.o: lepton/src/ExpressionTreeNode.cpp \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/Exception.h lepton/include/lepton/Operation.h \
+ lepton/include/lepton/CustomFunction.h lepton/include/lepton/Exception.h
+lepton/src/Operation.o: lepton/src/Operation.cpp \
+ lepton/include/lepton/Operation.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ExpressionTreeNode.h lepton/src/MSVC_erfc.h
+lepton/src/ParsedExpression.o: lepton/src/ParsedExpression.cpp \
+ lepton/include/lepton/ParsedExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CompiledExpression.h \
+ lepton/include/lepton/ExpressionProgram.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h
+lepton/src/Parser.o: lepton/src/Parser.cpp \
+ lepton/include/lepton/Parser.h lepton/include/lepton/windowsIncludes.h \
+ lepton/include/lepton/CustomFunction.h lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ExpressionTreeNode.h \
+ lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
+ lepton/include/lepton/Exception.h \
+ lepton/include/lepton/ParsedExpression.h \
+ lepton/include/lepton/ExpressionTreeNode.h
--- a/lib/colvars/README
+++ b/lib/colvars/README
@ -47,6 +47,10 @@ correct for your system, else the LAMMPS build will likely fail.
 If you want to set a debug flag recognized by the library, the
 settings in Makefile.common should work.

+Note: some Colvars functions use the Lepton mathematical expression parser,
+which is here included (no additional steps required).  For more details, see:
+  https://simtk.org/projects/lepton
+

 ## Documentation

--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@ -1008,6 +1008,8 @@ int colvar::calc()

 int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
 {
+  colvarproxy *proxy = cvm::main()->proxy;
+
  int error_code = COLVARS_OK;
  if (cvm::debug())
    cvm::log("Calculating colvar \""+this->name+"\", components "+
@ -1018,14 +1020,18 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
    return error_code;
  }

-  if (cvm::step_relative() > 0) {
-    // Total force depends on Jacobian derivative from previous timestep
+  if ((cvm::step_relative() > 0) && (!proxy->total_forces_same_step())){
+    // Use Jacobian derivative from previous timestep
    error_code |= calc_cvc_total_force(first_cvc, num_cvcs);
  }
  // atom coordinates are updated by the next line
  error_code |= calc_cvc_values(first_cvc, num_cvcs);
  error_code |= calc_cvc_gradients(first_cvc, num_cvcs);
  error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);
+  if (proxy->total_forces_same_step()){
+    // Use Jacobian derivative from this timestep
+    error_code |= calc_cvc_total_force(first_cvc, num_cvcs);
+  }

  if (cvm::debug())
    cvm::log("Done calculating colvar \""+this->name+"\".\n");
@ -1043,6 +1049,7 @@ int colvar::collect_cvc_data()

  if (cvm::step_relative() > 0) {
    // Total force depends on Jacobian derivative from previous timestep
+    // collect_cvc_total_forces() uses the previous value of jd
    error_code |= collect_cvc_total_forces();
  }
  error_code |= collect_cvc_values();
@ -1138,7 +1145,7 @@ int colvar::collect_cvc_values()
      if (!cvcs[i]->is_enabled()) continue;
      x += (cvcs[i])->sup_coeff *
      ( ((cvcs[i])->sup_np != 1) ?
-        std::pow((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
+        cvm::integer_power((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
        (cvcs[i])->value().real_value );
    }
  } else {
@ -1219,7 +1226,7 @@ int colvar::collect_cvc_gradients()
      if (!cvcs[i]->is_enabled()) continue;
      // Coefficient: d(a * x^n) = a * n * x^(n-1) * dx
      cvm::real coeff = (cvcs[i])->sup_coeff * cvm::real((cvcs[i])->sup_np) *
-        std::pow((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1);
+        cvm::integer_power((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1);

      for (size_t j = 0; j < cvcs[i]->atom_groups.size(); j++) {

@ -1471,9 +1478,15 @@ cvm::real colvar::update_forces_energy()
    // Coupling force is a slow force, to be applied to atomic coords impulse-style
    f *= cvm::real(time_step_factor);

-    // The total force acting on the extended variable is f_ext
-    // This will be used in the next timestep
-    ft_reported = f_ext;
+    if (is_enabled(f_cv_subtract_applied_force)) {
+      // Report a "system" force without the biases on this colvar
+      // that is, just the spring force
+      ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
+    } else {
+      // The total force acting on the extended variable is f_ext
+      // This will be used in the next timestep
+      ft_reported = f_ext;
+    }

    // leapfrog: starting from x_i, f_i, v_(i-1/2)
    vr  += (0.5 * dt) * f_ext / ext_mass;
@ -1580,9 +1593,9 @@ void colvar::communicate_forces()
    for (i = 0; i < cvcs.size(); i++) {
      if (!cvcs[i]->is_enabled()) continue;
      (cvcs[i])->apply_force(f * (cvcs[i])->sup_coeff *
-                              cvm::real((cvcs[i])->sup_np) *
-                              (std::pow((cvcs[i])->value().real_value,
-                                      (cvcs[i])->sup_np-1)) );
+                             cvm::real((cvcs[i])->sup_np) *
+                             (cvm::integer_power((cvcs[i])->value().real_value,
+                                                 (cvcs[i])->sup_np-1)) );
    }

  } else {
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@ -60,7 +60,10 @@ public:

  /// \brief Current actual value (not extended DOF)
  colvarvalue const & actual_value() const;
-
+  
+  /// \brief Force constant of the spring
+  cvm::real const & force_constant() const;
+   
  /// \brief Current velocity (previously set by calc() or by read_traj())
  colvarvalue const & velocity() const;

@ -96,6 +99,12 @@ public:
  {
    return cv_features;
  }
+  static void delete_features() {
+    for (size_t i=0; i < cv_features.size(); i++) {
+      delete cv_features[i];
+    }
+    cv_features.clear();
+  }

  /// Implements possible actions to be carried out
  /// when a given feature is enabled
@ -592,6 +601,10 @@ public:
  }
 };

+inline cvm::real const & colvar::force_constant() const
+{
+  return ext_force_k;
+}

