patch 17Jan17

Merge pull request #339 from akohlmey/fixes-for-srp-example
Fixes for srp example
2017-01-17 10:14:53 -07:00 · 2017-01-17 09:36:28 -07:00 · 2017-01-17 09:33:25 -07:00 · 2017-01-17 09:14:03 -07:00 · 2017-01-17 09:13:47 -07:00 · 2017-01-17 09:13:27 -07:00
677 changed files with 49969 additions and 31725 deletions
--- a/doc/src/JPG/tutorial_additional_changes.png
+++ b/doc/src/JPG/tutorial_additional_changes.png
--- a/doc/src/JPG/tutorial_automated_checks.png
+++ b/doc/src/JPG/tutorial_automated_checks.png
--- a/doc/src/JPG/tutorial_automated_checks_passed.png
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--- a/doc/src/JPG/tutorial_branch.png
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--- a/doc/src/JPG/tutorial_changes_others.png
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--- a/doc/src/JPG/tutorial_create_new_pull_request1.png
+++ b/doc/src/JPG/tutorial_create_new_pull_request1.png
--- a/doc/src/JPG/tutorial_create_new_pull_request2.png
+++ b/doc/src/JPG/tutorial_create_new_pull_request2.png
--- a/doc/src/JPG/tutorial_edits_maintainers.png
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--- a/doc/src/JPG/tutorial_fork.png
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--- a/doc/src/JPG/tutorial_https_block.png
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--- a/doc/src/JPG/tutorial_merged.png
+++ b/doc/src/JPG/tutorial_merged.png
--- a/doc/src/JPG/tutorial_new_pull_request.png
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--- a/doc/src/JPG/tutorial_reverse_pull_request.png
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--- a/doc/src/JPG/tutorial_reverse_pull_request2.png
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--- a/doc/src/JPG/tutorial_reverse_pull_request7.png
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--- a/doc/src/JPG/tutorial_steve_assignee.png
+++ b/doc/src/JPG/tutorial_steve_assignee.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="17 Dec 2016 version">
+<META NAME="docnumber" CONTENT="17 Jan 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
-17 Dec 2016 version :c,h4
+17 Jan 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
@ -581,8 +581,9 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "indent"_fix_indent.html,
 "langevin (k)"_fix_langevin.html,
 "lineforce"_fix_lineforce.html,
-"momentum"_fix_momentum.html,
+"momentum (k)"_fix_momentum.html,
 "move"_fix_move.html,
+"mscg"_fix_mscg.html,
 "msst"_fix_msst.html,
 "neb"_fix_neb.html,
 "nph (ko)"_fix_nh.html,
@ -702,6 +703,7 @@ package"_Section_start.html#start_3.
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
+"nvk"_fix_nvk.html,
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
 "nph/eff"_fix_nh_eff.html,
 "npt/eff"_fix_nh_eff.html,
@ -917,7 +919,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "dpd (go)"_pair_dpd.html,
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
-"eam (gkot)"_pair_eam.html,
+"eam (gkiot)"_pair_eam.html,
 "eam/alloy (gkot)"_pair_eam.html,
 "eam/fs (gkot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@ -55,12 +55,13 @@ LAMMPS errors are detected at setup time; others like a bond
 stretching too far may not occur until the middle of a run.

 LAMMPS tries to flag errors and print informative error messages so
-you can fix the problem.  Of course, LAMMPS cannot figure out your
-physics or numerical mistakes, like choosing too big a timestep,
-specifying erroneous force field coefficients, or putting 2 atoms on
-top of each other!  If you run into errors that LAMMPS doesn't catch
-that you think it should flag, please send an email to the
-"developers"_http://lammps.sandia.gov/authors.html.
+you can fix the problem.  For most errors it will also print the last
+input script command that it was processing.  Of course, LAMMPS cannot
+figure out your physics or numerical mistakes, like choosing too big a
+timestep, specifying erroneous force field coefficients, or putting 2
+atoms on top of each other!  If you run into errors that LAMMPS
+doesn't catch that you think it should flag, please send an email to
+the "developers"_http://lammps.sandia.gov/authors.html.

 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -1153,7 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
-"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
 "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@ -1610,11 +1610,12 @@ and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
 in this format.  See src/USER-NC-DUMP/README for more details.

 NetCDF files can be directly visualized with the following tools:
+
 Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
-  and all of the above extensions. :ulb,l
+and all of the above extensions. :ulb,l
 VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
 AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
-  a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule

 The person who created these files is Lars Pastewka at
 Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -1727,7 +1727,7 @@ thermodynamic state and a total run time for the simulation.  It then
 appends statistics about the CPU time and storage requirements for the
 simulation.  An example set of statistics is shown here:

-Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre

 Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
 97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
@ -1757,14 +1757,14 @@ Ave special neighs/atom = 2.34032
 Neighbor list builds = 26
 Dangerous builds = 0 :pre

-The first section provides a global loop timing summary. The loop time
+The first section provides a global loop timing summary. The {loop time}
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
-continuations required and for comparing performance with other
-similar MD codes.  The CPU use line provides the CPU utilzation per
+continuations required and for comparing performance with other,
+similar MD codes.  The {CPU use} line provides the CPU utilzation per
 MPI task; it should be close to 100% times the number of OpenMP
-threads (or 1). Lower numbers correspond to delays due to file I/O or
-insufficient thread utilization.
+threads (or 1 of no OpenMP). Lower numbers correspond to delays due
+to file I/O or insufficient thread utilization.

 The MPI task section gives the breakdown of the CPU run time (in
 seconds) into major categories:
@ -1791,7 +1791,7 @@ is present that also prints the CPU utilization in percent. In
 addition, when using {timer full} and the "package omp"_package.html
 command are active, a similar timing summary of time spent in threaded
 regions to monitor thread utilization and load balance is provided. A
-new entry is the {Reduce} section, which lists the time spend in
+new entry is the {Reduce} section, which lists the time spent in
 reducing the per-thread data elements to the storage for non-threaded
 computation. These thread timings are taking from the first MPI rank
 only and and thus, as the breakdown for MPI tasks can change from MPI
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -29,7 +29,7 @@ Bond Styles: fene, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
-Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
+Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
 charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
 K-Space Styles: pppm :l
 :ule
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@ -110,14 +110,14 @@ mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis :p
 [Required hardware/software:]

 Kokkos support within LAMMPS must be built with a C++11 compatible
-compiler.  If using gcc, version 4.8.1 or later is required.
+compiler.  If using gcc, version 4.7.2 or later is required.

 To build with Kokkos support for CPUs, your compiler must support the
 OpenMP interface.  You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.

 To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
-version 6.5 or later must be installed on your system.  See the
+version 7.5 or later must be installed on your system.  See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.

--- a/doc/src/commands.txt
+++ b/doc/src/commands.txt
@ -91,6 +91,7 @@ Commands :h1
   suffix
   tad
   temper
+   temper_grem
   thermo
   thermo_modify
   thermo_style
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@ -10,22 +10,34 @@ compute coord/atom command :h3

 [Syntax:]

-compute ID group-ID coord/atom cutoff type1 type2 ... :pre
+compute ID group-ID coord/atom cstyle args ... :pre

 ID, group-ID are documented in "compute"_compute.html command
 coord/atom = style name of this compute command
-cutoff = distance within which to count coordination neighbors (distance units)
-typeN = atom type for Nth coordination count (see asterisk form below) :ul
+one cstyle must be appended :ul
+
+cstyle = {cutoff} or {orientorder}
+
+{cutoff} args = cutoff typeN
+  cutoff = distance within which to count coordination neighbors (distance units)
+  typeN = atom type for Nth coordination count (see asterisk form below) :pre
+
+{orientorder} args = orientorderID threshold
+  orientorderID = ID of a previously defined orientorder/atom compute
+  threshold = minimum value of the scalar product between two 'connected' atoms (see text for explanation) :pre

 [Examples:]

-compute 1 all coord/atom 2.0
-compute 1 all coord/atom 6.0 1 2
-compute 1 all coord/atom 6.0 2*4 5*8 * :pre
+compute 1 all coord/atom cutoff 2.0
+compute 1 all coord/atom cutoff 6.0 1 2
+compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
+compute 1 all coord/atom orientorder 2 0.5 :pre

 [Description:]

-Define a computation that calculates one or more coordination numbers
+This compute performs generic calculations between neighboring atoms. So far,
+there are two cstyles implemented: {cutoff} and {orientorder}.
+The {cutoff} cstyle calculates one or more coordination numbers
 for each atom in a group.

 A coordination number is defined as the number of neighbor atoms with
@ -49,6 +61,14 @@ from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).

+The {orientorder} cstyle calculates the number of 'connected' atoms j 
+around each atom i. The atom j is connected to i if the scalar product
+({Ybar_lm(i)},{Ybar_lm(j)}) is larger than {threshold}. Thus, this cstyle
+will work only if a "compute orientorder/atom"_compute_orientorder_atom.html
+has been previously defined. This cstyle allows one to apply the 
+ten Wolde's criterion to identify cristal-like atoms in a system 
+(see "ten Wolde et al."_#tenWolde).
+
 The value of all coordination numbers will be 0.0 for atoms not in the
 specified compute group.

@ -83,10 +103,19 @@ options.
 The per-atom vector or array values will be a number >= 0.0, as
 explained above.

-[Restrictions:] none
+[Restrictions:]
+The cstyle {orientorder} can only be used if a 
+"compute orientorder/atom"_compute_orientorder_atom.html command
+was previously defined. Otherwise, an error message will be issued.

 [Related commands:]

 "compute cluster/atom"_compute_cluster_atom.html
+"compute orientorder/atom"_compute_orientorder_atom.html

 [Default:] none
+
+:line
+
+:link(tenWolde)
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@ -15,17 +15,19 @@ compute ID group-ID orientorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 orientorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {cutoff} or {nnn} or {degrees}
+keyword = {cutoff} or {nnn} or {degrees} or {components}
  {cutoff} value = distance cutoff
  {nnn} value = number of nearest neighbors
-  {degrees} values = nlvalues, l1, l2,...  :pre
+  {degrees} values = nlvalues, l1, l2,...
+  {components} value = l  :pre

 :ule

 [Examples:]

 compute 1 all orientorder/atom
-compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 :pre
+compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
+compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre

 [Description:]

@ -71,6 +73,13 @@ The numerical values of all order parameters up to {Q}12
 for a range of commonly encountered high-symmetry structures are given
 in Table I of "Mickel et al."_#Mickel.

+The optional keyword {components} will output the components of
+the normalized complex vector {Ybar_lm} of degree {l}, which must be
+explicitly included in the keyword {degrees}. This option can be used
+in conjunction with "compute coord_atom"_compute_coord_atom.html to
+calculate the ten Wolde's criterion to identify crystal-like particles
+(see "ten Wolde et al."_#tenWolde96).
+
 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
 {nnn} neighbors within the distance cutoff.
@ -98,6 +107,12 @@ the neighbor list.
 This compute calculates a per-atom array with {nlvalues} columns, giving the
 {Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.

+If the keyword {components} is set, then the real and imaginary parts of each
+component of (normalized) {Ybar_lm} will be added to the output array in the
+following order:
+Re({Ybar_-m}) Im({Ybar_-m}) Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}).
+This way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1) columns.
+
 These values can be accessed by any command that uses
 per-atom values from a compute as input.  See "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
@ -117,5 +132,9 @@ The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5

 :link(Steinhardt)
 [(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
+
 :link(Mickel)
 [(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
+
+:link(tenWolde96)
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@ -35,6 +35,7 @@ Computes :h1
   compute_erotate_sphere_atom
   compute_event_displace
   compute_fep
+   compute_global_atom
   compute_group_group
   compute_gyration
   compute_gyration_chunk
--- a/doc/src/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@ -31,21 +31,19 @@ fix abf all colvars colvars.inp tstat 1 :pre

 [Description:]

-This fix interfaces LAMMPS to a "collective variables" or "colvars"
-module library which allows to calculate potentials of mean force
+This fix interfaces LAMMPS to the collective variables "Colvars"
+library, which allows to calculate potentials of mean force
 (PMFs) for any set of colvars, using different sampling methods:
 currently implemented are the Adaptive Biasing Force (ABF) method,
 metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
-(US) via a flexible harmonic restraint bias. The colvars library is
-hosted at "http://colvars.github.io/"_http://colvars.github.io/
+(US) via a flexible harmonic restraint bias.

 This documentation describes only the fix colvars command itself and
 LAMMPS specific parts of the code.  The full documentation of the
 colvars library is available as "this supplementary PDF document"_PDF/colvars-refman-lammps.pdf

-A detailed discussion of the implementation of the portable collective
-variable library is in "(Fiorin)"_#Fiorin. Additional information can
-be found in "(Henin)"_#Henin.
+The Colvars library is developed at "https://github.com/colvars/colvars"_https://github.com/colvars/colvars
+A detailed discussion of its implementation is in "(Fiorin)"_#Fiorin.

 There are some example scripts for using this package with LAMMPS in the
 examples/USER/colvars directory.
@ -129,8 +127,3 @@ and tstat = NULL.

 :link(Fiorin)
 [(Fiorin)] Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
-
-:link(Henin)
-[(Henin)] Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
-35-47 (2010)
-
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@ -10,7 +10,7 @@ fix eos/table/rx command :h3

 [Syntax:]

-fix ID group-ID eos/table/rx style file1 N keyword file2 :pre
+fix ID group-ID eos/table/rx style file1 N keyword ... :pre

 ID, group-ID are documented in "fix"_fix.html command
 eos/table/rx = style name of this fix command
@ -18,11 +18,16 @@ style = {linear} = method of interpolation
 file1 = filename containing the tabulated equation of state
 N = use N values in {linear} tables
 keyword = name of table keyword correponding to table file
-file2 = filename containing the heats of formation of each species :ul
+file2 = filename containing the heats of formation of each species (optional)
+deltaHf = heat of formation for a single species in energy units (optional)
+energyCorr = energy correction in energy units (optional)
+tempCorrCoeff = temperature correction coefficient (optional) :ul

 [Examples:]

-fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table :pre
+fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table
+fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5
+fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 0.025 0.0 :pre

 [Description:]

@ -39,7 +44,15 @@ where {m} is the number of species, {c_i,j} is the concentration of
 species {j} in particle {i}, {u_j} is the internal energy of species j,
 {DeltaH_f,j} is the heat of formation of species {j}, N is the number of
 molecules represented by the coarse-grained particle, kb is the
-Boltzmann constant, and T is the temperature of the system.
+Boltzmann constant, and T is the temperature of the system.  Additionally,
+it is possible to modify the concentration-dependent particle internal 
+energy relation by adding an energy correction, temperature-dependent 
+correction, and/or a molecule-dependent correction.  An energy correction can
+be specified as a constant (in energy units).  A temperature correction can be 
+specified by multiplying a temperature correction coefficient by the 
+internal temperature.  A molecular correction can be specified by 
+by multiplying a molecule correction coefficient by the average number of 
+product gas particles in the coarse-grain particle. 

 Fix {eos/table/rx} creates interpolation tables of length {N} from {m}
 internal energy values of each species {u_j} listed in a file as a
@ -58,6 +71,14 @@ file is described below.
 The second filename specifies a file containing heat of formation
 {DeltaH_f,j} for each species.

+In cases where the coarse-grain particle represents a single molecular
+species (i.e., no reactions occur and fix {rx} is not present in the input file), 
+fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} 
+within a non-reactive DPD simulation.  In this case, the heat of formation 
+filename is replaced with the heat of formation value for the single species.
+Additionally, the energy correction and temperature correction coefficients may 
+also be specified as fix arguments.  
+
 :line

 The format of a tabulated file is as follows (without the
@ -116,6 +137,19 @@ Note that the species can be listed in any order.  The tag that is
 used as the species name must correspond with the tags used to define
 the reactions with the "fix rx"_fix_rx.html command.

+Alternatively, corrections to the EOS can be included by specifying
+three additional columns that correspond to the energy correction, 
+the temperature correction coefficient and molecule correction 
+coefficient.  In this case, the format of the file is as follows:
+
+# HEAT OF FORMATION TABLE     (one or more comment or blank lines) :pre
+                              (blank)
+h2      0.00 1.23 0.025  0.0  (species name, heat of formation, energy correction, temperature correction coefficient, molecule correction coefficient)
+no2     0.34 0.00 0.000 -1.76
+n2      0.00 0.00 0.000 -1.76
+...
+no      0.93 0.00 0.000 -1.76 :pre
+
 :line

 [Restrictions:]
--- a/doc/src/fix_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@ -151,7 +151,7 @@ The option default for the {energy} keyword is energy = no.
 :line

 :link(Strong)
-[(Strong)] Strong and Eaves, J. Phys. Chem. Lett. 7, 1907 (2016).
+[(Strong)] Strong and Eaves, J. Phys. Chem. B 121, 189 (2017).

 :link(Evans)
 [(Evans)] Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@ -29,7 +29,7 @@ fix             fxgREM all grem 502 -0.15 -80000 fxnvt :pre
 [Description:]

 This fix implements the molecular dynamics version of the generalized
-replica exchange method (gREM) originally developed by "(Kim)"_#Kim,
+replica exchange method (gREM) originally developed by "(Kim)"_#Kim2010,
 which uses non-Boltzmann ensembles to sample over first order phase
 transitions. The is done by defining replicas with an enthalpy
 dependent effective temperature
@ -103,7 +103,7 @@ npt"_fix_nh.html, "thermo_modify"_thermo_modify.html

 :line

-:link(Kim)
+:link(Kim2010)
 [(Kim)] Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).

 :link(Malolepsza)
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@ -7,6 +7,7 @@
 :line

 fix momentum command :h3
+fix momentum/kk command :h3

 [Syntax:]

@ -55,6 +56,29 @@ of atoms by rescaling the velocities after the momentum was removed.
 Note that the "velocity"_velocity.html command can be used to create
 initial velocities with zero aggregate linear and/or angular momentum.

+: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_7 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.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]

 No information about this fix is written to "binary restart
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@ -0,0 +1,130 @@
+"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 mscg command :h3
+
+[Syntax:]
+
+fix ID group-ID mscg N keyword args ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+mscg = style name of this fix command :l
+N = envoke this fix every this many timesteps :l
+zero or more keyword/value pairs may be appended :l
+keyword = {range} or {name} or {max} :l
+  {range} arg = {on} or {off}
+    {on} = range finding functionality is performed
+    {off} = force matching functionality is performed
+  {name} args = name1 ... nameN
+    name1,...,nameN = string names for each atom type (1-Ntype)
+  {max} args = maxb maxa maxd
+    maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom :pre
+:ule
+
+[Examples:]
+
+fix 1 all mscg 1
+fix 1 all mscg 1 range name A B
+fix 1 all mscg 1 max 4 8 20 :pre
+
+[Description:]
+
+This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
+snapshots from a dump file to generate potentials for coarse-grained
+simulations from all-atom simulations, using a force-matching
+technique ("Izvekov"_#Izvekov, "Noid"_#Noid).
+
+It makes use of the MS-CG library, written and maintained by Greg
+Voth's group at the University of Chicago, which is freely available
+on their "MS-CG GitHub
+site"_https://github.com/uchicago-voth/MSCG-release.  See instructions
+on obtaining and installing the MS-CG library in the src/MSCG/README
+file, which must be done before you build LAMMPS with this fix command
+and use the command in a LAMMPS input script.
+
+An example script using this fix is provided the examples/mscg
+directory.
+
+The general workflow for using LAMMPS in conjunction with the MS-CG
+library to create a coarse-grained model and run coarse-grained
+simulations is as follows:
+
+Perform all-atom simulations on the system to be coarse grained.
+Generate a trajectory mapped to the coarse-grained model.
+Create input files for the MS-CG library.
+Run the range finder functionality of the MS-CG library.  
+Run the force matching functionality of the MS-CG library.
+Check the results of the force matching.
+Run coarse-grained simulations using the new coarse-grained potentials. :ol
+
+This fix can perform the range finding and force matching steps 4 and
+5 of the above workflow when used in conjunction with the
+"rerun"_rerun.html command.  It does not perform steps 1-3 and 6-7.
+
+Step 2 can be performed using a Python script (what is the name?)
+provided with the MS-CG library which defines the coarse-grained model
+and converts a standard LAMMPS dump file for an all-atom simulation
+(step 1) into a LAMMPS dump file which has the positions of and forces
+on the coarse-grained beads.  
+
+In step 3, an input file named "control.in" is needed by the MS-CG
+library which sets parameters for the range finding and force matching
+functionalities.  See the examples/mscg/control.in file as an example.
+And see the documentation provided with the MS-CG library for more
+info on this file.
+
+When this fix is used to perform steps 4 and 5, the MS-CG library also
+produces additional output files.  The range finder functionality
+(step 4) outputs files defining pair and bonded interaction ranges.
+The force matching functionality (step 5) outputs tabulated force
+files for every interaction in the system. Other diagnostic files can
+also be output depending on the paramters in the MS-CG library input
+script.  Again, see the documentation provided with the MS-CG library
+for more info.
+
+:line
+
+The {range} keyword specifies which MS-CG library functionality should
+be invoked. If {on}, the step 4 range finder functionality is invoked.
+{off}, the step 5 force matching functionality is invoked.
+
+If the {name} keyword is used, string names are defined to associate
+with the integer atom types in LAMMPS.  {Ntype} names must be
+provided, one for each atom type (1-Ntype).
+
+The {max} keyword specifies the maximum number of bonds, angles, and
+dihedrals a bead can have in the coarse-grained model.
+
+[Restrictions:]
+
+This fix is part of the MSCG 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.
+
+The MS-CG library uses C++11, which may not be supported by older
+compilers. The MS-CG library also has some additional numeric library
+dependencies, which are describd in its documentation.
+
+Currently, the MS-CG library is not setup to run in parallel with MPI,
+so this fix can only be used in a serial LAMMPS build and run
+on a single processor.
+
+[Related commands:] none
+
+[Default:]
+
+The default keyword settings are range off, max 4 12 36.
+
+:line
+
+:link(Izvekov)
+[(Izvekov)] Izvekov, Voth, J Chem Phys 123, 134105 (2005).
+
+:link(Noid)
+[(Noid)] Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J
+Chem Phys 128, 134105 (2008).
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@ -0,0 +1,71 @@
+"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 nvk command :h3
+
+[Syntax:]
+
+fix ID group-ID nvk :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nvk = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all nvk :pre
+
+[Description:]
+
+Perform constant kinetic energy integration using the Gaussian
+thermostat to update position and velocity for atoms in the group each
+timestep.  V is volume; K is kinetic energy. This creates a system
+trajectory consistent with the isokinetic ensemble.
+
+The equations of motion used are those of Minary et al in
+"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in 
+"(Zhang)"_#nvk-Zhang.
+
+The kinetic energy will be held constant at its value given when fix
+nvk is initiated. If a different kinetic energy is desired, the
+"velocity"_velocity.html command should be used to change the kinetic
+energy prior to this fix.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output
+commands"_Section_howto.html#howto_15.  No parameter of this fix can
+be used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+The Gaussian thermostat only works when it is applied to all atoms in
+the simulation box. Therefore, the group must be set to all.
+
+This fix has not yet been implemented to work with the RESPA integrator.
+
+This fix is part of the USER-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:] none
+
+[Default:] none
+
+:line
+
+:link(nvk-Minary)
+[(Minary)] Minary, Martyna, and Tuckerman, J Chem Phys, 18, 2510 (2003).
+
+:link(nvk-Zhang)
+[(Zhang)] Zhang, J Chem Phys, 106, 6102 (1997).
--- a/doc/src/fix_spring.txt
+++ b/doc/src/fix_spring.txt
@ -89,11 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
 group can straddle a periodic boundary.  See the "dump"_dump.html doc
 page for a discussion of unwrapped coordinates.  It also means that a
 spring connecting two groups or a group and the tether point can cross
-a periodic boundary and its length be calculated correctly.  One
-exception is for rigid bodies, which should not be used with the fix
-spring command, if the rigid body will cross a periodic boundary.
-This is because image flags for rigid bodies are used in a different
-way, as explained on the "fix rigid"_fix_rigid.html doc page.
+a periodic boundary and its length be calculated correctly.  

 [Restart, fix_modify, output, run start/stop, minimize info:]

--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@ -68,6 +68,7 @@ Fixes :h1
   fix_meso_stationary
   fix_momentum
   fix_move
+   fix_mscg
   fix_msst
   fix_neb
   fix_nh
@ -90,6 +91,7 @@ Fixes :h1
   fix_nve_noforce
   fix_nve_sphere
   fix_nve_tri
+   fix_nvk
   fix_nvt_asphere
   fix_nvt_body
   fix_nvt_manifold_rattle
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -23,6 +23,7 @@ Section_history.html

 tutorial_drude.html
 tutorial_github.html
+tutorial_pylammps.html

 body.html
 manifolds.html
@ -113,6 +114,7 @@ special_bonds.html
 suffix.html
 tad.html
 temper.html
+temper_grem.html
 thermo.html
 thermo_modify.html
 thermo_style.html
@ -192,6 +194,7 @@ fix_meso.html
 fix_meso_stationary.html
 fix_momentum.html
 fix_move.html
+fix_mscg.html
 fix_msst.html
 fix_neb.html
 fix_nh.html
@ -214,6 +217,7 @@ fix_nve_manifold_rattle.html
 fix_nve_noforce.html
 fix_nve_sphere.html
 fix_nve_tri.html
+fix_nvk.html
 fix_nvt_asphere.html
 fix_nvt_body.html
 fix_nvt_manifold_rattle.html
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@ -8,6 +8,7 @@

 pair_style eam command :h3
 pair_style eam/gpu command :h3
+pair_style eam/intel command :h3
 pair_style eam/kk command :h3
 pair_style eam/omp command :h3
 pair_style eam/opt command :h3
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@ -10,16 +10,21 @@ pair_style exp6/rx command :h3

 [Syntax:]

-pair_style exp6/rx cutoff :pre
+pair_style exp6/rx cutoff ... :pre

-cutoff = global cutoff for DPD interactions (distance units) :ul
+cutoff = global cutoff for DPD interactions (distance units)
+weighting = fractional or molecular (optional) :ul

 [Examples:]

 pair_style exp6/rx 10.0
-pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0
-pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0
-pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 :pre
+pair_style exp6/rx 10.0 fractional
+pair_style exp6/rx 10.0 molecular
+pair_coeff * * exp6.params h2o h2o exponent 1.0 1.0 10.0
+pair_coeff * * exp6.params h2o 1fluid exponent 1.0 1.0 10.0
+pair_coeff * * exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0
+pair_coeff * * exp6.params 1fluid 1fluid none 10.0
+pair_coeff * * exp6.params 1fluid 1fluid polynomial filename 10.0 :pre

 [Description:]

@ -50,14 +55,36 @@ defined in the reaction kinetics files specified with the "fix
 rx"_fix_rx.html command or they must correspond to the tag "1fluid",
 signifying interaction with a product species mixture determined
 through a one-fluid approximation.  The interaction potential is
-weighted by the geometric average of the concentrations of the two
-species.  The coarse-grained potential is stored before and after the
+weighted by the geometric average of either the mole fraction concentrations 
+or the number of molecules associated with the interacting coarse-grained 
+particles (see the {fractional} or {molecular} weighting pair style options). 
+The coarse-grained potential is stored before and after the
 reaction kinetics solver is applied, where the difference is defined
 to be the internal chemical energy (uChem).

-The fourth and fifth arguments specify the {Rm} and {epsilon} scaling exponents.
+The fourth argument specifies the type of scaling that will be used 
+to scale the EXP-6 paramters as reactions occur.  Currently, there
+are three scaling options:  {exponent}, {polynomial} and {none}.

-The final argument specifies the interaction cutoff.
+Exponent scaling requires two additional arguments for scaling 
+the {Rm} and {epsilon} parameters, respectively.  The scaling factor
+is computed by phi^exponent, where phi is the number of molecules  
+represented by the coarse-grain particle and exponent is specified 
+as a pair coefficient argument for {Rm} and {epsilon}, respectively.
+The {Rm} and {epsilon} parameters are multiplied by the scaling 
+factor to give the scaled interaction paramters for the CG particle.
+
+Polynomial scaling requires a filename to be specified as a pair 
+coeff argument.  The file contains the coefficients to a fifth order
+polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend 
+upon phi (the number of molecules represented by the CG particle). 
+The format of a polynomial file is provided below.
+
+The {none} option to the scaling does not have any additional pair coeff
+arguments.  This is equivalent to specifying the {exponent} option with 
+{Rm} and {epsilon} exponents of 0.0 and 0.0, respectively.
+
+The final argument specifies the interaction cutoff (optional).

 :line

@ -70,6 +97,19 @@ no2  exp6  13.60 0.01 3.70
 ...
 co2  exp6  13.00 0.03 3.20 :pre

+The format of the polynomial scaling file as follows (without the
+parenthesized comments):
+
+# POLYNOMIAL FILE          (one or more comment or blank lines) :pre
+#  General Functional Form:
+#  A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F 
+#
+#  Parameter  A        B         C        D         E        F
+                           (blank)
+alpha        0.0000   0.00000   0.00008  0.04955  -0.73804  13.63201
+epsilon      0.0000   0.00478  -0.06283  0.24486  -0.33737   2.60097
+rm           0.0001  -0.00118  -0.00253  0.05812  -0.00509   1.50106 :pre
+
 A section begins with a non-blank line whose 1st character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.
@ -117,4 +157,4 @@ LAMMPS"_Section_start.html#start_3 section for more info.

 "pair_coeff"_pair_coeff.html

-[Default:] none
+[Default:] fractional weighting
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@ -13,11 +13,14 @@ pair_style multi/lucy/rx command :h3
 pair_style multi/lucy/rx style N keyword ... :pre

 style = {lookup} or {linear} = method of interpolation
-N = use N values in {lookup}, {linear} tables :ul
+N = use N values in {lookup}, {linear} tables
+weighting = fractional or molecular (optional) :ul

 [Examples:]

 pair_style multi/lucy/rx linear 1000
+pair_style multi/lucy/rx linear 1000 fractional
+pair_style multi/lucy/rx linear 1000 molecular
 pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0
 pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 :pre

@ -94,8 +97,10 @@ tags must either correspond to the species defined in the reaction
 kinetics files specified with the "fix rx"_fix_rx.html command or they
 must correspond to the tag "1fluid", signifying interaction with a
 product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of the
-concentrations of the two species.  The coarse-grained potential is
+The interaction potential is weighted by the geometric average of 
+either the mole fraction concentrations or the number of molecules 
+associated with the interacting coarse-grained particles (see the 
+{fractional} or {molecular} weighting pair style options). The coarse-grained potential is
 stored before and after the reaction kinetics solver is applied, where
 the difference is defined to be the internal chemical energy (uChem).

@ -205,7 +210,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.

 "pair_coeff"_pair_coeff.html

-[Default:] none
+[Default:] fractional weighting

 :line

--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@ -10,16 +10,17 @@ pair_style table/rx command :h3

 [Syntax:]

-pair_style table style N :pre
+pair_style table style N ... :pre

 style = {lookup} or {linear} or {spline} or {bitmap} = method of interpolation
 N = use N values in {lookup}, {linear}, {spline} tables
-N = use 2^N values in {bitmap} tables
+weighting = fractional or molecular (optional) :ul

 [Examples:]

 pair_style table/rx linear 1000
-pair_style table/rx bitmap 12
+pair_style table/rx linear 1000 fractional
+pair_style table/rx linear 1000 molecular
 pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0
 pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0
 pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0 :pre
@ -84,8 +85,10 @@ tags must either correspond to the species defined in the reaction
 kinetics files specified with the "fix rx"_fix_rx.html command or they
 must correspond to the tag "1fluid", signifying interaction with a
 product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of the
-concentrations of the two species.  The coarse-grained potential is
+The interaction potential is weighted by the geometric average of 
+either the mole fraction concentrations or the number of molecules 
+associated with the interacting coarse-grained particles (see the 
+{fractional} or {molecular} weighting pair style options). The coarse-grained potential is
 stored before and after the reaction kinetics solver is applied, where
 the difference is defined to be the internal chemical energy (uChem).

@ -230,7 +233,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.

