patch 6Jan17

enable pppm/tip4p to work with triclinic
Merge pull request #324 from ibaned/pair-table-kokkos-inherit
2017-01-06 11:14:48 -07:00 · 2017-01-06 10:38:32 -07:00 · 2017-01-06 10:10:59 -07:00 · 2017-01-06 10:10:09 -07:00 · 2017-01-06 10:03:32 -07:00 · 2017-01-06 10:03:05 -07:00
547 changed files with 30252 additions and 19975 deletions
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--- 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="30 Nov 2016 version">
+<META NAME="docnumber" CONTENT="6 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
-30 Nov 2016 version :c,h4
+6 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
@ -581,7 +581,7 @@ 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,
 "msst"_fix_msst.html,
 "neb"_fix_neb.html,
@ -702,6 +702,7 @@ 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,
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -1936,18 +1936,22 @@ documentation in the src/library.cpp file for details, including
 which quantities can be queried by name:

 void *lammps_extract_global(void *, char *)
+void lammps_extract_box(void *, double *, double *, 
+                        double *, double *, double *, int *, int *)
 void *lammps_extract_atom(void *, char *)
 void *lammps_extract_compute(void *, char *, int, int)
 void *lammps_extract_fix(void *, char *, int, int, int, int)
 void *lammps_extract_variable(void *, char *, char *) :pre

-int lammps_set_variable(void *, char *, char *)
-double lammps_get_thermo(void *, char *) :pre
+void lammps_reset_box(void *, double *, double *, double, double, double)
+int lammps_set_variable(void *, char *, char *) :pre

+double lammps_get_thermo(void *, char *)
 int lammps_get_natoms(void *)
 void lammps_gather_atoms(void *, double *)
 void lammps_scatter_atoms(void *, double *) :pre
-void lammps_create_atoms(void *, int, tagint *, int *, double *, double *) :pre
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
+                         imageint *, int) :pre

 The extract functions return a pointer to various global or per-atom
 quantities stored in LAMMPS or to values calculated by a compute, fix,
@ -1957,10 +1961,16 @@ the other extract functions, the underlying storage may be reallocated
 as LAMMPS runs, so you need to re-call the function to assure a
 current pointer or returned value(s).

+The lammps_reset_box() function resets the size and shape of the
+simulation box, e.g. as part of restoring a previously extracted and
+saved state of a simulation.
+
 The lammps_set_variable() function can set an existing string-style
 variable to a new string value, so that subsequent LAMMPS commands can
-access the variable.  The lammps_get_thermo() function returns the
-current value of a thermo keyword as a double.
+access the variable.
+
+The lammps_get_thermo() function returns the current value of a thermo
+keyword as a double precision value.

 The lammps_get_natoms() function returns the total number of atoms in
 the system and can be used by the caller to allocate space for the
@ -1973,10 +1983,13 @@ passed by the caller, to each atom owned by individual processors.

 The lammps_create_atoms() function takes a list of N atoms as input
 with atom types and coords (required), an optionally atom IDs and
-velocities.  It uses the coords of each atom to assign it as a new
-atom to the processor that owns it.  Additional properties for the new
-atoms can be assigned via the lammps_scatter_atoms() or
-lammps_extract_atom() functions.
+velocities and image flags.  It uses the coords of each atom to assign
+it as a new atom to the processor that owns it.  This function is
+useful to add atoms to a simulation or (in tandem with
+lammps_reset_box()) to restore a previously extracted and saved state
+of a simulation.  Additional properties for the new atoms can then be
+assigned via the lammps_scatter_atoms() or lammps_extract_atom()
+functions.

 The examples/COUPLE and python directories have example C++ and C and
 Python codes which show how a driver code can link to LAMMPS as a
--- a/doc/src/compute_bond_local.txt
+++ b/doc/src/compute_bond_local.txt
@ -51,12 +51,12 @@ relative to the center of mass (COM) velocity of the 2 atoms in the
 bond.

 The value {engvib} is the vibrational kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and
+in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
 v2 are the magnitude of the velocity of the 2 atoms along the bond
 direction, after the COM velocity has been subtracted from each.

 The value {engrot} is the rotationsl kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and
+in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
 v2 are the magnitude of the velocity of the 2 atoms perpendicular to
 the bond direction, after the COM velocity has been subtracted from
 each.
@ -67,7 +67,7 @@ Vcm^2 where Vcm = magnitude of the velocity of the COM.

 Note that these 3 kinetic energy terms are simply a partitioning of
 the summed kinetic energy of the 2 atoms themselves.  I.e. total KE =
-1/2 m1 v1^2 + 1/2 m2 v3^2 = engvib + engrot + engtrans, where v1,v2
+1/2 m1 v1^2 + 1/2 m2 v2^2 = engvib + engrot + engtrans, where v1,v2
 are the magnitude of the velocities of the 2 atoms, without any
 adjustment for the COM velocity.