 inline colvarvalue const & colvar::value() const
 {
--- a/lib/colvars/colvar_UIestimator.h
+++ b/lib/colvars/colvar_UIestimator.h
@ -0,0 +1,736 @@
+// -*- c++ -*-
+
+// This file is part of the Collective Variables module (Colvars).
+// The original version of Colvars and its updates are located at:
+// https://github.com/colvars/colvars
+// Please update all Colvars source files before making any changes.
+// If you wish to distribute your changes, please submit them to the
+// Colvars repository at GitHub.
+
+#ifndef COLVAR_UIESTIMATOR_H
+#define COLVAR_UIESTIMATOR_H
+
+#include <cmath>
+#include <vector>
+#include <iostream>
+#include <fstream>
+#include <string>
+
+#include <typeinfo>
+
+// only for colvar module!
+// when integrated into other code, just remove this line and "...cvm::backup_file(...)"
+#include "colvarmodule.h"
+
+namespace UIestimator {
+    const int Y_SIZE = 21;            // defines the range of extended CV with respect to a given CV
+                                      // For example, CV=10, width=1, Y_SIZE=21, then eCV=[0-20], having a size of 21
+    const int HALF_Y_SIZE = 10;
+    const int EXTENDED_X_SIZE = HALF_Y_SIZE;
+    const double EPSILON = 0.000001;   // for comparison of float numbers
+
+    class n_matrix {   // Stores the distribution matrix of n(x,y)
+
+    public:
+        n_matrix() {}
+        n_matrix(const std::vector<double> & lowerboundary,   // lowerboundary of x
+            const std::vector<double> & upperboundary,   // upperboundary of
+            const std::vector<double> & width,           // width of x
+            const int y_size) {          // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered
+
+            int i;
+
+            this->lowerboundary = lowerboundary;
+            this->upperboundary = upperboundary;
+            this->width = width;
+            this->dimension = lowerboundary.size();
+            this->y_size = y_size;     // keep in mind the internal (spare) matrix is stored in diagonal form
+            this->y_total_size = int(pow(double(y_size), dimension) + EPSILON);
+
+            // the range of the matrix is [lowerboundary, upperboundary]
+            x_total_size = 1;
+            for (i = 0; i < dimension; i++) {
+                x_size.push_back(int((upperboundary[i] - lowerboundary[i]) / width[i] + EPSILON));
+                x_total_size *= x_size[i];
+            }
+
+            // initialize the internal matrix
+            matrix.reserve(x_total_size);
+            for (i = 0; i < x_total_size; i++) {
+                matrix.push_back(std::vector<int>(y_total_size, 0));
+            }
+
+            temp.resize(dimension);
+        }
+
+        int inline get_value(const std::vector<double> & x, const std::vector<double> & y) {
+            return matrix[convert_x(x)][convert_y(x, y)];
+        }
+
+        void inline set_value(const std::vector<double> & x, const std::vector<double> & y, const int value) {
+            matrix[convert_x(x)][convert_y(x,y)] = value;
+        }
+
+        void inline increase_value(const std::vector<double> & x, const std::vector<double> & y, const int value) {
+            matrix[convert_x(x)][convert_y(x,y)] += value;
+        }
+
+    private:
+        std::vector<double> lowerboundary;
+        std::vector<double> upperboundary;
+        std::vector<double> width;
+        int dimension;
+        std::vector<int> x_size;       // the size of x in each dimension
+        int x_total_size;              // the size of x of the internal matrix
+        int y_size;                    // the size of y in each dimension
+        int y_total_size;              // the size of y of the internal matrix
+
+        std::vector<std::vector<int> > matrix;  // the internal matrix
+
+        std::vector<int> temp;         // this vector is used in convert_x and convert_y to save computational resource
+
+        int i, j;
+
+        int convert_x(const std::vector<double> & x) {       // convert real x value to its interal index
+            for (i = 0; i < dimension; i++) {
+                temp[i] = int((x[i] - lowerboundary[i]) / width[i] + EPSILON);
+            }
+
+            int index = 0;
+            for (i = 0; i < dimension; i++) {
+                if (i + 1 < dimension) {
+                    int x_temp = 1;
+                    for (j = i + 1; j < dimension; j++)
+                        x_temp *= x_size[j];
+                    index += temp[i] * x_temp;
+                }
+                else
+                    index += temp[i];
+            }
+            return index;
+        }
+
+        int convert_y(const std::vector<double> & x, const std::vector<double> & y) {       // convert real y value to its interal index
+
+            int i;
+
+            for (i = 0; i < dimension; i++) {
+                temp[i] = round((round(y[i] / width[i] + EPSILON) - round(x[i] / width[i] + EPSILON)) + (y_size - 1) / 2 + EPSILON);
+            }
+
+            int index = 0;
+            for (i = 0; i < dimension; i++) {
+                if (i + 1 < dimension)
+                    index += temp[i] * int(pow(double(y_size), dimension - i - 1) + EPSILON);
+                else
+                    index += temp[i];
+            }
+            return index;
+        }
+
+        double round(double r) {
+            return (r > 0.0) ? floor(r + 0.5) : ceil(r - 0.5);
+        }
+    };
+
+    // vector, store the sum_x, sum_x_square, count_y
+    template <typename T>
+    class n_vector {
+
+    public:
+        n_vector() {}
+        n_vector(const std::vector<double> & lowerboundary,   // lowerboundary of x
+            const std::vector<double> & upperboundary,   // upperboundary of
+            const std::vector<double> & width,                // width of x
+            const int y_size,           // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered
+            const T & default_value) {         //   the default value of T
+
+            this->width = width;
+            this->dimension = lowerboundary.size();
+
+            x_total_size = 1;
+            for (int i = 0; i < dimension; i++) {
+                this->lowerboundary.push_back(lowerboundary[i] - (y_size - 1) / 2 * width[i] - EPSILON);
+                this->upperboundary.push_back(upperboundary[i] + (y_size - 1) / 2 * width[i] + EPSILON);
+
+                x_size.push_back(int((this->upperboundary[i] - this->lowerboundary[i]) / this->width[i] + EPSILON));
+                x_total_size *= x_size[i];
+            }
+
+            // initialize the internal vector
+            vector.resize(x_total_size, default_value);
+
+            temp.resize(dimension);
+        }
+
+        const T inline get_value(const std::vector<double> & x) {
+            return vector[convert_x(x)];
+        }
+
+        void inline set_value(const std::vector<double> & x, const T value) {
+            vector[convert_x(x)] = value;
+        }
+
+        void inline increase_value(const std::vector<double> & x, const T value) {
+            vector[convert_x(x)] += value;
+        }
+    private:
+        std::vector<double> lowerboundary;
+        std::vector<double> upperboundary;
+        std::vector<double> width;
+        int dimension;
+        std::vector<int> x_size;       // the size of x in each dimension
+        int x_total_size;              // the size of x of the internal matrix
+
+        std::vector<T> vector;  // the internal vector
+
+        std::vector<int> temp;         // this vector is used in convert_x and convert_y to save computational resource
+
+        int convert_x(const std::vector<double> & x) {       // convert real x value to its interal index
+
+            int i, j;
+
+            for (i = 0; i < dimension; i++) {
+                temp[i] = int((x[i] - lowerboundary[i]) / width[i] + EPSILON);
+            }
+
+            int index = 0;
+            for (i = 0; i < dimension; i++) {
+                if (i + 1 < dimension) {
+                    int x_temp = 1;
+                    for (j = i + 1; j < dimension; j++)
+                        x_temp *= x_size[j];
+                    index += temp[i] * x_temp;
+                }
+                else
+                    index += temp[i];
+            }
+            return index;
+        }
+    };
+
+    class UIestimator {     // the implemension of UI estimator
+
+    public:
+        UIestimator() {}
+
+        //called when (re)start an eabf simulation
+        UIestimator(const std::vector<double> & lowerboundary,
+            const std::vector<double> & upperboundary,
+            const std::vector<double> & width,
+            const std::vector<double> & krestr,                // force constant in eABF
+            const std::string & output_filename,              // the prefix of output files
+            const int output_freq,
+            const bool restart,                              // whether restart from a .count and a .grad file
+            const std::vector<std::string> & input_filename,   // the prefixes of input files
+            const double temperature) {
+
+            // initialize variables
+            this->lowerboundary = lowerboundary;
+            this->upperboundary = upperboundary;
+            this->width = width;
+            this->krestr = krestr;
+            this->output_filename = output_filename;
+            this->output_freq = output_freq;
+            this->restart = restart;
+            this->input_filename = input_filename;
+            this->temperature = temperature;
+
+            int i, j;
+
+            dimension = lowerboundary.size();
+
+            for (i = 0; i < dimension; i++) {
+                sum_x.push_back(n_vector<double>(lowerboundary, upperboundary, width, Y_SIZE, 0.0));
+                sum_x_square.push_back(n_vector<double>(lowerboundary, upperboundary, width, Y_SIZE, 0.0));
+
+                x_av.push_back(n_vector<double>(lowerboundary, upperboundary, width, Y_SIZE, 0.0));
+                sigma_square.push_back(n_vector<double>(lowerboundary, upperboundary, width, Y_SIZE, 0.0));
+            }
+
+            count_y = n_vector<int>(lowerboundary, upperboundary, width, Y_SIZE, 0);
+            distribution_x_y = n_matrix(lowerboundary, upperboundary, width, Y_SIZE);
+
+            grad = n_vector<std::vector<double> >(lowerboundary, upperboundary, width, 1, std::vector<double>(dimension, 0.0));
+            count = n_vector<int>(lowerboundary, upperboundary, width, 1, 0);
+
+            written = false;
+            written_1D = false;
+
+            if (dimension == 1) {
+                std::vector<double> upperboundary_temp = upperboundary;
+                upperboundary_temp[0] = upperboundary[0] + width[0];
+                oneD_pmf = n_vector<double>(lowerboundary, upperboundary_temp, width, 1, 0.0);
+            }
+
+            if (restart == true) {
+                input_grad = n_vector<std::vector<double> >(lowerboundary, upperboundary, width, 1, std::vector<double>(dimension, 0.0));
+                input_count = n_vector<int>(lowerboundary, upperboundary, width, 1, 0);
+
+                // initialize input_Grad and input_count
+                // the loop_flag is a n-dimensional vector, increae from lowerboundary to upperboundary when looping
+                std::vector<double> loop_flag(dimension, 0);
+                for (i = 0; i < dimension; i++) {
+                    loop_flag[i] = lowerboundary[i];
+                }
+
+                i = 0;
+                while (i >= 0) {
+                    for (j = 0; j < dimension; j++) {
+                        input_grad.set_value(loop_flag, std::vector<double>(dimension,0));
+                    }
+                    input_count.set_value(loop_flag, 0);
+
+                    // iterate over any dimensions
+                    i = dimension - 1;
+                    while (i >= 0) {
+                        loop_flag[i] += width[i];
+                        if (loop_flag[i] > upperboundary[i] - width[i] + EPSILON) {
+                            loop_flag[i] = lowerboundary[i];
+                            i--;
+                        }
+                        else
+                            break;
+                    }
+                }
+                read_inputfiles(input_filename);
+            }
+        }
+
+        ~UIestimator() {}
+
+        // called from MD engine every step
+        bool update(const int step, std::vector<double> x, std::vector<double> y) {
+
+            int i;
+
+            if (step % output_freq == 0) {
+                calc_pmf();
+                write_files();
+                //write_interal_data();
+            }
+
+            for (i = 0; i < dimension; i++) {
+                // for dihedral RC, it is possible that x = 179 and y = -179, should correct it
+                // may have problem, need to fix
+                if (x[i] > 150 && y[i] < -150) {
+                    y[i] += 360;
+                }
+                if (x[i] < -150 && y[i] > 150) {
+                    y[i] -= 360;
+                }
+
+                if (x[i] < lowerboundary[i] - EXTENDED_X_SIZE * width[i] + EPSILON || x[i] > upperboundary[i] + EXTENDED_X_SIZE * width[i] - EPSILON \
+                    || y[i] - x[i] < -HALF_Y_SIZE * width[i] + EPSILON || y[i] - x[i] > HALF_Y_SIZE * width[i] - EPSILON \
+                    || y[i] - lowerboundary[i] < -HALF_Y_SIZE * width[i] + EPSILON || y[i] - upperboundary[i] > HALF_Y_SIZE * width[i] - EPSILON)
+                    return false;
+            }
+
+            for (i = 0; i < dimension; i++) {
+                sum_x[i].increase_value(y, x[i]);
+                sum_x_square[i].increase_value(y, x[i] * x[i]);
+            }
+            count_y.increase_value(y, 1);
+
+            for (i = 0; i < dimension; i++) {
+                // adapt colvars precision
+                if (x[i] < lowerboundary[i] + EPSILON || x[i] > upperboundary[i] - EPSILON)
+                    return false;
+            }
+            distribution_x_y.increase_value(x, y, 1);
+
+            return true;
+        }
+
+        // update the output_filename
+        void update_output_filename(const std::string& filename) {
+            output_filename = filename;
+        }
+
+    private:
+        std::vector<n_vector<double> > sum_x;                        // the sum of x in each y bin
+        std::vector<n_vector<double> > sum_x_square;                 // the sum of x in each y bin
+        n_vector<int> count_y;                              // the distribution of y
+        n_matrix distribution_x_y;   // the distribution of <x, y> pair
+
+        int dimension;
+
+        std::vector<double> lowerboundary;
+        std::vector<double> upperboundary;
+        std::vector<double> width;
+        std::vector<double> krestr;
+        std::string output_filename;
+        int output_freq;
+        bool restart;
+        std::vector<std::string> input_filename;
+        double temperature;
+
+        n_vector<std::vector<double> > grad;
+        n_vector<int> count;
+
+        n_vector<double> oneD_pmf;
+
+        n_vector<std::vector<double> > input_grad;
+        n_vector<int> input_count;
+
+        // used in double integration
+        std::vector<n_vector<double> > x_av;
+        std::vector<n_vector<double> > sigma_square;
+
+        bool written;
+        bool written_1D;
+
+        // calculate gradients from the internal variables
+        void calc_pmf() {
+            int norm;
+            int i, j, k;
+
+            std::vector<double> loop_flag(dimension, 0);
+            for (i = 0; i < dimension; i++) {
+                loop_flag[i] = lowerboundary[i] - HALF_Y_SIZE * width[i];
+            }
+
+            i = 0;
+            while (i >= 0) {
+                norm = count_y.get_value(loop_flag) > 0 ? count_y.get_value(loop_flag) : 1;
+                for (j = 0; j < dimension; j++) {
+                    x_av[j].set_value(loop_flag, sum_x[j].get_value(loop_flag) / norm);
+                    sigma_square[j].set_value(loop_flag, sum_x_square[j].get_value(loop_flag) / norm - x_av[j].get_value(loop_flag) * x_av[j].get_value(loop_flag));
+                }
+
+                // iterate over any dimensions
+                i = dimension - 1;
+                while (i >= 0) {
+                    loop_flag[i] += width[i];
+                    if (loop_flag[i] > upperboundary[i] + HALF_Y_SIZE * width[i] - width[i] + EPSILON) {
+                        loop_flag[i] = lowerboundary[i] - HALF_Y_SIZE * width[i];
+                        i--;
+                    }
+                    else
+                        break;
+                }
+            }
+
+            // double integration
+            std::vector<double> av(dimension, 0);
+            std::vector<double> diff_av(dimension, 0);
+
+            std::vector<double> loop_flag_x(dimension, 0);
+            std::vector<double> loop_flag_y(dimension, 0);
+            for (i = 0; i < dimension; i++) {
+                loop_flag_x[i] = lowerboundary[i];
+                loop_flag_y[i] = loop_flag_x[i] - HALF_Y_SIZE * width[i];
+            }
+
+            i = 0;
+            while (i >= 0) {
+                norm = 0;
+                for (k = 0; k < dimension; k++) {
+                    av[k] = 0;
+                    diff_av[k] = 0;
+                    loop_flag_y[k] = loop_flag_x[k] - HALF_Y_SIZE * width[k];
+                }
+
+                int j = 0;
+                while (j >= 0) {
+                    norm += distribution_x_y.get_value(loop_flag_x, loop_flag_y);
+                    for (k = 0; k < dimension; k++) {
+                        if (sigma_square[k].get_value(loop_flag_y) > EPSILON || sigma_square[k].get_value(loop_flag_y) < -EPSILON)
+                            av[k] += distribution_x_y.get_value(loop_flag_x, loop_flag_y) * ( (loop_flag_x[k] + 0.5 * width[k]) - x_av[k].get_value(loop_flag_y)) / sigma_square[k].get_value(loop_flag_y);
+
+                        diff_av[k] += distribution_x_y.get_value(loop_flag_x, loop_flag_y) * (loop_flag_x[k] - loop_flag_y[k]);
+                    }
+
+                    // iterate over any dimensions
+                    j = dimension - 1;
+                    while (j >= 0) {
+                        loop_flag_y[j] += width[j];
+                        if (loop_flag_y[j] > loop_flag_x[j] + HALF_Y_SIZE * width[j] - width[j] + EPSILON) {
+                            loop_flag_y[j] = loop_flag_x[j] - HALF_Y_SIZE * width[j];
+                            j--;
+                        }
+                        else
+                            break;
+                    }
+                }
+
+                std::vector<double> grad_temp(dimension, 0);
+                for (k = 0; k < dimension; k++) {
+                    diff_av[k] /= (norm > 0 ? norm : 1);
+                    av[k] = cvm::boltzmann() * temperature * av[k] / (norm > 0 ? norm : 1);
+                    grad_temp[k] = av[k] - krestr[k] * diff_av[k];
+                }
+                grad.set_value(loop_flag_x, grad_temp);
+                count.set_value(loop_flag_x, norm);
+
+                // iterate over any dimensions
+                i = dimension - 1;
+                while (i >= 0) {
+                    loop_flag_x[i] += width[i];
+                    if (loop_flag_x[i] > upperboundary[i] - width[i] + EPSILON) {
+                        loop_flag_x[i] = lowerboundary[i];
+                        i--;
+                    }
+                    else
+                        break;
+                }
+            }
+        }
+
+
+        // calculate 1D pmf
+        void calc_1D_pmf()
+        {
+            std::vector<double> last_position(1, 0);
+            std::vector<double> position(1, 0);
+
+            double min = 0;
+            double dG = 0;
+            double i;
+
+            oneD_pmf.set_value(lowerboundary, 0);
+            last_position = lowerboundary;
+            for (i = lowerboundary[0] + width[0]; i < upperboundary[0] + EPSILON; i += width[0]) {
+                position[0] = i + EPSILON;
+                if (restart == false || input_count.get_value(last_position) == 0) {
+                    dG = oneD_pmf.get_value(last_position) + grad.get_value(last_position)[0] * width[0];
+                }
+                else {
+                    dG = oneD_pmf.get_value(last_position) + ((grad.get_value(last_position)[0] * count.get_value(last_position) + input_grad.get_value(last_position)[0] * input_count.get_value(last_position)) / (count.get_value(last_position) + input_count.get_value(last_position))) * width[0];
+                }
+                if (dG < min)
+                    min = dG;
+                oneD_pmf.set_value(position, dG);
+                last_position[0] = i + EPSILON;
+            }
+
+            for (i = lowerboundary[0]; i < upperboundary[0] + EPSILON; i += width[0]) {
+                position[0] = i + EPSILON;
+                oneD_pmf.set_value(position, oneD_pmf.get_value(position) - min);
+            }
+        }
+
+        // write 1D pmf
+        void write_1D_pmf() {
+            std::string pmf_filename = output_filename + ".UI.pmf";
+
+            // only for colvars module!
+            if (written_1D) cvm::backup_file(pmf_filename.c_str());
+
+            std::ostream* ofile_pmf = cvm::proxy->output_stream(pmf_filename.c_str());
+
+            std::vector<double> position(1, 0);
+            for (double i = lowerboundary[0]; i < upperboundary[0] + EPSILON; i += width[0]) {
+                *ofile_pmf << i << " ";
+                position[0] = i + EPSILON;
+                *ofile_pmf << oneD_pmf.get_value(position) << std::endl;
+            }
+            cvm::proxy->close_output_stream(pmf_filename.c_str());
+
+            written_1D = true;
+        }
+
+        // write heads of the output files
+        void writehead(std::ostream& os) const {
+            os << "# " << dimension << std::endl;
+            for (int i = 0; i < dimension; i++) {
+                os << "# " << lowerboundary[i] << " " << width[i] << " " << int((upperboundary[i] - lowerboundary[i]) / width[i] + EPSILON) << " " << 0 << std::endl;
+            }
+            os << std::endl;
+        }
+
+        // write interal data, used for testing
+        void write_interal_data() {
+            std::string internal_filename = output_filename + ".UI.internal";
+
+            std::ostream* ofile_internal = cvm::proxy->output_stream(internal_filename.c_str());
+
+            std::vector<double> loop_flag(dimension, 0);
+            for (int i = 0; i < dimension; i++) {
+                loop_flag[i] = lowerboundary[i];
+            }
+
+            int n = 0;
+            while (n >= 0) {
+                for (int j = 0; j < dimension; j++) {
+                    *ofile_internal << loop_flag[j] + 0.5 * width[j] << " ";
+                }
+
+                for (int k = 0; k < dimension; k++) {
+                    *ofile_internal << grad.get_value(loop_flag)[k] << " ";
+                }
+
+                std::vector<double> ii(dimension,0);
+                for (double i = loop_flag[0] - 10; i < loop_flag[0] + 10 + EPSILON; i+= width[0]) {
+                    for (double j = loop_flag[1] - 10; j< loop_flag[1] + 10 + EPSILON; j+=width[1]) {
+                        ii[0] = i;
+                        ii[1] = j;
+                        *ofile_internal << i <<" "<<j<<" "<< distribution_x_y.get_value(loop_flag,ii)<< " ";
+                    }
+                }
+                *ofile_internal << std::endl;
+
+                // iterate over any dimensions
+                n = dimension - 1;
+                while (n >= 0) {
+                    loop_flag[n] += width[n];
+                    if (loop_flag[n] > upperboundary[n] - width[n] + EPSILON) {
+                        loop_flag[n] = lowerboundary[n];
+                        n--;
+                    }
+                    else
+                        break;
+                }
+            }
+            cvm::proxy->close_output_stream(internal_filename.c_str());
+        }
+
+        // write output files
+        void write_files() {
+            std::string grad_filename = output_filename + ".UI.grad";
+            std::string hist_filename = output_filename + ".UI.hist.grad";
+            std::string count_filename = output_filename + ".UI.count";
+
+            int i, j;
+//
+            // only for colvars module!
+            if (written) cvm::backup_file(grad_filename.c_str());
+            //if (written) cvm::backup_file(hist_filename.c_str());
+            if (written) cvm::backup_file(count_filename.c_str());
+
+            std::ostream* ofile = cvm::proxy->output_stream(grad_filename.c_str());
+            std::ostream* ofile_hist = cvm::proxy->output_stream(hist_filename.c_str(), std::ios::app);
+            std::ostream* ofile_count = cvm::proxy->output_stream(count_filename.c_str());
+
+            writehead(*ofile);
+            writehead(*ofile_hist);
+            writehead(*ofile_count);
+
+            if (dimension == 1) {
+                calc_1D_pmf();
+                write_1D_pmf();
+            }
+
+            std::vector<double> loop_flag(dimension, 0);
+            for (i = 0; i < dimension; i++) {
+                loop_flag[i] = lowerboundary[i];
+            }
+
+            i = 0;
+            while (i >= 0) {
+                for (j = 0; j < dimension; j++) {
+                    *ofile << loop_flag[j] + 0.5 * width[j] << " ";
+                    *ofile_hist << loop_flag[j] + 0.5 * width[j] << " ";
+                    *ofile_count << loop_flag[j] + 0.5 * width[j] << " ";
+                }
+
+                if (restart == false) {
+                    for (j = 0; j < dimension; j++) {
+                        *ofile << grad.get_value(loop_flag)[j] << " ";
+                        *ofile_hist << grad.get_value(loop_flag)[j] << " ";
+                    }
+                    *ofile << std::endl;
+                    *ofile_hist << std::endl;
+                    *ofile_count << count.get_value(loop_flag) << " " <<std::endl;
+                }
+                else {
+                    double final_grad = 0;
+                    for (j = 0; j < dimension; j++) {
+                        int total_count_temp = (count.get_value(loop_flag) + input_count.get_value(loop_flag));
+                        if (input_count.get_value(loop_flag) == 0)
+                            final_grad = grad.get_value(loop_flag)[j];
+                        else
+                            final_grad = ((grad.get_value(loop_flag)[j] * count.get_value(loop_flag) + input_grad.get_value(loop_flag)[j] * input_count.get_value(loop_flag)) / total_count_temp);
+                        *ofile << final_grad << " ";
+                        *ofile_hist << final_grad << " ";
+                    }
+                    *ofile << std::endl;
+                    *ofile_hist << std::endl;
+                    *ofile_count << (count.get_value(loop_flag) + input_count.get_value(loop_flag)) << " " <<std::endl;
+                }
+
+                // iterate over any dimensions
+                i = dimension - 1;
+                while (i >= 0) {
+                    loop_flag[i] += width[i];
+                    if (loop_flag[i] > upperboundary[i] - width[i] + EPSILON) {
+                        loop_flag[i] = lowerboundary[i];
+                        i--;
+                        *ofile << std::endl;
+                        *ofile_hist << std::endl;
+                        *ofile_count << std::endl;
+                    }
+                    else
+                        break;
+                }
+            }
+            cvm::proxy->close_output_stream(grad_filename.c_str());
+            cvm::proxy->close_output_stream(hist_filename.c_str());
+            cvm::proxy->close_output_stream(count_filename.c_str());
+
+            written = true;
+        }
+
+        // read input files
+        void read_inputfiles(const std::vector<std::string> input_filename)
+        {
+            char sharp;
+            double nothing;
+            int dimension_temp;
+            int i, j, k, l, m;
+
+            std::vector<double> loop_bin_size(dimension, 0);
+            std::vector<double> position_temp(dimension, 0);
+            std::vector<double> grad_temp(dimension, 0);
+            int count_temp = 0;
+            for (i = 0; i < int(input_filename.size()); i++) {
+                int size = 1 , size_temp = 0;
+
+                std::string count_filename = input_filename[i] + ".UI.count";
+                std::string grad_filename = input_filename[i] + ".UI.grad";
+
+                std::ifstream count_file(count_filename.c_str(), std::ios::in);
+                std::ifstream grad_file(grad_filename.c_str(), std::ios::in);
+
+                count_file >> sharp >> dimension_temp;
+                grad_file >> sharp >> dimension_temp;
+
+                for (j = 0; j < dimension; j++) {
+                    count_file >> sharp >> nothing >> nothing >> size_temp >> nothing;
+                    grad_file >> sharp >> nothing >> nothing >> nothing >> nothing;
+                    size *= size_temp;
+                }
+
+                for (j = 0; j < size; j++) {
+                    do {
+                        for (k = 0; k < dimension; k++) {
+                            count_file >> position_temp[k];
+                            grad_file >> nothing;
+                        }
+
+                        for (l = 0; l < dimension; l++) {
+                            grad_file >> grad_temp[l];
+                        }
+                        count_file >> count_temp;
+                    }
+                    while (position_temp[i] < lowerboundary[i] - EPSILON || position_temp[i] > upperboundary[i] + EPSILON);
+
+                    if (count_temp == 0) {
+                        continue;
+                    }
+
+                    for (m = 0; m < dimension; m++) {
+                        grad_temp[m] = (grad_temp[m] * count_temp + input_grad.get_value(position_temp)[m] * input_count.get_value(position_temp)) / (count_temp + input_count.get_value(position_temp));
+                    }
+                    input_grad.set_value(position_temp, grad_temp);
+                    input_count.increase_value(position_temp, count_temp);
+                }
+
+                count_file.close();
+                grad_file.close();
+            }
+        }
+    };
+};
+
+#endif
--- a/lib/colvars/colvaratoms.cpp
+++ b/lib/colvars/colvaratoms.cpp
@ -817,6 +817,18 @@ int cvm::atom_group::create_sorted_ids(void)
 }