 "pair_coeff"_pair_coeff.html

-[Default:] none
+[Default:] fractional weighting

 :line

--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@ -15,11 +15,12 @@ read_dump file Nstep field1 field2 ... keyword values ... :pre
 file = name of dump file to read :ulb,l
 Nstep = snapshot timestep to read from file :l
 one or more fields may be appended :l
-field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz}
+field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz} or {fx} or {fy} or {fz}
  {x},{y},{z} = atom coordinates
  {vx},{vy},{vz} = velocity components
  {q} = charge
-  {ix},{iy},{iz} = image flags in each dimension :pre
+  {ix},{iy},{iz} = image flags in each dimension
+  {fx},{fy},{fz} = force components :pre
 zero or more keyword/value pairs may be appended :l
 keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l
  {box} value = {yes} or {no} = replace simulation box with dump box
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@ -32,7 +32,7 @@ Run a parallel tempering or replica exchange simulation in LAMMPS
 partition mode using multiple generalized replicas (ensembles) of a
 system defined by "fix grem"_fix_grem.html, which stands for the
 generalized replica exchange method (gREM) originally developed by
-"(Kim)"_#Kim.  It uses non-Boltzmann ensembles to sample over first
+"(Kim)"_#KimStraub.  It uses non-Boltzmann ensembles to sample over first
 order phase transitions. The is done by defining replicas with an
 enthalpy dependent effective temperature

@ -105,5 +105,5 @@ This command must be used with "fix grem"_fix_grem.html.

 [Default:] none

-:link(Kim)
+:link(KimStraub)
 [(Kim)] Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010).
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@ -33,14 +33,14 @@ timer loop :pre
 Select the level of detail at which LAMMPS performs its CPU timings.
 Multiple keywords can be specified with the {timer} command.  For
 keywords that are mutually exclusive, the last one specified takes
-effect.
+precedence.

 During a simulation run LAMMPS collects information about how much
 time is spent in different sections of the code and thus can provide
 information for determining performance and load imbalance problems.
 This can be done at different levels of detail and accuracy.  For more
 information about the timing output, see this "discussion of screen
-output"_Section_start.html#start_8.
+output in Section 2.8"_Section_start.html#start_8.

 The {off} setting will turn all time measurements off. The {loop}
 setting will only measure the total time for a run and not collect any
@ -52,20 +52,22 @@ procsessors.  The {full} setting adds information about CPU
 utilization and thread utilization, when multi-threading is enabled.

 With the {sync} setting, all MPI tasks are synchronized at each timer
-call which meaures load imbalance more accuractly, though it can also
-slow down the simulation.  Using the {nosync} setting (which is the
-default) turns off this synchronization.
+call which measures load imbalance for each section more accuractly,
+though it can also slow down the simulation by prohibiting overlapping
+independent computations on different MPI ranks  Using the {nosync}
+setting (which is the default) turns this synchronization off.

-With the {timeout} keyword a walltime limit can be imposed that
+With the {timeout} keyword a walltime limit can be imposed, that
 affects the "run"_run.html and "minimize"_minimize.html commands.
-This can be convenient when runs have to confirm to time limits,
-e.g. when running under a batch system and you want to maximize
-the utilization of the batch time slot, especially when the time
-per timestep varies and is thus difficult to predict how many
-steps a simulation can perform, or for difficult to converge
-minimizations. The timeout {elapse} value should be somewhat smaller
-than the time requested from the batch system, as there is usually
-some overhead to launch jobs, and it may be advisable to write
+This can be convenient when calculations have to comply with execution
+time limits, e.g. when running under a batch system when you want to
+maximize the utilization of the batch time slot, especially for runs
+where the time per timestep varies much and thus it becomes difficult
+to predict how many steps a simulation can perform for a given walltime
+limit. This also applies for difficult to converge minimizations.
+The timeout {elapse} value should be somewhat smaller than the maximum
+wall time requested from the batch system, as there is usually
+some overhead to launch jobs, and it is advisable to write
 out a restart after terminating a run due to a timeout.

 The timeout timer starts when the command is issued. When the time
--- a/doc/src/tutorial_github.txt
+++ b/doc/src/tutorial_github.txt
@ -11,10 +11,22 @@ LAMMPS GitHub tutorial :h3

 :line

-This document briefly describes how to use GitHub to merge changes you
-make into LAMMPS, using GitHub. It assumes that you are familiar with
-git. You may want to have a look at the "Git
-book"_http://git-scm.com/book/ to reacquaint yourself.
+This document describes the process of how to use GitHub to integrate
+changes or additions you have made to LAMMPS into the official LAMMPS
+distribution.  It uses the process of updating this very tutorial as
+an example to describe the individual steps and options.  You need to
+be familiar with git and you may want to have a look at the
+"Git book"_http://git-scm.com/book/ to reacquaint yourself with some
+of the more advanced git features used below.
+
+As of fall 2016, submitting contributions to LAMMPS via pull requests
+on GitHub is the preferred option for integrating contributed features
+or improvements to LAMMPS, as it significantly reduces the amount of
+work required by the LAMMPS developers. Consequently, creating a pull
+request will increase your chances to have your contribution included
+and will reduce the time until the integration is complete. For more
+information on the requirements to have your code included into LAMMPS
+please see "Section 10.15"_Section_modify.html#mod_15

 :line

@ -30,106 +42,121 @@ username or e-mail address and password.

 [Forking the repository]

-To get changes into LAMMPS, you need to first fork the repository. At
-the time of writing, LAMMPS-ICMS is the preferred fork. Go to "LAMMPS
-on GitHub"_https://github.com/lammps/lammps and make sure branch is
-set to "lammps-icms", see the figure below.
+To get changes into LAMMPS, you need to first fork the `lammps/lammps`
+repository on GitHub. At the time of writing, {master} is the preferred
+target branch. Thus go to "LAMMPS on GitHub"_https://github.com/lammps/lammps
+and make sure branch is set to "master", as shown in the figure below.

 :c,image(JPG/tutorial_branch.png)

-Now, click on fork in the top right corner:
+If it is not, use the button to change it to {master}. Once it is, use the
+fork button to create a fork.

 :c,image(JPG/tutorial_fork.png)

-This will create your own fork of the LAMMPS repository. You can make
-changes in this fork and later file {pull requests} to allow the
-upstream repository to merge changes from your own fork into the one
-we just forked from. At the same time, you can set things up, so you
-can include changes from upstream into your repository.
+
+This will create a fork (which is essentially a copy, but uses less
+resources) of the LAMMPS repository under your own GitHub account. You
+can make changes in this fork and later file {pull requests} to allow
+the upstream repository to merge changes from your own fork into the one
+we just forked from (or others that were forked from the same repository).
+At the same time, you can set things up, so you can include changes from
+upstream into your repository and thus keep it in sync with the ongoing
+LAMMPS development.

 :line

 [Adding changes to your own fork]

-Before adding changes, it is better to first create a new branch that
-will contain these changes, a so-called feature branch.
+Additions to the upstream version of LAMMPS are handled using {feature
+branches}.  For every new feature, a so-called feature branch is
+created, which contains only those modification relevant to one specific
+feature. For example, adding a single fix would consist of creating a
+branch with only the fix header and source file and nothing else.  It is
+explained in more detail here: "feature branch
+workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow.

 [Feature branches]

-Since LAMMPS is such a big project and most user contributions come in
-small portions, the most ideal workflow for LAMMPS is the so-called
-"Feature branch" workflow. It is explained in great detail here:
-"feature branch
-workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow.
+First of all, create a clone of your version on github on your local
+machine via HTTPS:

-The idea is that every new feature for LAMMPS gets its own
-branch. This way, it is fairly painless to incorporate new features
-into the upstream repository. I will explain briefly here how to do
-it. In this feature branch, I will add a USER-package.
+  $ git clone https://github.com/<your user name>/lammps.git <some name> :pre

-I assume that git is installed on the local machine and you know how
-to use a command line.
+or, if you have set up your GitHub account for using SSH keys, via SSH:

-First of all, you need to clone your own fork of LAMMPS:
-
-  $ git clone https://github.com/<your user name>/lammps.git :pre
-
-You can find the proper url to the right of the "HTTPS" block, see figure.
+  $ git clone git@github.com:<your user name>/lammps.git :pre
+  
+You can find the proper URL by clicking the "Clone or download"-button:

 :c,image(JPG/tutorial_https_block.png)

 The above command copies ("clones") the git repository to your local
-machine. You can use this local clone to make changes and test them
-without interfering with the repository on github. First, however, it
-is recommended to make a new branch for a particular feature you would
-like added to LAMMPS. In this example, I will try adding a new
-USER-package called USER-MANIFOLD.
+machine to a directory with the name you chose. If none is given, it will
+default to "lammps". Typical names are "mylammps" or something similar.

-To create a new branch, run the following git command in your repository:
+You can use this local clone to make changes and
+test them without interfering with the repository on Github.

-$ git checkout -b add-user-manifold :pre
+To pull changes from upstream into this copy, you can go to the directory
+and use git pull:

-The name of this new branch is "add-user-manifold" in my case. Just
-name it after something that resembles the feature you want added to
-LAMMPS.
+  $ cd mylammps
+  $ git checkout master
+  $ git pull https://github.com/lammps/lammps :pre

-Now that you've changed branches, you can edit the files as you see
-fit, add new files, and commit as much as you would like. Just
-remember that if halfway you decide to add another, unrelated feature,
-you should switch branches!
+You can also add this URL as a remote:
+
+  $ git remote add lammps_upstream https://www.github.com/lammps/lammps :pre
+
+At this point, you typically make a feature branch from the updated master
+branch for the feature you want to work on. This tutorial contains the
+workflow that updated this tutorial, and hence we will call the branch
+"github-tutorial-update":
+
+ $ git checkout -b github-tutorial-update master :pre
+
+Now that we have changed branches, we can make our changes to our local
+repository. Just remember that if you want to start working on another,
+unrelated feature, you should switch branches!
+
+[After changes are made]

 After everything is done, add the files to the branch and commit them:

-  $ git add src/USER-MANIFOLD examples/USER/manifold/
-  $ git add doc/fix_nv\{t,e\}_manifold_rattle.txt
-  $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt :pre
+ $ git add doc/src/tutorial_github.txt
+ $ git add doc/src/JPG/tutorial*.png :pre

-After the files are added, the change should be comitted:
+IMPORTANT NOTE: Do not use {git commit -a} (or {git add -A}).  The -a
+flag (or -A flag) will automatically include _all_ modified or new files
+and that is rarely the behavior you want.  It can easily lead to
+accidentally adding unrelated and unwanted changes into the repository.
+Instead it is preferable to explicitly use {git add}, {git rm}, {git mv}
+for adding, removing, renaming individual files, respectively, and then
+{git commit} to finalize the commit.  Carefully check all pending
+changes with {git status} before committing them.  If you find doing
+this on the command line too tedious, consider using a GUI, for example
+the one included in git distributions written in Tk, i.e. use {git gui}
+(on some Linux distributions it may be required to install an additional
+package to use it).

-  $ git commit -m 'Added user-manifold package' :pre
+After adding all files, the change set can be committed with some
+useful message that explains the change.

-The "-m" switch is used to add a message to the commit. Use this to
-indicate what type of change was commited.
-
-[Wisdom by Axel]
-
-{"Do not use "git commit -a".  the -a flag will automatically include
-*all* modified or new files.  mercurial does that and it find it
-hugely annoying and often leading to accidental commits of files you
-don't want.  use git add, git rm, git mv for adding, removing,
-renaming and then git commit to finalize the commit.  personally, i
-find it very convenient to use the bundled gui for commits, i.e. git
-gui.  typically, i will do git add and other operations, but then
-verify and review them with git gui.  git gui also allows to do
-line-by-line unstaging and other convenient operations."}
+  $ git commit -m 'Finally updated the github tutorial' :pre

 After the commit, the changes can be pushed to the same branch on GitHub:

 $ git push :pre

 Git will ask you for your user name and password on GitHub if you have
-not configured anything. If you correctly type your user name and
-password, the change should be added to your fork on GitHub.
+not configured anything. If your local branch is not present on Github yet,
+it will ask you to add it by running
+
+  $ git push --set-upstream origin github-tutorial-update :pre
+
+If you correctly type your user name and
+password, the feature branch should be added to your fork on GitHub.

 If you want to make really sure you push to the right repository
 (which is good practice), you can provide it explicitly:
@ -140,16 +167,20 @@ or using an explicit URL:

 $ git push git@github.com:Pakketeretet2/lammps.git :pre

-After that, you can file a new pull request based on this
-branch. GitHub will now look like this:
+:line

-:c,image(JPG/tutorial_pull_request_feature_branch1.png)
+[Filing a pull request]
+
+Up to this point in the tutorial, all changes were to {your} clones of
+LAMMPS.  Eventually, however, you want this feature to be included into
+the official LAMMPS version.  To do this, you will want to file a pull
+request by clicking on the "New pull request" button:
+
+:c,image(JPG/tutorial_new_pull_request.png)

 Make sure that the current branch is set to the correct one, which, in
-this case, is "add-user-manifold". Now click "New pull request". If
-done correctly, the only changes you will see are those that were made
-on this branch, so in my case, I will see nothing related to
-$\mathrm{pair\_dzugatov}.$
+this case, is "github-tutorial-update". If done correctly, the only
+changes you will see are those that were made on this branch.

 This will open up a new window that lists changes made to the
 repository. If you are just adding new files, there is not much to do,
@ -158,36 +189,162 @@ changes in existing files. If all changes can automatically be merged,
 green text at the top will say so and you can click the "Create pull
 request" button, see image.

-:c,image(JPG/tutorial_pull_request2.png)
+:c,image(JPG/tutorial_create_new_pull_request1.png)

-After this you have to specify a short title and a comment with
-details about your pull request. I guess here you write what your
-modifications do and why they should be incorporated upstream. After
-that, click the "Create pull request" button, see image below.
+Before creating the pull request, make sure the short title is accurate
+and add a comment with details about your pull request.  Here you write
+what your modifications do and why they should be incorporated upstream.

-:c,image(JPG/tutorial_pull_request3.png)
+Note the checkbox that says "Allow edits from maintainers".
+This is checked by default checkbox (although in my version of Firefox, only the checkmark is visible):

-Now just write some nice comments, click "Comment", and that is it. It
-is now up to the maintainer(s) of the upstream repository to
-incorporate the changes into the repository and to close the pull
-request.
+:c,image(JPG/tutorial_edits_maintainers.png)

-:c,image(JPG/tutorial_pull_request4.png)
+If it is checked, maintainers can immediately add their own edits to the
+pull request.  This helps the inclusion of your branch significantly, as
+simple/trivial changes can be added directly to your pull request branch
+by the LAMMPS maintainers.  The alternative would be that they make
+changes on their own version of the branch and file a reverse pull
+request to you.  Just leave this box checked unless you have a very good
+reason not to.
+
+Now just write some nice comments and click on "Create pull request".
+
+:c,image(JPG/tutorial_create_new_pull_request2.png)

 :line

+[After filing a pull request]
+
+NOTE: When you submit a pull request (or ask for a pull request) for the
+first time, you will receive an invitation to become a LAMMPS project
+collaborator. Please accept this invite as being a collaborator will
+simplify certain administrative tasks and will probably speed up the
+merging of your feature, too.
+
+You will notice that after filing the pull request, some checks are
+performed automatically:
+
+:c,image(JPG/tutorial_automated_checks.png)
+
+If all is fine, you will see this:
+
+:c,image(JPG/tutorial_automated_checks_passed.png)
+
+If any of the checks are failing, your pull request will not be
+processed, as your changes may break compilation for certain
+configurations or may not merge cleanly. It is your responsibility
+to remove the reason(s) for the failed test(s). If you need help
+with this, please contact the LAMMPS developers by adding a comment
+explaining your problems with resolving the failed tests.
+
+A few further interesting things (can) happen to pull requests before
+they are included.
+
 [Additional changes]

-Before the pull request is accepted, any additional changes you push
-into your repository will automatically become part of the pull
-request.
+First of all, any additional changes you push into your branch in your
+repository will automatically become part of the pull request:
+
+:c,image(JPG/tutorial_additional_changes.png)
+
+This means you can add changes that should be part of the feature after
+filing the pull request, which is useful in case you have forgotten
+them, or if a developer has requested that something needs to be changed
+before the feature can be accepted into the official LAMMPS version.
+After each push, the automated checks are run again.
+
+[Assignees]
+
+There is an assignee label for pull requests. If the request has not
+been reviewed by any developer yet, it is not assigned to anyone. After
+revision, a developer can choose to assign it to either a) you, b) a
+LAMMPS developer (including him/herself) or c) Steve Plimpton (sjplimp).
+
+Case a) happens if changes are required on your part :ulb,l
+Case b) means that at the moment, it is being tested and reviewed by a
+LAMMPS developer with the expectation that some changes would be required.
+After the review, the developer can choose to implement changes directly
+or suggest them to you. :l
+Case c) means that the pull request has been assigned to the lead
+developer Steve Plimpton and means it is considered ready for merging. :ule,l
+
+In this case, Axel assigned the tutorial to Steve:
+
+:c,image(JPG/tutorial_steve_assignee.png)
+
+[Edits from LAMMPS maintainers]
+
+If you allowed edits from maintainers (the default), any LAMMPS
+maintainer can add changes to your pull request.  In this case, both
+Axel and Richard made changes to the tutorial:
+
+:c,image(JPG/tutorial_changes_others.png)
+
+[Reverse pull requests]
+
+Sometimes, however, you might not feel comfortable having other people
+push changes into your own branch, or maybe the maintainers are not sure
+their idea was the right one.  In such a case, they can make changes,
+reassign you as the assignee, and file a "reverse pull request", i.e.
+file a pull request in your GitHub repository to include changes in the
+branch, that you have submitted as a pull request yourself.  In that
+case, you can choose to merge their changes back into your branch,
+possibly make additional changes or corrections and proceed from there.
+It looks something like this:
+
+:c,image(JPG/tutorial_reverse_pull_request.png)
+
+For some reason, the highlighted button didn't work in my case, but I
+can go to my own repository and merge the pull request from there:
+
+:c,image(JPG/tutorial_reverse_pull_request2.png)
+
+Be sure to check the changes to see if you agree with them by clicking
+on the tab button:
+
+:c,image(JPG/tutorial_reverse_pull_request3.png)
+
+In this case, most of it is changes in the markup and a short rewrite of
+Axel's explanation of the "git gui" and "git add" commands.
+
+:c,image(JPG/tutorial_reverse_pull_request4.png)
+
+Because the changes are OK with us, we are going to merge by clicking on
+"Merge pull request".  After a merge it looks like this:
+
+:c,image(JPG/tutorial_reverse_pull_request5.png)
+
+Now, since in the meantime our local text for the tutorial also changed,
+we need to pull Axel's change back into our branch, and merge them:
+
+ $ git add tutorial_github.txt
+ $ git add JPG/tutorial_reverse_pull_request*.png
+ $ git commit -m "Updated text and images on reverse pull requests"
+ $ git pull :pre
+
+In this case, the merge was painless because git could auto-merge:
+
+:c,image(JPG/tutorial_reverse_pull_request6.png)
+
+With Axel's changes merged in and some final text updates, our feature
+branch is now perfect as far as we are concerned, so we are going to
+commit and push again:
+
+ $ git add tutorial_github.txt
+ $ git add JPG/tutorial_reverse_pull_request6.png
+ $ git commit -m "Merged Axel's suggestions and updated text"
+ $ git push git@github.com:Pakketeretet2/lammps :pre
+
+This merge also shows up on the lammps Github page:
+
+:c,image(JPG/tutorial_reverse_pull_request7.png)

 :line

 [After a merge]

-When everything is fine the feature branch is merged into the LAMMPS
-repositories:
+When everything is fine, the feature branch is merged into the master branch:

 :c,image(JPG/tutorial_merged.png)

@ -198,17 +355,29 @@ It is in principle safe to delete them from your own fork. This helps
 keep it a bit more tidy. Note that you first have to switch to another
 branch!

-$ git checkout lammps-icms
-$ git pull lammps-icms
-$ git branch -d add-user-manifold :pre
+$ git checkout master
+$ git pull master
+$ git branch -d github-tutorial-update :pre

 If you do not pull first, it is not really a problem but git will warn
 you at the next statement that you are deleting a local branch that
 was not yet fully merged into HEAD. This is because git does not yet
-know your branch just got merged into lammps-icms upstream. If you
+know your branch just got merged into LAMMPS upstream. If you
 first delete and then pull, everything should still be fine.

 Finally, if you delete the branch locally, you might want to push this
 to your remote(s) as well:

-$ git push origin :add-user-manifold :pre
+$ git push origin :github-tutorial-update :pre
+
+[Recent changes in the workflow]
+
+Some changes to the workflow are not captured in this tutorial.  For
+example, in addition to the master branch, to which all new features
+should be submitted, there is now also an "unstable" and a "stable"
+branch; these have the same content as "master", but are only updated
+after a patch release or stable release was made.
+Furthermore, the naming of the patches now follow the pattern
+"patch_<Day><Month><Year>" to simplify comparisons between releases.
+Finally, all patches and submissions are subject to automatic testing
+and code checks to make sure they at the very least compile.
--- a/examples/README
+++ b/examples/README
@ -82,6 +82,7 @@ meam:	  MEAM test for SiC and shear (same as shear examples)
 melt:	  rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:	  energy minimization of 2d LJ melt
+mscg:     parameterize a multi-scale coarse-graining (MSCG) model
 msst:	  MSST shock dynamics
 nb3b:     use of nonbonded 3-body harmonic pair style
 neb:	  nudged elastic band (NEB) calculation for barrier finding
--- a/examples/USER/dpd/dpde-vv/log.dpde-vv.reference
+++ b/examples/USER/dpd/dpde-vv/log.dpde-vv.reference
@ -35,129 +35,133 @@ thermo_modify   format float %24.16f

 run             1000
 Neighbor list info ...
-  1 neighbor list requests
  update every 1 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.6
  ghost atom cutoff = 10.6
-  binsize = 5.3 -> bins = 25 25 25
-Memory usage per processor = 3.36353 Mbytes
+  binsize = 5.3, bins = 25 25 25
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair dpd/fdt/energy, perpetual
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Memory usage per processor = 4.28221 Mbytes
 Step Temp Press PotEng KinEng c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4] 
-       0     301.4391322267262012    1636.1776395935085020    1188.6488072196075336     394.4722035796053206    7852.5601874986105031    7852.5601874986105031   17288.2413857964347699     299.9999999999841407 
-      10     301.4791572483523510    1486.4422375141198245    1188.7147620806101713     394.5245815119678241    7852.5601874999802021    7852.3731942333779443   17288.1727253259377903     299.9960221120699089 
-      20     301.4275643919337426    1677.9356110821624952    1188.7839634625399867     394.4570655673388728    7852.5601874999938445    7852.3711851933012440   17288.1724017231754260     299.9955485734552099 
-      30     301.2240988054542186    1452.7304951528931269    1188.8550809767796181     394.1908044563202225    7852.5601875000002110    7852.5679666239848302   17288.1740395570850524     299.9988968405210130 
-      40     301.1023506886409677    1527.9758363521380033    1188.9264527568634549     394.0314812537677653    7852.5601874999947540    7852.6574764573806533   17288.1755979680056043     300.0001694462812338 
-      50     301.0409654880461972    1597.1737251233498682    1188.9944523606982330     393.9511507566391515    7852.5601875000029395    7852.6700547249911324   17288.1758453423317405     299.9999653064982681 
-      60     301.2904978886139133    1610.8630327676828529    1189.0651026961211301     394.2776962691256131    7852.5601874999829306    7852.2734988976435488   17288.1764853628737910     299.9919857290491905 
-      70     300.8575037843163500    1489.3259312130880971    1189.1295686642290548     393.7110673208616731    7852.5601874999856591    7852.7707182199101226   17288.1715417049854295     300.0010992278233175 
-      80     300.5955830326474825    1449.3896097889587509    1189.1880764967559116     393.3683100440913449    7852.5601875000411383    7853.0484238882281716   17288.1649979291178170     300.0059513551503301 
-      90     301.0092332775843147    1553.9266324350364812    1189.2470037925052111     393.9096250433288446    7852.5601875000420478    7852.4452067113825251   17288.1620230472581170     299.9940347326859182 
-     100     301.0478004479094238    1539.2270336322194453    1189.3010269201699884     393.9600951881690207    7852.5601875000074870    7852.3416236045995902   17288.1629332129450631     299.9916385566916119 
-     110     300.9609384905550087    1500.0429484565006533    1189.3524514939088021     393.8464250502817663    7852.5601874999983920    7852.4114980357189779   17288.1705620799075405     299.9925626482005327 
-     120     300.9625536631411933    1630.5065919443034090    1189.4006029528841282     393.8485387131115658    7852.5601875000575092    7852.3600810123671181   17288.1694101784196391     299.9911580775880680 
-     130     301.0373750247310340    1539.2267307640183844    1189.4426173625224692     393.9464521696795032    7852.5601874999993015    7852.2178388309775983   17288.1670958631802932     299.9879581026651749 
-     140     300.7465104415114752    1550.8353679735087098    1189.4887352231000932     393.5658181350791551    7852.5601874999920256    7852.5559582333216895   17288.1706990914935886     299.9939749909034958 
-     150     300.6667173911141617    1634.8987162883277051    1189.5368575067818711     393.4613985788388959    7852.5601874999920256    7852.6079668015609059   17288.1664103871735279     299.9946423938895350 
-     160     300.4684731724562425    1462.9400882126803936    1189.5825022927965620     393.2019703048678707    7852.5601874999847496    7852.8265187980177870   17288.1711788956672535     299.9983600613423960 
-     170     300.1439323338466920    1510.2352578813552100    1189.6305700279478970     392.7772665220106774    7852.5601874999802021    7853.2009671047335360   17288.1689911546709482     300.0051118582463232 
-     180     300.1074244553407198    1529.6307083879951279    1189.6764977580119194     392.7294912276224181    7852.5601874999729262    7853.2047509722533505   17288.1709274578606710     300.0047089238623812 
-     190     300.4193298066089142    1546.3205495807171701    1189.7172820166240399     393.1376598363699486    7852.5601874999847496    7852.7461854379371289   17288.1613147909156396     299.9954451643528728 
-     200     300.3353919251508728    1532.5496449337254035    1189.7600175880224924     393.0278162310690391    7852.5601874999683787    7852.8107089913455638   17288.1587303104060993     299.9962707550171785 
-     210     300.3276568499739483    1504.8178651700843602    1189.7998299597820733     393.0176938818990493    7852.5601875000156724    7852.7810130200659842   17288.1587243617614149     299.9953436245502871 
-     220     300.5768315696971626    1592.5896084568344122    1189.8391466344742184     393.3437713226064716    7852.5601875000329528    7852.4205574703573802   17288.1636629274726147     299.9880321846658831 
-     230     300.6587445618569063    1672.3049358942289473    1189.8766340798690635     393.4509650976162334    7852.5601874999847496    7852.2733199687863817   17288.1611066462573945     299.9848228571166828 
-     240     300.7517707836825025    1527.1722267937811921    1189.9126240081129708     393.5727019751183207    7852.5601875000065775    7852.1160682173085661   17288.1615817005440476     299.9814952182625802 
-     250     300.8473715548367409    1589.1847713095248764    1189.9441342461948352     393.6978079843565865    7852.5601875000047585    7851.9625847797888127   17288.1647145103452203     299.9782210858571148 
-     260     300.8450266408960942    1623.1896863377055524    1189.9636161513917614     393.6947393603111891    7852.5601874999820211    7851.9471828473988353   17288.1657258590821584     299.9775302202895659 
-     270     300.6663619570709898    1564.5160171187899323    1189.9764081239700317     393.4609334472908131    7852.5601875000193104    7852.1708276117251444   17288.1683566830033669     299.9812899253168439 
-     280     300.7668534205726019    1618.5400526904263643    1189.9872008155405183     393.5924395618274048    7852.5601875000184009    7852.0271568534708422   17288.1669847308585304     299.9781169783826158 
-     290     300.8462727198648849    1562.6765776748122789    1189.9918265985252219     393.6963700162682471    7852.5601875000211294    7851.9189772084127981   17288.1673613232269417     299.9756806168044250 
-     300     300.8095414073812890    1525.1785808192844343    1189.9873922767767453     393.6483023295390922    7852.5601875000020300    7851.9657301693578120   17288.1616122756749974     299.9761279889730758 
-     310     300.9496330741350221    1566.5597234051326723    1189.9752299662607129     393.8316304464934774    7852.5601875000056680    7851.7898117189633922   17288.1568596317229094     299.9723726900590464 
-     320     301.2370566356515837    1513.6869483705047514    1189.9626455872523820     394.2077614578674343    7852.5601874999929350    7851.4248466706330873   17288.1554412157456682     299.9650543775110236 
-     330     301.3279721508968692    1549.0667862452519330    1189.9513389477854162     394.3267362020337146    7852.5601874999929350    7851.3129955581916875   17288.1512582080031279     299.9625537201162615 
-     340     301.1145736537583844    1414.7930515101759283    1189.9408691169965095     394.0474765890400590    7852.5601874999993015    7851.6028846074832472   17288.1514178135184920     299.9677356565828745 
-     350     301.1651600907370039    1529.8016115175887535    1189.9314470205476937     394.1136755032911196    7852.5601874999929350    7851.5441417268757505   17288.1494517507089768     299.9662576716461331 
-     360     301.0550563185083206    1536.7721716375504002    1189.9200519814730796     393.9695904359920178    7852.5601875000074870    7851.7101209691463737   17288.1599508866202086     299.9690811750865009 
-     370     301.1008976932964742    1522.3385843459479929    1189.9109162496640693     394.0295798208944120    7852.5601875000211294    7851.6603423306560217   17288.1610259012340975     299.9677565060027860 
-     380     301.1656898730700505    1505.0548721701993600    1189.9005648244351505     394.1143687921909304    7852.5601875000056680    7851.5816827598300733   17288.1568038764598896     299.9659906785156522 
-     390     300.8379322662876802    1740.9151205755624687    1189.8851457594087151     393.6854554509390596    7852.5601875000238579    7852.0268864110385039   17288.1576751214088290     299.9741278188615752 
-     400     300.8663790447546376    1564.9461156870302148    1189.8690133470408909     393.7226817503372445    7852.5601875000411383    7852.0043792319993372   17288.1562618294192362     299.9732593416579789 
-     410     300.6263441860635908    1564.2840871092373618    1189.8566574093877080     393.4085650033033517    7852.5601874999892971    7852.3284491703725507   17288.1538590830532485     299.9792095875052951 
-     420     300.5302259436974168    1438.1569922368764765    1189.8406936554465574     393.2827818158641549    7852.5601875000302243    7852.4696075433648730   17288.1532705147074012     299.9815165752025337 
-     430     300.5877786105220935    1503.3641639033023694    1189.8251514530138593     393.3580969454444016    7852.5601874999802021    7852.4023373559457468   17288.1457732543858583     299.9798346272511935 
-     440     300.7289160804472772    1689.2527029957295781    1189.8035410609209066     393.5427936314976591    7852.5601875000029395    7852.2436462415198548   17288.1501684339418716     299.9764596782897570 
-     450     300.9487198282456575    1497.3668092174791582    1189.7808137689632986     393.8304353457919547    7852.5601874999938445    7851.9788323927432430   17288.1502690074921702     299.9710227473042323 
-     460     300.9359942496024587    1625.1573864018491804    1189.7615359247627111     393.8137822755282400    7852.5601875000147629    7852.0165192783370003   17288.1520249786408385     299.9713565393226986 
-     470     301.0000133856357252    1486.1561922844011860    1189.7439269526955741     393.8975596188205941    7852.5601874999656502    7851.9561324572268859   17288.1578065287103527     299.9697143418395626 
-     480     300.8568627175957886    1535.6080526199095857    1189.7237810071801505     393.7102284019063063    7852.5601874999601932    7852.1697010727630186   17288.1638979818089865     299.9732503057674080 
-     490     301.0608040775520067    1497.3221544489886128    1189.7062242497636362     393.9771121242308709    7852.5601874999974825    7851.9258988739011329   17288.1694227478947141     299.9682362511933320 
-     500     301.0232592587148019    1517.5854528541199215    1189.6911287485861521     393.9279798589197981    7852.5601875000247674    7851.9823225510326665   17288.1616186585633841     299.9690333355835037 
-     510     300.7038579923685120    1420.2615974401142012    1189.6747661513456933     393.5100018730125839    7852.5601874999674692    7852.4114869568047652   17288.1564424811294884     299.9768186576545759 
-     520     300.5917863355052759    1537.4862082427132464    1189.6604754398756540     393.3633415734188361    7852.5601875000029395    7852.5789017095057716   17288.1629062228021212     299.9795694302102333 
-     530     300.4751352158502868    1481.1071694751799441    1189.6453243069925065     393.2106884527691477    7852.5601874999811116    7852.7451655714066874   17288.1613658311471227     299.9823181268525900 
-     540     300.5380123640739498    1547.3461372766389559    1189.6261485232855648     393.2929713568877332    7852.5601875000375003    7852.6850583598352387   17288.1643657400454686     299.9808112190538623 
-     550     300.4253885005187499    1544.3485889749692888    1189.6033595464525661     393.1455884232119047    7852.5601874999756546    7852.8598718466746504   17288.1690073163154011     299.9835860164698147 
-     560     300.3263552442093101    1556.5150300058251105    1189.5759163336824713     393.0159905619273673    7852.5601875000111249    7853.0148613782675966   17288.1669557738860021     299.9861837797674866 
-     570     300.1977324643196425    1511.2320626303917379    1189.5441090918316149     392.8476709710407704    7852.5601875000102154    7853.2098259401755058   17288.1617935030590161     299.9896761688499964 
-     580     300.3543631005173893    1588.9566243200433746    1189.5094471319721379     393.0526424747489500    7852.5601875000156724    7853.0374555421631158   17288.1597326488990802     299.9859298211933378 
-     590     300.5019108864805730    1504.4406939723214691    1189.4809412920112663     393.2457278908070748    7852.5601874999874781    7852.8704277855340479   17288.1572844683396397     299.9823573257917815 
-     600     300.4791158523048011    1540.4690749004150803    1189.4551948503105905     393.2158976318902432    7852.5601875000220389    7852.9312239063838206   17288.1625038886049879     299.9832002920041987 
-     610     300.5939139841889869    1368.0565839211087678    1189.4252547652590692     393.3661258776944578    7852.5601874999574648    7852.8130977336286378   17288.1646658765384927     299.9807742697515778 
-     620     300.7674247480806002    1483.2566452708945235    1189.3941250938435132     393.5931872179773450    7852.5601875000193104    7852.6187967208716145   17288.1662965327122947     299.9766963671718258 
-     630     300.7920034341021278    1543.0699124130637756    1189.3598279316649950     393.6253516166882491    7852.5601875000302243    7852.6219971866230480   17288.1673642350069713     299.9762538437230432 
-     640     300.8032734267029014    1423.2549819291616586    1189.3293074476885067     393.6400998638143278    7852.5601874999847496    7852.6384826097782934   17288.1680774212654796     299.9762118202994543 
-     650     300.7516995878241346    1542.6559695158523482    1189.3021161045705867     393.5726088061030055    7852.5601874999720167    7852.7361949473242930   17288.1711073579681397     299.9775656396505497 
-     660     300.8699697098109596    1675.5121937767839881    1189.2687179804190691     393.7273806013013768    7852.5601874999802021    7852.6179739687149777   17288.1742600504148868     299.9750492262036801 
-     670     301.0255004186900578    1520.7397686587873977    1189.2284265783687260     393.9309127074437242    7852.5601874999847496    7852.4592279727157802   17288.1787547585117863     299.9715123049731460 
-     680     301.1071983488760679    1651.9751417063259851    1189.1858967311386550     394.0378250459656329    7852.5601875000002110    7852.3982826328638112   17288.1821919099675142     299.9699481289110850 
-     690     301.0027086454253435    1496.1607274163641250    1189.1436949551202815     393.9010867158519886    7852.5601875000293148    7852.5788938360938118   17288.1838630070960789     299.9731939774295597 
-     700     300.9009090279179759    1551.8182127127668082    1189.0993919251338866     393.7678687121208441    7852.5601875000102154    7852.7513665452252098   17288.1788146824910655     299.9761043445071209 
-     710     301.2325536720837817    1678.1546953970853338    1189.0528341066981284     394.2018687459686817    7852.5601874999956635    7852.3633298995819132   17288.1782202522445004     299.9683013583347133 
-     720     301.2122298224125529    1524.1415452491430642    1189.0046957644285612     394.1752723525083866    7852.5601875000093059    7852.4351629896145823   17288.1753186065616319     299.9693315350040734 
-     730     301.0763282392692304    1547.1987029633166912    1188.9602551214045434     393.9974275034455218    7852.5601874999883876    7852.6518053705112834   17288.1696754953518393     299.9732715774841267 
-     740     301.3262401480515109    1544.7045314021493141    1188.9131307177485724     394.3244696516559884    7852.5601874999965730    7852.3694201272974169   17288.1672079966992897     299.9674666811455950 
-     750     301.5740779122830304    1591.1785078054851965    1188.8637580645938669     394.6487975126887022    7852.5601875000029395    7852.0919529470393172   17288.1646960243233480     299.9616008527094095 
-     760     301.4385361878654521    1547.3218422039201414    1188.8113669183098864     394.4714235854450521    7852.5601874999838401    7852.3161911124070684   17288.1591691161447670     299.9656339783694534 
-     770     301.6110125684814420    1494.5039561806622714    1188.7581685915934031     394.6971313010439530    7852.5601875000083965    7852.1351720579104949   17288.1506594505553949     299.9619855799395509 
-     780     301.8360352039435384    1588.1458619705292676    1188.7039178696472845     394.9916026067776329    7852.5601874999956635    7851.9015195838428554   17288.1572275602629816     299.9572350302977952 
-     790     302.1008324754310479    1545.4409171812178556    1188.6491103416560691     395.3381241828382144    7852.5601875000138534    7851.6150048936624444   17288.1624269181702402     299.9513959104631340 
-     800     301.9660372380565718    1563.9565804790736365    1188.5964649891604950     395.1617271307158035    7852.5601874999874781    7851.8461249560614306   17288.1645045759250934     299.9555810527747326 
-     810     302.0507207347627627    1511.4560763489957935    1188.5468477146612258     395.2725464702810996    7852.5601875000120344    7851.7904104899025697   17288.1699921748586348     299.9541551776504775 
-     820     302.4700213214911741    1458.5135514273570152    1188.4981381693974072     395.8212556746473751    7852.5601875000202199    7851.2935886962204677   17288.1731700402851857     299.9441803241180651 
-     830     302.2853997979337350    1496.2544527963129894    1188.4496917372191547     395.5796544641875698    7852.5601875000447762    7851.5862641793482908   17288.1757978808018379     299.9494768794835977 
-     840     302.0840465730901201    1518.8301331998704882    1188.3994383226176978     395.3161576523596636    7852.5601875000038490    7851.8962146812327774   17288.1719981562127941     299.9550476592922337 
-     850     301.8910942560261788    1469.8827850510901953    1188.3489956121345585     395.0636545180261692    7852.5601874999829306    7852.2025804631493884   17288.1754180932912277     299.9606927700139067 
-     860     301.7284384160519153    1657.6802015862324424    1188.3052233777652873     394.8507982536594341    7852.5601875000093059    7852.4644669022691232   17288.1806760337058222     299.9652835238809985 
-     870     301.6331619894115192    1501.5829953208524330    1188.2628815714097072     394.7261166912876433    7852.5601875000202199    7852.6378180648598573   17288.1870038275774277     299.9682811831179379 
-     880     301.3703918424367316    1499.1595903074553462    1188.2195190931643083     394.3822478705861272    7852.5601874999956635    7853.0266423250832304   17288.1885967888301820     299.9755099056966401 
-     890     301.4157954313303662    1598.8758859042511631    1188.1845892608291706     394.4416643558612918    7852.5601875000065775    7853.0036606192506952   17288.1901017359487014     299.9745322513492738 
-     900     301.4752150615485675    1621.2148728756822038    1188.1517520946135846     394.5194226492019993    7852.5601874999711072    7852.9579580608560718   17288.1893203046420240     299.9733125337182287 
-     910     301.4308816315938770    1538.4823217911632582    1188.1159856659232901     394.4614066057066566    7852.5601875000002110    7853.0558695713261841   17288.1934493429580471     299.9748317405193916 
-     920     301.4323110133492492    1594.7193046491217956    1188.0835779842032025     394.4632771371357762    7852.5601875000202199    7853.0942701464364291   17288.2013127677964803     299.9751127806911200 
-     930     301.4801256941950101    1387.6885377097617038    1188.0464206196895702     394.5258488489681099    7852.5601875000229484    7853.0656502842994087   17288.1981072529815719     299.9740698440909910 
-     940     301.8075611840245074    1534.2487040663793323    1188.0124217312886685     394.9543406584059539    7852.5601874999701977    7852.6729444202819650   17288.1998943099461030     299.9660570413493588 
-     950     301.6915970126173647    1567.7725992489238251    1187.9790455470049437     394.8025864986412898    7852.5601875000274958    7852.8619557087595240   17288.2037752544347313     299.9694678653150959 
-     960     301.6392594677008105    1504.8502165144939227    1187.9439133338105421     394.7340960325207675    7852.5601874999711072    7852.9728807988849439   17288.2110776651898050     299.9711546356286362 
-     970     301.6049535791644303    1514.0198965433548892    1187.9094123369413865     394.6892023276233772    7852.5601874999765641    7853.0497909819878259   17288.2085931465298927     299.9722547114341751 
-     980     301.2982841679705643    1634.1208149125807267    1187.8768454876480973     394.2878856256063500    7852.5601874999856591    7853.4862008383515786   17288.2111194515891839     299.9802110109069986 
-     990     301.2573007350166563    1489.7316698898257528    1187.8432331161868660     394.2342534877078606    7852.5601875000047585    7853.5840096862748396   17288.2216837901723920     299.9819468620868292 
-    1000     301.3195135766228532    1562.6587211933920116    1187.8034267774903583     394.3156670604516307    7852.5601874999356369    7853.5372636956635688   17288.2165450335414789     299.9807651637231629 
-Loop time of 21.3308 on 1 procs for 1000 steps with 10125 atoms
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+      60     301.2904978886138565    1610.8630327676828529    1189.0651026961211301     394.2776962691255562      -0.0000000000000000   15704.8336863976528548   17288.1764853628992569     299.9919857290491905 
+      70     300.8575037843164068    1489.3259312130892340    1189.1295686642290548     393.7110673208617300       0.0000000000000000   15705.3309057198275696   17288.1715417049199459     300.0010992278232607 
+      80     300.5955830326474825    1449.3896097889576140    1189.1880764967559116     393.3683100440913449      -0.0000000000000000   15705.6086113882302016   17288.1649979290777992     300.0059513551502164 
+      90     301.0092332775843147    1553.9266324350371633    1189.2470037925056658     393.9096250433288446      -0.0000000000000000   15705.0053942113881931   17288.1620230472217372     299.9940347326859182 
+     100     301.0478004479094238    1539.2270336322201274    1189.3010269201699884     393.9600951881690207      -0.0000000000000000   15704.9018111045588739   17288.1629332128977694     299.9916385566916119 
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+Loop time of 17.0881 on 1 procs for 1000 steps with 10125 atoms