--- 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_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@ -21,7 +21,7 @@ type = atom type for inserted atoms (must be 0 if mol keyword used) :l
 seed = random # seed (positive integer) :l
 T = temperature of the ideal gas reservoir (temperature units) :l
 mu = chemical potential of the ideal gas reservoir (energy units) :l
-translate = maximum Monte Carlo translation distance (length units) :l
+displace = maximum Monte Carlo translation distance (length units) :l
 zero or more keyword/value pairs may be appended to args :l
 keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, {charge}, {group}, {grouptype}, {intra_energy}, or {tfac_insert}
  {mol} value = template-ID
--- 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_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/fixes.txt
+++ b/doc/src/fixes.txt
@ -90,6 +90,7 @@ 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
@ -214,6 +214,7 @@ 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_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/python.txt
+++ b/doc/src/python.txt
@ -14,7 +14,7 @@ python func keyword args ... :pre

 func = name of Python function :ulb,l
 one or more keyword/args pairs must be appended :l
-keyword = {invoke} or {input} or {return} or {format} or {file} or {here} or {exists}
+keyword = {invoke} or {input} or {return} or {format} or {length} or {file} or {here} or {exists}
  {invoke} arg = none = invoke the previously defined Python function
  {input} args = N i1 i2 ... iN
    N = # of inputs to function
@ -29,6 +29,8 @@ keyword = {invoke} or {input} or {return} or {format} or {file} or {here} or {ex
    M = N+1 if there is a return value
    fstring = each character (i,f,s,p) corresponds in order to an input or return value
    'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
+  {length} arg = Nlen
+    Nlen = max length of string returned from Python function
  {file} arg = filename
    filename = file of Python code, which defines func
  {here} arg = inline
@ -165,6 +167,17 @@ equal-style variable as an argument, but only if the output of the
 Python function is flagged as a numeric value ("i" or "f") via the
 {format} keyword.

+If the {return} keyword is used and the {format} keyword specifies the
+output as a string, then the default maximum length of that string is
+63 characters (64-1 for the string terminator).  If you want to return
+a longer string, the {length} keyword can be specified with its {Nlen}
+value set to a larger number (the code allocates space for Nlen+1 to
+include the string terminator).  If the Python function generates a
+string longer than the default 63 or the specified {Nlen}, it will be
+trunctated.
+
+:line
+
 Either the {file}, {here}, or {exists} keyword must be used, but only
 one of them.  These keywords specify what Python code to load into the
 Python interpreter.  The {file} keyword gives the name of a file,
--- 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 +189,159 @@ 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
+

 :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 +352,29 @@ 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/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 
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+     910     301.4308816315937634    1538.4823217911621214    1188.1159856659228353     394.4614066057064861       0.0000000000000000   15705.6160570713091147   17288.1934493429398572     299.9748317405192779 
+     920     301.4323110133492492    1594.7193046491240693    1188.0835779842032025     394.4632771371357762       0.0000000000000000   15705.6544576464475540   17288.2013127677855664     299.9751127806913473 
+     930     301.4801256941949532    1387.6885377097596574    1188.0464206196900250     394.5258488489680531       0.0000000000000000   15705.6258377843460039   17288.1981072530033998     299.9740698440912183 
+     940     301.8075611840245074    1534.2487040663797870    1188.0124217312888959     394.9543406584059539       0.0000000000000000   15705.2331319202457962   17288.1998943099388271     299.9660570413491882 
+     950     301.6915970126175353    1567.7725992489226883    1187.9790455470049437     394.8025864986415172       0.0000000000000000   15705.4221432087451831   17288.2037752543910756     299.9694678653152096 
+     960     301.6392594677008105    1504.8502165144939227    1187.9439133338107695     394.7340960325207675       0.0000000000000000   15705.5330682989206252   17288.2110776652516506     299.9711546356285226 
+     970     301.6049535791644871    1514.0198965433535250    1187.9094123369409317     394.6892023276234909       0.0000000000000000   15705.6099784820144123   17288.2085931465771864     299.9722547114341751 
+     980     301.2982841679706780    1634.1208149125800446    1187.8768454876478700     394.2878856256065205       0.0000000000000000   15706.0463883383199573   17288.2111194515746320     299.9802110109068849 
+     990     301.2573007350166563    1489.7316698898262075    1187.8432331161866387     394.2342534877078606       0.0000000000000000   15706.1441971863041545   17288.2216837901978579     299.9819468620868292 
+    1000     301.3195135766228532    1562.6587211933931485    1187.8034267774903583     394.3156670604516307       0.0000000000000000   15706.0974511956701463   17288.2165450336106005     299.9807651637235040 
+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/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/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/lib/colvars/colvargrid.cpp
+++ b/lib/colvars/colvargrid.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"
@ -73,6 +80,21 @@ cvm::real colvar_grid_scalar::minimum_value() const
  return min;
 }