+int cvm::atom_group::overlap(const atom_group &g1, const atom_group &g2){
+  for (cvm::atom_const_iter ai1 = g1.begin(); ai1 != g1.end(); ai1++) {
+    for (cvm::atom_const_iter ai2 = g2.begin(); ai2 != g2.end(); ai2++) {
+      if (ai1->id == ai2->id) {
+        return (ai1->id + 1); // 1-based index to allow boolean usage
+      }
+    }
+  }
+  return 0;
+}
+
+
 void cvm::atom_group::center_ref_pos()
 {
  ref_pos_cog = cvm::atom_pos(0.0, 0.0, 0.0);
--- a/lib/colvars/colvaratoms.h
+++ b/lib/colvars/colvaratoms.h
@ -214,6 +214,12 @@ public:
  {
    return ag_features;
  }
+  static void delete_features() {
+    for (size_t i=0; i < ag_features.size(); i++) {
+      delete ag_features[i];
+    }
+    ag_features.clear();
+  }

 protected:

@ -280,6 +286,10 @@ public:
  /// Allocates and populates the sorted list of atom ids
  int create_sorted_ids(void);

+  /// Detect whether two groups share atoms
+  /// If yes, returns 1-based number of a common atom; else, returns 0
+  static int overlap(const atom_group &g1, const atom_group &g2);
+
  /// \brief When updating atomic coordinates, translate them to align with the
  /// center of mass of the reference coordinates
  bool b_center;
--- a/lib/colvars/colvarbias.cpp
+++ b/lib/colvars/colvarbias.cpp
@ -10,6 +10,7 @@
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarbias.h"
+#include "colvargrid.h"


 colvarbias::colvarbias(char const *key)
@ -31,12 +32,14 @@ int colvarbias::init(std::string const &conf)
 {
  colvarparse::init(conf);

+  size_t i = 0;
+
  if (name.size() == 0) {

    // first initialization

    cvm::log("Initializing a new \""+bias_type+"\" instance.\n");
-    rank = cvm::num_biases_type(bias_type);
+    rank = cvm::main()->num_biases_type(bias_type);
    get_keyval(conf, "name", name, bias_type+cvm::to_str(rank));

    {
@ -62,7 +65,7 @@ int colvarbias::init(std::string const &conf)
                     INPUT_ERROR);
          return INPUT_ERROR;
        }
-        for (size_t i = 0; i < colvar_names.size(); i++) {
+        for (i = 0; i < colvar_names.size(); i++) {
          add_colvar(colvar_names[i]);
        }
      }
@ -148,6 +151,13 @@ int colvarbias::clear()
 }


+int colvarbias::clear_state_data()
+{
+  // no mutable content to delete for base class
+  return COLVARS_OK;
+}
+
+
 int colvarbias::add_colvar(std::string const &cv_name)
 {
  if (colvar *cv = cvm::colvar_by_name(cv_name)) {
@ -164,6 +174,8 @@ int colvarbias::add_colvar(std::string const &cv_name)
    colvar_forces.back().is_derivative(); // colvar constraints are not applied to the force
    colvar_forces.back().reset();

+    previous_colvar_forces.push_back(colvar_forces.back());
+
    cv->biases.push_back(this); // add back-reference to this bias to colvar

    if (is_enabled(f_cvb_apply_force)) {
@ -204,7 +216,8 @@ int colvarbias::update()

 void colvarbias::communicate_forces()
 {
-  for (size_t i = 0; i < num_variables(); i++) {
+  size_t i = 0;
+  for (i = 0; i < num_variables(); i++) {
    if (cvm::debug()) {
      cvm::log("Communicating a force to colvar \""+
               variables(i)->name+"\".\n");
@ -216,6 +229,9 @@ void colvarbias::communicate_forces()
    // aware of this bias' time_step_factor
    variables(i)->add_bias_force(cvm::real(time_step_factor) * colvar_forces[i]);
  }
+  for (i = 0; i < num_variables(); i++) {
+    previous_colvar_forces[i] = colvar_forces[i];
+  }
 }


@ -389,6 +405,259 @@ std::ostream & colvarbias::write_traj(std::ostream &os)
  return os;
 }

+
+
+colvarbias_ti::colvarbias_ti(char const *key)
+  : colvarbias(key)
+{
+  provide(f_cvb_calc_ti_samples);
+  ti_avg_forces = NULL;
+  ti_count = NULL;
+}
+
+
+colvarbias_ti::~colvarbias_ti()
+{
+  colvarbias_ti::clear_state_data();
+}
+
+
+int colvarbias_ti::clear_state_data()
+{
+  if (ti_avg_forces != NULL) {
+    delete ti_avg_forces;
+    ti_avg_forces = NULL;
+  }
+  if (ti_count != NULL) {
+    delete ti_count;
+    ti_count = NULL;
+  }
+  return COLVARS_OK;
+}
+
+
+int colvarbias_ti::init(std::string const &conf)
+{
+  int error_code = COLVARS_OK;
+
+  get_keyval_feature(this, conf, "writeTISamples",
+                     f_cvb_write_ti_samples,
+                     is_enabled(f_cvb_write_ti_samples));
+
+  get_keyval_feature(this, conf, "writeTIPMF",
+                     f_cvb_write_ti_pmf,
+                     is_enabled(f_cvb_write_ti_pmf));
+
+  if ((num_variables() > 1) && is_enabled(f_cvb_write_ti_pmf)) {
+    return cvm::error("Error: only 1-dimensional PMFs can be written "
+                      "on the fly.\n"
+                      "Consider using writeTISamples instead and "
+                      "post-processing the sampled free-energy gradients.\n",
+                      COLVARS_NOT_IMPLEMENTED);
+  } else {
+    error_code |= init_grids();
+  }
+
+  if (is_enabled(f_cvb_write_ti_pmf)) {
+    enable(f_cvb_write_ti_samples);
+  }
+
+  if (is_enabled(f_cvb_calc_ti_samples)) {
+    std::vector<std::string> const time_biases =
+      cvm::main()->time_dependent_biases();
+    if (time_biases.size() > 0) {
+      if ((time_biases.size() > 1) || (time_biases[0] != this->name)) {
+        for (size_t i = 0; i < num_variables(); i++) {
+          if (! variables(i)->is_enabled(f_cv_subtract_applied_force)) {
+            return cvm::error("Error: cannot collect TI samples while other "
+                              "time-dependent biases are active and not all "
+                              "variables have subtractAppliedForces on.\n",
+                              INPUT_ERROR);
+          }
+        }
+      }
+    }
+  }
+
+  return error_code;
+}
+
+
+int colvarbias_ti::init_grids()
+{
+  if (is_enabled(f_cvb_calc_ti_samples)) {
+    if (ti_avg_forces == NULL) {
+      ti_bin.resize(num_variables());
+      ti_system_forces.resize(num_variables());
+      for (size_t icv = 0; icv < num_variables(); icv++) {
+        ti_system_forces[icv].type(variables(icv)->value());
+        ti_system_forces[icv].is_derivative();
+        ti_system_forces[icv].reset();
+      }
+      ti_avg_forces = new colvar_grid_gradient(colvars);
+      ti_count = new colvar_grid_count(colvars);
+      ti_avg_forces->samples = ti_count;
+      ti_count->has_parent_data = true;
+    }
+  }
+
+  return COLVARS_OK;
+}
+
+
+int colvarbias_ti::update()
+{
+  return update_system_forces(NULL);
+}
+
+
+int colvarbias_ti::update_system_forces(std::vector<colvarvalue> const
+                                        *subtract_forces)
+{
+  if (! is_enabled(f_cvb_calc_ti_samples)) {
+    return COLVARS_OK;
+  }
+
+  has_data = true;
+
+  if (cvm::debug()) {
+    cvm::log("Updating system forces for bias "+this->name+"\n");
+  }
+
+  colvarproxy *proxy = cvm::main()->proxy;
+
+  size_t i;
+
+  if (proxy->total_forces_same_step()) {
+    for (i = 0; i < num_variables(); i++) {
+      ti_bin[i] = ti_avg_forces->current_bin_scalar(i);
+    }
+  }
+
+  // Collect total colvar forces
+  if ((cvm::step_relative() > 0) || proxy->total_forces_same_step()) {
+    if (ti_avg_forces->index_ok(ti_bin)) {
+      for (i = 0; i < num_variables(); i++) {
+        if (variables(i)->is_enabled(f_cv_subtract_applied_force)) {
+          // this colvar is already subtracting all applied forces
+          ti_system_forces[i] = variables(i)->total_force();
+        } else {
+          ti_system_forces[i] = variables(i)->total_force() -
+            ((subtract_forces != NULL) ?
+             (*subtract_forces)[i] : previous_colvar_forces[i]);
+        }
+      }
+      ti_avg_forces->acc_value(ti_bin, ti_system_forces);
+    }
+  }
+
+  if (!proxy->total_forces_same_step()) {
+    // Set the index for use in the next iteration, when total forces come in
+    for (i = 0; i < num_variables(); i++) {
+      ti_bin[i] = ti_avg_forces->current_bin_scalar(i);
+    }
+  }
+
+  return COLVARS_OK;
+}
+
+
+std::string const colvarbias_ti::get_state_params() const
+{
+  return std::string("");
+}
+
+
+int colvarbias_ti::set_state_params(std::string const &state_conf)
+{
+  return COLVARS_OK;
+}
+
+
+std::ostream & colvarbias_ti::write_state_data(std::ostream &os)
+{
+  if (! is_enabled(f_cvb_calc_ti_samples)) {
+    return os;
+  }
+  os << "\nhistogram\n";
+  ti_count->write_raw(os);
+  os << "\nsystem_forces\n";
+  ti_avg_forces->write_raw(os);
+  return os;
+}
+
+
+std::istream & colvarbias_ti::read_state_data(std::istream &is)
+{
+  if (! is_enabled(f_cvb_calc_ti_samples)) {
+    return is;
+  }
+  if (cvm::debug()) {
+    cvm::log("Reading state data for the TI estimator.\n");
+  }
+  if (! read_state_data_key(is, "histogram")) {
+    return is;
+  }
+  if (! ti_count->read_raw(is)) {
+    return is;
+  }
+  if (! read_state_data_key(is, "system_forces")) {
+    return is;
+  }
+  if (! ti_avg_forces->read_raw(is)) {
+    return is;
+  }
+  if (cvm::debug()) {
+    cvm::log("Done reading state data for the TI estimator.\n");
+  }
+  return is;
+}
+
+
+int colvarbias_ti::write_output_files()
+{
+  if (!has_data) {
+    // nothing to write
+    return COLVARS_OK;
+  }
+
+  std::string const ti_output_prefix = cvm::output_prefix()+"."+this->name;
+
+  std::ostream *os = NULL;
+
+  if (is_enabled(f_cvb_write_ti_samples)) {
+    std::string const ti_count_file_name(ti_output_prefix+".ti.count");
+    os = cvm::proxy->output_stream(ti_count_file_name);
+    if (os) {
+      ti_count->write_multicol(*os);
+      cvm::proxy->close_output_stream(ti_count_file_name);
+    }
+
+    std::string const ti_grad_file_name(ti_output_prefix+".ti.grad");
+    os = cvm::proxy->output_stream(ti_grad_file_name);
+    if (os) {
+      ti_avg_forces->write_multicol(*os);
+      cvm::proxy->close_output_stream(ti_grad_file_name);
+    }
+  }
+
+  if (is_enabled(f_cvb_write_ti_pmf)) {
+    std::string const pmf_file_name(ti_output_prefix+".ti.pmf");
+    cvm::log("Writing TI PMF to file \""+pmf_file_name+"\".\n");
+    os = cvm::proxy->output_stream(pmf_file_name);
+    if (os) {
+      // get the FE gradient
+      ti_avg_forces->multiply_constant(-1.0);
+      ti_avg_forces->write_1D_integral(*os);
+      ti_avg_forces->multiply_constant(-1.0);
+      cvm::proxy->close_output_stream(pmf_file_name);
+    }
+  }
+
+  return COLVARS_OK;
+}
+
+
 // Static members

 std::vector<colvardeps::feature *> colvarbias::cvb_features;
--- a/lib/colvars/colvarbias.h
+++ b/lib/colvars/colvarbias.h
@ -109,6 +109,9 @@ public:
  /// \brief Delete everything
  virtual int clear();