-Performance: 4.050 ns/day, 5.925 hours/ns, 46.880 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 5.056 ns/day, 4.747 hours/ns, 58.520 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    | 10.099     | 10.099     | 10.099     |   0.0 | 47.34
-Neigh   | 10.145     | 10.145     | 10.145     |   0.0 | 47.56
-Comm    | 0.49807    | 0.49807    | 0.49807    |   0.0 |  2.33
-Output  | 0.011203   | 0.011203   | 0.011203   |   0.0 |  0.05
-Modify  | 0.28296    | 0.28296    | 0.28296    |   0.0 |  1.33
-Other   |            | 0.295      |            |       |  1.38
+Pair    | 8.0541     | 8.0541     | 8.0541     |   0.0 | 47.13
+Neigh   | 8.1306     | 8.1306     | 8.1306     |   0.0 | 47.58
+Comm    | 0.39415    | 0.39415    | 0.39415    |   0.0 |  2.31
+Output  | 0.01103    | 0.01103    | 0.01103    |   0.0 |  0.06
+Modify  | 0.24061    | 0.24061    | 0.24061    |   0.0 |  1.41
+Other   |            | 0.2576     |            |       |  1.51

 Nlocal:    10125 ave 10125 max 10125 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -170,4 +174,4 @@ Total # of neighbors = 114682
 Ave neighs/atom = 11.3266
 Neighbor list builds = 1000
 Dangerous builds not checked
-Total wall time: 0:00:21
+Total wall time: 0:00:17
--- a/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow
+++ b/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow
@ -18,7 +18,7 @@ neigh_modify    every 1 delay 0 check no once no
 timestep        0.001

 compute         dpdU all dpd
-variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[1]+press*vol
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]+press*vol

 thermo          1
 thermo_style    custom step temp press vol pe ke v_totEnergy cella cellb cellc
--- a/examples/USER/dpd/dpdh-shardlow/log.dpdh-shardlow.reference
+++ b/examples/USER/dpd/dpdh-shardlow/log.dpdh-shardlow.reference
@ -22,7 +22,7 @@ neigh_modify    every 1 delay 0 check no once no
 timestep        0.001

 compute         dpdU all dpd
-variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[1]+press*vol
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]+press*vol

 thermo          1
 thermo_style    custom step temp press vol pe ke v_totEnergy cella cellb cellc
@ -34,129 +34,137 @@ fix             2 all eos/cv 0.0005

 run             100
 Neighbor list info ...
-  1 neighbor list requests
  update every 1 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
-  binsize = 6 -> bins = 22 22 22
-Memory usage per processor = 6.48143 Mbytes
+  binsize = 6, bins = 22 22 22
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair dpd/fdt/energy, perpetual
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix shardlow, perpetual, ssa
+      pair build: half/bin/newton/ssa
+      stencil: half/bin/3d/newton/ssa
+      bin: ssa
+Memory usage per processor = 8.55503 Mbytes
 Step Temp Press Volume PotEng KinEng v_totEnergy Cella Cellb Cellc 
-       0  239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740  313.3218455755 6048176597.3066043854  129.0000000000  129.0000000000  129.0000000000 
-       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.9450111389  129.0000000012  129.0000000012  129.0000000012 
-       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391577.0431985855  129.0000000047  129.0000000047  129.0000000047 
-       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.5712032318  129.0000000105  129.0000000105  129.0000000105 
-       4  239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043  313.4653942786 6048377030.7404460907  129.0000000186  129.0000000186  129.0000000186 
-       5  239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340  313.6147686202 6048548267.9007377625  129.0000000291  129.0000000291  129.0000000291 
-       6  239.5617886781 2817.5624195435 2146689.0020948485 2639.8617493725  313.4976735610 6048434730.8592004776  129.0000000420  129.0000000420  129.0000000420 
-       7  239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407  313.4467287471 6048390900.5748577118  129.0000000571  129.0000000571  129.0000000571 
-       8  239.6066877934 2817.6008649264 2146689.0037241788 2639.8710757645  313.5564298772 6048517265.7987136841  129.0000000746  129.0000000746  129.0000000746 
-       9  239.5719861485 2817.5823530300 2146689.0047134170 2639.8752557893  313.5110182737 6048477529.2603597641  129.0000000944  129.0000000944  129.0000000944 
-      10  239.5800176776 2817.5915671176 2146689.0058190385 2639.8793778438  313.5215285712 6048497312.1706552505  129.0000001166  129.0000001166  129.0000001166 
-      11  239.6299830954 2817.6281223139 2146689.0070410441 2639.8829762049  313.5869148014 6048575788.3208351135  129.0000001410  129.0000001410  129.0000001410 
-      12  239.6011995911 2817.6132377273 2146689.0083794324 2639.8860704236  313.5492478526 6048543839.4788360596  129.0000001678  129.0000001678  129.0000001678 
-      13  239.6407681166 2817.6427924824 2146689.0098342048 2639.8889816934  313.6010284005 6048607288.5005025864  129.0000001970  129.0000001970  129.0000001970 
-      14  239.6981172055 2817.6844100046 2146689.0114053637 2639.8913405110  313.6760771219 6048696632.8825626373  129.0000002285  129.0000002285  129.0000002285 
-      15  239.8563971968 2817.7922519039 2146689.0130929090 2639.8934358481  313.8832070208 6048928140.8671455383  129.0000002623  129.0000002623  129.0000002623 
-      16  239.8561894618 2817.7971208197 2146689.0148968464 2639.8950496967  313.8829351726 6048938597.9994916916  129.0000002984  129.0000002984  129.0000002984 
-      17  239.8816520361 2817.8185621543 2146689.0168171758 2639.8961257823  313.9162562538 6048984631.3226108551  129.0000003369  129.0000003369  129.0000003369 
-      18  239.9099966096 2817.8417368960 2146689.0188538977 2639.8965743204  313.9533488047 6049034386.0627622604  129.0000003777  129.0000003777  129.0000003777 
-      19  240.0514024347 2817.9389205774 2146689.0210070144 2639.8966103811  314.1383966683 6049243015.4568052292  129.0000004208  129.0000004208  129.0000004208 
-      20  239.8802541140 2817.8327386176 2146689.0232765260 2639.8962085210  313.9144268914 6049015081.9802341461  129.0000004662  129.0000004662  129.0000004662 
-      21  239.8462621903 2817.8160306167 2146689.0256624296 2639.8953174755  313.8699440502 6048979221.7758703232  129.0000005140  129.0000005140  129.0000005140 
-      22  240.0487944678 2817.9533849157 2146689.0281647225 2639.8938590354  314.1349838054 6049274086.0571212769  129.0000005642  129.0000005642  129.0000005642 
-      23  240.0966314441 2817.9897873787 2146689.0307834130 2639.8918104774  314.1975846937 6049352238.2649183273  129.0000006166  129.0000006166  129.0000006166 
-      24  240.1765312516 2818.0463843765 2146689.0335185044 2639.8891292321  314.3021439554 6049473742.2287187576  129.0000006714  129.0000006714  129.0000006714 
-      25  240.1500705973 2818.0336048048 2146689.0363699966 2639.8858785483  314.2675167572 6049446316.4600162506  129.0000007285  129.0000007285  129.0000007285 
-      26  240.2681423500 2818.1151708195 2146689.0393378921 2639.8825176506  314.4220289603 6049621421.8445177078  129.0000007880  129.0000007880  129.0000007880 
-      27  240.4728815247 2818.2527327079 2146689.0424221945 2639.8784158747  314.6899567267 6049916733.3989181519  129.0000008498  129.0000008498  129.0000008498 
-      28  240.4793027032 2818.2613348477 2146689.0456229053 2639.8736089473  314.6983596717 6049935208.5421981812  129.0000009139  129.0000009139  129.0000009139 
-      29  240.5020619198 2818.2805472685 2146689.0489400285 2639.8681043704  314.7281430587 6049976461.0082206726  129.0000009803  129.0000009803  129.0000009803 
-      30  240.5513721776 2818.3167157263 2146689.0523735629 2639.8623484053  314.7926719270 6050054113.1760177612  129.0000010491  129.0000010491  129.0000010491 
-      31  240.7340393104 2818.4391703712 2146689.0559235099 2639.8563442170  315.0317155636 6050316995.4599781036  129.0000011202  129.0000011202  129.0000011202 
-      32  240.8254719483 2818.5014640740 2146689.0595898777 2639.8498122053  315.1513670299 6050450731.1168394089  129.0000011936  129.0000011936  129.0000011936 
-      33  240.9681573541 2818.5965480750 2146689.0633726656 2639.8425779528  315.3380893908 6050654857.7432861328  129.0000012694  129.0000012694  129.0000012694 
-      34  241.0039494187 2818.6217008564 2146689.0672718794 2639.8347174393  315.3849279499 6050708863.9733209610  129.0000013475  129.0000013475  129.0000013475 
-      35  241.0314566197 2818.6411150538 2146689.0712875174 2639.8262983643  315.4209246902 6050750551.5649127960  129.0000014279  129.0000014279  129.0000014279 
-      36  241.0829173424 2818.6763455617 2146689.0754195810 2639.8174397481  315.4882677207 6050826192.2165899277  129.0000015107  129.0000015107  129.0000015107 
-      37  241.2845682012 2818.8087982181 2146689.0796680767 2639.8080129872  315.7521540252 6051110539.1171846390  129.0000015958  129.0000015958  129.0000015958 
-      38  241.3214712920 2818.8336260248 2146689.0840330068 2639.7981963574  315.8004465062 6051163849.0412235260  129.0000016833  129.0000016833  129.0000016833 
-      39  241.3392127125 2818.8456991528 2146689.0885143690 2639.7879618658  315.8236634561 6051189778.9386901855  129.0000017730  129.0000017730  129.0000017730 
-      40  241.5383770555 2818.9753950055 2146689.0931121684 2639.7769824244  316.0842958321 6051468208.8210506439  129.0000018651  129.0000018651  129.0000018651 
-      41  241.5059730674 2818.9543817992 2146689.0978264087 2639.7656512498  316.0418910106 6051423113.2358427048  129.0000019595  129.0000019595  129.0000019595 
-      42  241.3907605672 2818.8793800508 2146689.1026570834 2639.7541331920  315.8911205101 6051262121.2551422119  129.0000020563  129.0000020563  129.0000020563 
-      43  241.5095917610 2818.9559595711 2146689.1076041958 2639.7424355740  316.0466265406 6051426527.7663059235  129.0000021554  129.0000021554  129.0000021554 
-      44  241.6271631762 2819.0312325531 2146689.1126677482 2639.7297705654  316.2004839873 6051588129.8722610474  129.0000022568  129.0000022568  129.0000022568 
-      45  241.5702411838 2818.9923790176 2146689.1178477411 2639.7163554760  316.1259941770 6051504737.9250564575  129.0000023606  129.0000023606  129.0000023606 
-      46  241.7029985068 2819.0771124986 2146689.1231441777 2639.7024246704  316.2997243538 6051686649.4576120377  129.0000024667  129.0000024667  129.0000024667 
-      47  241.7966144965 2819.1357830868 2146689.1285570571 2639.6882106593  316.4222330191 6051812612.3391046524  129.0000025751  129.0000025751  129.0000025751 
-      48  241.8573480255 2819.1726205120 2146689.1340863821 2639.6735287925  316.5017107195 6051891706.4921989441  129.0000026859  129.0000026859  129.0000026859 
-      49  241.9611147338 2819.2374095379 2146689.1397321564 2639.6583357477  316.6375029166 6052030804.4275226593  129.0000027990  129.0000027990  129.0000027990 
-      50  242.1023518806 2819.3259059811 2146689.1454943856 2639.6424863169  316.8223300428 6052220795.1955394745  129.0000029144  129.0000029144  129.0000029144 
-      51  242.1174105473 2819.3319633044 2146689.1513730693 2639.6264141131  316.8420362613 6052233814.9634265900  129.0000030321  129.0000030321  129.0000030321 
-      52  242.2534914901 2819.4164594322 2146689.1573682069 2639.6098392670  317.0201158259 6052415218.9485445023  129.0000031522  129.0000031522  129.0000031522 
-      53  242.3504633236 2819.4754119996 2146689.1634798055 2639.5930076506  317.1470160479 6052541789.1274013519  129.0000032746  129.0000032746  129.0000032746 
-      54  242.2982323323 2819.4368568264 2146689.1697078613 2639.5756353782  317.0786650211 6052459040.6286897659  129.0000033994  129.0000033994  129.0000033994 
-      55  242.3452896272 2819.4623310219 2146689.1760523771 2639.5575918586  317.1402455951 6052513743.7400159836  129.0000035265  129.0000035265  129.0000035265 
-      56  242.4181903333 2819.5048897011 2146689.1825133534 2639.5390347547  317.2356456249 6052605122.2894439697  129.0000036559  129.0000036559  129.0000036559 
-      57  242.5317091656 2819.5739975787 2146689.1890907930 2639.5199828249  317.3841997413 6052753494.0979280472  129.0000037876  129.0000037876  129.0000037876 
-      58  242.5478978740 2819.5796954935 2146689.1957846982 2639.5006137388  317.4053847660 6052765744.6257629395  129.0000039217  129.0000039217  129.0000039217 
-      59  242.6655316466 2819.6519225743 2146689.2025950695 2639.4808234811  317.5593238156 6052920813.0568208694  129.0000040582  129.0000040582  129.0000040582 
-      60  242.8126131177 2819.7431588157 2146689.2095219092 2639.4607996998  317.7517989980 6053116688.6155729294  129.0000041969  129.0000041969  129.0000041969 
-      61  242.7957124913 2819.7275989047 2146689.2165652174 2639.4406312730  317.7296823362 6053083306.1403274536  129.0000043380  129.0000043380  129.0000043380 
-      62  242.9276177041 2819.8088790098 2146689.2237249981 2639.4201279058  317.9022974164 6053257809.6067762375  129.0000044814  129.0000044814  129.0000044814 
-      63  243.0465445938 2819.8814758895 2146689.2310012528 2639.3991657500  318.0579286774 6053413673.1989650726  129.0000046272  129.0000046272  129.0000046272 
-      64  242.9890585501 2819.8387587817 2146689.2383939880 2639.3781767844  317.9827007328 6053321993.5937871933  129.0000047752  129.0000047752  129.0000047752 
-      65  242.9653746583 2819.8180104181 2146689.2459031967 2639.3568184374  317.9517072884 6053277474.4272727966  129.0000049256  129.0000049256  129.0000049256 
-      66  243.0259297024 2819.8514334947 2146689.2535288804 2639.3352568621  318.0309514181 6053349244.9473772049  129.0000050784  129.0000050784  129.0000050784 
-      67  242.9638979697 2819.8046112742 2146689.2612710390 2639.3134547096  317.9497748498 6053248753.9180717468  129.0000052335  129.0000052335  129.0000052335 
-      68  243.0283540775 2819.8395632725 2146689.2691296688 2639.2912303374  318.0341240273 6053323807.2197017670  129.0000053909  129.0000053909  129.0000053909 
-      69  243.2256418664 2819.9609646019 2146689.2771047787 2639.2684509205  318.2923006889 6053584440.8757400513  129.0000055506  129.0000055506  129.0000055506 
-      70  243.2507495334 2819.9706145524 2146689.2851963686 2639.2450126010  318.3251573278 6053605179.1483964920  129.0000057127  129.0000057127  129.0000057127 
-      71  243.4287155518 2820.0794853386 2146689.2934044413 2639.2213699915  318.5580489464 6053838914.2552747726  129.0000058771  129.0000058771  129.0000058771 
-      72  243.5097518574 2820.1249498194 2146689.3017290002 2639.1971212009  318.6640954635 6053936535.9274711609  129.0000060439  129.0000060439  129.0000060439 
-      73  243.5356790969 2820.1337977544 2146689.3101700447 2639.1723394661  318.6980246193 6053955553.5090074539  129.0000062130  129.0000062130  129.0000062130 
-      74  243.5479180498 2820.1331964183 2146689.3187275808 2639.1473868749  318.7140408766 6053954286.7515821457  129.0000063844  129.0000063844  129.0000063844 
-      75  243.7115573025 2820.2314361523 2146689.3274016059 2639.1220411207  318.9281840641 6054165201.5909118652  129.0000065581  129.0000065581  129.0000065581 
-      76  243.7457279618 2820.2454531429 2146689.3361921217 2639.0963868224  318.9729008040 6054195316.5254154205  129.0000067342  129.0000067342  129.0000067342 
-      77  243.8345031069 2820.2948644965 2146689.3450991292 2639.0700900389  319.0890745962 6054301412.5615310669  129.0000069126  129.0000069126  129.0000069126 
-      78  244.0193931195 2820.4067881628 2146689.3541226317 2639.0435094409  319.3310271594 6054541703.5689058304  129.0000070934  129.0000070934  129.0000070934 
-      79  243.9919100078 2820.3799166166 2146689.3632626338 2639.0164249037  319.2950619430 6054484044.4218587875  129.0000072765  129.0000072765  129.0000072765 
-      80  244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882  319.4320116291 6054610332.4174261093  129.0000074619  129.0000074619  129.0000074619 
-      81  244.1334315951 2820.4535208568 2146689.3818921377 2638.9608330195  319.4802612965 6054642102.5347270966  129.0000076496  129.0000076496  129.0000076496 
-      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858575.1664342880  129.0000078397  129.0000078397  129.0000078397 
-      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895140.1710596085  129.0000080321  129.0000080321  129.0000080321 
-      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768957.6739044189  129.0000082269  129.0000082269  129.0000082269 
-      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091776.5361995697  129.0000084240  129.0000084240  129.0000084240 
-      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136595.0767974854  129.0000086234  129.0000086234  129.0000086234 
-      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072877.2416200638  129.0000088251  129.0000088251  129.0000088251 
-      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271926.6536149979  129.0000090292  129.0000090292  129.0000090292 
-      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507852.1186332703  129.0000092356  129.0000092356  129.0000092356 
-      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482985.2258749008  129.0000094444  129.0000094444  129.0000094444 
-      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561333.3803453445  129.0000096555  129.0000096555  129.0000096555 
-      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590051.6433181763  129.0000098689  129.0000098689  129.0000098689 
-      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758210.2774200439  129.0000100846  129.0000100846  129.0000100846 
-      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948551.7882709503  129.0000103027  129.0000103027  129.0000103027 
-      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000363.5151576996  129.0000105232  129.0000105232  129.0000105232 
-      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176929.0169925690  129.0000107459  129.0000107459  129.0000107459 
-      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028008.1910057068  129.0000109710  129.0000109710  129.0000109710 
-      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991214.3494396210  129.0000111984  129.0000111984  129.0000111984 
-      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018909.4480972290  129.0000114282  129.0000114282  129.0000114282 
-     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403111.1006488800  129.0000116603  129.0000116603  129.0000116603 
-Loop time of 4.05006 on 1 procs for 100 steps with 10125 atoms
+       0  239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740  313.3218455755 6048176597.3066034317  129.0000000000  129.0000000000  129.0000000000 
+       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.8720483780  129.0000000012  129.0000000012  129.0000000012 
+       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391576.8485937119  129.0000000047  129.0000000047  129.0000000047 
+       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.2404479980  129.0000000105  129.0000000105  129.0000000105 
+       4  239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043  313.4653942786 6048377030.5689325333  129.0000000186  129.0000000186  129.0000000186 
+       5  239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340  313.6147686202 6048548267.5742130280  129.0000000291  129.0000000291  129.0000000291 
+       6  239.5617886781 2817.5624195435 2146689.0020948485 2639.8617493725  313.4976735610 6048434730.6441593170  129.0000000420  129.0000000420  129.0000000420 
+       7  239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407  313.4467287471 6048390900.4058599472  129.0000000571  129.0000000571  129.0000000571 
+       8  239.6066877934 2817.6008649264 2146689.0037241788 2639.8710757645  313.5564298772 6048517265.5155982971  129.0000000746  129.0000000746  129.0000000746 
+       9  239.5719861485 2817.5823530300 2146689.0047134170 2639.8752557893  313.5110182737 6048477529.0184717178  129.0000000944  129.0000000944  129.0000000944 
+      10  239.5800176776 2817.5915671176 2146689.0058190385 2639.8793778438  313.5215285712 6048497311.9141387939  129.0000001166  129.0000001166  129.0000001166 
+      11  239.6299830954 2817.6281223139 2146689.0070410441 2639.8829762049  313.5869148014 6048575787.9953098297  129.0000001410  129.0000001410  129.0000001410 
+      12  239.6011995911 2817.6132377273 2146689.0083794324 2639.8860704236  313.5492478526 6048543839.1878814697  129.0000001678  129.0000001678  129.0000001678 
+      13  239.6407681166 2817.6427924824 2146689.0098342048 2639.8889816934  313.6010284005 6048607288.1548709869  129.0000001970  129.0000001970  129.0000001970 
+      14  239.6981172055 2817.6844100046 2146689.0114053637 2639.8913405110  313.6760771219 6048696632.4595127106  129.0000002285  129.0000002285  129.0000002285 
+      15  239.8563971968 2817.7922519039 2146689.0130929090 2639.8934358481  313.8832070208 6048928140.2348766327  129.0000002623  129.0000002623  129.0000002623 
+      16  239.8561894618 2817.7971208196 2146689.0148968464 2639.8950496967  313.8829351726 6048938597.3658657074  129.0000002984  129.0000002984  129.0000002984 
+      17  239.8816520361 2817.8185621543 2146689.0168171758 2639.8961257823  313.9162562538 6048984630.6545839310  129.0000003369  129.0000003369  129.0000003369 
+      18  239.9099966096 2817.8417368960 2146689.0188538977 2639.8965743204  313.9533488047 6049034385.3571958542  129.0000003777  129.0000003777  129.0000003777 
+      19  240.0514024347 2817.9389205774 2146689.0210070144 2639.8966103811  314.1383966683 6049243014.5661621094  129.0000004208  129.0000004208  129.0000004208 
+      20  239.8802541140 2817.8327386176 2146689.0232765260 2639.8962085210  313.9144268914 6049015081.3139505386  129.0000004662  129.0000004662  129.0000004662 
+      21  239.8462621903 2817.8160306167 2146689.0256624296 2639.8953174755  313.8699440502 6048979221.1549577713  129.0000005140  129.0000005140  129.0000005140 
+      22  240.0487944678 2817.9533849157 2146689.0281647225 2639.8938590354  314.1349838054 6049274085.1726217270  129.0000005642  129.0000005642  129.0000005642 
+      23  240.0966314441 2817.9897873787 2146689.0307834130 2639.8918104774  314.1975846937 6049352237.3198652267  129.0000006166  129.0000006166  129.0000006166 
+      24  240.1765312516 2818.0463843765 2146689.0335185044 2639.8891292321  314.3021439554 6049473741.1817827225  129.0000006714  129.0000006714  129.0000006714 
+      25  240.1500705973 2818.0336048048 2146689.0363699966 2639.8858785483  314.2675167572 6049446315.4509468079  129.0000007285  129.0000007285  129.0000007285 
+      26  240.2681423500 2818.1151708195 2146689.0393378921 2639.8825176506  314.4220289603 6049621420.6842966080  129.0000007880  129.0000007880  129.0000007880 
+      27  240.4728815247 2818.2527327079 2146689.0424221945 2639.8784158747  314.6899567267 6049916731.9748563766  129.0000008498  129.0000008498  129.0000008498 
+      28  240.4793027032 2818.2613348477 2146689.0456229053 2639.8736089473  314.6983596717 6049935207.1145420074  129.0000009139  129.0000009139  129.0000009139 
+      29  240.5020619198 2818.2805472685 2146689.0489400285 2639.8681043704  314.7281430587 6049976459.5562763214  129.0000009803  129.0000009803  129.0000009803 
+      30  240.5513721776 2818.3167157263 2146689.0523735629 2639.8623484053  314.7926719270 6050054111.6652946472  129.0000010491  129.0000010491  129.0000010491 
+      31  240.7340393104 2818.4391703712 2146689.0559235099 2639.8563442170  315.0317155636 6050316993.7162160873  129.0000011202  129.0000011202  129.0000011202 
+      32  240.8254719483 2818.5014640740 2146689.0595898777 2639.8498122053  315.1513670299 6050450729.2599506378  129.0000011936  129.0000011936  129.0000011936 
+      33  240.9681573541 2818.5965480750 2146689.0633726656 2639.8425779528  315.3380893908 6050654855.7068986893  129.0000012694  129.0000012694  129.0000012694 
+      34  241.0039494187 2818.6217008564 2146689.0672718794 2639.8347174393  315.3849279499 6050708861.8979463577  129.0000013475  129.0000013475  129.0000013475 
+      35  241.0314566197 2818.6411150538 2146689.0712875174 2639.8262983643  315.4209246902 6050750549.4619541168  129.0000014279  129.0000014279  129.0000014279 
+      36  241.0829173424 2818.6763455617 2146689.0754195810 2639.8174397481  315.4882677207 6050826190.0551443100  129.0000015107  129.0000015107  129.0000015107 
+      37  241.2845682012 2818.8087982181 2146689.0796680767 2639.8080129872  315.7521540252 6051110536.7012710571  129.0000015958  129.0000015958  129.0000015958 
+      38  241.3214712920 2818.8336260248 2146689.0840330068 2639.7981963574  315.8004465062 6051163846.5868301392  129.0000016833  129.0000016833  129.0000016833 
+      39  241.3392127125 2818.8456991528 2146689.0885143690 2639.7879618658  315.8236634561 6051189776.4712991714  129.0000017730  129.0000017730  129.0000017730 
+      40  241.5383770555 2818.9753950055 2146689.0931121684 2639.7769824244  316.0842958321 6051468206.1039972305  129.0000018651  129.0000018651  129.0000018651 
+      41  241.5059730674 2818.9543817992 2146689.0978264087 2639.7656512498  316.0418910106 6051423110.5725250244  129.0000019595  129.0000019595  129.0000019595 
+      42  241.3907605672 2818.8793800508 2146689.1026570834 2639.7541331920  315.8911205101 6051262118.7541017532  129.0000020563  129.0000020563  129.0000020563 
+      43  241.5095917610 2818.9559595711 2146689.1076041958 2639.7424355740  316.0466265406 6051426525.1214485168  129.0000021554  129.0000021554  129.0000021554 
+      44  241.6271631762 2819.0312325531 2146689.1126677482 2639.7297705654  316.2004839873 6051588127.0861988068  129.0000022568  129.0000022568  129.0000022568 
+      45  241.5702411838 2818.9923790176 2146689.1178477411 2639.7163554760  316.1259941770 6051504735.2269029617  129.0000023606  129.0000023606  129.0000023606 
+      46  241.7029985068 2819.0771124986 2146689.1231441777 2639.7024246704  316.2997243538 6051686646.5996389389  129.0000024667  129.0000024667  129.0000024667 
+      47  241.7966144965 2819.1357830868 2146689.1285570571 2639.6882106593  316.4222330191 6051812609.3728218079  129.0000025751  129.0000025751  129.0000025751 
+      48  241.8573480255 2819.1726205120 2146689.1340863821 2639.6735287925  316.5017107195 6051891703.4611186981  129.0000026859  129.0000026859  129.0000026859 
+      49  241.9611147338 2819.2374095379 2146689.1397321564 2639.6583357477  316.6375029166 6052030801.2758235931  129.0000027990  129.0000027990  129.0000027990 
+      50  242.1023518806 2819.3259059811 2146689.1454943856 2639.6424863169  316.8223300428 6052220791.8748512268  129.0000029144  129.0000029144  129.0000029144 
+      51  242.1174105473 2819.3319633044 2146689.1513730693 2639.6264141131  316.8420362613 6052233811.6391019821  129.0000030321  129.0000030321  129.0000030321 
+      52  242.2534914901 2819.4164594322 2146689.1573682069 2639.6098392671  317.0201158259 6052415215.4627037048  129.0000031522  129.0000031522  129.0000031522 
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+      54  242.2982323323 2819.4368568264 2146689.1697078613 2639.5756353782  317.0786650211 6052459037.1184797287  129.0000033994  129.0000033994  129.0000033994 
+      55  242.3452896272 2819.4623310219 2146689.1760523771 2639.5575918586  317.1402455951 6052513740.1862611771  129.0000035265  129.0000035265  129.0000035265 
+      56  242.4181903333 2819.5048897011 2146689.1825133534 2639.5390347547  317.2356456249 6052605118.6588287354  129.0000036559  129.0000036559  129.0000036559 
+      57  242.5317091656 2819.5739975787 2146689.1890907930 2639.5199828249  317.3841997413 6052753490.3378009796  129.0000037876  129.0000037876  129.0000037876 
+      58  242.5478978740 2819.5796954935 2146689.1957846982 2639.5006137388  317.4053847660 6052765740.8638200760  129.0000039217  129.0000039217  129.0000039217 
+      59  242.6655316466 2819.6519225743 2146689.2025950695 2639.4808234811  317.5593238156 6052920809.1607065201  129.0000040582  129.0000040582  129.0000040582 
+      60  242.8126131177 2819.7431588157 2146689.2095219092 2639.4607996998  317.7517989980 6053116684.5470046997  129.0000041969  129.0000041969  129.0000041969 
+      61  242.7957124913 2819.7275989047 2146689.2165652174 2639.4406312730  317.7296823362 6053083302.1140241623  129.0000043380  129.0000043380  129.0000043380 
+      62  242.9276177041 2819.8088790098 2146689.2237249981 2639.4201279058  317.9022974164 6053257805.4283437729  129.0000044814  129.0000044814  129.0000044814 
+      63  243.0465445938 2819.8814758895 2146689.2310012528 2639.3991657500  318.0579286774 6053413668.8858547211  129.0000046272  129.0000046272  129.0000046272 
+      64  242.9890585501 2819.8387587817 2146689.2383939880 2639.3781767844  317.9827007328 6053321989.3768787384  129.0000047752  129.0000047752  129.0000047752 
+      65  242.9653746583 2819.8180104181 2146689.2459031967 2639.3568184374  317.9517072884 6053277470.2627182007  129.0000049256  129.0000049256  129.0000049256 
+      66  243.0259297024 2819.8514334947 2146689.2535288804 2639.3352568621  318.0309514181 6053349240.7251205444  129.0000050784  129.0000050784  129.0000050784 
+      67  242.9638979697 2819.8046112742 2146689.2612710390 2639.3134547096  317.9497748498 6053248749.7987766266  129.0000052335  129.0000052335  129.0000052335 
+      68  243.0283540775 2819.8395632725 2146689.2691296688 2639.2912303374  318.0341240273 6053323803.0382738113  129.0000053909  129.0000053909  129.0000053909 
+      69  243.2256418664 2819.9609646019 2146689.2771047787 2639.2684509205  318.2923006889 6053584436.4588871002  129.0000055506  129.0000055506  129.0000055506 
+      70  243.2507495334 2819.9706145524 2146689.2851963686 2639.2450126010  318.3251573278 6053605174.7221174240  129.0000057127  129.0000057127  129.0000057127 
+      71  243.4287155518 2820.0794853386 2146689.2934044413 2639.2213699915  318.5580489464 6053838909.6197280884  129.0000058771  129.0000058771  129.0000058771 
+      72  243.5097518574 2820.1249498194 2146689.3017290002 2639.1971212009  318.6640954635 6053936531.2101163864  129.0000060439  129.0000060439  129.0000060439 
+      73  243.5356790969 2820.1337977544 2146689.3101700447 2639.1723394661  318.6980246193 6053955548.7824945450  129.0000062130  129.0000062130  129.0000062130 
+      74  243.5479180498 2820.1331964183 2146689.3187275808 2639.1473868749  318.7140408766 6053954282.0339813232  129.0000063844  129.0000063844  129.0000063844 
+      75  243.7115573025 2820.2314361523 2146689.3274016059 2639.1220411207  318.9281840641 6054165196.6845111847  129.0000065581  129.0000065581  129.0000065581 
+      76  243.7457279618 2820.2454531429 2146689.3361921217 2639.0963868224  318.9729008040 6054195311.5999307632  129.0000067342  129.0000067342  129.0000067342 
+      77  243.8345031069 2820.2948644965 2146689.3450991292 2639.0700900389  319.0890745962 6054301407.5461502075  129.0000069126  129.0000069126  129.0000069126 
+      78  244.0193931195 2820.4067881628 2146689.3541226317 2639.0435094409  319.3310271594 6054541698.3381366730  129.0000070934  129.0000070934  129.0000070934 
+      79  243.9919100078 2820.3799166166 2146689.3632626338 2639.0164249037  319.2950619430 6054484039.2541246414  129.0000072765  129.0000072765  129.0000072765 
+      80  244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882  319.4320116291 6054610327.1403293610  129.0000074619  129.0000074619  129.0000074619 
+      81  244.1334315951 2820.4535208568 2146689.3818921377 2638.9608330195  319.4802612965 6054642097.2373485565  129.0000076496  129.0000076496  129.0000076496 
+      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858569.6761827469  129.0000078397  129.0000078397  129.0000078397 
+      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895134.6560049057  129.0000080321  129.0000080321  129.0000080321 
+      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768952.2869329453  129.0000082269  129.0000082269  129.0000082269 
+      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091770.8571672440  129.0000084240  129.0000084240  129.0000084240 
+      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136589.3662166595  129.0000086234  129.0000086234  129.0000086234 
+      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072871.6007261276  129.0000088251  129.0000088251  129.0000088251 
+      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271920.8364210129  129.0000090292  129.0000090292  129.0000090292 
+      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507846.0901927948  129.0000092356  129.0000092356  129.0000092356 
+      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482979.2295818329  129.0000094444  129.0000094444  129.0000094444 
+      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561327.3181543350  129.0000096555  129.0000096555  129.0000096555 
+      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590045.5610351562  129.0000098689  129.0000098689  129.0000098689 
+      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758204.0434722900  129.0000100846  129.0000100846  129.0000100846 
+      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948545.3822879791  129.0000103027  129.0000103027  129.0000103027 
+      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000357.0671482086  129.0000105232  129.0000105232  129.0000105232 
+      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176922.4099712372  129.0000107459  129.0000107459  129.0000107459 
+      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028001.7295455933  129.0000109710  129.0000109710  129.0000109710 
+      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991207.9293851852  129.0000111984  129.0000111984  129.0000111984 
+      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018903.0102539062  129.0000114282  129.0000114282  129.0000114282 
+     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403104.3106222153  129.0000116603  129.0000116603  129.0000116603 
+Loop time of 5.22601 on 1 procs for 100 steps with 10125 atoms