+  /// \brief Delete only the allocatable data (save memory)
+  virtual int clear_state_data();
+
  /// Destructor
  virtual ~colvarbias();

@ -183,6 +186,12 @@ public:
  {
    return cvb_features;
  }
+  static void delete_features() {
+    for (size_t i=0; i < cvb_features.size(); i++) {
+      delete cvb_features[i];
+    }
+    cvb_features.clear();
+  }

 protected:

@ -194,6 +203,9 @@ protected:
  /// \brief Current forces from this bias to the variables
  std::vector<colvarvalue> colvar_forces;

+  /// \brief Forces last applied by this bias to the variables
+  std::vector<colvarvalue> previous_colvar_forces;
+
  /// \brief Current energy of this bias (colvar_forces should be obtained by deriving this)
  cvm::real                bias_energy;

@ -209,4 +221,48 @@ protected:

 };

+
+class colvar_grid_gradient;
+class colvar_grid_count;
+
+/// \brief Base class for unconstrained thermodynamic-integration FE estimator
+class colvarbias_ti : public virtual colvarbias {
+public:
+
+  colvarbias_ti(char const *key);
+  virtual ~colvarbias_ti();
+
+  virtual int clear_state_data();
+
+  virtual int init(std::string const &conf);
+  virtual int init_grids();
+  virtual int update();
+
+  /// Subtract applied forces (either last forces or argument) from the total
+  /// forces
+  virtual int update_system_forces(std::vector<colvarvalue> const
+                                   *subtract_forces);
+
+  virtual std::string const get_state_params() const;
+  virtual int set_state_params(std::string const &state_conf);
+  virtual std::ostream & write_state_data(std::ostream &os);
+  virtual std::istream & read_state_data(std::istream &is);
+  virtual int write_output_files();
+
+protected:
+
+  /// \brief Forces exerted from the system to the associated variables
+  std::vector<colvarvalue> ti_system_forces;
+
+  /// Averaged system forces
+  colvar_grid_gradient *ti_avg_forces;
+
+  /// Histogram of sampled data
+  colvar_grid_count *ti_count;
+
+  /// Because total forces may be from the last simulation step,
+  /// store the index of the variables then
+  std::vector<int> ti_bin;
+};
+
 #endif
--- a/lib/colvars/colvarbias_abf.cpp
+++ b/lib/colvars/colvarbias_abf.cpp
@ -14,6 +14,8 @@

 colvarbias_abf::colvarbias_abf(char const *key)
  : colvarbias(key),
+    b_UI_estimator(false),
+    b_CZAR_estimator(false),
    system_force(NULL),
    gradients(NULL),
    samples(NULL),
@ -159,6 +161,7 @@ int colvarbias_abf::init(std::string const &conf)

  // Data for eABF z-based estimator
  if (b_extended) {
+    get_keyval(conf, "CZARestimator", b_CZAR_estimator, true);
    // CZAR output files for stratified eABF
    get_keyval(conf, "writeCZARwindowFile", b_czar_window_file, false,
               colvarparse::parse_silent);
@ -187,8 +190,38 @@ int colvarbias_abf::init(std::string const &conf)
    read_gradients_samples();
  }

-  cvm::log("Finished ABF setup.\n");
+  // if extendedLangrangian is on, then call UI estimator
+  if (b_extended) {
+    get_keyval(conf, "UIestimator", b_UI_estimator, false);

+    if (b_UI_estimator) {
+    std::vector<double> UI_lowerboundary;
+    std::vector<double> UI_upperboundary;
+    std::vector<double> UI_width;
+    std::vector<double> UI_krestr;
+
+    bool UI_restart = (input_prefix.size() > 0);
+
+    for (size_t i = 0; i < colvars.size(); i++)
+    {
+      UI_lowerboundary.push_back(colvars[i]->lower_boundary);
+      UI_upperboundary.push_back(colvars[i]->upper_boundary);
+      UI_width.push_back(colvars[i]->width);
+      UI_krestr.push_back(colvars[i]->force_constant());
+    }
+      eabf_UI = UIestimator::UIestimator(UI_lowerboundary,
+                                         UI_upperboundary,
+                                         UI_width,
+                                         UI_krestr,                // force constant in eABF
+                                         output_prefix,              // the prefix of output files
+                                         cvm::restart_out_freq,
+                                         UI_restart,                    // whether restart from a .count and a .grad file
+                                         input_prefix,   // the prefixes of input files
+                                         cvm::temperature());
+    }
+  }
+
+  cvm::log("Finished ABF setup.\n");
  return COLVARS_OK;
 }

@ -271,6 +304,10 @@ int colvarbias_abf::update()
        // and subtract previous ABF force if necessary
        update_system_force(i);
      }
+      if (cvm::proxy->total_forces_same_step()) {
+        // e.g. in LAMMPS, total forces are current
+        force_bin = bin;
+      }
      gradients->acc_force(force_bin, system_force);
    }
    if ( z_gradients && update_bias ) {
@ -288,8 +325,11 @@ int colvarbias_abf::update()
    }
  }

-  // save bin for next timestep
-  force_bin = bin;
+  if (!cvm::proxy->total_forces_same_step()) {
+    // e.g. in NAMD, total forces will be available for next timestep
+    // hence we store the current colvar bin
+    force_bin = bin;
+  }

  // Reset biasing forces from previous timestep
  for (size_t i = 0; i < colvars.size(); i++) {
@ -332,7 +372,7 @@ int colvarbias_abf::update()
  }

  // update the output prefix; TODO: move later to setup_output() function
-  if (cvm::num_biases_feature(colvardeps::f_cvb_calc_pmf) == 1) {
+  if (cvm::main()->num_biases_feature(colvardeps::f_cvb_calc_pmf) == 1) {
    // This is the only bias computing PMFs
    output_prefix = cvm::output_prefix();
  } else {
@ -364,6 +404,20 @@ int colvarbias_abf::update()
    cvm::log("Prepared sample and gradient buffers at step "+cvm::to_str(cvm::step_absolute())+".");
  }

+  // update UI estimator every step
+  if (b_UI_estimator)
+  {
+    std::vector<double> x(colvars.size(),0);
+    std::vector<double> y(colvars.size(),0);
+    for (size_t i = 0; i < colvars.size(); i++)
+    {
+      x[i] = colvars[i]->actual_value();
+      y[i] = colvars[i]->value();
+    }
+    eabf_UI.update_output_filename(output_prefix);
+    eabf_UI.update(cvm::step_absolute(), x, y);
+  }
+
  return COLVARS_OK;
 }

@ -479,8 +533,8 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
    cvm::proxy->close_output_stream(pmf_out_name);
  }

-  if (z_gradients) {
-    // Write eABF-related quantities
+  if (b_CZAR_estimator) {
+    // Write eABF CZAR-related quantities

    std::string  z_samples_out_name = prefix + ".zcount";

@ -588,7 +642,7 @@ void colvarbias_abf::read_gradients_samples()
      is.close();
    }

-    if (z_gradients) {
+    if (b_CZAR_estimator) {
      // Read eABF z-averaged data for CZAR
      cvm::log("Reading z-histogram from " + z_samples_in_name + " and z-gradient from " + z_gradients_in_name);

@ -621,7 +675,7 @@ std::ostream & colvarbias_abf::write_state_data(std::ostream& os)
  os << "\ngradient\n";
  gradients->write_raw(os, 8);

-  if (z_gradients) {
+  if (b_CZAR_estimator) {
    os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format
    os << "\nz_samples\n";
    z_samples->write_raw(os, 8);
@ -655,7 +709,7 @@ std::istream & colvarbias_abf::read_state_data(std::istream& is)
    return is;
  }

-  if (z_gradients) {
+  if (b_CZAR_estimator) {

    if (! read_state_data_key(is, "z_samples")) {
      return is;
--- a/lib/colvars/colvarbias_abf.h
+++ b/lib/colvars/colvarbias_abf.h
@ -17,6 +17,7 @@

 #include "colvarbias.h"
 #include "colvargrid.h"
+#include "colvar_UIestimator.h"

 typedef cvm::real* gradient_t;

@ -50,6 +51,12 @@ private:
  /// Write CZAR output file for stratified eABF (.zgrad)
  bool      b_czar_window_file;
  size_t    history_freq;
+  /// Umbrella Integration estimator of free energy from eABF
+  UIestimator::UIestimator eabf_UI;
+  // Run UI estimator?
+  bool b_UI_estimator;
+  // Run CZAR estimator?
+  bool b_CZAR_estimator;

  /// Cap applied biasing force?
  bool                    cap_force;
--- a/lib/colvars/colvarbias_meta.cpp
+++ b/lib/colvars/colvarbias_meta.cpp
@ -33,7 +33,7 @@


 colvarbias_meta::colvarbias_meta(char const *key)
-  : colvarbias(key)
+  : colvarbias(key), colvarbias_ti(key)
 {
  new_hills_begin = hills.end();
  hills_traj_os = NULL;
@ -44,6 +44,7 @@ colvarbias_meta::colvarbias_meta(char const *key)
 int colvarbias_meta::init(std::string const &conf)
 {
  colvarbias::init(conf);
+  colvarbias_ti::init(conf);

  enable(f_cvb_calc_pmf);

@ -104,7 +105,7 @@ int colvarbias_meta::init(std::string const &conf)
      get_keyval(conf, "dumpFreeEnergyFile", dump_fes, true, colvarparse::parse_silent);
    if (get_keyval(conf, "saveFreeEnergyFile", dump_fes_save, false, colvarparse::parse_silent)) {
      cvm::log("Option \"saveFreeEnergyFile\" is deprecated, "
-               "please use \"keepFreeEnergyFile\" instead.");
+               "please use \"keepFreeEnergyFiles\" instead.");
    }
    get_keyval(conf, "keepFreeEnergyFiles", dump_fes_save, dump_fes_save);

@ -230,15 +231,7 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)

 colvarbias_meta::~colvarbias_meta()
 {
-  if (hills_energy) {
-    delete hills_energy;
-    hills_energy = NULL;
-  }
-
-  if (hills_energy_gradients) {
-    delete hills_energy_gradients;
-    hills_energy_gradients = NULL;
-  }
+  colvarbias_meta::clear_state_data();

  if (replica_hills_os) {
    cvm::proxy->close_output_stream(replica_hills_file);
@ -250,13 +243,31 @@ colvarbias_meta::~colvarbias_meta()
    hills_traj_os = NULL;
  }

-  if(target_dist) {
+  if (target_dist) {
    delete target_dist;
    target_dist = NULL;
  }
 }


+int colvarbias_meta::clear_state_data()
+{
+  if (hills_energy) {
+    delete hills_energy;
+    hills_energy = NULL;
+  }
+
+  if (hills_energy_gradients) {
+    delete hills_energy_gradients;
+    hills_energy_gradients = NULL;
+  }
+
+  hills.clear();
+  hills_off_grid.clear();
+
+  return COLVARS_OK;
+}
+

 // **********************************************************************
 // Hill management member functions
@ -336,6 +347,9 @@ int colvarbias_meta::update()
  // update base class
  error_code |= colvarbias::update();

+  // update the TI estimator (if defined)
+  error_code |= colvarbias_ti::update();
+
  // update grid definition, if needed
  error_code |= update_grid_params();
  // add new biasing energy/forces
@ -1000,6 +1014,10 @@ void colvarbias_meta::update_replicas_registry()
          (replicas.back())->hills_energy           = new colvar_grid_scalar(colvars);
          (replicas.back())->hills_energy_gradients = new colvar_grid_gradient(colvars);
        }
+        if (is_enabled(f_cvb_calc_ti_samples)) {
+          (replicas.back())->enable(f_cvb_calc_ti_samples);
+          (replicas.back())->colvarbias_ti::init_grids();
+        }
      }
    }
  } else {
@ -1374,6 +1392,8 @@ std::istream & colvarbias_meta::read_state_data(std::istream& is)
    }
  }

+  colvarbias_ti::read_state_data(is);
+
  if (cvm::debug())
    cvm::log("colvarbias_meta::read_restart() done\n");

@ -1474,7 +1494,7 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
 int colvarbias_meta::setup_output()
 {
  output_prefix = cvm::output_prefix();
-  if (cvm::num_biases_feature(colvardeps::f_cvb_calc_pmf) > 1) {
+  if (cvm::main()->num_biases_feature(colvardeps::f_cvb_calc_pmf) > 1) {
    // if this is not the only free energy integrator, append
    // this bias's name, to distinguish it from the output of the other
    // biases producing a .pmf file
@ -1631,6 +1651,7 @@ std::ostream & colvarbias_meta::write_state_data(std::ostream& os)
    }
  }

+  colvarbias_ti::write_state_data(os);
  return os;
 }

@ -1651,6 +1672,7 @@ int colvarbias_meta::write_state_to_replicas()

 int colvarbias_meta::write_output_files()
 {
+  colvarbias_ti::write_output_files();
  if (dump_fes) {
    write_pmf();
  }
--- a/lib/colvars/colvarbias_meta.h
+++ b/lib/colvars/colvarbias_meta.h
@ -19,7 +19,10 @@
 #include "colvargrid.h"

 /// Metadynamics bias (implementation of \link colvarbias \endlink)
-class colvarbias_meta : public colvarbias {
+class colvarbias_meta 
+  : public virtual colvarbias, 
+    public virtual colvarbias_ti
+{

 public:

@ -35,10 +38,13 @@ public:
  Communication comm;

  colvarbias_meta(char const *key);
+  virtual ~colvarbias_meta();
+
  virtual int init(std::string const &conf);
  virtual int init_well_tempered_params(std::string const &conf);
  virtual int init_ebmeta_params(std::string const &conf);
-  virtual ~colvarbias_meta();
+
+  virtual int clear_state_data();

  virtual int update();
  virtual int update_grid_params();
--- a/lib/colvars/colvarbias_restraint.cpp
+++ b/lib/colvars/colvarbias_restraint.cpp
@ -14,7 +14,7 @@


 colvarbias_restraint::colvarbias_restraint(char const *key)
-  : colvarbias(key)
+  : colvarbias(key), colvarbias_ti(key)
 {
 }

@ -24,6 +24,8 @@ int colvarbias_restraint::init(std::string const &conf)
  colvarbias::init(conf);
  enable(f_cvb_apply_force);

+  colvarbias_ti::init(conf);
+
  if (cvm::debug())
    cvm::log("Initializing a new restraint bias.\n");

@ -86,7 +88,7 @@ std::ostream & colvarbias_restraint::write_traj(std::ostream &os)


 colvarbias_restraint_centers::colvarbias_restraint_centers(char const *key)
-  : colvarbias(key), colvarbias_restraint(key)
+  : colvarbias(key), colvarbias_ti(key), colvarbias_restraint(key)
 {
 }

@ -145,7 +147,7 @@ int colvarbias_restraint_centers::change_configuration(std::string const &conf)


 colvarbias_restraint_k::colvarbias_restraint_k(char const *key)
-  : colvarbias(key), colvarbias_restraint(key)
+  : colvarbias(key), colvarbias_ti(key), colvarbias_restraint(key)
 {
  force_k = -1.0;
 }
@ -237,6 +239,7 @@ int colvarbias_restraint_moving::set_state_params(std::string const &conf)

 colvarbias_restraint_centers_moving::colvarbias_restraint_centers_moving(char const *key)
  : colvarbias(key),
+    colvarbias_ti(key),
    colvarbias_restraint(key),
    colvarbias_restraint_centers(key),
    colvarbias_restraint_moving(key)
@ -284,14 +287,17 @@ int colvarbias_restraint_centers_moving::init(std::string const &conf)
                                 target_centers[i],
                                 0.5);
    }
+
+    get_keyval(conf, "outputAccumulatedWork", b_output_acc_work,
+               b_output_acc_work); // TODO this conflicts with stages
+
  } else {
    target_centers.clear();
-    return COLVARS_OK;
  }

+  // Output restraint centers even when they do not change; some NAMD REUS
+  // scripts expect this behavior
  get_keyval(conf, "outputCenters", b_output_centers, b_output_centers);
-  get_keyval(conf, "outputAccumulatedWork", b_output_acc_work,
-             b_output_acc_work); // TODO this conflicts with stages

  return COLVARS_OK;
 }
@ -475,6 +481,7 @@ std::ostream & colvarbias_restraint_centers_moving::write_traj(std::ostream &os)

 colvarbias_restraint_k_moving::colvarbias_restraint_k_moving(char const *key)
  : colvarbias(key),
+    colvarbias_ti(key),
    colvarbias_restraint(key),
    colvarbias_restraint_k(key),
    colvarbias_restraint_moving(key)
@ -712,6 +719,7 @@ std::ostream & colvarbias_restraint::write_state(std::ostream &os)

 colvarbias_restraint_harmonic::colvarbias_restraint_harmonic(char const *key)
  : colvarbias(key),
+    colvarbias_ti(key),
    colvarbias_restraint(key),
    colvarbias_restraint_centers(key),
    colvarbias_restraint_moving(key),
@ -743,17 +751,22 @@ int colvarbias_restraint_harmonic::init(std::string const &conf)

 int colvarbias_restraint_harmonic::update()
 {
+  int error_code = COLVARS_OK;
+
+  // update the TI estimator (if defined)
+  error_code |= colvarbias_ti::update();
+
  // update parameters (centers or force constant)
-  colvarbias_restraint_centers_moving::update();
-  colvarbias_restraint_k_moving::update();
+  error_code |= colvarbias_restraint_centers_moving::update();
+  error_code |= colvarbias_restraint_k_moving::update();

  // update restraint energy and forces
-  colvarbias_restraint::update();
+  error_code |= colvarbias_restraint::update();

  // update accumulated work using the current forces
-  colvarbias_restraint_centers_moving::update_acc_work();
+  error_code |= colvarbias_restraint_centers_moving::update_acc_work();

-  return COLVARS_OK;
+  return error_code;
 }


@ -798,6 +811,18 @@ int colvarbias_restraint_harmonic::set_state_params(std::string const &conf)
 }


+std::ostream & colvarbias_restraint_harmonic::write_state_data(std::ostream &os)
+{
+  return colvarbias_ti::write_state_data(os);
+}
+
+
+std::istream & colvarbias_restraint_harmonic::read_state_data(std::istream &is)
+{
+  return colvarbias_ti::read_state_data(is);
+}
+
+
 std::ostream & colvarbias_restraint_harmonic::write_traj_label(std::ostream &os)
 {
  colvarbias_restraint::write_traj_label(os);
@ -845,6 +870,7 @@ cvm::real colvarbias_restraint_harmonic::energy_difference(std::string const &co

 colvarbias_restraint_harmonic_walls::colvarbias_restraint_harmonic_walls(char const *key)
  : colvarbias(key),
+    colvarbias_ti(key),
    colvarbias_restraint(key),
    colvarbias_restraint_k(key),
    colvarbias_restraint_moving(key),
@ -967,11 +993,15 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)

 int colvarbias_restraint_harmonic_walls::update()
 {
-  colvarbias_restraint_k_moving::update();
+  int error_code = COLVARS_OK;

-  colvarbias_restraint::update();
+  error_code |= colvarbias_ti::update();

-  return COLVARS_OK;
+  error_code |= colvarbias_restraint_k_moving::update();
+
+  error_code |= colvarbias_restraint::update();
+
+  return error_code;
 }


@ -1065,6 +1095,18 @@ int colvarbias_restraint_harmonic_walls::set_state_params(std::string const &con
 }


+std::ostream & colvarbias_restraint_harmonic_walls::write_state_data(std::ostream &os)
+{
+  return colvarbias_ti::write_state_data(os);
+}
+
+
+std::istream & colvarbias_restraint_harmonic_walls::read_state_data(std::istream &is)
+{
+  return colvarbias_ti::read_state_data(is);
+}
+
+
 std::ostream & colvarbias_restraint_harmonic_walls::write_traj_label(std::ostream &os)
 {
  colvarbias_restraint::write_traj_label(os);
@ -1084,6 +1126,7 @@ std::ostream & colvarbias_restraint_harmonic_walls::write_traj(std::ostream &os)

 colvarbias_restraint_linear::colvarbias_restraint_linear(char const *key)
  : colvarbias(key),
+    colvarbias_ti(key),
    colvarbias_restraint(key),
    colvarbias_restraint_centers(key),
    colvarbias_restraint_moving(key),
@ -1120,17 +1163,22 @@ int colvarbias_restraint_linear::init(std::string const &conf)

 int colvarbias_restraint_linear::update()
 {
+  int error_code = COLVARS_OK;
+
+  // update the TI estimator (if defined)
+  error_code |= colvarbias_ti::update();
+
  // update parameters (centers or force constant)
-  colvarbias_restraint_centers_moving::update();
-  colvarbias_restraint_k_moving::update();
+  error_code |= colvarbias_restraint_centers_moving::update();
+  error_code |= colvarbias_restraint_k_moving::update();

  // update restraint energy and forces
-  colvarbias_restraint::update();
+  error_code |= colvarbias_restraint::update();

  // update accumulated work using the current forces
-  colvarbias_restraint_centers_moving::update_acc_work();
+  error_code |= colvarbias_restraint_centers_moving::update_acc_work();

-  return COLVARS_OK;
+  return error_code;
 }


@ -1196,6 +1244,18 @@ int colvarbias_restraint_linear::set_state_params(std::string const &conf)
 }


+std::ostream & colvarbias_restraint_linear::write_state_data(std::ostream &os)
+{
+  return colvarbias_ti::write_state_data(os);
+}
+
+
+std::istream & colvarbias_restraint_linear::read_state_data(std::istream &is)
+{
+  return colvarbias_ti::read_state_data(is);
+}
+
+
 std::ostream & colvarbias_restraint_linear::write_traj_label(std::ostream &os)
 {
  colvarbias_restraint::write_traj_label(os);
--- a/lib/colvars/colvarbias_restraint.h
+++ b/lib/colvars/colvarbias_restraint.h
@ -16,7 +16,8 @@
 /// see derived classes for specific types
 /// (implementation of \link colvarbias \endlink)
 class colvarbias_restraint
-  : public virtual colvarbias
+  : public virtual colvarbias,
+    public virtual colvarbias_ti
 {

 public:
@ -95,7 +96,7 @@ protected:

 /// Options to change the restraint configuration over time (shared between centers and k moving)
 class colvarbias_restraint_moving
-  : public virtual colvarparse {
+  : public virtual colvarparse, public virtual colvardeps {
 public:

  colvarbias_restraint_moving(char const *key);
@ -226,6 +227,8 @@ public:
  virtual int update();
  virtual std::string const get_state_params() const;
  virtual int set_state_params(std::string const &conf);
+  virtual std::ostream & write_state_data(std::ostream &os);
+  virtual std::istream & read_state_data(std::istream &os);
  virtual std::ostream & write_traj_label(std::ostream &os);
  virtual std::ostream & write_traj(std::ostream &os);
  virtual int change_configuration(std::string const &conf);
@ -252,6 +255,8 @@ public:
  virtual void communicate_forces();
  virtual std::string const get_state_params() const;
  virtual int set_state_params(std::string const &conf);
+  virtual std::ostream & write_state_data(std::ostream &os);
+  virtual std::istream & read_state_data(std::istream &os);
  virtual std::ostream & write_traj_label(std::ostream &os);
  virtual std::ostream & write_traj(std::ostream &os);

@ -292,6 +297,8 @@ public:

  virtual std::string const get_state_params() const;
  virtual int set_state_params(std::string const &conf);
+  virtual std::ostream & write_state_data(std::ostream &os);
+  virtual std::istream & read_state_data(std::istream &os);
  virtual std::ostream & write_traj_label(std::ostream &os);
  virtual std::ostream & write_traj(std::ostream &os);

--- a/lib/colvars/colvarcomp.h
+++ b/lib/colvars/colvarcomp.h
@ -140,7 +140,12 @@ public:
  {
    return cvc_features;
  }
-
+  static void delete_features() {
+    for (size_t i=0; i < cvc_features.size(); i++) {
+      delete cvc_features[i];
+    }
+    cvc_features.clear();
+  }

  /// \brief Obtain data needed for the calculation for the backend
  virtual void read_data();
--- a/lib/colvars/colvarcomp_coordnums.cpp
+++ b/lib/colvars/colvarcomp_coordnums.cpp
@ -18,6 +18,7 @@



+
 template<bool calculate_gradients>
 cvm::real colvar::coordnum::switching_function(cvm::real const &r0,
                                               int const &en,
@ -32,8 +33,8 @@ cvm::real colvar::coordnum::switching_function(cvm::real const &r0,
  int const en2 = en/2;
  int const ed2 = ed/2;

-  cvm::real const xn = std::pow(l2, en2);
-  cvm::real const xd = std::pow(l2, ed2);
+  cvm::real const xn = cvm::integer_power(l2, en2);
+  cvm::real const xd = cvm::integer_power(l2, ed2);
  cvm::real const func = (1.0-xn)/(1.0-xd);

  if (calculate_gradients) {
@ -62,8 +63,8 @@ cvm::real colvar::coordnum::switching_function(cvm::rvector const &r0_vec,
  int const en2 = en/2;
  int const ed2 = ed/2;

-  cvm::real const xn = std::pow(l2, en2);
-  cvm::real const xd = std::pow(l2, ed2);
+  cvm::real const xn = cvm::integer_power(l2, en2);
+  cvm::real const xd = cvm::integer_power(l2, ed2);
  cvm::real const func = (1.0-xn)/(1.0-xd);

  if (calculate_gradients) {
@ -87,6 +88,12 @@ colvar::coordnum::coordnum(std::string const &conf)
  group1 = parse_group(conf, "group1");
  group2 = parse_group(conf, "group2");

+  if (int atom_number = cvm::atom_group::overlap(*group1, *group2)) {
+    cvm::error("Error: group1 and group2 share a common atom (number: " +
+      cvm::to_str(atom_number) + ")\n");
+    return;
+  }
+
  if (group1->b_dummy) {
    cvm::error("Error: only group2 is allowed to be a dummy atom\n");
    return;
@ -111,11 +118,17 @@ colvar::coordnum::coordnum(std::string const &conf)
    if (r0_vec.z < 0.0) r0_vec.z *= -1.0;
  }

-  get_keyval(conf, "expNumer", en, int(6) );
-  get_keyval(conf, "expDenom", ed, int(12));
+  get_keyval(conf, "expNumer", en, 6);
+  get_keyval(conf, "expDenom", ed, 12);

  if ( (en%2) || (ed%2) ) {
-    cvm::error("Error: odd exponents provided, can only use even ones.\n", INPUT_ERROR);
+    cvm::error("Error: odd exponent(s) provided, can only use even ones.\n",
+               INPUT_ERROR);
+  }
+
+  if ( (en <= 0) || (ed <= 0) ) {
+    cvm::error("Error: negative exponent(s) provided.\n",
+               INPUT_ERROR);
  }

  if (!is_enabled(f_cvc_pbc_minimum_image)) {
@ -250,8 +263,13 @@ colvar::h_bond::h_bond(std::string const &conf)
  get_keyval(conf, "expDenom", ed, 8);

  if ( (en%2) || (ed%2) ) {
-    cvm::error("Error: odd exponents provided, can only use even ones.\n");
-    return;
+    cvm::error("Error: odd exponent(s) provided, can only use even ones.\n",
+               INPUT_ERROR);
+  }
+
+  if ( (en <= 0) || (ed <= 0) ) {
+    cvm::error("Error: negative exponent(s) provided.\n",
+               INPUT_ERROR);
  }

  if (cvm::debug())
@ -318,12 +336,18 @@ colvar::selfcoordnum::selfcoordnum(std::string const &conf)
  group1 = parse_group(conf, "group1");

  get_keyval(conf, "cutoff", r0, cvm::real(4.0 * cvm::unit_angstrom()));
-  get_keyval(conf, "expNumer", en, int(6) );
-  get_keyval(conf, "expDenom", ed, int(12));
+  get_keyval(conf, "expNumer", en, 6);
+  get_keyval(conf, "expDenom", ed, 12);
+

  if ( (en%2) || (ed%2) ) {
-    cvm::error("Error: odd exponents provided, can only use even ones.\n");
-    return;
+    cvm::error("Error: odd exponent(s) provided, can only use even ones.\n",
+               INPUT_ERROR);
+  }
+
+  if ( (en <= 0) || (ed <= 0) ) {
+    cvm::error("Error: negative exponent(s) provided.\n",
+               INPUT_ERROR);
  }

  if (!is_enabled(f_cvc_pbc_minimum_image)) {
@ -401,12 +425,17 @@ colvar::groupcoordnum::groupcoordnum(std::string const &conf)
    if (r0_vec.z < 0.0) r0_vec.z *= -1.0;
  }