-Performance: 2.133 ns/day, 11.250 hours/ns, 24.691 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.653 ns/day, 14.517 hours/ns, 19.135 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads

 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.46587    | 0.46587    | 0.46587    |   0.0 | 11.50
-Neigh   | 1.4713     | 1.4713     | 1.4713     |   0.0 | 36.33
-Comm    | 0.05567    | 0.05567    | 0.05567    |   0.0 |  1.37
-Output  | 0.011364   | 0.011364   | 0.011364   |   0.0 |  0.28
-Modify  | 2.0158     | 2.0158     | 2.0158     |   0.0 | 49.77
-Other   |            | 0.03004    |            |       |  0.74
+Pair    | 0.44045    | 0.44045    | 0.44045    |   0.0 |  8.43
+Neigh   | 2.669      | 2.669      | 2.669      |   0.0 | 51.07
+Comm    | 0.056143   | 0.056143   | 0.056143   |   0.0 |  1.07
+Output  | 0.012469   | 0.012469   | 0.012469   |   0.0 |  0.24
+Modify  | 2.0163     | 2.0163     | 2.0163     |   0.0 | 38.58
+Other   |            | 0.03168    |            |       |  0.61

 Nlocal:    10125 ave 10125 max 10125 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -172,4 +180,4 @@ Dangerous builds not checked

 Please see the log.cite file for references relevant to this simulation

-Total wall time: 0:00:04
+Total wall time: 0:00:05
--- a/examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow
+++ b/examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow
@ -37,7 +37,7 @@ timestep        0.001

 pair_style      hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
 pair_coeff      * * dpd/fdt/energy 0.0 0.05 10.0 16.00
-pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
+pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid exponent 1.0 1.0 16.00

 fix             1 all shardlow
 fix             2 all nve
--- a/examples/USER/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference
+++ b/examples/USER/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference
@ -48,7 +48,7 @@ timestep        0.001

 pair_style      hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
 pair_coeff      * * dpd/fdt/energy 0.0 0.05 10.0 16.00
-pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
+pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid exponent 1.0 1.0 16.00

 fix             1 all shardlow
 fix             2 all nve
@ -69,39 +69,51 @@ dump_modify     2 sort id

 run             10
 Neighbor list info ...
-  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 18
  ghost atom cutoff = 18
-  binsize = 9 -> bins = 8 8 5
-Memory usage per processor = 6.52436 Mbytes
+  binsize = 9, bins = 8 8 5
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair dpd/fdt/energy, perpetual
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair exp6/rx, perpetual, copy from (1)
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) fix shardlow, perpetual, ssa
+      pair build: half/bin/newton/ssa
+      stencil: half/bin/3d/newton/ssa
+      bin: ssa
+Memory usage per processor = 8.39564 Mbytes
 Step Temp Press Volume PotEng KinEng c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4] 
-       0   2065.00000000   1368.17463335 179834.51777865      0.00000000    230.35385810   3841.42393279   3841.42393279      0.00000000   7682.84786557   2065.00000000 
-       1   2064.93210437   1368.12964881 179834.51777865      0.00000000    230.34628424   3841.42393279   3841.43150665      0.00000000   7682.85543943   2065.20275230 
-       2   2067.82089565   1370.04362990 179834.51777865     -0.00000000    230.66853326   3841.42393279   3841.10925763      0.00000000   7682.53319042   2065.32453473 
-       3   2070.45225169   1371.78704616 179834.51777865     -0.00000000    230.96206499   3841.42393279   3840.81572590      0.00000000   7682.23965869   2065.45336917 
-       4   2075.00241157   1374.80177416 179834.51777865     -0.00000000    231.46964217   3841.42393279   3840.30814872      0.00000000   7681.73208151   2065.52973333 
-       5   2073.96509212   1374.11449370 179834.51777865     -0.00000000    231.35392762   3841.42393279   3840.42386327      0.00000000   7681.84779605   2065.76011517 
-       6   2074.26516936   1374.31331117 179834.51777865     -0.00000000    231.38740169   3841.42393279   3840.39038920      0.00000000   7681.81432198   2065.95399323 
-       7   2071.41069700   1372.42206822 179834.51777865     -0.00000000    231.06898100   3841.42393279   3840.70880989      0.00000000   7682.13274267   2066.23407076 
-       8   2071.35844957   1372.38745146 179834.51777865     -0.00000000    231.06315272   3841.42393279   3840.71463817      0.00000000   7682.13857095   2066.43766287 
-       9   2071.35676496   1372.38633532 179834.51777865     -0.00000000    231.06296480   3841.42393279   3840.71482609      0.00000000   7682.13875887   2066.64001166 
-      10   2066.53172340   1369.18948328 179834.51777865     -0.00000000    230.52472415   3841.42393279   3841.25306673      0.00000000   7682.67699952   2066.97516855 
-Loop time of 0.289778 on 1 procs for 10 steps with 864 atoms
+       0   2065.00000000   1368.17463335 179834.51777865      0.00000000    230.35385810      0.00000000   7682.84786557      0.00000000   7682.84786557   2065.00000000 
+       1   2064.93210437   1368.12964881 179834.51777865      0.00000000    230.34628424      0.00000000   7682.85543943      0.00000000   7682.85543943   2065.20275230 
+       2   2067.82089565   1370.04362990 179834.51777865     -0.00000000    230.66853326      0.00000000   7682.53319042      0.00000000   7682.53319042   2065.32453473 
+       3   2070.45225169   1371.78704616 179834.51777865     -0.00000000    230.96206499      0.00000000   7682.23965869      0.00000000   7682.23965869   2065.45336917 
+       4   2075.00241157   1374.80177416 179834.51777865     -0.00000000    231.46964217      0.00000000   7681.73208151      0.00000000   7681.73208151   2065.52973333 
+       5   2073.96509212   1374.11449370 179834.51777865     -0.00000000    231.35392762     -0.00000000   7681.84779605      0.00000000   7681.84779605   2065.76011517 
+       6   2074.26516936   1374.31331117 179834.51777865     -0.00000000    231.38740169     -0.00000000   7681.81432198      0.00000000   7681.81432198   2065.95399323 
+       7   2071.41069700   1372.42206822 179834.51777865     -0.00000000    231.06898100     -0.00000000   7682.13274267      0.00000000   7682.13274267   2066.23407076 
+       8   2071.35844957   1372.38745146 179834.51777865     -0.00000000    231.06315272      0.00000000   7682.13857095      0.00000000   7682.13857095   2066.43766287 
+       9   2071.35676496   1372.38633532 179834.51777865     -0.00000000    231.06296480      0.00000000   7682.13875887      0.00000000   7682.13875887   2066.64001166 
+      10   2066.53172340   1369.18948328 179834.51777865     -0.00000000    230.52472415      0.00000000   7682.67699952      0.00000000   7682.67699952   2066.97516855 
+Loop time of 0.611304 on 1 procs for 10 steps with 864 atoms

-Performance: 2.982 ns/day, 8.049 hours/ns, 34.509 timesteps/s
-99.4% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.413 ns/day, 16.981 hours/ns, 16.358 timesteps/s
+98.2% CPU use with 1 MPI tasks x no OpenMP threads

 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.16405    | 0.16405    | 0.16405    |   0.0 | 56.61
+Pair    | 0.34177    | 0.34177    | 0.34177    |   0.0 | 55.91
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00066328 | 0.00066328 | 0.00066328 |   0.0 |  0.23
-Output  | 0.037718   | 0.037718   | 0.037718   |   0.0 | 13.02
-Modify  | 0.087281   | 0.087281   | 0.087281   |   0.0 | 30.12
-Other   |            | 7.057e-05  |            |       |  0.02
+Comm    | 0.0013342  | 0.0013342  | 0.0013342  |   0.0 |  0.22
+Output  | 0.083583   | 0.083583   | 0.083583   |   0.0 | 13.67
+Modify  | 0.18451    | 0.18451    | 0.18451    |   0.0 | 30.18
+Other   |            | 0.0001087  |            |       |  0.02

 Nlocal:    864 ave 864 max 864 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
--- a/examples/USER/misc/basal/in.basal
+++ b/examples/USER/misc/basal/in.basal
@ -1,163 +1,163 @@
-############################################################################
-# Input file for investigating twinning nucleation under uniaxial loading with basal plane vector analysis
-# Christopher Barrett, March 2013
-# This script requires a Mg pair potential file to be in the same directory.
-
-# fname is the file name.  It is necessary for loops to work correctly. (See jump command)
-variable fname index in.basal
-
-######################################
-# POTENTIAL VARIABLES
-# lattice parameters and the minimum energy per atom which should be obtained with the current pair potential and homogeneous lattice
-variable lx equal 3.181269601 
-variable b equal sqrt(3)
-variable c equal sqrt(8/3)
-variable ly equal ${b}*${lx}
-variable lz equal ${c}*${lx}
-variable pairlocation index almg.liu
-variable pairstyle index eam/alloy/opt
-
-######################################
-# EQUILIBRATION/DEFORMATION VARIABLES
-# eqpress = 10 bar = 1 MPa
-# tstep (the timestep) is set to a default value of 0.001 (1 fs) 
-# seed randomizes the velocity
-# srate is the rate of strain in 1/s
-# Ndump is the number of timesteps in between each dump of the atom coordinates
-variable tstep equal 0.001
-variable seed equal 95812384
-variable srate equal 1e9
-
-######################################
-# INITIALIZATION
-units 		metal
-dimension		3
-boundary		s	s	s
-atom_style		atomic
-
-######################################
-# ATOM BUILD
-atom_modify map array
-
-# lattice custom scale a1 "coordinates of a1" a2 "coordinates of a2" a3 "coordinates of a3" basis "atom1 coordinates" basis "atom2 coordinates" basis "atom3 coordinates" basis "atom4 coordinates" orient x "crystallagraphic orientation of x axis" orient y "crystallagraphic orientation of y axis" z "crystallagraphic orientation of z axis"
-lattice custom 3.181269601 a1 1 0 0 a2 0 1.732050808 0 a3 0 0 1.632993162 basis 0.0 0.0 0.0 basis 0.5 0.5 0 basis 0 0.3333333 0.5 basis 0.5 0.833333 0.5 orient x 0 1 1 orient y 1 0 0 orient z 0 1 -1
-variable multiple equal 20
-variable mx equal "v_lx*v_multiple"
-variable my equal "v_ly*v_multiple"
-variable mz equal "v_lz*v_multiple"
-
-# the simulation region should be from 0 to a multiple of the periodic boundary in x, y and z.
-region		whole block 0 ${mz} 0 ${mx} 0 ${my} units box 
-create_box		2 whole
-create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 
-
-region fixed1 block INF INF INF INF INF 10 units box
-region fixed2 block INF INF INF INF  100 INF units box
-group lower region fixed1
-group upper region fixed2
-group boundary union upper lower
-group mobile subtract all boundary
-
-variable natoms equal "count(all)"
-print "# of atoms are: ${natoms}"
-
-######################################
-# INTERATOMIC POTENTIAL
-pair_style	${pairstyle}
-pair_coeff	* * ${pairlocation} Mg Mg
-
-######################################
-# COMPUTES REQUIRED
-compute csym all centro/atom 12
-compute eng all pe/atom
-compute eatoms all reduce sum c_eng
-compute basal all basal/atom
-
-######################################
-# MINIMIZATION
-# Primarily adjusts the c/a ratio to value predicted by EAM potential
-reset_timestep	0
-thermo 1
-thermo_style custom step pe c_eatoms
-min_style cg
-minimize	1e-15 1e-15 1000 2000
-variable eminimum equal "c_eatoms / count(all)"
-print "%%e(it,1)=${eminimum}"
-
-######################################
-# EQUILIBRATION
-reset_timestep	0
-timestep ${tstep}
-# atoms are given a random velocity based on a temperature of 100K.
-velocity all create 100 ${seed} mom yes rot no
-
-# temperature and pressure are set to 100 and 0
-fix 1 all nve
-
-# Set thermo output
-thermo 100
-thermo_style custom step lx ly lz press pxx pyy pzz pe temp
-
-# Run for at least 2 picosecond (assuming 1 fs timestep)
-run 2000
-
-# Loop to run until pressure is below the variable eqpress (defined at beginning of file)
-label loopeq 
-variable eq loop 100 
-run 250
-variable converge equal press
-if "${converge} <= 0" then "variable converge equal -press" else "variable converge equal press" 
-if "${converge} <= 50" then "jump ${fname} breakeq" 
-next eq 
-jump ${fname} loopeq 
-label breakeq 
-
-# Store length for strain rate calculations
-variable tmp equal "lx"
-variable L0 equal ${tmp}
-print "Initial Length, L0: ${L0}"
-unfix 1
-
-######################################
-# DEFORMATION
-reset_timestep	0
-timestep ${tstep}
-
-# Impose constant strain rate 
-variable srate1 equal "v_srate / 1.0e10"
-velocity	upper set 0.0 NULL 0.0 units box
-velocity        lower set 0.0 NULL 0.0 units box
-
-fix 2 upper setforce 0.0 NULL 0.0
-fix 3 lower setforce 0.0 NULL 0.0
-fix 1 all nve
-
-# Output strain and stress info to file
-# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
-# p2 is in GPa
-variable strain equal "(lx - v_L0)/v_L0"
-variable p1 equal "v_strain"
-variable p2 equal "-pxz/10000"
-variable p3 equal "lx"
-variable p4 equal "temp"
-variable p5 equal "pe"
-variable p6 equal "ke"
-fix def1 all print 100 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6}" file output.def1.txt screen no
-# Dump coordinates to file (for void size calculations)
-dump 		1 all custom 1000 output.dump.* id x y z c_basal[1] c_basal[2] c_basal[3]
-
-# Display thermo
-thermo_style	custom step v_strain pxz lx temp pe ke
-restart 50000 output.restart
-
-# run deformation for 100000 timesteps (10% strain assuming 1 fs timestep and 1e9/s strainrate)
-variable runtime equal 0
-label loop
-displace_atoms	all ramp x 0.0 ${srate1} z 10 100 units box
-run		100
-variable runtime equal ${runtime}+100
-if "${runtime} < 100000" then "jump ${fname} loop"
-
-######################################
-# SIMULATION DONE
-print "All done"
+############################################################################
+# Input file for investigating twinning nucleation under uniaxial loading with basal plane vector analysis
+# Christopher Barrett, March 2013
+# This script requires a Mg pair potential file to be in the same directory.
+
+# fname is the file name.  It is necessary for loops to work correctly. (See jump command)
+variable fname index in.basal
+
+######################################
+# POTENTIAL VARIABLES
+# lattice parameters and the minimum energy per atom which should be obtained with the current pair potential and homogeneous lattice
+variable lx equal 3.181269601 
+variable b equal sqrt(3)
+variable c equal sqrt(8/3)
+variable ly equal ${b}*${lx}
+variable lz equal ${c}*${lx}
+variable pairlocation index almg.liu
+variable pairstyle index eam/alloy/opt
+
+######################################
+# EQUILIBRATION/DEFORMATION VARIABLES
+# eqpress = 10 bar = 1 MPa
+# tstep (the timestep) is set to a default value of 0.001 (1 fs) 
+# seed randomizes the velocity
+# srate is the rate of strain in 1/s
+# Ndump is the number of timesteps in between each dump of the atom coordinates
+variable tstep equal 0.001
+variable seed equal 95812384
+variable srate equal 1e9
+
+######################################
+# INITIALIZATION
+units 		metal
+dimension		3
+boundary		s	s	s
+atom_style		atomic
+
+######################################
+# ATOM BUILD
+atom_modify map array
+
+# lattice custom scale a1 "coordinates of a1" a2 "coordinates of a2" a3 "coordinates of a3" basis "atom1 coordinates" basis "atom2 coordinates" basis "atom3 coordinates" basis "atom4 coordinates" orient x "crystallagraphic orientation of x axis" orient y "crystallagraphic orientation of y axis" z "crystallagraphic orientation of z axis"
+lattice custom 3.181269601 a1 1 0 0 a2 0 1.732050808 0 a3 0 0 1.632993162 basis 0.0 0.0 0.0 basis 0.5 0.5 0 basis 0 0.3333333 0.5 basis 0.5 0.833333 0.5 orient x 0 1 1 orient y 1 0 0 orient z 0 1 -1
+variable multiple equal 20
+variable mx equal "v_lx*v_multiple"
+variable my equal "v_ly*v_multiple"
+variable mz equal "v_lz*v_multiple"
+
+# the simulation region should be from 0 to a multiple of the periodic boundary in x, y and z.
+region		whole block 0 ${mz} 0 ${mx} 0 ${my} units box 
+create_box		2 whole
+create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 
+
+region fixed1 block INF INF INF INF INF 10 units box
+region fixed2 block INF INF INF INF  100 INF units box
+group lower region fixed1
+group upper region fixed2
+group boundary union upper lower
+group mobile subtract all boundary
+
+variable natoms equal "count(all)"
+print "# of atoms are: ${natoms}"
+
+######################################
+# INTERATOMIC POTENTIAL
+pair_style	${pairstyle}
+pair_coeff	* * ${pairlocation} Mg Mg
+
+######################################
+# COMPUTES REQUIRED
+compute csym all centro/atom 12
+compute eng all pe/atom
+compute eatoms all reduce sum c_eng
+compute basal all basal/atom
+
+######################################
+# MINIMIZATION
+# Primarily adjusts the c/a ratio to value predicted by EAM potential
+reset_timestep	0
+thermo 1
+thermo_style custom step pe c_eatoms
+min_style cg
+minimize	1e-15 1e-15 1000 2000
+variable eminimum equal "c_eatoms / count(all)"
+print "%%e(it,1)=${eminimum}"
+
+######################################
+# EQUILIBRATION
+reset_timestep	0
+timestep ${tstep}
+# atoms are given a random velocity based on a temperature of 100K.
+velocity all create 100 ${seed} mom yes rot no
+
+# temperature and pressure are set to 100 and 0
+fix 1 all nve
+
+# Set thermo output
+thermo 100
+thermo_style custom step lx ly lz press pxx pyy pzz pe temp
+
+# Run for at least 2 picosecond (assuming 1 fs timestep)
+run 2000
+
+# Loop to run until pressure is below the variable eqpress (defined at beginning of file)
+label loopeq 
+variable eq loop 100 
+run 250
+variable converge equal press
+if "${converge} <= 0" then "variable converge equal -press" else "variable converge equal press" 
+if "${converge} <= 50" then "jump ${fname} breakeq" 
+next eq 
+jump ${fname} loopeq 
+label breakeq 
+
+# Store length for strain rate calculations
+variable tmp equal "lx"
+variable L0 equal ${tmp}
+print "Initial Length, L0: ${L0}"
+unfix 1
+
+######################################
+# DEFORMATION
+reset_timestep	0
+timestep ${tstep}
+
+# Impose constant strain rate 
+variable srate1 equal "v_srate / 1.0e10"
+velocity	upper set 0.0 NULL 0.0 units box
+velocity        lower set 0.0 NULL 0.0 units box
+
+fix 2 upper setforce 0.0 NULL 0.0
+fix 3 lower setforce 0.0 NULL 0.0
+fix 1 all nve
+
+# Output strain and stress info to file
+# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
+# p2 is in GPa
+variable strain equal "(lx - v_L0)/v_L0"
+variable p1 equal "v_strain"
+variable p2 equal "-pxz/10000"
+variable p3 equal "lx"
+variable p4 equal "temp"
+variable p5 equal "pe"
+variable p6 equal "ke"
+fix def1 all print 100 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6}" file output.def1.txt screen no
+# Dump coordinates to file (for void size calculations)
+dump 		1 all custom 1000 output.dump.* id x y z c_basal[1] c_basal[2] c_basal[3]
+
+# Display thermo
+thermo_style	custom step v_strain pxz lx temp pe ke
+restart 50000 output.restart
+
+# run deformation for 100000 timesteps (10% strain assuming 1 fs timestep and 1e9/s strainrate)
+variable runtime equal 0
+label loop
+displace_atoms	all ramp x 0.0 ${srate1} z 10 100 units box
+run		100
+variable runtime equal ${runtime}+100
+if "${runtime} < 100000" then "jump ${fname} loop"
+
+######################################
+# SIMULATION DONE
+print "All done"
--- a/examples/USER/misc/srp/in.srp
+++ b/examples/USER/misc/srp/in.srp
@ -15,6 +15,7 @@ bond_style      harmonic
 bond_coeff      * 225.0 0.85