-  get_keyval(conf, "expNumer", en, int(6) );
-  get_keyval(conf, "expDenom", ed, int(12));
+  get_keyval(conf, "expNumer", en, 6);
+  get_keyval(conf, "expDenom", ed, 12);

  if ( (en%2) || (ed%2) ) {
-    cvm::error("Error: odd exponents provided, can only use even ones.\n");
-    return;
+    cvm::error("Error: odd exponent(s) provided, can only use even ones.\n",
+               INPUT_ERROR);
+  }
+
+  if ( (en <= 0) || (ed <= 0) ) {
+    cvm::error("Error: negative exponent(s) provided.\n",
+               INPUT_ERROR);
  }

  if (!is_enabled(f_cvc_pbc_minimum_image)) {
@ -438,8 +467,8 @@ cvm::real colvar::groupcoordnum::switching_function(cvm::real const &r0,
  int const en2 = en/2;
  int const ed2 = ed/2;

-  cvm::real const xn = std::pow(l2, en2);
-  cvm::real const xd = std::pow(l2, ed2);
+  cvm::real const xn = cvm::integer_power(l2, en2);
+  cvm::real const xd = cvm::integer_power(l2, ed2);
  cvm::real const func = (1.0-xn)/(1.0-xd);

  if (calculate_gradients) {
@ -471,8 +500,8 @@ cvm::real colvar::groupcoordnum::switching_function(cvm::rvector const &r0_vec,
  int const en2 = en/2;
  int const ed2 = ed/2;

-  cvm::real const xn = std::pow(l2, en2);
-  cvm::real const xd = std::pow(l2, ed2);
+  cvm::real const xn = cvm::integer_power(l2, en2);
+  cvm::real const xd = cvm::integer_power(l2, ed2);
  cvm::real const func = (1.0-xn)/(1.0-xd);

  if (calculate_gradients) {
--- a/lib/colvars/colvarcomp_distances.cpp
+++ b/lib/colvars/colvarcomp_distances.cpp
@ -1066,8 +1066,9 @@ void colvar::rmsd::calc_force_invgrads()
 void colvar::rmsd::calc_Jacobian_derivative()
 {
  // divergence of the rotated coordinates (including only derivatives of the rotation matrix)
-  cvm::real divergence = 0.0;
+  cvm::real rotation_term = 0.0;

+  // The rotation term only applies is coordinates are rotated
  if (atoms->b_rotate) {

    // gradient of the rotation matrix
@ -1104,7 +1105,7 @@ void colvar::rmsd::calc_Jacobian_derivative()

      for (size_t alpha = 0; alpha < 3; alpha++) {
        for (size_t beta = 0; beta < 3; beta++) {
-          divergence += grad_rot_mat[beta][alpha][alpha] * y[beta];
+          rotation_term += grad_rot_mat[beta][alpha][alpha] * y[beta];
        // Note: equation was derived for inverse rotation (see colvars paper)
        // so here the matrix is transposed
        // (eq would give   divergence += grad_rot_mat[alpha][beta][alpha] * y[beta];)
@ -1112,7 +1113,13 @@ void colvar::rmsd::calc_Jacobian_derivative()
      }
    }
  }
-  jd.real_value = x.real_value > 0.0 ? (3.0 * atoms->size() - 4.0 - divergence) / x.real_value : 0.0;
+
+  // The translation term only applies is coordinates are centered
+  cvm::real translation_term = atoms->b_center ? 3.0 : 0.0;
+
+  jd.real_value = x.real_value > 0.0 ?
+    (3.0 * atoms->size() - 1.0 - translation_term - rotation_term) / x.real_value :
+    0.0;
 }


--- a/lib/colvars/colvarcomp_protein.cpp
+++ b/lib/colvars/colvarcomp_protein.cpp
@ -150,8 +150,8 @@ void colvar::alpha_angles::calc_value()
      (theta[i])->calc_value();

      cvm::real const t = ((theta[i])->value().real_value-theta_ref)/theta_tol;
-      cvm::real const f = ( (1.0 - std::pow(t, (int) 2)) /
-                            (1.0 - std::pow(t, (int) 4)) );
+      cvm::real const f = ( (1.0 - (t*t)) /
+                            (1.0 - (t*t*t*t)) );

      x.real_value += theta_norm * f;

@ -202,12 +202,12 @@ void colvar::alpha_angles::apply_force(colvarvalue const &force)
    for (size_t i = 0; i < theta.size(); i++) {

      cvm::real const t = ((theta[i])->value().real_value-theta_ref)/theta_tol;
-      cvm::real const f = ( (1.0 - std::pow(t, (int) 2)) /
-                            (1.0 - std::pow(t, (int) 4)) );
+      cvm::real const f = ( (1.0 - (t*t)) /
+                            (1.0 - (t*t*t*t)) );

      cvm::real const dfdt =
-        1.0/(1.0 - std::pow(t, (int) 4)) *
-        ( (-2.0 * t) + (-1.0*f)*(-4.0 * std::pow(t, (int) 3)) );
+        1.0/(1.0 - (t*t*t*t)) *
+        ( (-2.0 * t) + (-1.0*f)*(-4.0 * (t*t*t)) );

      (theta[i])->apply_force(theta_norm *
                               dfdt * (1.0/theta_tol) *
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@ -413,15 +413,27 @@ void colvardeps::init_cvb_requires() {
    init_feature(f_cvb_apply_force, "apply force", f_type_user);
    f_req_children(f_cvb_apply_force, f_cv_gradient);

-    init_feature(f_cvb_get_total_force, "obtain total force");
+    init_feature(f_cvb_get_total_force, "obtain total force", f_type_dynamic);
    f_req_children(f_cvb_get_total_force, f_cv_total_force);

    init_feature(f_cvb_history_dependent, "history-dependent", f_type_static);

+    init_feature(f_cvb_time_dependent, "time-dependent", f_type_static);
+
    init_feature(f_cvb_scalar_variables, "require scalar variables", f_type_static);
    f_req_children(f_cvb_scalar_variables, f_cv_scalar);

    init_feature(f_cvb_calc_pmf, "calculate a PMF", f_type_static);
+
+    init_feature(f_cvb_calc_ti_samples, "calculate TI samples", f_type_dynamic);
+    f_req_self(f_cvb_calc_ti_samples, f_cvb_get_total_force);
+    f_req_children(f_cvb_calc_ti_samples, f_cv_grid);
+
+    init_feature(f_cvb_write_ti_samples, "write TI samples ", f_type_user);
+    f_req_self(f_cvb_write_ti_samples, f_cvb_calc_ti_samples);
+
+    init_feature(f_cvb_write_ti_pmf, "write TI PMF", f_type_user);
+    f_req_self(f_cvb_write_ti_pmf, f_cvb_calc_ti_samples);
  }

  // Initialize feature_states for each instance
@ -431,6 +443,9 @@ void colvardeps::init_cvb_requires() {
    // Most features are available, so we set them so
    // and list exceptions below
  }
+
+  // only compute TI samples when deriving from colvarbias_ti
+  feature_states[f_cvb_calc_ti_samples].available = false;
 }


@ -504,9 +519,6 @@ void colvardeps::init_cv_requires() {

    init_feature(f_cv_subtract_applied_force, "subtract applied force from total force", f_type_user);
    f_req_self(f_cv_subtract_applied_force, f_cv_total_force);
-    // There is no well-defined way to implement f_cv_subtract_applied_force
-    // in the case of extended-Lagrangian colvars
-    f_req_exclude(f_cv_subtract_applied_force, f_cv_extended_Lagrangian);

    init_feature(f_cv_lower_boundary, "lower boundary", f_type_user);
    f_req_self(f_cv_lower_boundary, f_cv_scalar);
@ -514,7 +526,7 @@ void colvardeps::init_cv_requires() {
    init_feature(f_cv_upper_boundary, "upper boundary", f_type_user);
    f_req_self(f_cv_upper_boundary, f_cv_scalar);

-    init_feature(f_cv_grid, "grid", f_type_user);
+    init_feature(f_cv_grid, "grid", f_type_dynamic);
    f_req_self(f_cv_grid, f_cv_lower_boundary);
    f_req_self(f_cv_grid, f_cv_upper_boundary);

@ -693,7 +705,6 @@ void colvardeps::print_state() {
 }


-
 void colvardeps::add_child(colvardeps *child) {

  children.push_back(child);
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@ -180,8 +180,6 @@ public:

 protected:

-
-
  /// Parse a keyword and enable a feature accordingly
  bool get_keyval_feature(colvarparse *cvp,
                          std::string const &conf, char const *key,
@ -229,10 +227,18 @@ public:
    f_cvb_get_total_force,
    /// \brief depends on simulation history
    f_cvb_history_dependent,
+    /// \brief depends on time
+    f_cvb_time_dependent,
    /// \brief requires scalar colvars
    f_cvb_scalar_variables,
    /// \brief whether this bias will compute a PMF
    f_cvb_calc_pmf,
+    /// \brief whether this bias will compute TI samples
+    f_cvb_calc_ti_samples,
+    /// \brief whether this bias will write TI samples
+    f_cvb_write_ti_samples,
+    /// \brief whether this bias should write the TI PMF
+    f_cvb_write_ti_pmf,
    f_cvb_ntot
  };

--- a/lib/colvars/colvargrid.h
+++ b/lib/colvars/colvargrid.h
@ -1403,6 +1403,15 @@ public:
  /// Constructor from a vector of colvars
  colvar_grid_gradient(std::vector<colvar *>  &colvars);

+  /// \brief Accumulate the value
+  inline void acc_value(std::vector<int> const &ix, std::vector<colvarvalue> const &values) {
+    for (size_t imult = 0; imult < mult; imult++) {
+      data[address(ix) + imult] += values[imult].real_value;
+    }
+    if (samples)
+      samples->incr_count(ix);
+  }
+
  /// \brief Accumulate the gradient
  inline void acc_grad(std::vector<int> const &ix, cvm::real const *grads) {
    for (size_t imult = 0; imult < mult; imult++) {
--- a/lib/colvars/colvarmodule.cpp
+++ b/lib/colvars/colvarmodule.cpp
@ -22,7 +22,7 @@
 #include "colvarbias_restraint.h"
 #include "colvarscript.h"
 #include "colvaratoms.h"
-
+#include "colvarcomp.h"

 colvarmodule::colvarmodule(colvarproxy *proxy_in)
 {
@ -274,9 +274,9 @@ int colvarmodule::parse_global_params(std::string const &conf)
  parse->get_keyval(conf, "colvarsRestartFrequency",
                    restart_out_freq, restart_out_freq);

-  // if this is true when initializing, it means
-  // we are continuing after a reset(): default to true
-  parse->get_keyval(conf, "colvarsTrajAppend", cv_traj_append, cv_traj_append);
+  // Deprecate append flag
+  parse->get_keyval(conf, "colvarsTrajAppend",
+                    cv_traj_append, cv_traj_append, colvarparse::parse_silent);

  parse->get_keyval(conf, "scriptedColvarForces", use_scripted_forces, false);

@ -409,22 +409,12 @@ int colvarmodule::parse_biases(std::string const &conf)
    cvm::decrease_depth();
  }

-  size_t i;
-
-  size_t n_hist_dep_biases = 0;
-  std::vector<std::string> hist_dep_biases_names;
-  for (i = 0; i < biases.size(); i++) {
-    if (biases[i]->is_enabled(colvardeps::f_cvb_apply_force) &&
-        biases[i]->is_enabled(colvardeps::f_cvb_history_dependent)) {
-      n_hist_dep_biases++;
-      hist_dep_biases_names.push_back(biases[i]->name);
-    }
-  }
-  if (n_hist_dep_biases > 1) {
-    cvm::log("WARNING: there are "+cvm::to_str(n_hist_dep_biases)+
-             " history-dependent biases with non-zero force parameters:\n"+
-             cvm::to_str(hist_dep_biases_names)+"\n"+
-             "Please make sure that their forces do not counteract each other.\n");
+  std::vector<std::string> const time_biases = time_dependent_biases();
+  if (time_biases.size() > 1) {
+    cvm::log("WARNING: there are "+cvm::to_str(time_biases.size())+
+             " time-dependent biases with non-zero force parameters:\n"+
+             cvm::to_str(time_biases)+"\n"+
+             "Please ensure that their forces do not counteract each other.\n");
  }

  if (biases.size() || use_scripted_forces) {
@ -441,7 +431,7 @@ int colvarmodule::parse_biases(std::string const &conf)
 }


-int colvarmodule::num_biases_feature(int feature_id)
+int colvarmodule::num_biases_feature(int feature_id) const
 {
  colvarmodule *cv = cvm::main();
  size_t n = 0;
@ -456,7 +446,7 @@ int colvarmodule::num_biases_feature(int feature_id)
 }


-int colvarmodule::num_biases_type(std::string const &type)
+int colvarmodule::num_biases_type(std::string const &type) const
 {
  colvarmodule *cv = cvm::main();
  size_t n = 0;
@ -471,6 +461,22 @@ int colvarmodule::num_biases_type(std::string const &type)
 }


+std::vector<std::string> const colvarmodule::time_dependent_biases() const
+{
+  size_t i;
+  std::vector<std::string> biases_names;
+  for (i = 0; i < biases.size(); i++) {
+    if (biases[i]->is_enabled(colvardeps::f_cvb_apply_force) &&
+        biases[i]->is_enabled(colvardeps::f_cvb_active) &&
+        (biases[i]->is_enabled(colvardeps::f_cvb_history_dependent) ||
+         biases[i]->is_enabled(colvardeps::f_cvb_time_dependent))) {
+      biases_names.push_back(biases[i]->name);
+    }
+  }
+  return biases_names;
+}
+
+
 int colvarmodule::catch_input_errors(int result)
 {
  if (result != COLVARS_OK || get_error()) {
@ -673,8 +679,15 @@ int colvarmodule::calc()
  }

  // write restart files, if needed
-  if (restart_out_freq && restart_out_name.size()) {
-    error_code |= write_restart_files();
+  if (restart_out_freq && (cvm::step_relative() > 0) &&
+      ((cvm::step_absolute() % restart_out_freq) == 0) ) {
+    if (restart_out_name.size()) {
+      // Write restart file, if different from main output
+      error_code |= write_restart_file(restart_out_name);
+    } else {
+      error_code |= write_restart_file(output_prefix()+".colvars.state");
+    }
+    write_output_files();
  }

  return error_code;
@ -916,21 +929,16 @@ int colvarmodule::calc_scripted_forces()
 }