 comm_modify vel yes
+comm_modify cutoff 3.6

 # must use pair hybrid, since srp bond particles
 # do not interact with other atoms types
--- a/examples/mscg/README
+++ b/examples/mscg/README
@ -0,0 +1,10 @@
+Running this example requires that LAMMPS be built with the MSCG
+package and its fix mscg command.  The fix uses the Multi-Scale
+Coarse-Graining (MS-CG) library, freely available at
+https://github.com/uchicago-voth/MSCG-release, to compute optimized
+coarse-grained force field parameters.  The MS-CG library was
+developed by Jacob Wagner in Greg Voth's group at the University of
+Chicago.
+
+See the lib/mscg/README file for instructions on how to download and
+install the MS-CG library for use with LAMMPS.
--- a/examples/mscg/control.in
+++ b/examples/mscg/control.in
@ -0,0 +1,12 @@
+block_size 1
+start_frame 1
+n_frames 19
+nonbonded_cutoff 10.0
+basis_type 0
+primary_output_style 0
+output_solution_flag 1
+output_spline_coeffs_flag 1
+pair_nonbonded_bspline_basis_order 6
+pair_nonbonded_basis_set_resolution 0.7
+pair_nonbonded_output_binwidth 0.1
+matrix_type 0
--- a/examples/mscg/data.meoh
+++ b/examples/mscg/data.meoh
--- a/examples/mscg/dump.meoh
+++ b/examples/mscg/dump.meoh
--- a/examples/mscg/in.mscg
+++ b/examples/mscg/in.mscg
@ -0,0 +1,22 @@
+units real
+atom_style full
+pair_style zero 10.0
+
+read_data data.meoh
+pair_coeff * *
+
+thermo 1
+thermo_style custom step
+
+# Test 1a: range finder functionality
+fix 1 all mscg 1 range on
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+print "TEST_1a mscg range finder"
+unfix 1
+
+# Test 1b: force matching functionality
+fix 1 all mscg 1
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+print "TEST_1b mscg force matching"
+
+print TEST_DONE
--- a/examples/mscg/output_9Jan17/1_1.dat
+++ b/examples/mscg/output_9Jan17/1_1.dat
@ -0,0 +1,77 @@
+2.500000 5.670970817963099e+02
+2.600000 2.404059283529051e+02
+2.700000 9.157060823529977e+01
+2.800000 3.428273061369140e+01
+2.900000 1.619868149395266e+01
+3.000000 1.039607214301755e+01
+3.100000 6.830187514267188e+00
+3.200000 3.861970842349535e+00
+3.300000 1.645948643278161e+00
+3.400000 2.395428971623918e-01
+3.500000 -4.276763637833773e-01
+3.600000 -5.132022977965877e-01
+3.700000 -2.208024961234051e-01
+3.800000 2.402697744243800e-01
+3.900000 6.956064296165573e-01
+4.000000 1.034070044257954e+00
+4.100000 1.205997975111669e+00
+4.200000 1.209501102128581e+00
+4.300000 1.076304670380924e+00
+4.400000 8.575891319958883e-01
+4.500000 6.098309880892070e-01
+4.600000 3.807992942746473e-01
+4.700000 1.995994191469442e-01
+4.800000 7.699059877424269e-02
+4.900000 9.750744163981299e-03
+5.000000 -1.480308769532222e-02
+5.100000 -1.429422279228416e-02
+5.200000 -6.765899050869768e-03
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+5.600000 -8.376292122940529e-02
+5.700000 -1.226699982917263e-01
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+5.900000 -1.737865035767736e-01
+6.000000 -1.738272491408507e-01
+6.100000 -1.546779867768825e-01
+6.200000 -1.193171291488982e-01
+6.300000 -7.321054075616322e-02
+6.400000 -2.317411193286228e-02
+6.500000 2.376366715221714e-02
+6.600000 6.149913249600215e-02
+6.700000 8.597538938112201e-02
+6.800000 9.590170060736655e-02
+6.900000 9.245100462148878e-02
+7.000000 7.855487875847664e-02
+7.100000 5.818301960249692e-02
+7.200000 3.562272334783877e-02
+7.300000 1.475836615985744e-02
+7.400000 -1.639617536128255e-03
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+7.600000 -1.768202571195587e-02
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+8.600000 -4.553187949229211e-02
+8.700000 -4.629269831051163e-02
+8.800000 -4.327548798226762e-02
+8.900000 -3.674131754868225e-02
+9.000000 -2.758883541814894e-02
+9.100000 -1.712151838480657e-02
+9.200000 -6.810600249997737e-03
+9.300000 1.941999556272785e-03
+9.400000 8.040747353879739e-03
+9.500000 1.092691524686838e-02
+9.600000 1.063606620723048e-02
+9.700000 7.416550438142138e-03
+9.800000 1.175066786686231e-03
+9.900000 -9.084427187675534e-03
+10.000000 -2.582180514463068e-02
+10.100000 -5.352186189454393e-02
--- a/examples/mscg/output_9Jan17/1_1.table
+++ b/examples/mscg/output_9Jan17/1_1.table
@ -0,0 +1,82 @@
+# Header information on force file
+
+1_1
+N 77 R 2.500000 10.100000
+
+1 2.500000 69.428523 567.097082
+2 2.600000 29.053372 240.405928
+3 2.700000 12.454545 91.570608
+4 2.800000 6.161878 34.282731
+5 2.900000 3.637808 16.198681
+6 3.000000 2.308070 10.396072
+7 3.100000 1.446757 6.830188
+8 3.200000 0.912149 3.861971
+9 3.300000 0.636753 1.645949
+10 3.400000 0.542478 0.239543
+11 3.500000 0.551885 -0.427676
+12 3.600000 0.598929 -0.513202
+13 3.700000 0.635629 -0.220802
+14 3.800000 0.634656 0.240270
+15 3.900000 0.587862 0.695606
+16 4.000000 0.501378 1.034070
+17 4.100000 0.389375 1.205998
+18 4.200000 0.268600 1.209501
+19 4.300000 0.154310 1.076305
+20 4.400000 0.057615 0.857589
+21 4.500000 -0.015756 0.609831
+22 4.600000 -0.065288 0.380799
+23 4.700000 -0.094307 0.199599
+24 4.800000 -0.108137 0.076991
+25 4.900000 -0.112474 0.009751
+26 5.000000 -0.112221 -0.014803
+27 5.100000 -0.110767 -0.014294
+28 5.200000 -0.109714 -0.006766
+29 5.300000 -0.109065 -0.006214
+30 5.400000 -0.107778 -0.019516
+31 5.500000 -0.104458 -0.046891
+32 5.600000 -0.097925 -0.083763
+33 5.700000 -0.087603 -0.122670
+34 5.800000 -0.073711 -0.155177
+35 5.900000 -0.057263 -0.173787
+36 6.000000 -0.039882 -0.173827
+37 6.100000 -0.023457 -0.154678
+38 6.200000 -0.009757 -0.119317
+39 6.300000 -0.000131 -0.073211
+40 6.400000 0.004688 -0.023174
+41 6.500000 0.004659 0.023764
+42 6.600000 0.000396 0.061499
+43 6.700000 -0.006978 0.085975
+44 6.800000 -0.016072 0.095902
+45 6.900000 -0.025489 0.092451
+46 7.000000 -0.034040 0.078555
+47 7.100000 -0.040877 0.058183
+48 7.200000 -0.045567 0.035623
+49 7.300000 -0.048086 0.014758
+50 7.400000 -0.048742 -0.001640
+51 7.500000 -0.048041 -0.012379
+52 7.600000 -0.046538 -0.017682
+53 7.700000 -0.044715 -0.018778
+54 7.800000 -0.042902 -0.017480
+55 7.900000 -0.041239 -0.015771
+56 8.000000 -0.039682 -0.015380
+57 8.100000 -0.038044 -0.017370
+58 8.200000 -0.036082 -0.021879
+59 8.300000 -0.033576 -0.028240
+60 8.400000 -0.030401 -0.035257
+61 8.500000 -0.026564 -0.041490
+62 8.600000 -0.022213 -0.045532
+63 8.700000 -0.017621 -0.046293
+64 8.800000 -0.013143 -0.043275
+65 8.900000 -0.009142 -0.036741
+66 9.000000 -0.005926 -0.027589
+67 9.100000 -0.003690 -0.017122
+68 9.200000 -0.002494 -0.006811
+69 9.300000 -0.002250 0.001942
+70 9.400000 -0.002749 0.008041
+71 9.500000 -0.003698 0.010927
+72 9.600000 -0.004776 0.010636
+73 9.700000 -0.005678 0.007417
+74 9.800000 -0.006108 0.001175
+75 9.900000 -0.005712 -0.009084
+76 10.000000 -0.003967 -0.025822
+77 10.100000 0.000000 -0.053522
--- a/examples/mscg/output_9Jan17/b-spline.out
+++ b/examples/mscg/output_9Jan17/b-spline.out
@ -0,0 +1,2 @@
+n: 1 1 6 12 2.400000000000002e+00 1.010000000000000e+01
+1.200460787805587e+03 2.169623423326193e+01 2.388396964379328e+01 -1.197754948555067e+01 6.472482422420378e+00 -1.483711824891365e+00 7.768139601662113e-01 -7.869494711740244e-01 4.830820182054661e-01 -1.892989444995645e-01 1.021275453070386e-01 -1.637649039972671e-01 5.570978712841167e-02 7.637188693695119e-03 -4.109175461195019e-03 -5.352186189455146e-02 
--- a/examples/mscg/output_9Jan17/rmin.in
+++ b/examples/mscg/output_9Jan17/rmin.in
@ -0,0 +1 @@
+1 1 2.852369 10.000000 fm
--- a/examples/mscg/output_9Jan17/rmin_b.in
+++ b/examples/mscg/output_9Jan17/rmin_b.in
--- a/examples/mscg/output_9Jan17/sol_info.out
+++ b/examples/mscg/output_9Jan17/sol_info.out
@ -0,0 +1,18 @@
+fm_matrix_rows:3000; fm_matrix_columns:16;
+Singular vector:
+2.442317e+00
+2.105009e+00
+1.433251e+00
+1.184602e+00
+9.739627e-01
+6.944898e-01
+5.376709e-01
+4.616070e-01
+3.257062e-01
+2.683729e-01
+1.530153e-01
+9.336288e-02
+5.042150e-02
+2.126912e-02
+1.446682e-02
+4.167763e-05
--- a/examples/mscg/output_9Jan17/x.out
+++ b/examples/mscg/output_9Jan17/x.out
@ -0,0 +1 @@
+<EFBFBD>-<2D><><EFBFBD><EFBFBD><EFBFBD>@47h<<3C>5@<40><><EFBFBD><EFBFBD>K<EFBFBD>7@<40>R<EFBFBD>]<5D><>'<27><><EFBFBD><EFBFBD>n<EFBFBD><6E>@݌I<DD8C>H<EFBFBD><48><EFBFBD><19>?<3F><><EFBFBD><EFBFBD>?r<>I<EFBFBD><49>.<2E><><11>^<5E><><EFBFBD><EFBFBD>?W<57><7F><EFBFBD>:ȿ(O<1D>%<25>?<3F>Ns<4E>?<3F>Ŀ<EFBFBD>:<3A>C<EFBFBD><43><EFBFBD>?<3F><><EFBFBD>:,H?<3F>}<7D>c<EFBFBD><63>p<EFBFBD><70><EFBFBD><EFBFBD><EFBFBD>7g<37><67>
--- a/examples/prd/in.prd
+++ b/examples/prd/in.prd
@ -78,7 +78,7 @@ run             100

 # only output atoms near vacancy

-compute coord all coord/atom $r
+compute coord all coord/atom cutoff $r

 #dump events all custom 1 dump.prd id type x y z
 #dump_modify events thresh c_coord != 4
--- a/examples/tad/in.tad
+++ b/examples/tad/in.tad
@ -80,7 +80,7 @@ velocity all zero linear

 # only output atoms near vacancy

-compute coord all coord/atom $r
+compute coord all coord/atom cutoff $r

 #dump events all custom 1 dump.prd id type x y z
 #dump_modify events thresh c_coord != 4
--- a/examples/voronoi/README
+++ b/examples/voronoi/README
@ -0,0 +1,10 @@
+Running this example requires that LAMMPS be built with the VORONOI
+package and its compute voronoi command.  The compute uses the Voro++
+library, freely available at http://math.lbl.gov/voro++, to compute
+the Voronoi tesselation locally on each processor.  Voro++ was
+developed by Chris H. Rycroft while at UC Berkeley / Lawrence Berkeley
+Laboratory.
+
+See the lib/voronoi/README file for instructions on how to download
+and install the Voro++ library for use with LAMMPS.
+
--- a/lib/README
+++ b/lib/README
@ -39,6 +39,8 @@ meam	      modified embedded atom method (MEAM) potential, MEAM package
                from Greg Wagner (Sandia)
 molfile       hooks to VMD molfile plugins, used by the USER-MOLFILE package
                from Axel Kohlmeyer (Temple U) and the VMD development team
+mscg          hooks to the MSCG library, used by fix_mscg command
+                from Jacob Wagner and Greg Voth group (U Chicago)
 python        hooks to the system Python library, used by the PYTHON package
                from the LAMMPS development team
 qmmm	      quantum mechanics/molecular mechanics coupling interface
--- a/lib/colvars/Makefile.colvars
+++ b/lib/colvars/Makefile.colvars
@ -0,0 +1,119 @@
+# library build -*- makefile -*- for colvars module
+
+# which file will be copied to Makefile.lammps
+
+EXTRAMAKE = Makefile.lammps.empty
+
+# ------ SETTINGS ------
+
+CXX =		g++
+CXXFLAGS =	-O2 -g -Wall -fPIC -funroll-loops # -DCOLVARS_DEBUG
+ARCHIVE =	ar
+ARCHFLAG =	-rscv
+SHELL =		/bin/sh
+
+# ------ DEFINITIONS ------
+
+SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias_alb.cpp colvarbias.cpp  \
+ colvarbias_histogram.cpp colvarbias_meta.cpp colvarbias_restraint.cpp      \
+ colvarcomp_angles.cpp colvarcomp_coordnums.cpp colvarcomp.cpp              \
+ colvarcomp_distances.cpp colvarcomp_protein.cpp colvarcomp_rotations.cpp   \
+ colvardeps.cpp colvar.cpp colvargrid.cpp colvarmodule.cpp colvarparse.cpp  \
+ colvarscript.cpp colvartypes.cpp colvarvalue.cpp
+
+LIB = libcolvars.a
+OBJ = $(SRC:.cpp=.o)
+EXE = #colvars_standalone
+
+# ------ MAKE PROCEDURE ------
+
+default: $(LIB) $(EXE) Makefile.lammps
+
+Makefile.lammps:
+	@cp $(EXTRAMAKE) Makefile.lammps
+
+$(LIB):	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
+
+colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
+	$(CXX) -o $@ $(CXXFLAGS) $^
+
+# ------ MAKE FLAGS ------
+
+.SUFFIXES:
+.SUFFIXES: .cpp .o
+
+.PHONY: default clean
+
+# ------ COMPILE RULES ------
+
+.cpp.o:
+	$(CXX) $(CXXFLAGS) -c $<
+
+# ------ DEPENDENCIES ------
+#
+colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvarparse.h colvardeps.h colvaratoms.h
+colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
+ colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarbias_abf.h colvarbias.h colvargrid.h
+colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
+ colvarproxy.h colvarvalue.h colvarbias_alb.h colvar.h colvarparse.h \
+ colvardeps.h colvarbias_restraint.h colvarbias.h
+colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h
+colvarbias_histogram.o: colvarbias_histogram.cpp colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
+ colvardeps.h colvarbias_histogram.h colvarbias.h colvargrid.h
+colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvarbias_meta.h colvarbias.h colvargrid.h
+colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \
+ colvarbias.h colvar.h colvarparse.h colvardeps.h
+colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
+ colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarcomp.h colvaratoms.h
+colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvaratoms.h colvar.h colvarcomp.h
+colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarcomp.h \
+ colvaratoms.h
+colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvar.h colvarcomp.h colvaratoms.h
+colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
+ colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
+ colvarcomp.h colvaratoms.h
+colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
+ colvar.h colvarcomp.h colvaratoms.h
+colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
+ colvaratoms.h colvarscript.h colvarbias.h
+colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \
+ colvarproxy.h colvarvalue.h colvarparse.h
+colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
+ colvaratoms.h colvargrid.h
+colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
+ colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
+ colvarbias.h colvarbias_abf.h colvargrid.h colvarbias_alb.h \
+ colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
+ colvarscript.h
+colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvarparse.h
+colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
+ colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
+ colvarparse.h colvardeps.h
+colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h colvarparse.h
+colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
+ colvarvalue.h
+
+# ------ CLEAN ------
+
+clean:
+	-rm *.o *~ $(LIB)
+
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarparse.h"
@ -163,38 +170,38 @@ colvar::colvar(std::string const &conf)
    }
    feature_states[f_cv_homogeneous]->enabled = homogeneous;
  }
-  // Colvar is deemed periodic iff:
+
+  // Colvar is deemed periodic if:
  // - it is homogeneous
  // - all cvcs are periodic
  // - all cvcs have the same period
-
-  b_periodic = cvcs[0]->b_periodic && is_enabled(f_cv_homogeneous);
-  period = cvcs[0]->period;
-  for (i = 1; i < cvcs.size(); i++) {
-    if (!cvcs[i]->b_periodic || cvcs[i]->period != period) {
-      b_periodic = false;
-      period = 0.0;
+  if (cvcs[0]->b_periodic) { // TODO make this a CVC feature
+    bool b_periodic = true;
+    period = cvcs[0]->period;
+    for (i = 1; i < cvcs.size(); i++) {
+      if (!cvcs[i]->b_periodic || cvcs[i]->period != period) {
+        b_periodic = false;
+        period = 0.0;
+        cvm::log("Warning: although one component is periodic, this colvar will "
+                 "not be treated as periodic, either because the exponent is not "
+                 "1, or because components of different periodicity are defined.  "
+                 "Make sure that you know what you are doing!");
+      }
    }
+    feature_states[f_cv_periodic]->enabled = b_periodic;
  }
-  feature_states[f_cv_periodic]->enabled = b_periodic;

  // check that cvcs are compatible

  for (i = 0; i < cvcs.size(); i++) {
-    if ((cvcs[i])->b_periodic && !b_periodic) {
-        cvm::log("Warning: although this component is periodic, the colvar will "
-                  "not be treated as periodic, either because the exponent is not "
-                  "1, or because multiple components are present. Make sure that "
-                  "you know what you are doing!");
-    }

    // components may have different types only for scripted functions
    if (!is_enabled(f_cv_scripted) && (colvarvalue::check_types(cvcs[i]->value(),
-                                                           cvcs[0]->value())) ) {
+                                                                cvcs[0]->value())) ) {
      cvm::error("ERROR: you are definining this collective variable "
                 "by using components of different types. "
                 "You must use the same type in order to "
-                 " sum them together.\n", INPUT_ERROR);
+                 "sum them together.\n", INPUT_ERROR);
      return;
    }
  }
@ -207,16 +214,15 @@ colvar::colvar(std::string const &conf)
  // at this point, the colvar's type is defined
  f.type(value());
  f_accumulated.type(value());
-  fb.type(value());
+
+  reset_bias_force();

  get_keyval(conf, "width", width, 1.0);
  if (width <= 0.0) {
    cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
+    return;
  }

-  // NOTE: not porting wall stuff to new deps, as this will change to a separate bias
-  // the grid functions will wait a little as well
-
  lower_boundary.type(value());
  lower_wall.type(value());

@ -308,6 +314,9 @@ colvar::colvar(std::string const &conf)
      enable(f_cv_extended_Lagrangian);
      provide(f_cv_Langevin);

+      // The extended mass will apply forces
+      enable(f_cv_gradient);
+
      xr.type(value());
      vr.type(value());
      fr.type(value());
@ -400,6 +409,9 @@ colvar::colvar(std::string const &conf)
  f_old.type(value());
  f_old.reset();

+  x_restart.type(value());
+  after_restart = false;
+
  if (cvm::b_analysis)
    parse_analysis(conf);

@ -761,9 +773,13 @@ 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
+    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_total_force(first_cvc, num_cvcs);
  error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);

  if (cvm::debug())
@ -780,9 +796,12 @@ int colvar::collect_cvc_data()

  int error_code = COLVARS_OK;

+  if (cvm::step_relative() > 0) {
+    // Total force depends on Jacobian derivative from previous timestep
+    error_code |= collect_cvc_total_forces();
+  }
  error_code |= collect_cvc_values();
  error_code |= collect_cvc_gradients();
-  error_code |= collect_cvc_total_forces();
  error_code |= collect_cvc_Jacobians();
  error_code |= calc_colvar_properties();

@ -872,6 +891,22 @@ int colvar::collect_cvc_values()
    cvm::log("Colvar \""+this->name+"\" has value "+
              cvm::to_str(x, cvm::cv_width, cvm::cv_prec)+".\n");

+  if (after_restart) {
+    after_restart = false;
+    if (cvm::proxy->simulation_running()) {
+      cvm::real const jump2 = dist2(x, x_restart) / (width*width);
+      if (jump2 > 0.25) {
+        cvm::error("Error: the calculated value of colvar \""+name+
+                   "\":\n"+cvm::to_str(x)+"\n differs greatly from the value "
+                   "last read from the state file:\n"+cvm::to_str(x_restart)+
+                   "\nPossible causes are changes in configuration, "
+                   "wrong state file, or how PBC wrapping is handled.\n",
+                   INPUT_ERROR);
+        return INPUT_ERROR;
+      }
+    }
+  }
+
  return COLVARS_OK;
 }

@ -979,22 +1014,17 @@ int colvar::calc_cvc_total_force(int first_cvc, size_t num_cvcs)
    if (cvm::debug())
      cvm::log("Calculating total force of colvar \""+this->name+"\".\n");

-    // if (!tasks[task_extended_lagrangian] && (cvm::step_relative() > 0)) {
-   // Disabled check to allow for explicit total force calculation
-    // even with extended Lagrangian
+    cvm::increase_depth();

-    if (cvm::step_relative() > 0) {
-      cvm::increase_depth();
-      // get from the cvcs the total forces from the PREVIOUS step
-      for (i = first_cvc, cvc_count = 0;
-          (i < cvcs.size()) && (cvc_count < cvc_max_count);
-          i++) {
-        if (!cvcs[i]->is_enabled()) continue;
-        cvc_count++;
-        (cvcs[i])->calc_force_invgrads();
-      }
-      cvm::decrease_depth();
+    for (i = first_cvc, cvc_count = 0;
+        (i < cvcs.size()) && (cvc_count < cvc_max_count);
+        i++) {
+      if (!cvcs[i]->is_enabled()) continue;
+      cvc_count++;
+      (cvcs[i])->calc_force_invgrads();
    }
+    cvm::decrease_depth();
+

    if (cvm::debug())
      cvm::log("Done calculating total force of colvar \""+this->name+"\".\n");
@ -1013,6 +1043,11 @@ int colvar::collect_cvc_total_forces()
      // get from the cvcs the total forces from the PREVIOUS step
      for (size_t i = 0; i < cvcs.size();  i++) {
        if (!cvcs[i]->is_enabled()) continue;
+            if (cvm::debug())
+            cvm::log("Colvar component no. "+cvm::to_str(i+1)+
+                " within colvar \""+this->name+"\" has total force "+
+                cvm::to_str((cvcs[i])->total_force(),
+                cvm::cv_width, cvm::cv_prec)+".\n");
        // linear combination is assumed
        ft += (cvcs[i])->total_force() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
      }
@ -1056,6 +1091,11 @@ int colvar::collect_cvc_Jacobians()
    fj.reset();
    for (size_t i = 0; i < cvcs.size(); i++) {
      if (!cvcs[i]->is_enabled()) continue;
+        if (cvm::debug())
+          cvm::log("Colvar component no. "+cvm::to_str(i+1)+
+            " within colvar \""+this->name+"\" has Jacobian derivative"+
+            cvm::to_str((cvcs[i])->Jacobian_derivative(),
+            cvm::cv_width, cvm::cv_prec)+".\n");
      // linear combination is assumed
      fj += (cvcs[i])->Jacobian_derivative() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
    }
@ -1085,7 +1125,7 @@ int colvar::calc_colvar_properties()
    // TODO: put it in the restart information
    if (cvm::step_relative() == 0) {
      xr = x;
-      vr = 0.0; // (already 0; added for clarity)
+      vr.reset(); // (already 0; added for clarity)
    }

    // report the restraint center as "value"
@ -1128,15 +1168,16 @@ cvm::real colvar::update_forces_energy()
  if (is_enabled(f_cv_Jacobian)) {
    // the instantaneous Jacobian force was not included in the reported total force;
    // instead, it is subtracted from the applied force (silent Jacobian correction)
+    // This requires the Jacobian term for the *current* timestep
    if (is_enabled(f_cv_hide_Jacobian))
      f -= fj;
  }

-  if (is_enabled(f_cv_lower_wall) || is_enabled(f_cv_upper_wall)) {
+  // Wall force
+  colvarvalue fw(x);
+  fw.reset();

-    // Wall force
-    colvarvalue fw(x);
-    fw.reset();
+  if (is_enabled(f_cv_lower_wall) || is_enabled(f_cv_upper_wall)) {

    if (cvm::debug())
      cvm::log("Calculating wall forces for colvar \""+this->name+"\".\n");
@ -1144,12 +1185,11 @@ cvm::real colvar::update_forces_energy()
    // For a periodic colvar, both walls may be applicable at the same time
    // in which case we pick the closer one
    if ( (!is_enabled(f_cv_upper_wall)) ||
-         (this->dist2(x_reported, lower_wall) < this->dist2(x_reported, upper_wall)) ) {
+         (this->dist2(x, lower_wall) < this->dist2(x, upper_wall)) ) {

-      cvm::real const grad = this->dist2_lgrad(x_reported, lower_wall);
+      cvm::real const grad = this->dist2_lgrad(x, lower_wall);
      if (grad < 0.0) {
        fw = -0.5 * lower_wall_k * grad;
-        f += fw;
        if (cvm::debug())
          cvm::log("Applying a lower wall force("+
                    cvm::to_str(fw)+") to \""+this->name+"\".\n");
@ -1157,10 +1197,9 @@ cvm::real colvar::update_forces_energy()

    } else {

-      cvm::real const grad = this->dist2_lgrad(x_reported, upper_wall);
+      cvm::real const grad = this->dist2_lgrad(x, upper_wall);
      if (grad > 0.0) {
        fw = -0.5 * upper_wall_k * grad;
-        f += fw;
        if (cvm::debug())
          cvm::log("Applying an upper wall force("+
                    cvm::to_str(fw)+") to \""+this->name+"\".\n");
@ -1168,17 +1207,26 @@ cvm::real colvar::update_forces_energy()
    }
  }

+  // At this point f is the force f from external biases that will be applied to the
+  // extended variable if there is one
+
  if (is_enabled(f_cv_extended_Lagrangian)) {

+    if (cvm::debug()) {
+      cvm::log("Updating extended-Lagrangian degrees of freedom.\n");
+    }
+
    cvm::real dt = cvm::dt();
-    cvm::real f_ext;
+    colvarvalue f_ext(fr.type());
+    f_ext.reset();

    // the total force is applied to the fictitious mass, while the
-    // atoms only feel the harmonic force
+    // atoms only feel the harmonic force + wall force
    // fr: bias force on extended variable (without harmonic spring), for output in trajectory
    // f_ext: total force on extended variable (including harmonic spring)
-    // f: - initially, external biasing force (including wall forces)
-    //    - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
+    // f: - initially, external biasing force
+    //    - after this code block, colvar force to be applied to atomic coordinates
+    //      ie. spring force + wall force
    fr    = f;
    f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
    f     =     (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
@ -1200,15 +1248,24 @@ cvm::real colvar::update_forces_energy()
    potential_energy = 0.5 * ext_force_k * this->dist2(xr, x);
    // leap to v_(i+1/2)
    if (is_enabled(f_cv_Langevin)) {
-      vr -= dt * ext_gamma * vr.real_value;
-      vr += dt * ext_sigma * cvm::rand_gaussian() / ext_mass;
+      vr -= dt * ext_gamma * vr;
+      colvarvalue rnd(x);
+      rnd.set_random();
+      vr += dt * ext_sigma * rnd / ext_mass;
    }
    vr  += (0.5 * dt) * f_ext / ext_mass;
    xr  += dt * vr;
    xr.apply_constraints();
-    if (this->b_periodic) this->wrap(xr);
+    if (this->is_enabled(f_cv_periodic)) this->wrap(xr);
  }

+  // TODO remove the wall force
+  f += fw;
+  // Now adding the force on the actual colvar (for those biases who
+  // bypass the extended Lagrangian mass)
+  f += fb_actual;
+
+  // Store force to be applied, possibly summed over several timesteps
  f_accumulated += f;

  if (is_enabled(f_cv_fdiff_velocity)) {
@ -1425,14 +1482,15 @@ std::istream & colvar::read_restart(std::istream &is)
    }
  }

-  if ( !(get_keyval(conf, "x", x,
-                    colvarvalue(x.type()), colvarparse::parse_silent)) ) {
+  if ( !(get_keyval(conf, "x", x, x, colvarparse::parse_silent)) ) {
    cvm::log("Error: restart file does not contain "
             "the value of the colvar \""+
             name+"\" .\n");
  } else {
    cvm::log("Restarting collective variable \""+name+"\" from value: "+
             cvm::to_str(x)+"\n");
+    x_restart = x;
+    after_restart = true;
  }

  if (is_enabled(f_cv_extended_Lagrangian)) {
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@ -1,5 +1,12 @@
 // -*- 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_H
 #define COLVAR_H

@ -170,6 +177,9 @@ public:
  /// the biases are updated
  colvarvalue fb;

+  /// \brief Bias force to the actual value (only useful with extended Lagrangian)
+  colvarvalue fb_actual;
+
  /// \brief Total \em applied force; fr (if extended_lagrangian
  /// is defined), fb (if biases are applied) and the walls' forces
  /// (if defined) contribute to it
@ -183,13 +193,9 @@ public:
  colvarvalue ft;


-  /// Period, if it is a constant
+  /// Period, if this variable is periodic
  cvm::real period;

-  /// \brief Same as above, but also takes into account components
-  /// with a variable period, such as distanceZ
-  bool b_periodic;
-

  /// \brief Expand the boundaries of multiples of width, to keep the
  /// value always within range
@ -290,6 +296,9 @@ public:
  /// Add to the total force from biases
  void add_bias_force(colvarvalue const &force);

+  /// Apply a force to the actual value (only meaningful with extended Lagrangian)
+  void add_bias_force_actual_value(colvarvalue const &force);
+
  /// \brief Collect all forces on this colvar, integrate internal
  /// equations of motion of internal degrees of freedom; see also
  /// colvar::communicate_forces()
@ -386,6 +395,12 @@ protected:
  /// Previous value (to calculate velocities during analysis)
  colvarvalue            x_old;

+  /// Value read from the most recent state file (if any)
+  colvarvalue            x_restart;
+
+  /// True if a state file was just read
+  bool                   after_restart;
+
  /// Time series of values and velocities used in correlation
  /// functions
  std::list< std::list<colvarvalue> > acf_x_history, acf_v_history;
@ -577,9 +592,20 @@ inline void colvar::add_bias_force(colvarvalue const &force)
 }


+inline void colvar::add_bias_force_actual_value(colvarvalue const &force)
+{
+  if (cvm::debug()) {
+    cvm::log("Adding biasing force "+cvm::to_str(force)+" to colvar \""+name+"\".\n");
+  }
+  fb_actual += force;
+}
+
+
 inline void colvar::reset_bias_force() {
  fb.type(value());
  fb.reset();
+  fb_actual.type(value());
+  fb_actual.reset();
 }

 #endif
--- a/lib/colvars/colvaratoms.cpp
+++ b/lib/colvars/colvaratoms.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include "colvarmodule.h"
 #include "colvarparse.h"
 #include "colvaratoms.h"
@ -171,7 +178,10 @@ int cvm::atom_group::remove_atom(cvm::atom_iter ai)

 int cvm::atom_group::init()
 {
-  if (!key.size()) key = "atoms";
+  if (!key.size()) key = "unnamed";
+  description = "atom group " + key;
+  // These will be overwritten by parse(), if initializing from a config string
+
  atoms.clear();

  // TODO: check with proxy whether atom forces etc are available
@ -179,6 +189,7 @@ int cvm::atom_group::init()

  index = -1;

+  b_dummy = false;
  b_center = false;
  b_rotate = false;
  b_user_defined_fit = false;
@ -440,6 +451,7 @@ int cvm::atom_group::parse(std::string const &conf)

  if (b_print_atom_ids) {
    cvm::log("Internal definition of the atom group:\n");
+    cvm::log(print_atom_ids());
  }

  cvm::decrease_depth();
--- a/lib/colvars/colvaratoms.h
+++ b/lib/colvars/colvaratoms.h
@ -1,5 +1,12 @@
 // -*- 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 COLVARATOMS_H
 #define COLVARATOMS_H

@ -64,7 +71,7 @@ public:

  /// \brief Initialize an atom for collective variable calculation
  /// and get its internal identifier \param atom_number Atom index in
-  /// the system topology (starting from 1)
+  /// the system topology (1-based)
  atom(int atom_number);

  /// \brief Initialize an atom for collective variable calculation
@ -453,6 +460,8 @@ public:
  /// are not used, either because they were not defined (e.g because
  /// the colvar has not a scalar value) or the biases require to
  /// micromanage the force.
+  /// This function will be phased out eventually, in favor of
+  /// apply_colvar_force() once that is implemented for non-scalar values
  void apply_force(cvm::rvector const &force);

 };
--- a/lib/colvars/colvarbias.cpp
+++ b/lib/colvars/colvarbias.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarbias.h"
@ -29,6 +36,7 @@ colvarbias::colvarbias(char const *key)
  has_data = false;
  b_output_energy = false;
  reset();
+  state_file_step = 0;

  // Start in active state by default
  enable(f_cvb_active);
@ -141,20 +149,25 @@ int colvarbias::clear()
 int colvarbias::add_colvar(std::string const &cv_name)
 {
  if (colvar *cv = cvm::colvar_by_name(cv_name)) {
-    // Removed this as nor all biases apply forces eg histogram
-    // cv->enable(colvar::task_gradients);
+
    if (cvm::debug()) {
      cvm::log("Applying this bias to collective variable \""+
               cv->name+"\".\n");
    }
+
    colvars.push_back(cv);

    colvar_forces.push_back(colvarvalue());
    colvar_forces.back().type(cv->value()); // make sure each force is initialized to zero
+    colvar_forces.back().is_derivative(); // colvar constraints are not applied to the force
    colvar_forces.back().reset();

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

+    if (is_enabled(f_cvb_apply_force)) {
+      cv->enable(f_cv_gradient);
+    }
+
    // Add dependency link.
    // All biases need at least the value of each colvar
    // although possibly not at all timesteps
@ -165,6 +178,7 @@ int colvarbias::add_colvar(std::string const &cv_name)
               cv_name+"\".\n", INPUT_ERROR);
    return INPUT_ERROR;
  }
+
  return COLVARS_OK;
 }

@ -190,16 +204,19 @@ void colvarbias::communicate_forces()
 }


-void colvarbias::change_configuration(std::string const &conf)
+int colvarbias::change_configuration(std::string const &conf)
 {
-  cvm::error("Error: change_configuration() not implemented.\n");
+  cvm::error("Error: change_configuration() not implemented.\n",
+             COLVARS_NOT_IMPLEMENTED);
+  return COLVARS_NOT_IMPLEMENTED;
 }


 cvm::real colvarbias::energy_difference(std::string const &conf)
 {
-  cvm::error("Error: energy_difference() not implemented.\n");
-  return 0.;
+  cvm::error("Error: energy_difference() not implemented.\n",
+             COLVARS_NOT_IMPLEMENTED);
+  return 0.0;
 }


@ -225,6 +242,118 @@ int colvarbias::replica_share()
  return COLVARS_NOT_IMPLEMENTED;
 }

+
+std::string const colvarbias::get_state_params() const
+{
+  std::ostringstream os;
+  os << "step " << cvm::step_absolute() << "\n"
+     << "name " << this->name << "\n";
+  return os.str();
+}
+
+
+int colvarbias::set_state_params(std::string const &conf)
+{
+  std::string new_name = "";
+  if (colvarparse::get_keyval(conf, "name", new_name,
+                              std::string(""), colvarparse::parse_silent) &&
+      (new_name != this->name)) {
+    cvm::error("Error: in the state file, the "
+               "\""+bias_type+"\" block has a different name, \""+new_name+
+               "\": different system?\n", INPUT_ERROR);
+  }
+
+  if (name.size() == 0) {
+    cvm::error("Error: \""+bias_type+"\" block within the restart file "
+               "has no identifiers.\n", INPUT_ERROR);
+  }
+
+  colvarparse::get_keyval(conf, "step", state_file_step,
+                          cvm::step_absolute(), colvarparse::parse_silent);
+
+  return COLVARS_OK;
+}
+
+
+std::ostream & colvarbias::write_state(std::ostream &os)
+{
+  if (cvm::debug()) {
+    cvm::log("Writing state file for bias \""+name+"\"\n");
+  }
+  os.setf(std::ios::scientific, std::ios::floatfield);
+  os.precision(cvm::cv_prec);
+  os << bias_type << " {\n"
+     << "  configuration {\n";
+  std::istringstream is(get_state_params());
+  std::string line;
+  while (std::getline(is, line)) {
+    os << "    " << line << "\n";
+  }
+  os << "  }\n";
+  write_state_data(os);
+  os << "}\n\n";
+  return os;
+}
+
+
+std::istream & colvarbias::read_state(std::istream &is)
+{
+  size_t const start_pos = is.tellg();
+
+  std::string key, brace, conf;
+  if ( !(is >> key)   || !(key == bias_type) ||
+       !(is >> brace) || !(brace == "{") ||
+       !(is >> colvarparse::read_block("configuration", conf)) ||
+       (set_state_params(conf) != COLVARS_OK) ) {
+    cvm::error("Error: in reading state configuration for \""+bias_type+"\" bias \""+
+               this->name+"\" at position "+
+               cvm::to_str(is.tellg())+" in stream.\n", INPUT_ERROR);
+    is.clear();
+    is.seekg(start_pos, std::ios::beg);
+    is.setstate(std::ios::failbit);
+    return is;
+  }
+
+  if (!read_state_data(is)) {
+    cvm::error("Error: in reading state data for \""+bias_type+"\" bias \""+
+               this->name+"\" at position "+
+               cvm::to_str(is.tellg())+" in stream.\n", INPUT_ERROR);
+    is.clear();
+    is.seekg(start_pos, std::ios::beg);
+    is.setstate(std::ios::failbit);
+  }
+
+  is >> brace;
+  if (brace != "}") {
+    cvm::error("Error: corrupt restart information for \""+bias_type+"\" bias \""+
+               this->name+"\": no matching brace at position "+
+               cvm::to_str(is.tellg())+" in stream.\n");
+    is.setstate(std::ios::failbit);
+  }
+
+  return is;
+}
+
+
+std::istream & colvarbias::read_state_data_key(std::istream &is, char const *key)
+{
+  size_t const start_pos = is.tellg();
+  std::string key_in;
+  if ( !(is >> key_in) ||
+       !(key_in == to_lower_cppstr(std::string(key))) ) {
+    cvm::error("Error: in reading restart configuration for "+
+               bias_type+" bias \""+this->name+"\" at position "+
+               cvm::to_str(is.tellg())+" in stream.\n", INPUT_ERROR);
+    is.clear();
+    is.seekg(start_pos, std::ios::beg);
+    is.setstate(std::ios::failbit);
+    return is;
+  }
+  return is;
+}
+
+
+
 std::ostream & colvarbias::write_traj_label(std::ostream &os)
 {
  os << " ";
--- a/lib/colvars/colvarbias.h
+++ b/lib/colvars/colvarbias.h
@ -1,5 +1,12 @@
 // -*- 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 COLVARBIAS_H
 #define COLVARBIAS_H

@ -9,7 +16,8 @@


 /// \brief Collective variable bias, base class
-class colvarbias : public colvarparse, public colvardeps {
+class colvarbias
+  : public virtual colvarparse, public virtual colvardeps {
 public:

  /// Name of this bias
@ -24,6 +32,12 @@ public:
  /// Add a new collective variable to this bias
  int add_colvar(std::string const &cv_name);

+  /// Add a new collective variable to this bias
+  size_t number_of_colvars() const
+  {
+    return colvars.size();
+  }
+
  /// Retrieve colvar values and calculate their biasing forces
  /// Return bias energy
  virtual int update();
@ -31,7 +45,7 @@ public:
  // TODO: move update_bias here (share with metadynamics)

  /// Load new configuration - force constant and/or centers only
-  virtual void change_configuration(std::string const &conf);
+  virtual int change_configuration(std::string const &conf);

  /// Calculate change in energy from using alternate configuration
  virtual cvm::real energy_difference(std::string const &conf);
@ -49,7 +63,7 @@ public:
  virtual void analyze() {}

  /// Send forces to the collective variables
-  void communicate_forces();
+  virtual void communicate_forces();

  /// \brief Constructor
  colvarbias(char const *key);
@ -60,13 +74,11 @@ public:
  /// \brief Set to zero all mutable data
  virtual int reset();

-protected:
+private:

  /// Default constructor
  colvarbias();

-private:
-
  /// Copy constructor
  colvarbias(colvarbias &);

@ -78,28 +90,59 @@ public:
  /// Destructor
  virtual ~colvarbias();

-  /// Read the bias configuration from a restart file
-  virtual std::istream & read_restart(std::istream &is) = 0;
+  /// Write the values of specific mutable properties to a string
+  virtual std::string const get_state_params() const;

-  /// Write the bias configuration to a restart file
-  virtual std::ostream & write_restart(std::ostream &os) = 0;
+  /// Read the values of specific mutable properties from a string
+  virtual int set_state_params(std::string const &state_conf);
+
+  /// Write all mutable data not already written by get_state_params()
+  virtual std::ostream & write_state_data(std::ostream &os)
+  {
+    return os;
+  }
+
+  /// Read all mutable data not already set by set_state_params()
+  virtual std::istream & read_state_data(std::istream &is)
+  {
+    return is;
+  }
+
+  /// Read a keyword from the state data (typically a header)
+  std::istream & read_state_data_key(std::istream &is, char const *key);
+
+  /// Write the bias configuration to a restart file or other stream
+  virtual std::ostream & write_state(std::ostream &os);
+
+  /// Read the bias configuration from a restart file or other stream
+  virtual std::istream & read_state(std::istream &is);

  /// Write a label to the trajectory file (comment line)
  virtual std::ostream & write_traj_label(std::ostream &os);

-  /// (Re)initialize the output files (does not write them yet)
-  virtual int setup_output() { return COLVARS_OK; }
-
  /// Output quantities such as the bias energy to the trajectory file
  virtual std::ostream & write_traj(std::ostream &os);

-  /// Write output files (if defined, e.g. in analysis mode)
+  /// (Re)initialize the output files (does not write them yet)
+  virtual int setup_output()
+  {
+    return COLVARS_OK;
+  }
+
+  /// Write any output files that this bias may have (e.g. PMF files)
  virtual int write_output_files()
  {
    return COLVARS_OK;
  }

-  inline cvm::real get_energy() {
+  /// If this bias is communicating with other replicas through files, send it to them
+  virtual int write_state_to_replicas()
+  {
+    return COLVARS_OK;
+  }
+
+  inline cvm::real get_energy()
+  {
    return bias_energy;
  }

@ -107,9 +150,11 @@ public:
  static std::vector<feature *> cvb_features;

  /// \brief Implementation of the feature list accessor for colvarbias
-  virtual std::vector<feature *> &features() {
+  virtual std::vector<feature *> &features()
+  {
    return cvb_features;
  }
+
 protected:

  /// \brief Pointers to collective variables to which the bias is
@ -130,6 +175,9 @@ protected:
  /// (for history-dependent biases)
  bool                     has_data;

+  /// \brief Step number read from the last state file
+  size_t                   state_file_step;
+
 };

 #endif
--- a/lib/colvars/colvarbias_abf.cpp
+++ b/lib/colvars/colvarbias_abf.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include "colvarmodule.h"
 #include "colvar.h"
 #include "colvarbias_abf.h"
@ -23,6 +30,8 @@ int colvarbias_abf::init(std::string const &conf)
 {
  colvarbias::init(conf);

+  provide(f_cvb_scalar_variables);
+  enable(f_cvb_scalar_variables);
  provide(f_cvb_history_dependent);

  // TODO relax this in case of VMD plugin
@ -590,16 +599,10 @@ void colvarbias_abf::read_gradients_samples()
 }


-std::ostream & colvarbias_abf::write_restart(std::ostream& os)
+std::ostream & colvarbias_abf::write_state_data(std::ostream& os)
 {
-
  std::ios::fmtflags flags(os.flags());

-  os << "abf {\n"
-     << "  configuration {\n"
-     << "    name " << this->name << "\n";
-  os << "  }\n";
-
  os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format
  os << "\nsamples\n";
  samples->write_raw(os, 8);
@ -617,117 +620,47 @@ std::ostream & colvarbias_abf::write_restart(std::ostream& os)
    z_gradients->write_raw(os, 8);
  }

-  os << "}\n\n";
-
  os.flags(flags);
  return os;
 }


-std::istream & colvarbias_abf::read_restart(std::istream& is)
+std::istream & colvarbias_abf::read_state_data(std::istream& is)
 {
  if ( input_prefix.size() > 0 ) {
    cvm::error("ERROR: cannot provide both inputPrefix and a colvars state file.\n", INPUT_ERROR);
  }

-  size_t const start_pos = is.tellg();
-
-  cvm::log("Restarting ABF bias \""+
-            this->name+"\".\n");
-  std::string key, brace, conf;
-
-  if ( !(is >> key)   || !(key == "abf") ||
-       !(is >> brace) || !(brace == "{") ||
-       !(is >> colvarparse::read_block("configuration", conf)) ) {
-    cvm::log("Error: in reading restart configuration for ABF bias \""+
-              this->name+"\" at position "+
-              cvm::to_str(is.tellg())+" in stream.\n");
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
-    return is;
-  }
-
-  std::string name = "";
-  if ( (colvarparse::get_keyval(conf, "name", name, std::string(""), colvarparse::parse_silent)) &&
-         (name != this->name) )
-    cvm::error("Error: in the restart file, the "
-                      "\"abf\" block has wrong name(" + name + ")\n");
-  if ( name == "" ) {
-    cvm::error("Error: \"abf\" block in the restart file has no name.\n");
-  }
-
-  if ( !(is >> key)   || !(key == "samples")) {
-    cvm::log("Error: in reading restart configuration for ABF bias \""+
-              this->name+"\" at position "+
-              cvm::to_str(is.tellg())+" in stream.\n");
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
+  if (! read_state_data_key(is, "samples")) {
    return is;
  }
  if (! samples->read_raw(is)) {
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
    return is;
  }

-  if ( !(is >> key)   || !(key == "gradient")) {
-    cvm::log("Error: in reading restart configuration for ABF bias \""+
-              this->name+"\" at position "+
-              cvm::to_str(is.tellg())+" in stream.\n");
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
+  if (! read_state_data_key(is, "gradient")) {
    return is;
  }
  if (! gradients->read_raw(is)) {
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
    return is;
  }

  if (z_gradients) {
-    if ( !(is >> key) || !(key == "z_samples")) {
-      cvm::log("Error: in reading restart configuration for ABF bias \""+
-                this->name+"\" at position "+
-                cvm::to_str(is.tellg())+" in stream.\n");
-      is.clear();
-      is.seekg(start_pos, std::ios::beg);
-      is.setstate(std::ios::failbit);
+
+    if (! read_state_data_key(is, "z_samples")) {
      return is;
    }
    if (! z_samples->read_raw(is)) {
-      is.clear();
-      is.seekg(start_pos, std::ios::beg);
-      is.setstate(std::ios::failbit);
      return is;
    }

-    if ( !(is >> key)   || !(key == "z_gradient")) {
-      cvm::log("Error: in reading restart configuration for ABF bias \""+
-                this->name+"\" at position "+
-                cvm::to_str(is.tellg())+" in stream.\n");
-      is.clear();
-      is.seekg(start_pos, std::ios::beg);
-      is.setstate(std::ios::failbit);
+    if (! read_state_data_key(is, "z_gradient")) {
      return is;
    }
    if (! z_gradients->read_raw(is)) {
-      is.clear();
-      is.seekg(start_pos, std::ios::beg);
-      is.setstate(std::ios::failbit);
      return is;
    }
  }
-  is >> brace;
-  if (brace != "}") {
-    cvm::error("Error: corrupt restart information for ABF bias \""+
-                      this->name+"\": no matching brace at position "+
-                      cvm::to_str(is.tellg())+" in the restart file.\n");
-    is.setstate(std::ios::failbit);
-  }
+
  return is;
 }
--- a/lib/colvars/colvarbias_abf.h
+++ b/lib/colvars/colvarbias_abf.h
@ -1,5 +1,12 @@
 // -*- 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 COLVARBIAS_ABF_H
 #define COLVARBIAS_ABF_H

@ -107,8 +114,8 @@ private:
  /// Read human-readable FE gradients and sample count (if not using restart)
  void		  read_gradients_samples();

-  std::istream& read_restart(std::istream&);
-  std::ostream& write_restart(std::ostream&);
+  std::istream& read_state_data(std::istream&);
+  std::ostream& write_state_data(std::ostream&);
 };

 #endif
--- a/lib/colvars/colvarbias_alb.cpp
+++ b/lib/colvars/colvarbias_alb.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <math.h>
@ -33,6 +40,9 @@ int colvarbias_alb::init(std::string const &conf)
 {
  colvarbias::init(conf);

+  provide(f_cvb_scalar_variables);
+  enable(f_cvb_scalar_variables);
+
  provide(f_cvb_history_dependent);

  size_t i;
@ -239,37 +249,8 @@ int colvarbias_alb::update()
 }


-std::istream & colvarbias_alb::read_restart(std::istream &is)
+int colvarbias_alb::set_state_params(std::string const &conf)
 {
-  size_t const start_pos = is.tellg();
-
-  cvm::log("Restarting adaptive linear bias \""+
-            this->name+"\".\n");
-
-  std::string key, brace, conf;
-  if ( !(is >> key)   || !(key == "ALB") ||
-       !(is >> brace) || !(brace == "{") ||
-       !(is >> colvarparse::read_block("configuration", conf)) ) {
-
-    cvm::log("Error: in reading restart configuration for restraint bias \""+
-              this->name+"\" at position "+
-              cvm::to_str(is.tellg())+" in stream.\n");
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
-    return is;
-  }
-
-  std::string name = "";
-  if ( (colvarparse::get_keyval(conf, "name", name, std::string(""), colvarparse::parse_silent)) &&
-       (name != this->name) )
-    cvm::fatal_error("Error: in the restart file, the "
-                      "\"ALB\" block has a wrong name\n");
-  if (name.size() == 0) {
-    cvm::fatal_error("Error: \"ALB\" block in the restart file "
-                      "has no identifiers.\n");
-  }
-
  if (!get_keyval(conf, "setCoupling", set_coupling))
    cvm::fatal_error("Error: current setCoupling  is missing from the restart.\n");

@ -299,23 +280,13 @@ std::istream & colvarbias_alb::read_restart(std::istream &is)
  if (!get_keyval(conf, "b_equilibration", b_equilibration))
    cvm::fatal_error("Error: current updateCalls is missing from the restart.\n");

-  is >> brace;
-  if (brace != "}") {
-    cvm::fatal_error("Error: corrupt restart information for adaptive linear bias \""+
-                      this->name+"\": no matching brace at position "+
-                      cvm::to_str(is.tellg())+" in the restart file.\n");
-    is.setstate(std::ios::failbit);
-  }
-
-  return is;
+  return COLVARS_OK;
 }


-std::ostream & colvarbias_alb::write_restart(std::ostream &os)
+std::string const colvarbias_alb::get_state_params() const
 {
-  os << "ALB {\n"
-     << "  configuration {\n"
-     << "    name " << this->name << "\n";
+  std::ostringstream os;
  os << "    setCoupling ";
  size_t i;
  for (i = 0; i < colvars.size(); i++) {
@ -358,10 +329,7 @@ std::ostream & colvarbias_alb::write_restart(std::ostream &os)
  else
    os << "    b_equilibration no\n";

-  os << "  }\n"
-     << "}\n\n";
-
-  return os;
+  return os.str();
 }


--- a/lib/colvars/colvarbias_alb.h
+++ b/lib/colvars/colvarbias_alb.h
@ -1,10 +1,18 @@
 // -*- 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 COLVARBIAS_ALB_H
 #define COLVARBIAS_ALB_H

 #include "colvar.h"
-#include "colvarbias_restraint.h"
+#include "colvarbias.h"
+

 class colvarbias_alb : public colvarbias {

@ -15,8 +23,8 @@ public:
  virtual int init(std::string const &conf);
  virtual int update();

-  virtual std::istream & read_restart(std::istream &is);
-  virtual std::ostream & write_restart(std::ostream &os);
+  virtual std::string const get_state_params() const;
+  virtual int set_state_params(std::string const &conf);
  virtual std::ostream & write_traj_label(std::ostream &os);
  virtual std::ostream & write_traj(std::ostream &os);

--- a/lib/colvars/colvarbias_histogram.cpp
+++ b/lib/colvars/colvarbias_histogram.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include "colvarmodule.h"
 #include "colvar.h"
 #include "colvarbias_histogram.h"
@ -17,6 +24,9 @@ int colvarbias_histogram::init(std::string const &conf)
 {
  colvarbias::init(conf);

+  provide(f_cvb_scalar_variables);
+  enable(f_cvb_scalar_variables);
+
  provide(f_cvb_history_dependent);
  enable(f_cvb_history_dependent);

@ -196,78 +206,25 @@ int colvarbias_histogram::write_output_files()
 }


-std::istream & colvarbias_histogram::read_restart(std::istream& is)
+std::istream & colvarbias_histogram::read_state_data(std::istream& is)
 {
-  size_t const start_pos = is.tellg();
-
-  cvm::log("Restarting collective variable histogram \""+
-            this->name+"\".\n");
-  std::string key, brace, conf;
-
-  if ( !(is >> key)   || !(key == "histogram") ||
-       !(is >> brace) || !(brace == "{") ||
-       !(is >> colvarparse::read_block("configuration", conf)) ) {
-    cvm::log("Error: in reading restart configuration for histogram \""+
-              this->name+"\" at position "+
-              cvm::to_str(is.tellg())+" in stream.\n");
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
-    return is;
-  }
-
-  int id = -1;
-  std::string name = "";
-  if ( (colvarparse::get_keyval(conf, "name", name, std::string(""), colvarparse::parse_silent)) &&
-         (name != this->name) )
-    cvm::error("Error: in the restart file, the "
-                      "\"histogram\" block has a wrong name: different system?\n");
-  if ( (id == -1) && (name == "") ) {
-    cvm::error("Error: \"histogram\" block in the restart file "
-                      "has no name.\n");
-  }
-
-  if ( !(is >> key)   || !(key == "grid")) {
-    cvm::error("Error: in reading restart configuration for histogram \""+
-              this->name+"\" at position "+
-              cvm::to_str(is.tellg())+" in stream.\n");
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
+  if (! read_state_data_key(is, "grid")) {
    return is;
  }
  if (! grid->read_raw(is)) {
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
    return is;
  }

-  is >> brace;
-  if (brace != "}") {
-    cvm::error("Error: corrupt restart information for ABF bias \""+
-                this->name+"\": no matching brace at position "+
-                cvm::to_str(is.tellg())+" in the restart file.\n");
-    is.setstate(std::ios::failbit);
-  }
  return is;
 }

-std::ostream & colvarbias_histogram::write_restart(std::ostream& os)
+
+std::ostream & colvarbias_histogram::write_state_data(std::ostream& os)
 {
  std::ios::fmtflags flags(os.flags());
  os.setf(std::ios::fmtflags(0), std::ios::floatfield);
-
-  os << "histogram {\n"
-     << "  configuration {\n"
-     << "    name " << this->name << "\n";
-  os << "  }\n";
-
  os << "grid\n";
  grid->write_raw(os, 8);
-
-  os << "}\n\n";
-
  os.flags(flags);
  return os;
 }
--- a/lib/colvars/colvarbias_histogram.h
+++ b/lib/colvars/colvarbias_histogram.h
@ -1,5 +1,12 @@
 // -*- 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 COLVARBIAS_HISTOGRAM_H
 #define COLVARBIAS_HISTOGRAM_H

@ -35,8 +42,8 @@ protected:
  /// If colvar_array_size is larger than 1, weigh each one by this number before accumulating the histogram
  std::vector<cvm::real> weights;

-  virtual std::istream& read_restart(std::istream&);
-  virtual std::ostream& write_restart(std::ostream&);
+  virtual std::istream & read_state_data(std::istream &is);
+  virtual std::ostream & write_state_data(std::ostream &os);
 };

 #endif
--- a/lib/colvars/colvarbias_meta.cpp
+++ b/lib/colvars/colvarbias_meta.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include <iostream>
 #include <sstream>
 #include <fstream>
@ -26,10 +33,9 @@


 colvarbias_meta::colvarbias_meta(char const *key)
-  : colvarbias(key),
-    new_hills_begin(hills.end()),
-    state_file_step(0)
+  : colvarbias(key)
 {
+  new_hills_begin = hills.end();
 }


@ -164,11 +170,32 @@ int colvarbias_meta::init(std::string const &conf)
  target_dist = NULL;
  get_keyval(conf, "ebMeta", ebmeta, false);
  if(ebmeta){
+    if (use_grids && expand_grids) {
+      cvm::fatal_error("Error: expandBoundaries is not supported with "
+                       "ebMeta please allocate wide enough boundaries for "
+                       "each colvar ahead of time and set targetdistfile "
+                       "accordingly. \n");
+    }
    target_dist = new colvar_grid_scalar();
    target_dist->init_from_colvars(colvars);
    get_keyval(conf, "targetdistfile", target_dist_file);
    std::ifstream targetdiststream(target_dist_file.c_str());
    target_dist->read_multicol(targetdiststream);
+    cvm::real min_val = target_dist->minimum_value();
+    if(min_val<0){
+      cvm::error("Error: Target distribution of ebMeta "
+                 "has negative values!.\n", INPUT_ERROR);
+    }
+    cvm::real min_pos_val = target_dist->minimum_pos_value();
+    if(min_pos_val<=0){
+      cvm::error("Error: Target distribution of ebMeta has negative "
+                 "or zero minimum positive value!.\n", INPUT_ERROR);
+    }
+    if(min_val==0){
+      cvm::log("WARNING: Target distribution has zero values.\n");
+      cvm::log("Zeros will be converted to the minimum positive value.\n");
+      target_dist->remove_zeros(min_pos_val);
+    }
    // normalize target distribution and multiply by effective volume = exp(differential entropy)
    target_dist->multiply_constant(1.0/target_dist->integral());
    cvm::real volume = std::exp(target_dist->entropy());
@ -404,8 +431,10 @@ int colvarbias_meta::update()

    if (ebmeta) {
       hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index());
-       if(cvm::step_absolute() <= ebmeta_equil_steps) {
-         cvm::real const hills_lambda=(cvm::real(ebmeta_equil_steps - cvm::step_absolute()))/(cvm::real(ebmeta_equil_steps));
+       if(cvm::step_absolute() <= long(ebmeta_equil_steps)) {
+         cvm::real const hills_lambda =
+           (cvm::real(long(ebmeta_equil_steps) - cvm::step_absolute())) /
+           (cvm::real(ebmeta_equil_steps));
         hills_scale = hills_lambda + (1-hills_lambda)*hills_scale;
       }
    }
@ -972,7 +1001,7 @@ void colvarbias_meta::read_replica_files()
               (replicas[ir])->replica_state_file+"\".\n");

      std::ifstream is((replicas[ir])->replica_state_file.c_str());
-      if (! (replicas[ir])->read_restart(is)) {
+      if (! (replicas[ir])->read_state(is)) {
        cvm::log("Reading from file \""+(replicas[ir])->replica_state_file+
                 "\" failed or incomplete: will try again in "+
                 cvm::to_str(replica_update_freq)+" steps.\n");
@ -1068,63 +1097,24 @@ void colvarbias_meta::read_replica_files()
 }


-// **********************************************************************
-// input functions
-// **********************************************************************
-
-
-std::istream & colvarbias_meta::read_restart(std::istream& is)
+int colvarbias_meta::set_state_params(std::string const &state_conf)
 {
-  size_t const start_pos = is.tellg();
-
-  if (comm == single_replica) {
-    // if using a multiple replicas scheme, output messages
-    // are printed before and after calling this function
-    cvm::log("Restarting metadynamics bias \""+this->name+"\""+
-             ".\n");
-  }
-  std::string key, brace, conf;
-  if ( !(is >> key)   || !(key == "metadynamics") ||
-       !(is >> brace) || !(brace == "{") ||
-       !(is >> colvarparse::read_block("configuration", conf)) ) {
-
-    if (comm == single_replica)
-      cvm::log("Error: in reading restart configuration for metadynamics bias \""+
-               this->name+"\""+
-               ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
-               (replica_state_file_in_sync ? ("at position "+
-                                              cvm::to_str(start_pos)+
-                                              " in the state file") : "")+".\n");
-    is.clear();
-    is.seekg(start_pos, std::ios::beg);
-    is.setstate(std::ios::failbit);
-    return is;
+  std::string new_replica = "";
+  if (colvarparse::get_keyval(state_conf, "replicaID", new_replica,
+                              std::string(""), colvarparse::parse_silent) &&
+      (new_replica != this->replica_id)) {
+    cvm::error("Error: in the state file, the "
+               "\"metadynamics\" block has a different replicaID: different system?\n",
+               INPUT_ERROR);
+    return INPUT_ERROR;
  }

-  std::string name = "";
-  if ( colvarparse::get_keyval(conf, "name", name,
-                               std::string(""), colvarparse::parse_silent) &&
-       (name != this->name) )
-    cvm::fatal_error("Error: in the restart file, the "
-                     "\"metadynamics\" block has a different name: different system?\n");
+  return COLVARS_OK;
+}

-  if (name.size() == 0) {
-    cvm::fatal_error("Error: \"metadynamics\" block within the restart file "
-                     "has no identifiers.\n");
-  }
-
-  if (comm != single_replica) {
-    std::string replica = "";
-    if (colvarparse::get_keyval(conf, "replicaID", replica,
-                                std::string(""), colvarparse::parse_silent) &&
-        (replica != this->replica_id))
-      cvm::fatal_error("Error: in the restart file, the "
-                       "\"metadynamics\" block has a different replicaID: different system?\n");
-
-    colvarparse::get_keyval(conf, "step", state_file_step,
-                            cvm::step_absolute(), colvarparse::parse_silent);
-  }

+std::istream & colvarbias_meta::read_state_data(std::istream& is)
+{
  bool grids_from_restart_file = use_grids;

  if (use_grids) {
@ -1155,6 +1145,7 @@ std::istream & colvarbias_meta::read_restart(std::istream& is)
    }

    size_t const hills_energy_pos = is.tellg();
+    std::string key;
    if (!(is >> key)) {
      if (hills_energy_backup != NULL) {
        delete hills_energy;
@ -1316,17 +1307,6 @@ std::istream & colvarbias_meta::read_restart(std::istream& is)
    }
  }

-  is >> brace;
-  if (brace != "}") {
-    cvm::log("Incomplete restart information for metadynamics bias \""+
-             this->name+"\""+
-             ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
-             ": no closing brace at position "+
-             cvm::to_str(is.tellg())+" in the file.\n");
-    is.setstate(std::ios::failbit);
-    return is;
-  }
-
  if (cvm::debug())
    cvm::log("colvarbias_meta::read_restart() done\n");

@ -1424,13 +1404,6 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
 }


-
-
-// **********************************************************************
-// output functions
-// **********************************************************************
-
-
 int colvarbias_meta::setup_output()
 {

@ -1537,16 +1510,17 @@ int colvarbias_meta::setup_output()
 }


-std::ostream & colvarbias_meta::write_restart(std::ostream& os)
+std::string const colvarbias_meta::get_state_params() const
 {
-  os << "metadynamics {\n"
-     << "  configuration {\n"
-     << "    step " << cvm::step_absolute() << "\n"
-     << "    name " << this->name << "\n";
+  std::ostringstream os;
  if (this->comm != single_replica)
-    os << "    replicaID " << this->replica_id << "\n";
-  os << "  }\n\n";
+    os << "replicaID " << this->replica_id << "\n";
+  return (colvarbias::get_state_params() + os.str());
+}

+
+std::ostream & colvarbias_meta::write_state_data(std::ostream& os)
+{
  if (use_grids) {

    // this is a very good time to project hills, if you haven't done
@ -1578,8 +1552,12 @@ std::ostream & colvarbias_meta::write_restart(std::ostream& os)
    }
  }