-int colvarmodule::write_restart_files()
+int colvarmodule::write_restart_file(std::string const &out_name)
 {
-  if ( (cvm::step_relative() > 0) &&
-       ((cvm::step_absolute() % restart_out_freq) == 0) ) {
-    cvm::log("Writing the state file \""+
-             restart_out_name+"\".\n");
-    proxy->backup_file(restart_out_name);
-    std::ostream *restart_out_os = proxy->output_stream(restart_out_name);
-    if (!restart_out_os) return cvm::get_error();
-    if (!write_restart(*restart_out_os)) {
-      return cvm::error("Error: in writing restart file.\n", FILE_ERROR);
-    }
-    proxy->close_output_stream(restart_out_name);
+  cvm::log("Saving collective variables state to \""+out_name+"\".\n");
+  proxy->backup_file(out_name);
+  std::ostream *restart_out_os = proxy->output_stream(out_name);
+  if (!restart_out_os) return cvm::get_error();
+  if (!write_restart(*restart_out_os)) {
+    return cvm::error("Error: in writing restart file.\n", FILE_ERROR);
  }
-
+  proxy->close_output_stream(out_name);
  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
 }

@ -1011,7 +1019,15 @@ colvarmodule::~colvarmodule()
 {
  if ((proxy->smp_thread_id() == COLVARS_NOT_IMPLEMENTED) ||
      (proxy->smp_thread_id() == 0)) {
+
    reset();
+
+    // Delete contents of static arrays
+    colvarbias::delete_features();
+    colvar::delete_features();
+    colvar::cvc::delete_features();
+    atom_group::delete_features();
+
    delete parse;
    parse = NULL;
    proxy = NULL;
@ -1261,7 +1277,7 @@ continue the previous simulation.\n\n");
 to:\n\
 \""+ proxy->input_prefix()+".colvars.state\"\n");
    output_prefix() = output_prefix()+".tmp";
-    write_output_files();
+    write_restart_file(output_prefix()+".colvars.state");
    cvm::error("Exiting with error until issue is addressed.\n", FATAL_ERROR);
  }

@ -1277,24 +1293,13 @@ int colvarmodule::backup_file(char const *filename)

 int colvarmodule::write_output_files()
 {
-  // if this is a simulation run (i.e. not a postprocessing), output data
-  // must be written to be able to restart the simulation
-  std::string const out_name =
-    (output_prefix().size() ?
-     std::string(output_prefix()+".colvars.state") :
-     std::string("colvars.state"));
-  cvm::log("Saving collective variables state to \""+out_name+"\".\n");
-
-  std::ostream * os = proxy->output_stream(out_name);
-  os->setf(std::ios::scientific, std::ios::floatfield);
-  this->write_restart(*os);
-  proxy->close_output_stream(out_name);
+  int error_code = COLVARS_OK;

  cvm::increase_depth();
  for (std::vector<colvar *>::iterator cvi = colvars.begin();
       cvi != colvars.end();
       cvi++) {
-    (*cvi)->write_output_files();
+    error_code |= (*cvi)->write_output_files();
  }
  cvm::decrease_depth();

@ -1302,8 +1307,8 @@ int colvarmodule::write_output_files()
  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
-    (*bi)->write_output_files();
-    (*bi)->write_state_to_replicas();
+    error_code |= (*bi)->write_output_files();
+    error_code |= (*bi)->write_state_to_replicas();
  }
  cvm::decrease_depth();

@ -1403,15 +1408,12 @@ std::ostream & colvarmodule::write_restart(std::ostream &os)
       cvi != colvars.end();
       cvi++) {
    (*cvi)->write_restart(os);
-    error_code |= (*cvi)->write_output_files();
  }

  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
    (*bi)->write_state(os);
-    error_code |= (*bi)->write_state_to_replicas();
-    error_code |= (*bi)->write_output_files();
  }
  cvm::decrease_depth();

--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@ -83,6 +83,15 @@ public:

  /// Defining an abstract real number allows to switch precision
  typedef  double    real;
+
+  /// Override std::pow with a product for n positive integer
+  static inline real integer_power(real x, int n)
+  {
+    real result = 1.0;
+    for (int i = 0; i < n; i++) result *= x;
+    return result;
+  }
+
  /// Residue identifier
  typedef  int       residue_id;

@ -293,10 +302,13 @@ private:
 public:

  /// Return how many biases have this feature enabled
-  static int num_biases_feature(int feature_id);
+  int num_biases_feature(int feature_id) const;

  /// Return how many biases are defined with this type
-  static int num_biases_type(std::string const &type);
+  int num_biases_type(std::string const &type) const;
+
+  /// Return the names of time-dependent biases with forces enabled
+  std::vector<std::string> const time_dependent_biases() const;

 private:
  /// Useful wrapper to interrupt parsing if any error occurs
@ -334,9 +346,9 @@ public:

  /// Write all trajectory files
  int write_traj_files();
-  /// Write all restart files
-  int write_restart_files();
-  /// Write all FINAL output files
+  /// Write a state file useful to resume the simulation
+  int write_restart_file(std::string const &out_name);
+  /// Write all other output files
  int write_output_files();
  /// Backup a file before writing it
  static int backup_file(char const *filename);
@ -580,7 +592,7 @@ public:
  /// from static functions in the colvarmodule class
  static colvarproxy *proxy;

-  /// \brief Accessor for the above
+  /// \brief Access the one instance of the Colvars module
  static colvarmodule *main();

 };
--- a/lib/colvars/colvarproxy.cpp
+++ b/lib/colvars/colvarproxy.cpp
@ -10,6 +10,10 @@
 #include <sstream>
 #include <string.h>

+#if defined(_OPENMP)
+#include <omp.h>
+#endif
+
 #include "colvarmodule.h"
 #include "colvarproxy.h"
 #include "colvarscript.h"
@ -40,6 +44,12 @@ bool colvarproxy_system::total_forces_enabled() const
 }


+bool colvarproxy_system::total_forces_same_step() const
+{
+  return false;
+}
+
+
 cvm::real colvarproxy_system::position_dist2(cvm::atom_pos const &pos1,
                                             cvm::atom_pos const &pos2)
 {
@ -204,7 +214,13 @@ void colvarproxy_atom_groups::clear_atom_group(int index)

 colvarproxy_smp::colvarproxy_smp()
 {
-  b_smp_active = true;
+  b_smp_active = true; // May be disabled by user option
+  omp_lock_state = NULL;
+#if defined(_OPENMP)
+  if (smp_thread_id() == 0) {
+    omp_init_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
+  }
+#endif
 }


@ -213,60 +229,143 @@ colvarproxy_smp::~colvarproxy_smp() {}

 int colvarproxy_smp::smp_enabled()
 {
+#if defined(_OPENMP)
+  if (b_smp_active) {
+    return COLVARS_OK;
+  }
+  return COLVARS_ERROR;
+#else
  return COLVARS_NOT_IMPLEMENTED;
+#endif
 }


 int colvarproxy_smp::smp_colvars_loop()
 {
+#if defined(_OPENMP)
+  colvarmodule *cv = cvm::main();
+  colvarproxy *proxy = cv->proxy;
+#pragma omp parallel for
+  for (size_t i = 0; i < cv->variables_active_smp()->size(); i++) {
+    colvar *x = (*(cv->variables_active_smp()))[i];
+    int x_item = (*(cv->variables_active_smp_items()))[i];
+    if (cvm::debug()) {
+      cvm::log("["+cvm::to_str(proxy->smp_thread_id())+"/"+
+               cvm::to_str(proxy->smp_num_threads())+
+               "]: calc_colvars_items_smp(), i = "+cvm::to_str(i)+", cv = "+
+               x->name+", cvc = "+cvm::to_str(x_item)+"\n");
+    }
+    x->calc_cvcs(x_item, 1);
+  }
+  return cvm::get_error();
+#else
  return COLVARS_NOT_IMPLEMENTED;
+#endif
 }


 int colvarproxy_smp::smp_biases_loop()
 {
+#if defined(_OPENMP)
+  colvarmodule *cv = cvm::main();
+#pragma omp parallel
+  {
+#pragma omp for
+    for (size_t i = 0; i < cv->biases_active()->size(); i++) {
+      colvarbias *b = (*(cv->biases_active()))[i];
+      if (cvm::debug()) {
+        cvm::log("Calculating bias \""+b->name+"\" on thread "+
+                 cvm::to_str(smp_thread_id())+"\n");
+      }
+      b->update();
+    }
+  }
+  return cvm::get_error();
+#else
  return COLVARS_NOT_IMPLEMENTED;
+#endif
 }


 int colvarproxy_smp::smp_biases_script_loop()
 {
+#if defined(_OPENMP)
+  colvarmodule *cv = cvm::main();
+#pragma omp parallel
+  {
+#pragma omp single nowait
+    {
+      cv->calc_scripted_forces();
+    }
+#pragma omp for
+    for (size_t i = 0; i < cv->biases_active()->size(); i++) {
+      colvarbias *b = (*(cv->biases_active()))[i];
+      if (cvm::debug()) {
+        cvm::log("Calculating bias \""+b->name+"\" on thread "+
+                 cvm::to_str(smp_thread_id())+"\n");
+      }
+      b->update();
+    }
+  }
+  return cvm::get_error();
+#else
  return COLVARS_NOT_IMPLEMENTED;
+#endif
 }


+
+
 int colvarproxy_smp::smp_thread_id()
 {
+#if defined(_OPENMP)
+  return omp_get_thread_num();
+#else
  return COLVARS_NOT_IMPLEMENTED;
+#endif
 }


 int colvarproxy_smp::smp_num_threads()
 {
+#if defined(_OPENMP)
+  return omp_get_max_threads();
+#else
  return COLVARS_NOT_IMPLEMENTED;
+#endif
 }


 int colvarproxy_smp::smp_lock()
 {
+#if defined(_OPENMP)
+  omp_set_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
+#endif
  return COLVARS_OK;
 }


 int colvarproxy_smp::smp_trylock()
 {
+#if defined(_OPENMP)
+  return omp_test_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state)) ?
+    COLVARS_OK : COLVARS_ERROR;
+#else
  return COLVARS_OK;
+#endif
 }


 int colvarproxy_smp::smp_unlock()
 {
+#if defined(_OPENMP)
+  omp_unset_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
+#endif
  return COLVARS_OK;
 }



-
 colvarproxy_replicas::colvarproxy_replicas() {}


--- a/lib/colvars/colvarproxy.h
+++ b/lib/colvars/colvarproxy.h
@ -80,6 +80,9 @@ public:

  /// Are total forces being used?
  virtual bool total_forces_enabled() const;
+
+  /// Are total forces from the current step available?
+  virtual bool total_forces_same_step() const;
 };


@ -372,6 +375,11 @@ public:

  /// Release the lock
  virtual int smp_unlock();
+
+protected:
+
+  /// Lock state for OpenMP
+  void *omp_lock_state;
 };


--- a/lib/colvars/colvars_version.h
+++ b/lib/colvars/colvars_version.h
@ -1,5 +1,5 @@
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2017-08-06"
+#define COLVARS_VERSION "2017-10-20"
 // This file is part of the Collective Variables module (Colvars).
 // The original version of Colvars and its updates are located at:
 // https://github.com/colvars/colvars
--- a/lib/colvars/colvarscript.cpp
+++ b/lib/colvars/colvarscript.cpp
@ -11,7 +11,10 @@
 #include <stdlib.h>
 #include <string.h>

+#define COLVARSCRIPT_CPP
 #include "colvarscript.h"
+#undef COLVARSCRIPT_CPP
+
 #include "colvarproxy.h"
 #include "colvardeps.h"

@ -21,6 +24,11 @@ colvarscript::colvarscript(colvarproxy *p)
   colvars(p->colvars),
   proxy_error(0)
 {
+  comm_help.resize(colvarscript::cv_n_commands);
+  comm_fns.resize(colvarscript::cv_n_commands);
+#define COLVARSCRIPT_INIT_FN
+#include "colvarscript.h"
+#undef COLVARSCRIPT_INIT_FN
 }


@ -66,8 +74,7 @@ int colvarscript::run(int objc, unsigned char *const objv[])
  }

  if (objc < 2) {
-    result = help_string();
-    return COLVARS_OK;
+    return exec_command(cv_help, NULL, objc, objv);
  }

  std::string const cmd(obj_to_str(objv[1]));
@ -167,17 +174,7 @@ int colvarscript::run(int objc, unsigned char *const objv[])

  /// Parse config from string
  if (cmd == "config") {
-    if (objc < 3) {
-      result = "Missing arguments\n" + help_string();
-      return COLVARSCRIPT_ERROR;
-    }
-    std::string const conf(obj_to_str(objv[2]));
-    if (colvars->read_config_string(conf) == COLVARS_OK) {
-      return COLVARS_OK;
-    } else {
-      result = "Error parsing configuration string";
-      return COLVARSCRIPT_ERROR;
-    }
+    return exec_command(cv_config, NULL, objc, objv);
  }

  /// Load an input state file
@ -204,6 +201,8 @@ int colvarscript::run(int objc, unsigned char *const objv[])
    proxy->output_prefix() = obj_to_str(objv[2]);
    int error = 0;
    error |= colvars->setup_output();
+    error |= colvars->write_restart_file(colvars->output_prefix()+
+                                         ".colvars.state");
    error |= colvars->write_output_files();
    return error ? COLVARSCRIPT_ERROR : COLVARS_OK;
  }
@ -255,6 +254,10 @@ int colvarscript::run(int objc, unsigned char *const objv[])
    }
  }

+  if (cmd == "help") {
+    return exec_command(cv_help, NULL, objc, objv);
+  }
+
  result = "Syntax error\n" + help_string();
  return COLVARSCRIPT_ERROR;
 }
@ -295,7 +298,9 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[])
    // colvar destructor is tasked with the cleanup
    delete cv;
    // TODO this could be done by the destructors
-    colvars->write_traj_label(*(colvars->cv_traj_os));
+    if (colvars->cv_traj_os != NULL) {
+      colvars->write_traj_label(*(colvars->cv_traj_os));
+    }
    return COLVARS_OK;
  }

@ -374,7 +379,6 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[])

 int colvarscript::proc_bias(colvarbias *b, int objc, unsigned char *const objv[]) {

-  std::string const key(obj_to_str(objv[0]));
  std::string const subcmd(obj_to_str(objv[2]));

  if (subcmd == "energy") {
@ -425,7 +429,9 @@ int colvarscript::proc_bias(colvarbias *b, int objc, unsigned char *const objv[]
    // the bias destructor takes care of the cleanup at cvm level
    delete b;
    // TODO this could be done by the destructors
-    colvars->write_traj_label(*(colvars->cv_traj_os));
+    if (colvars->cv_traj_os != NULL) {
+      colvars->write_traj_label(*(colvars->cv_traj_os));
+    }
    return COLVARS_OK;
  }

@ -528,7 +534,7 @@ int colvarscript::proc_features(colvardeps *obj,
 }


-std::string colvarscript::help_string()
+std::string colvarscript::help_string() const
 {
  std::string buf;
  buf = "Usage: cv <subcommand> [args...]\n\
@ -538,7 +544,7 @@ Managing the Colvars module:\n\
  config <string>             -- read configuration from the given string\n\
  reset                       -- delete all internal configuration\n\
  delete                      -- delete this Colvars module instance\n\
-  version                     -- return version of colvars code\n\
+  version                     -- return version of Colvars code\n\
  \n\
 Input and output:\n\
  list                        -- return a list of all variables\n\
@ -564,6 +570,8 @@ Accessing collective variables:\n\
  colvar <name> type          -- return the type of colvar <name>\n\
  colvar <name> delete        -- delete colvar <name>\n\
  colvar <name> addforce <F>  -- apply given force on colvar <name>\n\
+  colvar <name> getappliedforce -- return applied force of colvar <name>\n\
+  colvar <name> gettotalforce -- return total force of colvar <name>\n\
  colvar <name> getconfig     -- return config string of colvar <name>\n\
  colvar <name> cvcflags <fl> -- enable or disable cvcs according to 0/1 flags\n\
  colvar <name> get <f>       -- get the value of the colvar feature <f>\n\
--- a/lib/colvars/colvarscript.h
+++ b/lib/colvars/colvarscript.h
@ -8,21 +8,27 @@
 // Colvars repository at GitHub.