-  os << "}\n\n";
+  return os;
+}

+
+int colvarbias_meta::write_state_to_replicas()
+{
  if (comm != single_replica) {
    write_replica_state_file();
    // schedule to reread the state files of the other replicas (they
@ -1588,12 +1566,16 @@ std::ostream & colvarbias_meta::write_restart(std::ostream& os)
      (replicas[ir])->replica_state_file_in_sync = false;
    }
  }
+  return COLVARS_OK;
+}

+
+int colvarbias_meta::write_output_files()
+{
  if (dump_fes) {
    write_pmf();
  }
-
-  return os;
+  return COLVARS_OK;
 }


@ -1665,53 +1647,67 @@ void colvarbias_meta::write_pmf()



-void colvarbias_meta::write_replica_state_file()
+int colvarbias_meta::write_replica_state_file()
 {
-  // write down also the restart for the other replicas: TODO: this
-  // is duplicated code, that could be cleaned up later
+  if (cvm::debug()) {
+    cvm::log("Writing replica state file for bias \""+name+"\"\n");
+  }
+  // write down also the restart for the other replicas
  cvm::backup_file(replica_state_file.c_str());
-  cvm::ofstream rep_state_os(replica_state_file.c_str());
-  if (!rep_state_os.is_open())
-    cvm::fatal_error("Error: in opening file \""+
-                     replica_state_file+"\" for writing.\n");
-
-  rep_state_os.setf(std::ios::scientific, std::ios::floatfield);
-  rep_state_os << "\n"
-               << "metadynamics {\n"
-               << "  configuration {\n"
-               << "    name " << this->name << "\n"
-               << "    step " << cvm::step_absolute() << "\n";
-  if (this->comm != single_replica) {
-    rep_state_os << "    replicaID " << this->replica_id << "\n";
-  }
-  rep_state_os << "  }\n\n";
-  rep_state_os << "  hills_energy\n";
-  rep_state_os << std::setprecision(cvm::cv_prec)
-               << std::setw(cvm::cv_width);
-  hills_energy->write_restart(rep_state_os);
-  rep_state_os << "  hills_energy_gradients\n";
-  rep_state_os << std::setprecision(cvm::cv_prec)
-               << std::setw(cvm::cv_width);
-  hills_energy_gradients->write_restart(rep_state_os);
-
-  if ( (!use_grids) || keep_hills ) {
-    // write all hills currently in memory
-    for (std::list<hill>::const_iterator h = this->hills.begin();
-         h != this->hills.end();
-         h++) {
-      rep_state_os << *h;
-    }
-  } else {
-    // write just those that are near the grid boundaries
-    for (std::list<hill>::const_iterator h = this->hills_off_grid.begin();
-         h != this->hills_off_grid.end();
-         h++) {
-      rep_state_os << *h;
-    }
+  std::ostream *rep_state_os = cvm::proxy->output_stream(replica_state_file);
+  if (rep_state_os == NULL) {
+    cvm::error("Error: in opening file \""+
+               replica_state_file+"\" for writing.\n", FILE_ERROR);
+    return FILE_ERROR;
  }

-  rep_state_os << "}\n\n";
-  rep_state_os.close();
+  rep_state_os->setf(std::ios::scientific, std::ios::floatfield);
+
+  if (!write_state(*rep_state_os)) {
+    cvm::error("Error: in writing to file \""+
+               replica_state_file+"\".\n", FILE_ERROR);
+    cvm::proxy->close_output_stream(replica_state_file);
+    return FILE_ERROR;
+  }
+
+  cvm::proxy->close_output_stream(replica_state_file);
+
+  // rep_state_os.setf(std::ios::scientific, std::ios::floatfield);
+  // rep_state_os << "\n"
+  //              << "metadynamics {\n"
+  //              << "  configuration {\n"
+  //              << "    name " << this->name << "\n"
+  //              << "    step " << cvm::step_absolute() << "\n";
+  // if (this->comm != single_replica) {
+  //   rep_state_os << "    replicaID " << this->replica_id << "\n";
+  // }
+  // rep_state_os << "  }\n\n";
+  // rep_state_os << "  hills_energy\n";
+  // rep_state_os << std::setprecision(cvm::cv_prec)
+  //              << std::setw(cvm::cv_width);
+  // hills_energy->write_restart(rep_state_os);
+  // rep_state_os << "  hills_energy_gradients\n";
+  // rep_state_os << std::setprecision(cvm::cv_prec)
+  //              << std::setw(cvm::cv_width);
+  // hills_energy_gradients->write_restart(rep_state_os);
+
+  // if ( (!use_grids) || keep_hills ) {
+  //   // write all hills currently in memory
+  //   for (std::list<hill>::const_iterator h = this->hills.begin();
+  //        h != this->hills.end();
+  //        h++) {
+  //     rep_state_os << *h;
+  //   }
+  // } else {
+  //   // write just those that are near the grid boundaries
+  //   for (std::list<hill>::const_iterator h = this->hills_off_grid.begin();
+  //        h != this->hills_off_grid.end();
+  //        h++) {
+  //     rep_state_os << *h;
+  //   }
+  // }
+  // rep_state_os << "}\n\n";
+  // rep_state_os.close();

  // reopen the hills file
  replica_hills_os.close();
@ -1721,8 +1717,11 @@ void colvarbias_meta::write_replica_state_file()
    cvm::fatal_error("Error: in opening file \""+
                     replica_hills_file+"\" for writing.\n");
  replica_hills_os.setf(std::ios::scientific, std::ios::floatfield);
+
+  return COLVARS_OK;
 }

+
 std::string colvarbias_meta::hill::output_traj()
 {
  std::ostringstream os;
--- a/lib/colvars/colvarbias_meta.h
+++ b/lib/colvars/colvarbias_meta.h
@ -1,5 +1,12 @@
 // -*- 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 COLVARBIAS_META_H
 #define COLVARBIAS_META_H

@ -31,10 +38,16 @@ public:
  virtual int init(std::string const &conf);
  virtual ~colvarbias_meta();
  virtual int update();
-  virtual std::istream & read_restart(std::istream &is);
-  virtual std::ostream & write_restart(std::ostream &os);
+
+  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 &os);
+
  virtual int setup_output();
+  virtual int write_output_files();
  virtual void write_pmf();
+  virtual int write_state_to_replicas();

  class hill;
  typedef std::list<hill>::iterator hill_iter;
@ -77,13 +90,6 @@ protected:
  /// Read a hill from a file
  std::istream & read_hill(std::istream &is);

-  /// \brief step present in a state file
-  ///
-  /// When using grids and reading state files containing them
-  /// (multiple replicas), this is used to check whether a hill is
-  /// newer or older than the grids
-  size_t                   state_file_step;
-
  /// \brief Add a new hill; if a .hills trajectory is written,
  /// write it there; if there is more than one replica, communicate
  /// it to the others
@ -187,7 +193,7 @@ protected:
  virtual void read_replica_files();

  /// \brief Write data to other replicas
-  virtual void write_replica_state_file();
+  virtual int write_replica_state_file();

  /// \brief Additional, "mirror" metadynamics biases, to collect info
  /// from the other replicas
--- a/lib/colvars/colvarbias_restraint.cpp
+++ b/lib/colvars/colvarbias_restraint.cpp
--- a/lib/colvars/colvarbias_restraint.h
+++ b/lib/colvars/colvarbias_restraint.h
@ -1,36 +1,43 @@
 // -*- 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 COLVARBIAS_RESTRAINT_H
 #define COLVARBIAS_RESTRAINT_H

 #include "colvarbias.h"

-/// \brief Bias restraint, optionally moving towards a target
+/// \brief Most general definition of a colvar restraint:
+/// see derived classes for specific types
 /// (implementation of \link colvarbias \endlink)
-class colvarbias_restraint : public colvarbias {
+class colvarbias_restraint
+  : public virtual colvarbias
+{

 public:

  /// Retrieve colvar values and calculate their biasing forces
  virtual int update();

-  // TODO the following can be supplanted by a new call to init()
  /// Load new configuration - force constant and/or centers only
-  virtual void change_configuration(std::string const &conf);
+  virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }

  /// Calculate change in energy from using alternate configuration
-  virtual cvm::real energy_difference(std::string const &conf);
+  virtual cvm::real energy_difference(std::string const &conf) { return 0.0; }

-  /// Read the bias configuration from a restart file
-  virtual std::istream & read_restart(std::istream &is);
+  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_state(std::ostream &os);
+  virtual std::istream & read_state(std::istream &is);

-  /// Write the bias configuration to a restart file
-  virtual std::ostream & write_restart(std::ostream &os);
-
-  /// Write a label to the trajectory file (comment line)
  virtual std::ostream & write_traj_label(std::ostream &os);
-
-  /// Output quantities such as the bias energy to the trajectory file
  virtual std::ostream & write_traj(std::ostream &os);

  /// \brief Constructor
@ -42,26 +49,110 @@ public:

 protected:

-  /// \brief Potential function
-  virtual cvm::real restraint_potential(cvm::real k, colvar const *x,
-                                        colvarvalue const &xcenter) const = 0;
+  /// \brief Potential function for the i-th colvar
+  virtual cvm::real restraint_potential(size_t i) const = 0;

-  /// \brief Force function
-  virtual colvarvalue restraint_force(cvm::real k, colvar const *x,
-                                      colvarvalue const &xcenter) const = 0;
+  /// \brief Force function for the i-th colvar
+  virtual colvarvalue const restraint_force(size_t i) const = 0;

-  ///\brief Unit scaling
-  virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const = 0;
+  /// \brief Derivative of the potential function with respect to the force constant
+  virtual cvm::real d_restraint_potential_dk(size_t i) const = 0;
+};
+
+
+/// Definition and parsing of the restraint centers
+class colvarbias_restraint_centers
+  : public virtual colvarbias_restraint
+{
+public:
+
+  colvarbias_restraint_centers(char const *key);
+  virtual int init(std::string const &conf);
+  virtual int change_configuration(std::string const &conf);
+
+protected:

  /// \brief Restraint centers
  std::vector<colvarvalue> colvar_centers;

-  /// \brief Restraint centers without wrapping or constraints applied
+  /// \brief Restraint centers outside the domain of the colvars (no wrapping or constraints applied)
  std::vector<colvarvalue> colvar_centers_raw;
+};
+
+
+/// Definition and parsing of the force constant
+class colvarbias_restraint_k
+  : public virtual colvarbias_restraint
+{
+public:
+
+  colvarbias_restraint_k(char const *key);
+  virtual int init(std::string const &conf);
+  virtual int change_configuration(std::string const &conf);
+
+protected:
+  /// \brief Restraint force constant
+  cvm::real force_k;
+};
+
+
+/// Options to change the restraint configuration over time (shared between centers and k moving)
+class colvarbias_restraint_moving
+  : public virtual colvarparse {
+public:
+
+  colvarbias_restraint_moving(char const *key);
+  // Note: despite the diamond inheritance, most of this function gets only executed once
+  virtual int init(std::string const &conf);
+  virtual int update() { return COLVARS_OK; }
+  virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
+
+  virtual std::string const get_state_params() const;
+  virtual int set_state_params(std::string const &conf);
+
+protected:

  /// \brief Moving target?
  bool b_chg_centers;

+  /// \brief Changing force constant?
+  bool b_chg_force_k;
+
+  /// \brief Number of stages over which to perform the change
+  /// If zero, perform a continuous change
+  int target_nstages;
+
+  /// \brief Number of current stage of the perturbation
+  int stage;
+
+    /// \brief Lambda-schedule for custom varying force constant
+  std::vector<cvm::real> lambda_schedule;
+
+  /// \brief Number of steps required to reach the target force constant
+  /// or restraint centers
+  long target_nsteps;
+};
+
+
+/// Options to change the restraint centers over time
+class colvarbias_restraint_centers_moving
+  : public virtual colvarbias_restraint_centers,
+    public virtual colvarbias_restraint_moving
+{
+public:
+
+  colvarbias_restraint_centers_moving(char const *key);
+  virtual int init(std::string const &conf);
+  virtual int update();
+  virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
+
+  virtual std::string const get_state_params() const;
+  virtual int set_state_params(std::string const &conf);
+  virtual std::ostream & write_traj_label(std::ostream &os);
+  virtual std::ostream & write_traj(std::ostream &os);
+
+protected:
+
  /// \brief New restraint centers
  std::vector<colvarvalue> target_centers;

@ -78,11 +169,29 @@ protected:
  /// \brief Accumulated work
  cvm::real acc_work;

-  /// \brief Restraint force constant
-  cvm::real force_k;
+  /// Update the accumulated work
+  int update_acc_work();
+};

-  /// \brief Changing force constant?
-  bool b_chg_force_k;
+
+/// Options to change the restraint force constant over time
+class colvarbias_restraint_k_moving
+  : public virtual colvarbias_restraint_k,
+    public virtual colvarbias_restraint_moving
+{
+public:
+
+  colvarbias_restraint_k_moving(char const *key);
+  virtual int init(std::string const &conf);
+  virtual int update();
+  virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
+
+  virtual std::string const get_state_params() const;
+  virtual int set_state_params(std::string const &conf);
+  virtual std::ostream & write_traj_label(std::ostream &os);
+  virtual std::ostream & write_traj(std::ostream &os);
+
+protected:

  /// \brief Restraint force constant (target value)
  cvm::real target_force_k;
@ -90,9 +199,6 @@ protected:
  /// \brief Restraint force constant (starting value)
  cvm::real starting_force_k;

-  /// \brief Lambda-schedule for custom varying force constant
-  std::vector<cvm::real> lambda_schedule;
-
  /// \brief Exponent for varying the force constant
  cvm::real force_k_exp;

@ -100,71 +206,91 @@ protected:
  /// (in TI, would be the accumulating FE derivative)
  cvm::real restraint_FE;

-
  /// \brief Equilibration steps for restraint FE calculation through TI
  cvm::real target_equil_steps;
-
-  /// \brief Number of stages over which to perform the change
-  /// If zero, perform a continuous change
-  int target_nstages;
-
-  /// \brief Number of current stage of the perturbation
-  int stage;
-
-  /// \brief Number of steps required to reach the target force constant
-  /// or restraint centers
-  long target_nsteps;
 };


 /// \brief Harmonic bias restraint
 /// (implementation of \link colvarbias_restraint \endlink)
-class colvarbias_restraint_harmonic : public colvarbias_restraint {
-
+class colvarbias_restraint_harmonic
+  : public colvarbias_restraint_centers_moving,
+    public colvarbias_restraint_k_moving
+{
 public:
-
  colvarbias_restraint_harmonic(char const *key);
  virtual int init(std::string const &conf);
-  // no additional members, destructor not needed
+  virtual int update();
+  virtual std::string const get_state_params() const;
+  virtual int set_state_params(std::string const &conf);
+  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);
+  virtual cvm::real energy_difference(std::string const &conf);

 protected:

-  /// \brief Potential function
-  virtual cvm::real restraint_potential(cvm::real k, colvar const *x,
-                                        colvarvalue const &xcenter) const;
+  virtual cvm::real restraint_potential(size_t i) const;
+  virtual colvarvalue const restraint_force(size_t i) const;
+  virtual cvm::real d_restraint_potential_dk(size_t i) const;
+};

-  /// \brief Force function
-  virtual colvarvalue restraint_force(cvm::real k, colvar const *x,
-                                      colvarvalue const &xcenter) const;

-  ///\brief Unit scaling
-  virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const;
+/// \brief Wall restraint
+/// (implementation of \link colvarbias_restraint \endlink)
+class colvarbias_restraint_harmonic_walls
+  : public colvarbias_restraint_k_moving
+{
+public:

+  colvarbias_restraint_harmonic_walls(char const *key);
+  virtual int init(std::string const &conf);
+  virtual int update();
+  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_traj_label(std::ostream &os);
+  virtual std::ostream & write_traj(std::ostream &os);
+
+protected:
+
+  /// \brief Location of the lower walls
+  std::vector<colvarvalue> lower_walls;
+
+  /// \brief Location of the upper walls
+  std::vector<colvarvalue> upper_walls;
+
+  virtual cvm::real colvar_distance(size_t i) const;
+  virtual cvm::real restraint_potential(size_t i) const;
+  virtual colvarvalue const restraint_force(size_t i) const;
+  virtual cvm::real d_restraint_potential_dk(size_t i) const;
 };


 /// \brief Linear bias restraint
 /// (implementation of \link colvarbias_restraint \endlink)
-class colvarbias_restraint_linear : public colvarbias_restraint {
+class colvarbias_restraint_linear
+  : public colvarbias_restraint_centers_moving,
+    public colvarbias_restraint_k_moving
+{

 public:
  colvarbias_restraint_linear(char const *key);
  virtual int init(std::string const &conf);
-  // no additional members, destructor not needed
+  virtual int update();
+  virtual int change_configuration(std::string const &conf);
+  virtual cvm::real energy_difference(std::string const &conf);
+
+  virtual std::string const get_state_params() const;
+  virtual int set_state_params(std::string const &conf);
+  virtual std::ostream & write_traj_label(std::ostream &os);
+  virtual std::ostream & write_traj(std::ostream &os);

 protected:

-  /// \brief Potential function
-  virtual cvm::real restraint_potential(cvm::real k, colvar const *x,
-                                        colvarvalue const &xcenter) const;
-
-  /// \brief Force function
-  virtual colvarvalue restraint_force(cvm::real k, colvar const *x,
-                                      colvarvalue const &xcenter) const;
-
-  ///\brief Unit scaling
-  virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const;
-
+  virtual cvm::real restraint_potential(size_t i) const;
+  virtual colvarvalue const restraint_force(size_t i) const;
+  virtual cvm::real d_restraint_potential_dk(size_t i) const;
 };


--- a/lib/colvars/colvarcomp.cpp
+++ b/lib/colvars/colvarcomp.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvar.h"
@ -154,15 +161,17 @@ void colvar::cvc::read_data()

 void colvar::cvc::calc_force_invgrads()
 {
-  cvm::fatal_error("Error: calculation of inverse gradients is not implemented "
-                    "for colvar components of type \""+function_type+"\".\n");
+  cvm::error("Error: calculation of inverse gradients is not implemented "
+             "for colvar components of type \""+function_type+"\".\n",
+             COLVARS_NOT_IMPLEMENTED);
 }


 void colvar::cvc::calc_Jacobian_derivative()
 {
-  cvm::fatal_error("Error: calculation of inverse gradients is not implemented "
-                    "for colvar components of type \""+function_type+"\".\n");
+  cvm::error("Error: calculation of inverse gradients is not implemented "
+             "for colvar components of type \""+function_type+"\".\n",
+             COLVARS_NOT_IMPLEMENTED);
 }


@ -281,6 +290,33 @@ void colvar::cvc::debug_gradients(cvm::atom_group *group)
 }


+cvm::real colvar::cvc::dist2(colvarvalue const &x1,
+                             colvarvalue const &x2) const
+{
+  return x1.dist2(x2);
+}
+
+
+colvarvalue colvar::cvc::dist2_lgrad(colvarvalue const &x1,
+                                     colvarvalue const &x2) const
+{
+  return x1.dist2_grad(x2);
+}
+
+
+colvarvalue colvar::cvc::dist2_rgrad(colvarvalue const &x1,
+                                     colvarvalue const &x2) const
+{
+  return x2.dist2_grad(x1);
+}
+
+
+void colvar::cvc::wrap(colvarvalue &x) const
+{
+  return;
+}
+
+
 // Static members

 std::vector<colvardeps::feature *> colvar::cvc::cvc_features;
--- a/lib/colvars/colvarcomp.h
+++ b/lib/colvars/colvarcomp.h
@ -1,5 +1,12 @@
 // -*- 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 COLVARCOMP_H
 #define COLVARCOMP_H

@ -105,8 +112,8 @@ public:
  /// options from the provided configuration string
  /// Returns reference to new group
  cvm::atom_group *parse_group(std::string const &conf,
-                   char const *group_key,
-                   bool optional = false);
+                               char const *group_key,
+                               bool optional = false);

  /// \brief Parse options pertaining to total force calculation
  virtual int init_total_force_params(std::string const &conf);
@ -130,7 +137,7 @@ public:
  }

  /// \brief Obtain data needed for the calculation for the backend
-  void read_data();
+  virtual void read_data();

  /// \brief Calculate the variable
  virtual void calc_value() = 0;
@ -151,17 +158,14 @@ public:


  /// \brief Return the previously calculated value
-  virtual colvarvalue const & value() const;
-
-  // /// \brief Return const pointer to the previously calculated value
-  // virtual const colvarvalue *p_value() const;
+  colvarvalue const & value() const;

  /// \brief Return the previously calculated total force
-  virtual colvarvalue const & total_force() const;
+  colvarvalue const & total_force() const;

  /// \brief Return the previously calculated divergence of the
  /// inverse atomic gradients
-  virtual colvarvalue const & Jacobian_derivative() const;
+  colvarvalue const & Jacobian_derivative() const;

  /// \brief Apply the collective variable force, by communicating the
  /// atomic forces to the simulation program (\b Note: the \link ft
@ -247,52 +251,24 @@ protected:
 };


-
-
 inline colvarvalue const & colvar::cvc::value() const
 {
  return x;
 }

-// inline const colvarvalue * colvar::cvc::p_value() const
-// {
-//   return &x;
-// }

 inline colvarvalue const & colvar::cvc::total_force() const
 {
  return ft;
 }

+
 inline colvarvalue const & colvar::cvc::Jacobian_derivative() const
 {
  return jd;
 }


-inline cvm::real colvar::cvc::dist2(colvarvalue const &x1,
-                                    colvarvalue const &x2) const
-{
-  return x1.dist2(x2);
-}
-
-inline colvarvalue colvar::cvc::dist2_lgrad(colvarvalue const &x1,
-                                            colvarvalue const &x2) const
-{
-  return x1.dist2_grad(x2);
-}
-
-inline colvarvalue colvar::cvc::dist2_rgrad(colvarvalue const &x1,
-                                            colvarvalue const &x2) const
-{
-  return x2.dist2_grad(x1);
-}
-
-inline void colvar::cvc::wrap(colvarvalue &x) const
-{
-  return;
-}
-

 /// \brief Colvar component: distance between the centers of mass of
 /// two groups (colvarvalue::type_scalar type, range [0:*))
@ -312,7 +288,7 @@ protected:
 public:
  distance(std::string const &conf);
  distance();
-  virtual inline ~distance() {}
+  virtual ~distance() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void calc_force_invgrads();
@ -327,6 +303,7 @@ public:
 };


+
 // \brief Colvar component: distance vector between centers of mass
 // of two groups (\link colvarvalue::type_3vector \endlink type,
 // range (-*:*)x(-*:*)x(-*:*))
@ -336,7 +313,7 @@ class colvar::distance_vec
 public:
  distance_vec(std::string const &conf);
  distance_vec();
-  virtual inline ~distance_vec() {}
+  virtual ~distance_vec() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -352,6 +329,7 @@ public:
 };


+
 /// \brief Colvar component: distance unit vector (direction) between
 /// centers of mass of two groups (colvarvalue::type_unit3vector type,
 /// range [-1:1]x[-1:1]x[-1:1])
@ -361,19 +339,14 @@ class colvar::distance_dir
 public:
  distance_dir(std::string const &conf);
  distance_dir();
-  virtual inline ~distance_dir() {}
+  virtual ~distance_dir() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
-  virtual cvm::real dist2(colvarvalue const &x1,
-                          colvarvalue const &x2) const;
-  virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
-                                  colvarvalue const &x2) const;
-  virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
-                                  colvarvalue const &x2) const;
 };


+
 /// \brief Colvar component: projection of the distance vector along
 /// an axis(colvarvalue::type_scalar type, range (-*:*))
 class colvar::distance_z
@ -399,7 +372,7 @@ protected:
 public:
  distance_z(std::string const &conf);
  distance_z();
-  virtual inline ~distance_z() {}
+  virtual ~distance_z() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void calc_force_invgrads();
@ -416,6 +389,7 @@ public:
 };


+
 /// \brief Colvar component: projection of the distance vector on a
 /// plane (colvarvalue::type_scalar type, range [0:*))
 class colvar::distance_xy
@ -429,7 +403,7 @@ protected:
 public:
  distance_xy(std::string const &conf);
  distance_xy();
-  virtual inline ~distance_xy() {}
+  virtual ~distance_xy() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void calc_force_invgrads();
@ -444,6 +418,7 @@ public:
 };


+
 /// \brief Colvar component: average distance between two groups of atoms, weighted as the sixth power,
 /// as in NMR refinements(colvarvalue::type_scalar type, range (0:*))
 class colvar::distance_inv
@ -455,7 +430,7 @@ protected:
 public:
  distance_inv(std::string const &conf);
  distance_inv();
-  virtual inline ~distance_inv() {}
+  virtual ~distance_inv() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -468,6 +443,7 @@ public:
 };


+
 /// \brief Colvar component: N1xN2 vector of pairwise distances
 /// (colvarvalue::type_vector type, range (0:*) for each component)
 class colvar::distance_pairs
@ -483,16 +459,10 @@ protected:
 public:
  distance_pairs(std::string const &conf);
  distance_pairs();
-  virtual inline ~distance_pairs() {}
+  virtual ~distance_pairs() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
-  virtual cvm::real dist2(colvarvalue const &x1,
-                          colvarvalue const &x2) const;
-  virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
-                                  colvarvalue const &x2) const;
-  virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
-                                  colvarvalue const &x2) const;
 };


@ -509,7 +479,7 @@ public:
  /// Constructor
  gyration(std::string const &conf);
  gyration();
-  virtual inline ~gyration() {}
+  virtual ~gyration() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void calc_force_invgrads();
@ -524,6 +494,7 @@ public:
 };


+
 /// \brief Colvar component: moment of inertia of an atom group
 /// (colvarvalue::type_scalar type, range [0:*))
 class colvar::inertia
@ -533,7 +504,7 @@ public:
  /// Constructor
  inertia(std::string const &conf);
  inertia();
-  virtual inline ~inertia() {}
+  virtual ~inertia() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -546,6 +517,7 @@ public:
 };


+
 /// \brief Colvar component: moment of inertia of an atom group
 /// around a user-defined axis (colvarvalue::type_scalar type, range [0:*))
 class colvar::inertia_z
@ -558,7 +530,7 @@ public:
  /// Constructor
  inertia_z(std::string const &conf);
  inertia_z();
-  virtual inline ~inertia_z() {}
+  virtual ~inertia_z() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -571,6 +543,7 @@ public:
 };


+
 /// \brief Colvar component: projection of 3N coordinates onto an
 /// eigenvector(colvarvalue::type_scalar type, range (-*:*))
 class colvar::eigenvector
@ -597,7 +570,7 @@ public:

  /// Constructor
  eigenvector(std::string const &conf);
-  virtual inline ~eigenvector() {}
+  virtual ~eigenvector() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void calc_force_invgrads();
@ -645,7 +618,7 @@ public:
  /// \brief Initialize the three groups after three atoms
  angle(cvm::atom const &a1, cvm::atom const &a2, cvm::atom const &a3);
  angle();
-  virtual inline ~angle() {}
+  virtual ~angle() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void calc_force_invgrads();
@ -659,6 +632,8 @@ public:
                                  colvarvalue const &x2) const;
 };

+
+
 /// \brief Colvar component: angle between the dipole of a molecule and an axis
 /// formed by two groups of atoms(colvarvalue::type_scalar type, range [0:PI])
 class colvar::dipole_angle
@ -691,7 +666,7 @@ public:
  /// \brief Initialize the three groups after three atoms
  dipole_angle (cvm::atom const &a1, cvm::atom const &a2, cvm::atom const &a3);
  dipole_angle();
-  virtual inline ~dipole_angle() {}
+  virtual ~dipole_angle() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force (colvarvalue const &force);
@ -703,6 +678,8 @@ public:
                                   colvarvalue const &x2) const;
 };

+
+
 /// \brief Colvar component: dihedral between the centers of mass of
 /// four groups (colvarvalue::type_scalar type, range [-PI:PI])
 class colvar::dihedral
@ -732,7 +709,7 @@ public:
  /// \brief Initialize the four groups after four atoms
  dihedral(cvm::atom const &a1, cvm::atom const &a2, cvm::atom const &a3, cvm::atom const &a4);
  dihedral();
-  virtual inline ~dihedral() {}
+  virtual ~dihedral() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void calc_force_invgrads();
@ -753,6 +730,7 @@ public:
 };


+
 /// \brief Colvar component: coordination number between two groups
 /// (colvarvalue::type_scalar type, range [0:N1*N2])
 class colvar::coordnum
@ -781,7 +759,7 @@ public:
  /// Constructor
  coordnum(std::string const &conf);
  coordnum();
-  virtual inline ~coordnum() {}
+  virtual ~coordnum() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -812,6 +790,8 @@ public:
                                  colvarvalue const &x2) const;
 };

+
+
 /// \brief Colvar component: self-coordination number within a group
 /// (colvarvalue::type_scalar type, range [0:N*(N-1)/2])
 class colvar::selfcoordnum
@ -830,7 +810,7 @@ public:
  /// Constructor
  selfcoordnum(std::string const &conf);
  selfcoordnum();
-  virtual inline ~selfcoordnum() {}
+  virtual ~selfcoordnum() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -852,6 +832,7 @@ public:
 };


+
 /// \brief Colvar component: coordination number between two groups
 /// (colvarvalue::type_scalar type, range [0:N1*N2])
 class colvar::groupcoordnum
@ -873,7 +854,7 @@ public:
  /// Constructor
  groupcoordnum(std::string const &conf);
  groupcoordnum();
-  virtual inline ~groupcoordnum() {}
+  virtual ~groupcoordnum() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -896,6 +877,7 @@ public:
  static cvm::real switching_function(cvm::rvector const &r0_vec,
                                      int const &exp_num, int const &exp_den,
                                      cvm::atom &A1, cvm::atom &A2);
+  */

  virtual cvm::real dist2(colvarvalue const &x1,
                          colvarvalue const &x2) const;
@ -903,10 +885,10 @@ public:
                                  colvarvalue const &x2) const;
  virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
                                  colvarvalue const &x2) const;
-  */
 };


+
 /// \brief Colvar component: hydrogen bond, defined as the product of
 /// a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol))
 /// (colvarvalue::type_scalar type, range [0:1])
@ -941,6 +923,7 @@ public:
 };


+
 /// \brief Colvar component: alpha helix content of a contiguous
 /// segment of 5 or more residues, implemented as a sum of phi/psi
 /// dihedral angles and hydrogen bonds (colvarvalue::type_scalar type,
@ -969,7 +952,7 @@ public:

 //   alpha_dihedrals (std::string const &conf);
 //   alpha_dihedrals();
-//   virtual inline ~alpha_dihedrals() {}
+//   virtual ~alpha_dihedrals() {}
 //   virtual void calc_value();
 //   virtual void calc_gradients();
 //   virtual void apply_force (colvarvalue const &force);
@ -982,6 +965,7 @@ public:
 // };


+
 /// \brief Colvar component: alpha helix content of a contiguous
 /// segment of 5 or more residues, implemented as a sum of Ca-Ca-Ca
 /// angles and hydrogen bonds (colvarvalue::type_scalar type, range
@ -1022,6 +1006,8 @@ public:
                                  colvarvalue const &x2) const;
 };

+
+
 /// \brief Colvar component: dihedPC
 /// Projection of the config onto a dihedral principal component
 /// See e.g. Altis et al., J. Chem. Phys 126, 244111 (2007)
@ -1050,6 +1036,8 @@ public:
                                  colvarvalue const &x2) const;
 };

+
+
 /// \brief Colvar component: orientation in space of an atom group,
 /// with respect to a set of reference coordinates
 /// (colvarvalue::type_quaternion type, range
@ -1078,7 +1066,7 @@ public:

  orientation(std::string const &conf);
  orientation();
-  virtual inline ~orientation() {}
+  virtual ~orientation() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -1091,6 +1079,7 @@ public:
 };


+
 /// \brief Colvar component: angle of rotation with respect to a set
 /// of reference coordinates (colvarvalue::type_scalar type, range
 /// [0:PI))
@ -1101,7 +1090,7 @@ public:

  orientation_angle(std::string const &conf);
  orientation_angle();
-  virtual inline ~orientation_angle() {}
+  virtual ~orientation_angle() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -1114,6 +1103,7 @@ public:
 };


+
 /// \brief Colvar component: cosine of the angle of rotation with respect to a set
 /// of reference coordinates (colvarvalue::type_scalar type, range
 /// [-1:1])
@ -1124,7 +1114,7 @@ public:

  orientation_proj(std::string const &conf);
  orientation_proj();
-  virtual inline ~orientation_proj() {}
+  virtual ~orientation_proj() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -1137,6 +1127,7 @@ public:
 };