 #ifndef COLVARSCRIPT_H
-#define COLVARSCRIPT_H
+//#define COLVARSCRIPT_H // Delay definition until later

 #include <string>
+#include <vector>
+#include <map>
+
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarbias.h"
 #include "colvarproxy.h"

+
 // Only these error values are part of the scripting interface
 #define COLVARSCRIPT_ERROR -1
 #define COLVARSCRIPT_OK 0

+
 class colvarscript  {

 private:
+
  colvarproxy *proxy;
  colvarmodule *colvars;

@ -35,16 +41,93 @@ public:
  colvarscript(colvarproxy * p);
  inline ~colvarscript() {}

-  /// If an error is caught by the proxy through fatal_error(), this is set to COLVARSCRIPT_ERROR
+  /// If an error is caught by the proxy through fatal_error(), this is set to
+  /// COLVARSCRIPT_ERROR
  int proxy_error;

-  /// If an error is returned by one of the methods, it should set this to the error message
+  /// If an error is returned by one of the methods, it should set this to the
+  /// error message
  std::string result;

  /// Run script command with given positional arguments (objects)
  int run(int objc, unsigned char *const objv[]);

+  /// Set the return value of the script command to the given string
+  inline void set_str_result(std::string const &s)
+  {
+    result = s;
+  }
+
+  /// Build and return a short help
+  std::string help_string(void) const;
+
+  /// Use scripting language to get the string representation of an object
+  inline char const *obj_to_str(unsigned char *const obj)
+  {
+    return cvm::proxy->script_obj_to_str(obj);
+  }
+
+  enum command {
+    cv_help,
+    cv_version,
+    cv_config,
+    cv_configfile,
+    cv_reset,
+    cv_delete,
+    cv_list,
+    cv_list_biases,
+    cv_load,
+    cv_save,
+    cv_update,
+    cv_addenergy,
+    cv_getenergy,
+    cv_printframe,
+    cv_printframelabels,
+    cv_frame,
+    cv_colvar,
+    cv_colvar_value,
+    cv_colvar_update,
+    cv_colvar_type,
+    cv_colvar_delete,
+    cv_colvar_addforce,
+    cv_colvar_getappliedforce,
+    cv_colvar_gettotalforce,
+    cv_colvar_cvcflags,
+    cv_colvar_getconfig,
+    cv_colvar_get,
+    cv_colvar_set,
+    cv_bias,
+    cv_bias_energy,
+    cv_bias_update,
+    cv_bias_delete,
+    cv_bias_getconfig,
+    cv_bias_get,
+    cv_bias_set,
+    cv_n_commands
+  };
+
+  /// Execute a script command
+  inline int exec_command(command c,
+                          void *pobj,
+                          int objc, unsigned char * const *objv)
+  {
+    return (*(comm_fns[c]))(pobj, objc, objv);
+  }
+
+  /// Get help for a command (TODO reformat for each language?)
+  inline std::string command_help(colvarscript::command c) const
+  {
+    return comm_help[c];
+  }
+
+  /// Clear all object results
+  inline void clear_results()
+  {
+    result.clear();
+  }
+
 private:
+
  /// Run subcommands on colvar
  int proc_colvar(colvar *cv, int argc, unsigned char *const argv[]);

@ -55,17 +138,146 @@ private:
  int proc_features(colvardeps *obj,
                    int argc, unsigned char *const argv[]);

-  /// Build and return a short help
-  std::string help_string(void);
+  /// Internal identifiers of command strings
+  std::map<std::string, command> comm_str_map;

-public:
+  /// Help strings for each command
+  std::vector<std::string> comm_help;

-  inline char const *obj_to_str(unsigned char *const obj)
-  {
-    return cvm::proxy->script_obj_to_str(obj);
-  }
+  /// Number of arguments for each command
+  std::vector<size_t> comm_n_args;
+
+  /// Arguments for each command
+  std::vector< std::vector<std::string> > comm_args;
+
+  /// Implementations of each command
+  std::vector<int (*)(void *, int, unsigned char * const *)> comm_fns;

 };


+/// Get a pointer to the main colvarscript object
+inline static colvarscript *colvarscript_obj()
+{
+  return cvm::main()->proxy->script;
+}
+
+/// Get a pointer to the colvar object pointed to by pobj
+inline static colvar *colvar_obj(void *pobj)
+{
+  return reinterpret_cast<colvar *>(pobj);
+}
+
+/// Get a pointer to the colvarbias object pointed to by pobj
+inline static colvarbias *colvarbias_obj(void *pobj)
+{
+  return reinterpret_cast<colvarbias *>(pobj);
+}
+
+
+#define CVSCRIPT_COMM_FNAME(COMM) cvscript_ ## COMM
+
+#define CVSCRIPT_COMM_PROTO(COMM)                                       \
+  int CVSCRIPT_COMM_FNAME(COMM)(void *, int, unsigned char *const *);
+
+#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY)  \
+  CVSCRIPT_COMM_PROTO(COMM)
+
+#undef COLVARSCRIPT_H
+#endif // #ifndef COLVARSCRIPT_H
+
+
+#ifdef COLVARSCRIPT_CPP
+#define CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY)       \
+  int CVSCRIPT_COMM_FNAME(COMM)(void *pobj,                             \
+                                int objc, unsigned char *const objv[])  \
+  {                                                                     \
+    colvarscript *script = colvarscript_obj();                          \
+    script->clear_results();                                            \
+    if (objc < 2+N_ARGS_MIN) /* "cv" and "COMM" are 1st and 2nd */ {    \
+      script->set_str_result("Missing arguments\n" +                    \
+                             script->command_help(colvarscript::COMM)); \
+      return COLVARSCRIPT_ERROR;                                        \
+    }                                                                   \
+    if (objc > 2+N_ARGS_MAX) {                                          \
+      script->set_str_result("Too many arguments\n" +                   \
+                             script->command_help(colvarscript::COMM)); \
+      return COLVARSCRIPT_ERROR;                                        \
+    }                                                                   \
+    FN_BODY;                                                            \
+  }
+#undef CVSCRIPT
+#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
+  CVSCRIPT_COMM_FN(COMM,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY)
+#endif // #ifdef COLVARSCRIPT_CPP
+
+
+#ifdef COLVARSCRIPT_INIT_FN
+#define CVSCRIPT_COMM_INIT(COMM,HELP,ARGS) {                    \
+    comm_str_map[#COMM] = COMM;                                 \
+    comm_help[COMM] = HELP;                                     \
+    comm_fns[COMM] = &(CVSCRIPT_COMM_FNAME(COMM));              \
+  }
+#undef CVSCRIPT
+#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY)  \
+  CVSCRIPT_COMM_INIT(COMM,HELP,ARGS)
 #endif
+
+
+#if !defined(COLVARSCRIPT_H) || defined(COLVARSCRIPT_INIT_FN)
+#define COLVARSCRIPT_H
+
+#ifndef COLVARSCRIPT_INIT_FN
+#ifdef __cplusplus
+extern "C" {
+#endif
+#endif
+
+  // Add optional arguments for command-specific help?
+  CVSCRIPT(cv_help,
+           "Print the help message",
+           0, 0,
+           {},
+           script->set_str_result(script->help_string());
+           return COLVARS_OK;
+           )
+
+  CVSCRIPT(cv_config,
+           "Read configuration from the given string",
+           1, 1,
+           { "conf (str) - Configuration string" },
+           std::string const conf(script->obj_to_str(objv[2]));
+           if (cvm::main()->read_config_string(conf) == COLVARS_OK) {
+             return COLVARS_OK;
+           }
+           script->set_str_result("Error parsing configuration string");
+           return COLVARSCRIPT_ERROR;
+           )
+
+  CVSCRIPT(cv_addenergy,
+           "Add an energy to the MD engine",
+           1, 1,
+           { "E (float) - Amount of energy to add" },
+           cvm::main()->total_bias_energy +=
+             strtod(script->obj_to_str(objv[2]), NULL);
+           return COLVARS_OK;
+           )
+
+  CVSCRIPT(cv_getenergy,
+           "Get the current Colvars energy",
+           1, 1,
+           { "E (float) - Store the energy in this variable" },
+           double *energy = reinterpret_cast<double *>(objv[2]);
+           *energy = cvm::main()->total_bias_energy;
+           return COLVARS_OK;
+           )
+
+#ifndef COLVARSCRIPT_INIT_FN
+#ifdef __cplusplus
+} // extern "C"
+#endif
+#endif
+
+#undef CVSCRIPT
+
+#endif // #ifndef COLVARSCRIPT_H
--- a/lib/colvars/colvartypes.cpp
+++ b/lib/colvars/colvartypes.cpp
@ -312,7 +312,7 @@ void colvarmodule::rotation::diagonalize_matrix(cvm::matrix2d<cvm::real> &S,
    cvm::real norm2 = 0.0;
    size_t i;
    for (i = 0; i < 4; i++) {
-      norm2 += std::pow(S_eigvec[ie][i], int(2));
+      norm2 += S_eigvec[ie][i] * S_eigvec[ie][i];
    }
    cvm::real const norm = std::sqrt(norm2);
    for (i = 0; i < 4; i++) {
--- a/lib/colvars/colvartypes.h
+++ b/lib/colvars/colvartypes.h
@ -705,7 +705,7 @@ public:
  {
    std::stringstream stream(s);
    size_t i = 0;
-    while ((stream >> data[i]) && (i < data.size())) {
+    while ((i < data.size()) && (stream >> data[i])) {
      i++;
    }
    if (i < data.size()) {
--- a/lib/colvars/lepton/include/Lepton.h
+++ b/lib/colvars/lepton/include/Lepton.h
@ -0,0 +1,43 @@
+#ifndef LEPTON_H_
+#define LEPTON_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   Lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the Lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "lepton/CompiledExpression.h"
+#include "lepton/CustomFunction.h"
+#include "lepton/ExpressionProgram.h"
+#include "lepton/ExpressionTreeNode.h"
+#include "lepton/Operation.h"
+#include "lepton/ParsedExpression.h"
+#include "lepton/Parser.h"
+
+#endif /*LEPTON_H_*/
--- a/lib/colvars/lepton/include/lepton/CompiledExpression.h
+++ b/lib/colvars/lepton/include/lepton/CompiledExpression.h
@ -0,0 +1,113 @@
+#ifndef LEPTON_COMPILED_EXPRESSION_H_
+#define LEPTON_COMPILED_EXPRESSION_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   Lepton                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the Lepton expression parser originating from              *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ExpressionTreeNode.h"
+#include "windowsIncludes.h"
+#include <map>
+#include <set>
+#include <string>
+#include <utility>
+#include <vector>
+#ifdef LEPTON_USE_JIT
+    #include "asmjit.h"
+#endif
+
+namespace Lepton {
+
+class Operation;
+class ParsedExpression;
+
+/**
+ * A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate
+ * it many times as quickly as possible.  You should treat it as an opaque object; none of the internal representation
+ * is visible.
+ * 
+ * A CompiledExpression is created by calling createCompiledExpression() on a ParsedExpression.
+ * 
+ * WARNING: CompiledExpression is NOT thread safe.  You should never access a CompiledExpression from two threads at
+ * the same time.
+ */
+
+class LEPTON_EXPORT CompiledExpression {
+public:
+    CompiledExpression();
+    CompiledExpression(const CompiledExpression& expression);
+    ~CompiledExpression();
+    CompiledExpression& operator=(const CompiledExpression& expression);
+    /**
+     * Get the names of all variables used by this expression.
+     */
+    const std::set<std::string>& getVariables() const;
+    /**
+     * Get a reference to the memory location where the value of a particular variable is stored.  This can be used
+     * to set the value of the variable before calling evaluate().
+     */
+    double& getVariableReference(const std::string& name);
+    /**
+     * You can optionally specify the memory locations from which the values of variables should be read.
+     * This is useful, for example, when several expressions all use the same variable.  You can then set
+     * the value of that variable in one place, and it will be seen by all of them.
+     */
+    void setVariableLocations(std::map<std::string, double*>& variableLocations);
+    /**
+     * Evaluate the expression.  The values of all variables should have been set before calling this.
+     */
+    double evaluate() const;
+private:
+    friend class ParsedExpression;
+    CompiledExpression(const ParsedExpression& expression);
+    void compileExpression(const ExpressionTreeNode& node, std::vector<std::pair<ExpressionTreeNode, int> >& temps);
+    int findTempIndex(const ExpressionTreeNode& node, std::vector<std::pair<ExpressionTreeNode, int> >& temps);
+    std::map<std::string, double*> variablePointers;
+    std::vector<std::pair<double*, double*> > variablesToCopy;
+    std::vector<std::vector<int> > arguments;
+    std::vector<int> target;
+    std::vector<Operation*> operation;
+    std::map<std::string, int> variableIndices;
+    std::set<std::string> variableNames;
+    mutable std::vector<double> workspace;
+    mutable std::vector<double> argValues;
+    std::map<std::string, double> dummyVariables;
+    void* jitCode;
+#ifdef LEPTON_USE_JIT
+    void generateJitCode();
+    void generateSingleArgCall(asmjit::X86Compiler& c, asmjit::X86XmmVar& dest, asmjit::X86XmmVar& arg, double (*function)(double));
+    std::vector<double> constants;
+    asmjit::JitRuntime runtime;
+#endif
+};
+
+} // namespace Lepton
+
+#endif /*LEPTON_COMPILED_EXPRESSION_H_*/
--- a/Show More
+++ b/Show More