+
 /// \brief Colvar component: projection of the orientation vector onto
 /// a predefined axis (colvarvalue::type_scalar type, range [-1:1])
 class colvar::tilt
@ -1150,7 +1141,7 @@ public:

  tilt(std::string const &conf);
  tilt();
-  virtual inline ~tilt() {}
+  virtual ~tilt() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -1177,7 +1168,7 @@ public:

  spin_angle(std::string const &conf);
  spin_angle();
-  virtual inline ~spin_angle() {}
+  virtual ~spin_angle() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -1215,7 +1206,7 @@ public:

  /// Constructor
  rmsd(std::string const &conf);
-  virtual inline ~rmsd() {}
+  virtual ~rmsd() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void calc_force_invgrads();
@ -1230,6 +1221,7 @@ public:
 };


+
 // \brief Colvar component: flat vector of Cartesian coordinates
 // Mostly useful to compute scripted colvar values
 class colvar::cartesian
@ -1243,7 +1235,7 @@ protected:
 public:
  cartesian(std::string const &conf);
  cartesian();
-  virtual inline ~cartesian() {}
+  virtual ~cartesian() {}
  virtual void calc_value();
  virtual void calc_gradients();
  virtual void apply_force(colvarvalue const &force);
@ -1260,255 +1252,26 @@ public:

 #define simple_scalar_dist_functions(TYPE)                              \
                                                                        \
-  inline cvm::real colvar::TYPE::dist2(colvarvalue const &x1,           \
-                                       colvarvalue const &x2) const     \
+                                                                        \
+  cvm::real colvar::TYPE::dist2(colvarvalue const &x1,                  \
+                                colvarvalue const &x2) const            \
  {                                                                     \
    return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
  }                                                                     \
                                                                        \
-  inline colvarvalue colvar::TYPE::dist2_lgrad(colvarvalue const &x1,   \
-                                               colvarvalue const &x2) const \
+                                                                        \
+  colvarvalue colvar::TYPE::dist2_lgrad(colvarvalue const &x1,          \
+                                        colvarvalue const &x2) const    \
  {                                                                     \
    return 2.0 * (x1.real_value - x2.real_value);                       \
  }                                                                     \
                                                                        \
-  inline colvarvalue colvar::TYPE::dist2_rgrad(colvarvalue const &x1,   \
-                                               colvarvalue const &x2) const \
+                                                                        \
+  colvarvalue colvar::TYPE::dist2_rgrad(colvarvalue const &x1,          \
+                                        colvarvalue const &x2) const    \
  {                                                                     \
    return this->dist2_lgrad(x2, x1);                                   \
  }                                                                     \
                                                                        \

-simple_scalar_dist_functions(distance)
-// NOTE: distance_z has explicit functions, see below
-simple_scalar_dist_functions(distance_xy)
-simple_scalar_dist_functions(distance_inv)
-simple_scalar_dist_functions(angle)
-simple_scalar_dist_functions(dipole_angle)
-simple_scalar_dist_functions(coordnum)
-simple_scalar_dist_functions(selfcoordnum)
-simple_scalar_dist_functions(h_bond)
-simple_scalar_dist_functions(gyration)
-simple_scalar_dist_functions(inertia)
-simple_scalar_dist_functions(inertia_z)
-simple_scalar_dist_functions(rmsd)
-simple_scalar_dist_functions(orientation_angle)
-simple_scalar_dist_functions(orientation_proj)
-simple_scalar_dist_functions(tilt)
-simple_scalar_dist_functions(eigenvector)
-//  simple_scalar_dist_functions (alpha_dihedrals)
-simple_scalar_dist_functions(alpha_angles)
-simple_scalar_dist_functions(dihedPC)
-
-
-// metrics functions for cvc implementations with a periodicity
-
-inline cvm::real colvar::dihedral::dist2(colvarvalue const &x1,
-                                           colvarvalue const &x2) const
-{
-cvm::real diff = x1.real_value - x2.real_value;
-diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
-return diff * diff;
-}
-
-inline colvarvalue colvar::dihedral::dist2_lgrad(colvarvalue const &x1,
-                                                   colvarvalue const &x2) const
-{
-cvm::real diff = x1.real_value - x2.real_value;
-diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
-return 2.0 * diff;
-}
-
-inline colvarvalue colvar::dihedral::dist2_rgrad(colvarvalue const &x1,
-                                                   colvarvalue const &x2) const
-{
-cvm::real diff = x1.real_value - x2.real_value;
-diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
-return (-2.0) * diff;
-}
-
-inline void colvar::dihedral::wrap(colvarvalue &x) const
-{
-if ((x.real_value - wrap_center) >= 180.0) {
-x.real_value -= 360.0;
-return;
-}
-
-if ((x.real_value - wrap_center) < -180.0) {
-x.real_value += 360.0;
-return;
-}
-
-return;
-}
-
-inline cvm::real colvar::spin_angle::dist2(colvarvalue const &x1,
-                                             colvarvalue const &x2) const
-{
-cvm::real diff = x1.real_value - x2.real_value;
-diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
-return diff * diff;
-}
-
-inline colvarvalue colvar::spin_angle::dist2_lgrad(colvarvalue const &x1,
-                                                     colvarvalue const &x2) const
-{
-cvm::real diff = x1.real_value - x2.real_value;
-diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
-return 2.0 * diff;
-}
-
-inline colvarvalue colvar::spin_angle::dist2_rgrad(colvarvalue const &x1,
-                                                     colvarvalue const &x2) const
-{
-cvm::real diff = x1.real_value - x2.real_value;
-diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
-return (-2.0) * diff;
-}
-
-inline void colvar::spin_angle::wrap(colvarvalue &x) const
-{
-if ((x.real_value - wrap_center) >= 180.0) {
-x.real_value -= 360.0;
-return;
-}
-
-if ((x.real_value - wrap_center) < -180.0) {
-x.real_value += 360.0;
-return;
-}
-
-return;
-}
-
-
-// Projected distance
-// Differences should always be wrapped around 0 (ignoring wrap_center)
-inline cvm::real colvar::distance_z::dist2(colvarvalue const &x1,
-                                             colvarvalue const &x2) const
-{
-  cvm::real diff = x1.real_value - x2.real_value;
-  if (period != 0.0) {
-    cvm::real shift = std::floor(diff/period + 0.5);
-    diff -= shift * period;
-  }
-  return diff * diff;
-}
-
-inline colvarvalue colvar::distance_z::dist2_lgrad(colvarvalue const &x1,
-                                                   colvarvalue const &x2) const
-{
-  cvm::real diff = x1.real_value - x2.real_value;
-  if (period != 0.0) {
-    cvm::real shift = std::floor(diff/period + 0.5);
-    diff -= shift * period;
-  }
-  return 2.0 * diff;
-}
-
-inline colvarvalue colvar::distance_z::dist2_rgrad(colvarvalue const &x1,
-                                                   colvarvalue const &x2) const
-{
-  cvm::real diff = x1.real_value - x2.real_value;
-  if (period != 0.0) {
-    cvm::real shift = std::floor(diff/period + 0.5);
-    diff -= shift * period;
-  }
-  return (-2.0) * diff;
-}
-
-inline void colvar::distance_z::wrap(colvarvalue &x) const
-{
-  if (! this->b_periodic) {
-    // don't wrap if the period has not been set
-    return;
-  }
-
-  cvm::real shift = std::floor((x.real_value - wrap_center) / period + 0.5);
-  x.real_value -= shift * period;
-  return;
-}
-
-
-// distance between three dimensional vectors
-//
-// TODO apply PBC to distance_vec
-// Note: differences should be centered around (0, 0, 0)!
-
-inline cvm::real colvar::distance_vec::dist2(colvarvalue const &x1,
-                                             colvarvalue const &x2) const
-{
-  return cvm::position_dist2(x1.rvector_value, x2.rvector_value);
-}
-
-inline colvarvalue colvar::distance_vec::dist2_lgrad(colvarvalue const &x1,
-                                                     colvarvalue const &x2) const
-{
-  return 2.0 * cvm::position_distance(x2.rvector_value, x1.rvector_value);
-}
-
-inline colvarvalue colvar::distance_vec::dist2_rgrad(colvarvalue const &x1,
-                                                     colvarvalue const &x2) const
-{
-  return 2.0 * cvm::position_distance(x2.rvector_value, x1.rvector_value);
-}
-
-inline cvm::real colvar::distance_dir::dist2(colvarvalue const &x1,
-                                             colvarvalue const &x2) const
-{
-  return (x1.rvector_value - x2.rvector_value).norm2();
-}
-
-inline colvarvalue colvar::distance_dir::dist2_lgrad(colvarvalue const &x1,
-                                                     colvarvalue const &x2) const
-{
-  return colvarvalue((x1.rvector_value - x2.rvector_value), colvarvalue::type_unit3vector);
-}
-
-inline colvarvalue colvar::distance_dir::dist2_rgrad(colvarvalue const &x1,
-                                                     colvarvalue const &x2) const
-{
-  return colvarvalue((x2.rvector_value - x1.rvector_value), colvarvalue::type_unit3vector);
-}
-
-inline cvm::real colvar::distance_pairs::dist2(colvarvalue const &x1,
-                                               colvarvalue const &x2) const
-{
-  return (x1.vector1d_value - x2.vector1d_value).norm2();
-}
-
-inline colvarvalue colvar::distance_pairs::dist2_lgrad(colvarvalue const &x1,
-                                                       colvarvalue const &x2) const
-{
-  return colvarvalue((x1.vector1d_value - x2.vector1d_value), colvarvalue::type_vector);
-}
-
-inline colvarvalue colvar::distance_pairs::dist2_rgrad(colvarvalue const &x1,
-                                                       colvarvalue const &x2) const
-{
-  return colvarvalue((x2.vector1d_value - x1.vector1d_value), colvarvalue::type_vector);
-}
-
-
-// distance between quaternions
-
-inline cvm::real colvar::orientation::dist2(colvarvalue const &x1,
-                                            colvarvalue const &x2) const
-{
-  return x1.quaternion_value.dist2(x2);
-}
-
-inline colvarvalue colvar::orientation::dist2_lgrad(colvarvalue const &x1,
-                                                    colvarvalue const &x2) const
-{
-  return x1.quaternion_value.dist2_grad(x2);
-}
-
-inline colvarvalue colvar::orientation::dist2_rgrad(colvarvalue const &x1,
-                                                    colvarvalue const &x2) const
-{
-  return x2.quaternion_value.dist2_grad(x1);
-}
-
-
 #endif
--- a/lib/colvars/colvarcomp_angles.cpp
+++ b/lib/colvars/colvarcomp_angles.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include "colvarmodule.h"
 #include "colvar.h"
 #include "colvarcomp.h"
@ -7,6 +14,7 @@
 #include <cmath>


+
 colvar::angle::angle(std::string const &conf)
  : cvc(conf)
 {
@ -85,6 +93,7 @@ void colvar::angle::calc_gradients()
  group3->set_weighted_gradient(dxdr3);
 }

+
 void colvar::angle::calc_force_invgrads()
 {
  // This uses a force measurement on groups 1 and 3 only
@ -107,6 +116,7 @@ void colvar::angle::calc_force_invgrads()
  return;
 }

+
 void colvar::angle::calc_Jacobian_derivative()
 {
  // det(J) = (2 pi) r^2 * sin(theta)
@ -129,6 +139,8 @@ void colvar::angle::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(angle)
+


 colvar::dipole_angle::dipole_angle(std::string const &conf)
@ -235,6 +247,8 @@ void colvar::dipole_angle::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(dipole_angle)
+


 colvar::dihedral::dihedral(std::string const &conf)
@ -453,3 +467,46 @@ void colvar::dihedral::apply_force(colvarvalue const &force)
 }


+// metrics functions for cvc implementations with a periodicity
+
+cvm::real colvar::dihedral::dist2(colvarvalue const &x1,
+                                  colvarvalue const &x2) const
+{
+  cvm::real diff = x1.real_value - x2.real_value;
+  diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
+  return diff * diff;
+}
+
+
+colvarvalue colvar::dihedral::dist2_lgrad(colvarvalue const &x1,
+                                          colvarvalue const &x2) const
+{
+  cvm::real diff = x1.real_value - x2.real_value;
+  diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
+  return 2.0 * diff;
+}
+
+
+colvarvalue colvar::dihedral::dist2_rgrad(colvarvalue const &x1,
+                                          colvarvalue const &x2) const
+{
+  cvm::real diff = x1.real_value - x2.real_value;
+  diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
+  return (-2.0) * diff;
+}
+
+
+void colvar::dihedral::wrap(colvarvalue &x) const
+{
+  if ((x.real_value - wrap_center) >= 180.0) {
+    x.real_value -= 360.0;
+    return;
+  }
+
+  if ((x.real_value - wrap_center) < -180.0) {
+    x.real_value += 360.0;
+    return;
+  }
+
+  return;
+}
--- a/lib/colvars/colvarcomp_coordnums.cpp
+++ b/lib/colvars/colvarcomp_coordnums.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include <cmath>

 #include "colvarmodule.h"
@ -13,10 +20,10 @@

 template<bool calculate_gradients>
 cvm::real colvar::coordnum::switching_function(cvm::real const &r0,
-                                                int const &en,
-                                                int const &ed,
-                                                cvm::atom &A1,
-                                                cvm::atom &A2)
+                                               int const &en,
+                                               int const &ed,
+                                               cvm::atom &A1,
+                                               cvm::atom &A2)
 {
  cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
  cvm::real const l2 = diff.norm2()/(r0*r0);
@ -42,10 +49,10 @@ cvm::real colvar::coordnum::switching_function(cvm::real const &r0,

 template<bool calculate_gradients>
 cvm::real colvar::coordnum::switching_function(cvm::rvector const &r0_vec,
-                                                int const &en,
-                                                int const &ed,
-                                                cvm::atom &A1,
-                                                cvm::atom &A2)
+                                               int const &en,
+                                               int const &ed,
+                                               cvm::atom &A1,
+                                               cvm::atom &A2)
 {
  cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
  cvm::rvector const scal_diff(diff.x/r0_vec.x, diff.y/r0_vec.y, diff.z/r0_vec.z);
@ -190,6 +197,7 @@ void colvar::coordnum::calc_gradients()
  }
 }

+
 void colvar::coordnum::apply_force(colvarvalue const &force)
 {
  if (!group1->noforce)
@ -200,6 +208,9 @@ void colvar::coordnum::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(coordnum)
+
+

 // h_bond member functions

@ -252,6 +263,7 @@ colvar::h_bond::h_bond(cvm::atom const &acceptor,
  atom_groups[0]->add_atom(donor);
 }

+
 colvar::h_bond::h_bond()
  : cvc()
 {
@ -284,6 +296,8 @@ void colvar::h_bond::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(h_bond)
+


 colvar::selfcoordnum::selfcoordnum(std::string const &conf)
@ -339,6 +353,9 @@ void colvar::selfcoordnum::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(selfcoordnum)
+
+
 // groupcoordnum member functions
 colvar::groupcoordnum::groupcoordnum(std::string const &conf)
  : distance(conf), b_anisotropic(false)
@ -448,7 +465,6 @@ cvm::real colvar::groupcoordnum::switching_function(cvm::rvector const &r0_vec,
 #endif


-
 void colvar::groupcoordnum::calc_value()
 {

@ -460,7 +476,6 @@ void colvar::groupcoordnum::calc_value()

  x.real_value = coordnum::switching_function<false>(r0, en, ed,
                                                     group1_com_atom, group2_com_atom);
-
 }


@ -486,3 +501,6 @@ void colvar::groupcoordnum::apply_force(colvarvalue const &force)
  if (!group2->noforce)
    group2->apply_colvar_force(force.real_value);
 }
+
+
+simple_scalar_dist_functions(groupcoordnum)
--- a/lib/colvars/colvarcomp_distances.cpp
+++ b/lib/colvars/colvarcomp_distances.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include <cmath>

 #include "colvarmodule.h"
@ -91,6 +98,9 @@ void colvar::distance::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(distance)
+
+

 colvar::distance_vec::distance_vec(std::string const &conf)
  : distance(conf)
@ -138,6 +148,27 @@ void colvar::distance_vec::apply_force(colvarvalue const &force)
 }


+cvm::real colvar::distance_vec::dist2(colvarvalue const &x1,
+                                      colvarvalue const &x2) const
+{
+  return cvm::position_dist2(x1.rvector_value, x2.rvector_value);
+}
+
+
+colvarvalue colvar::distance_vec::dist2_lgrad(colvarvalue const &x1,
+                                              colvarvalue const &x2) const
+{
+  return 2.0 * cvm::position_distance(x2.rvector_value, x1.rvector_value);
+}
+
+
+colvarvalue colvar::distance_vec::dist2_rgrad(colvarvalue const &x1,
+                                              colvarvalue const &x2) const
+{
+  return 2.0 * cvm::position_distance(x2.rvector_value, x1.rvector_value);
+}
+
+

 colvar::distance_z::distance_z(std::string const &conf)
  : cvc(conf)
@ -191,6 +222,7 @@ colvar::distance_z::distance_z(std::string const &conf)

 }

+
 colvar::distance_z::distance_z()
 {
  function_type = "distance_z";
@ -200,6 +232,7 @@ colvar::distance_z::distance_z()
  x.type(colvarvalue::type_scalar);
 }

+
 void colvar::distance_z::calc_value()
 {
  if (fixed_axis) {
@ -227,6 +260,7 @@ void colvar::distance_z::calc_value()
  this->wrap(x);
 }

+
 void colvar::distance_z::calc_gradients()
 {
  main->set_weighted_gradient( axis );
@ -248,6 +282,7 @@ void colvar::distance_z::calc_gradients()
  }
 }

+
 void colvar::distance_z::calc_force_invgrads()
 {
  main->read_total_forces();
@ -260,11 +295,13 @@ void colvar::distance_z::calc_force_invgrads()
  }
 }

+
 void colvar::distance_z::calc_Jacobian_derivative()
 {
  jd.real_value = 0.0;
 }

+
 void colvar::distance_z::apply_force(colvarvalue const &force)
 {
  if (!ref1->noforce)
@ -278,6 +315,56 @@ void colvar::distance_z::apply_force(colvarvalue const &force)
 }


+// Differences should always be wrapped around 0 (ignoring wrap_center)
+cvm::real colvar::distance_z::dist2(colvarvalue const &x1,
+                                    colvarvalue const &x2) const
+{
+  cvm::real diff = x1.real_value - x2.real_value;
+  if (b_periodic) {
+    cvm::real shift = std::floor(diff/period + 0.5);
+    diff -= shift * period;
+  }
+  return diff * diff;
+}
+
+
+colvarvalue colvar::distance_z::dist2_lgrad(colvarvalue const &x1,
+                                            colvarvalue const &x2) const
+{
+  cvm::real diff = x1.real_value - x2.real_value;
+  if (b_periodic) {
+    cvm::real shift = std::floor(diff/period + 0.5);
+    diff -= shift * period;
+  }
+  return 2.0 * diff;
+}
+
+
+colvarvalue colvar::distance_z::dist2_rgrad(colvarvalue const &x1,
+                                            colvarvalue const &x2) const
+{
+  cvm::real diff = x1.real_value - x2.real_value;
+  if (b_periodic) {
+    cvm::real shift = std::floor(diff/period + 0.5);
+    diff -= shift * period;
+  }
+  return (-2.0) * diff;
+}
+
+
+void colvar::distance_z::wrap(colvarvalue &x) const
+{
+  if (!b_periodic) {
+    // don't wrap if the period has not been set
+    return;
+  }
+
+  cvm::real shift = std::floor((x.real_value - wrap_center) / period + 0.5);
+  x.real_value -= shift * period;
+  return;
+}
+
+

 colvar::distance_xy::distance_xy(std::string const &conf)
  : distance_z(conf)
@ -289,6 +376,7 @@ colvar::distance_xy::distance_xy(std::string const &conf)
  x.type(colvarvalue::type_scalar);
 }

+
 colvar::distance_xy::distance_xy()
  : distance_z()
 {
@ -299,6 +387,7 @@ colvar::distance_xy::distance_xy()
  x.type(colvarvalue::type_scalar);
 }

+
 void colvar::distance_xy::calc_value()
 {
  if (b_no_PBC) {
@ -321,6 +410,7 @@ void colvar::distance_xy::calc_value()
  x.real_value = dist_v_ortho.norm();
 }

+
 void colvar::distance_xy::calc_gradients()
 {
  // Intermediate quantity (r_P3 / r_12 where P is the projection
@ -348,6 +438,7 @@ void colvar::distance_xy::calc_gradients()
  }
 }

+
 void colvar::distance_xy::calc_force_invgrads()
 {
  main->read_total_forces();
@ -360,11 +451,13 @@ void colvar::distance_xy::calc_force_invgrads()
  }
 }

+
 void colvar::distance_xy::calc_Jacobian_derivative()
 {
  jd.real_value = x.real_value ? (1.0 / x.real_value) : 0.0;
 }

+
 void colvar::distance_xy::apply_force(colvarvalue const &force)
 {
  if (!ref1->noforce)
@ -378,6 +471,9 @@ void colvar::distance_xy::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(distance_xy)
+
+

 colvar::distance_dir::distance_dir(std::string const &conf)
  : distance(conf)
@ -403,7 +499,7 @@ void colvar::distance_dir::calc_value()
    dist_v = group2->center_of_mass() - group1->center_of_mass();
  } else {
    dist_v = cvm::position_distance(group1->center_of_mass(),
-                                     group2->center_of_mass());
+                                    group2->center_of_mass());
  }
  x.rvector_value = dist_v.unit();
 }
@ -460,6 +556,7 @@ colvar::distance_inv::distance_inv(std::string const &conf)
  x.type(colvarvalue::type_scalar);
 }

+
 colvar::distance_inv::distance_inv()
 {
  function_type = "distance_inv";
@ -467,6 +564,7 @@ colvar::distance_inv::distance_inv()
  x.type(colvarvalue::type_scalar);
 }

+
 void colvar::distance_inv::calc_value()
 {
  x.real_value = 0.0;
@ -504,6 +602,7 @@ void colvar::distance_inv::calc_value()
  x.real_value = std::pow(x.real_value, -1.0/(cvm::real(exponent)));
 }

+
 void colvar::distance_inv::calc_gradients()
 {
  cvm::real const dxdsum = (-1.0/(cvm::real(exponent))) * std::pow(x.real_value, exponent+1) / cvm::real(group1->size() * group2->size());
@ -515,6 +614,7 @@ void colvar::distance_inv::calc_gradients()
  }
 }

+
 void colvar::distance_inv::apply_force(colvarvalue const &force)
 {
  if (!group1->noforce)
@ -525,6 +625,9 @@ void colvar::distance_inv::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(distance_inv)
+
+

 colvar::distance_pairs::distance_pairs(std::string const &conf)
  : cvc(conf)
@ -579,11 +682,13 @@ void colvar::distance_pairs::calc_value()
  }
 }

+
 void colvar::distance_pairs::calc_gradients()
 {
  // will be calculated on the fly in apply_force()
 }

+
 void colvar::distance_pairs::apply_force(colvarvalue const &force)
 {
  if (b_no_PBC) {
@ -608,6 +713,7 @@ void colvar::distance_pairs::apply_force(colvarvalue const &force)
 }


+
 colvar::gyration::gyration(std::string const &conf)
  : cvc(conf)
 {
@ -621,6 +727,7 @@ colvar::gyration::gyration(std::string const &conf)
  } else {
    atoms->b_center = true;
    atoms->ref_pos.assign(1, cvm::atom_pos(0.0, 0.0, 0.0));
+    atoms->fit_gradients.assign(atoms->size(), cvm::rvector(0.0, 0.0, 0.0));
  }

  x.type(colvarvalue::type_scalar);
@ -681,6 +788,9 @@ void colvar::gyration::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(gyration)
+
+

 colvar::inertia::inertia(std::string const &conf)
  : gyration(conf)
@ -721,6 +831,10 @@ void colvar::inertia::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(inertia_z)
+
+
+
 colvar::inertia_z::inertia_z(std::string const &conf)
  : inertia(conf)
 {
@ -771,6 +885,10 @@ void colvar::inertia_z::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(inertia)
+
+
+

 colvar::rmsd::rmsd(std::string const &conf)
  : cvc(conf)
@ -970,6 +1088,8 @@ void colvar::rmsd::calc_Jacobian_derivative()
 }


+simple_scalar_dist_functions(rmsd)
+


 colvar::eigenvector::eigenvector(std::string const &conf)
@ -1254,6 +1374,10 @@ void colvar::eigenvector::calc_Jacobian_derivative()
 }


+simple_scalar_dist_functions(eigenvector)
+
+
+
 colvar::cartesian::cartesian(std::string const &conf)
  : cvc(conf)
 {
--- a/lib/colvars/colvarcomp_protein.cpp
+++ b/lib/colvars/colvarcomp_protein.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include <cmath>

 #include "colvarmodule.h"
@ -119,6 +126,7 @@ colvar::alpha_angles::alpha_angles()
  x.type(colvarvalue::type_scalar);
 }

+
 colvar::alpha_angles::~alpha_angles()
 {
  while (theta.size() != 0) {
@ -131,6 +139,7 @@ colvar::alpha_angles::~alpha_angles()
  }
 }

+
 void colvar::alpha_angles::calc_value()
 {
  x.real_value = 0.0;
@ -222,6 +231,10 @@ void colvar::alpha_angles::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(alpha_angles)
+
+
+
 //////////////////////////////////////////////////////////////////////
 // dihedral principal component
 //////////////////////////////////////////////////////////////////////
@ -337,14 +350,22 @@ colvar::dihedPC::dihedPC(std::string const &conf)
  for (size_t i = 0; i < residues.size()-1; i++) {
    // Psi
    theta.push_back(new colvar::dihedral(cvm::atom(r[i  ], "N", sid),
-                                           cvm::atom(r[i  ], "CA", sid),
-                                           cvm::atom(r[i  ], "C", sid),
-                                           cvm::atom(r[i+1], "N", sid)));
+                                         cvm::atom(r[i  ], "CA", sid),
+                                         cvm::atom(r[i  ], "C", sid),
+                                         cvm::atom(r[i+1], "N", sid)));
+    atom_groups.push_back(theta.back()->atom_groups[0]);
+    atom_groups.push_back(theta.back()->atom_groups[1]);
+    atom_groups.push_back(theta.back()->atom_groups[2]);
+    atom_groups.push_back(theta.back()->atom_groups[3]);
    // Phi (next res)
    theta.push_back(new colvar::dihedral(cvm::atom(r[i  ], "C", sid),
-                                           cvm::atom(r[i+1], "N", sid),
-                                           cvm::atom(r[i+1], "CA", sid),
-                                           cvm::atom(r[i+1], "C", sid)));
+                                         cvm::atom(r[i+1], "N", sid),
+                                         cvm::atom(r[i+1], "CA", sid),
+                                         cvm::atom(r[i+1], "C", sid)));
+    atom_groups.push_back(theta.back()->atom_groups[0]);
+    atom_groups.push_back(theta.back()->atom_groups[1]);
+    atom_groups.push_back(theta.back()->atom_groups[2]);
+    atom_groups.push_back(theta.back()->atom_groups[3]);
  }

  if (cvm::debug())
@ -400,3 +421,6 @@ void colvar::dihedPC::apply_force(colvarvalue const &force)
                           coeffs[2*i+1] * dsindt) * force);
  }
 }
+
+
+simple_scalar_dist_functions(dihedPC)
--- a/lib/colvars/colvarcomp_rotations.cpp
+++ b/lib/colvars/colvarcomp_rotations.cpp
@ -1,5 +1,12 @@
 // -*- 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.
+
 #include <cmath>

 #include "colvarmodule.h"
@ -123,6 +130,27 @@ void colvar::orientation::apply_force(colvarvalue const &force)
 }


+cvm::real colvar::orientation::dist2(colvarvalue const &x1,
+                                     colvarvalue const &x2) const
+{
+  return x1.quaternion_value.dist2(x2);
+}
+
+
+colvarvalue colvar::orientation::dist2_lgrad(colvarvalue const &x1,
+                                             colvarvalue const &x2) const
+{
+  return x1.quaternion_value.dist2_grad(x2);
+}
+
+
+colvarvalue colvar::orientation::dist2_rgrad(colvarvalue const &x1,
+                                             colvarvalue const &x2) const
+{
+  return x2.quaternion_value.dist2_grad(x1);
+}
+
+

 colvar::orientation_angle::orientation_angle(std::string const &conf)
  : orientation(conf)
@ -176,6 +204,9 @@ void colvar::orientation_angle::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(orientation_angle)
+
+

 colvar::orientation_proj::orientation_proj(std::string const &conf)
  : orientation(conf)
@ -220,6 +251,9 @@ void colvar::orientation_proj::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(orientation_proj)
+
+

 colvar::tilt::tilt(std::string const &conf)
  : orientation(conf)
@ -278,6 +312,9 @@ void colvar::tilt::apply_force(colvarvalue const &force)
 }


+simple_scalar_dist_functions(tilt)
+
+

 colvar::spin_angle::spin_angle(std::string const &conf)
  : orientation(conf)
@ -339,3 +376,46 @@ void colvar::spin_angle::apply_force(colvarvalue const &force)
    atoms->apply_colvar_force(fw);
  }
 }
+
+
+cvm::real colvar::spin_angle::dist2(colvarvalue const &x1,
+                                    colvarvalue const &x2) const
+{
+  cvm::real diff = x1.real_value - x2.real_value;
+  diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
+  return diff * diff;
+}
+
+
+colvarvalue colvar::spin_angle::dist2_lgrad(colvarvalue const &x1,
+                                            colvarvalue const &x2) const
+{
+  cvm::real diff = x1.real_value - x2.real_value;
+  diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
+  return 2.0 * diff;
+}
+
+
+colvarvalue colvar::spin_angle::dist2_rgrad(colvarvalue const &x1,
+                                            colvarvalue const &x2) const
+{
+  cvm::real diff = x1.real_value - x2.real_value;
+  diff = (diff < -180.0 ? diff + 360.0 : (diff > 180.0 ? diff - 360.0 : diff));
+  return (-2.0) * diff;
+}
+
+
+void colvar::spin_angle::wrap(colvarvalue &x) const
+{
+  if ((x.real_value - wrap_center) >= 180.0) {
+    x.real_value -= 360.0;
+    return;
+  }
+
+  if ((x.real_value - wrap_center) < -180.0) {
+    x.real_value += 360.0;
+    return;
+  }
+
+  return;
+}
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@ -1,3 +1,13 @@
+// -*- 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.
+
+
 #include "colvardeps.h"


@ -219,6 +229,9 @@ void colvardeps::init_cvb_requires() {

  f_description(f_cvb_history_dependent, "history-dependent");

+  f_description(f_cvb_scalar_variables, "require scalar variables");
+  f_req_children(f_cvb_scalar_variables, f_cv_scalar);
+
  // Initialize feature_states for each instance
  feature_states.reserve(f_cvb_ntot);
  for (i = 0; i < f_cvb_ntot; i++) {
@ -229,6 +242,9 @@ void colvardeps::init_cvb_requires() {

  // some biases are not history-dependent
  feature_states[f_cvb_history_dependent]->available = false;
+
+  // by default, biases should work with vector variables, too
+  feature_states[f_cvb_scalar_variables]->available = false;
 }


@ -321,6 +337,7 @@ void colvardeps::init_cv_requires() {
    // The features below are set programmatically
    f_description(f_cv_scripted, "scripted");
    f_description(f_cv_periodic, "periodic");
+    f_req_self(f_cv_periodic, f_cv_homogeneous);
    f_description(f_cv_scalar, "scalar");
    f_description(f_cv_linear, "linear");
    f_description(f_cv_homogeneous, "homogeneous");
@ -407,6 +424,11 @@ void colvardeps::init_cvc_requires() {
  // Each cvc specifies what other features are available
  feature_states[f_cvc_active]->available = true;
  feature_states[f_cvc_gradient]->available = true;
+
+  // Features that are implemented by default if their requirements are
+  feature_states[f_cvc_one_site_total_force]->available = true;
+
+  // Features That are implemented only for certain simulation engine configurations
  feature_states[f_cvc_scalable_com]->available = (cvm::proxy->scalable_group_coms() == COLVARS_OK);
  feature_states[f_cvc_scalable]->available = feature_states[f_cvc_scalable_com]->available;
 }
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@ -1,5 +1,12 @@
 // -*- 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 COLVARDEPS_H
 #define COLVARDEPS_H

@ -157,6 +164,7 @@ public:
    f_cvb_apply_force, // will apply forces
    f_cvb_get_total_force, // requires total forces
    f_cvb_history_dependent, // depends on simulation history
+    f_cvb_scalar_variables, // requires scalar colvars
    f_cvb_ntot
  };

--- a/Show More
+++ b/Show More
				`@ -0,0 +1 @@`
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