+cvm::real colvar_grid_scalar::minimum_pos_value() const
+{
+  cvm::real minpos = data[0];
+  size_t i;
+  for (i = 0; i < nt; i++) {
+    if(data[i] > 0) {
+      minpos = data[i];
+      break;
+    }
+  }
+  for (i = 0; i < nt; i++) {
+    if (data[i] > 0 && data[i] < minpos) minpos = data[i];
+  }
+  return minpos;
+}

 cvm::real colvar_grid_scalar::integral() const
 {
--- a/lib/colvars/colvargrid.h
+++ b/lib/colvars/colvargrid.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 COLVARGRID_H
 #define COLVARGRID_H

@ -378,6 +385,13 @@ public:
    return value_to_bin_scalar(actual_value[i] ? cv[i]->actual_value() : cv[i]->value(), i);
  }

+  /// \brief Report the bin corresponding to the current value of variable i
+  /// and assign first or last bin if out of boundaries
+  inline int current_bin_scalar_bound(int const i) const
+  {
+    return value_to_bin_scalar_bound(actual_value[i] ? cv[i]->actual_value() : cv[i]->value(), i);
+  }
+
  /// \brief Report the bin corresponding to the current value of item iv in variable i
  inline int current_bin_scalar(int const i, int const iv) const
  {
@ -393,6 +407,16 @@ public:
    return (int) std::floor( (value.real_value - lower_boundaries[i].real_value) / widths[i] );
  }

+  /// \brief Use the lower boundary and the width to report which bin
+  /// the provided value is in and assign first or last bin if out of boundaries
+  inline int value_to_bin_scalar_bound(colvarvalue const &value, const int i) const
+  {
+    int bin_index = std::floor( (value.real_value - lower_boundaries[i].real_value) / widths[i] );
+    if (bin_index < 0) bin_index=0;
+    if (bin_index >=int(nx[i])) bin_index=int(nx[i])-1;
+    return (int) bin_index;
+  }
+
  /// \brief Same as the standard version, but uses another grid definition
  inline int value_to_bin_scalar(colvarvalue const &value,
                                 colvarvalue const &new_offset,
@ -514,6 +538,13 @@ public:
      data[i] *= a;
  }

+  /// \brief Assign all zero elements a scalar constant (fast loop)
+  inline void remove_zeros(cvm::real const &a)
+  {
+    for (size_t i = 0; i < nt; i++)
+      if(data[i]==0) data[i] = a;
+  }
+

  /// \brief Get the bin indices corresponding to the provided values of
  /// the colvars
@ -537,6 +568,17 @@ public:
    return index;
  }

+  /// \brief Get the bin indices corresponding to the provided values of
+  /// the colvars and assign first or last bin if out of boundaries
+  inline std::vector<int> const get_colvars_index_bound() const
+  {
+    std::vector<int> index = new_index();
+    for (size_t i = 0; i < nd; i++) {
+      index[i] = current_bin_scalar_bound(i);
+    }
+    return index;
+  }
+
  /// \brief Get the minimal distance (in number of bins) from the
  /// boundaries; a negative number is returned if the given point is
  /// off-grid
@ -1071,7 +1113,7 @@ public:
  {
    // write the header
    os << "object 1 class gridpositions counts";
-    int icv;
+    size_t icv;
    for (icv = 0; icv < number_of_colvars(); icv++) {
      os << " " << number_of_points(icv);
    }
@ -1166,45 +1208,49 @@ public:

  /// \brief Return the log-gradient from finite differences
  /// on the *same* grid for dimension n
-  inline const cvm::real log_gradient_finite_diff( const std::vector<int> &ix0,
-                                                   int n = 0)
+  inline cvm::real log_gradient_finite_diff(const std::vector<int> &ix0,
+                                            int n = 0)
  {
-    cvm::real A0, A1;
-    std::vector<int> ix;
-
-    // factor for mesh width, 2.0 for central finite difference
-    // but only 1.0 on edges for non-PBC coordinates
-    cvm::real factor;
+    int A0, A1, A2;
+    std::vector<int> ix = ix0;

    if (periodic[n]) {
-      factor = 2.;
-      ix = ix0;
      ix[n]--; wrap(ix);
      A0 = data[address(ix)];
      ix = ix0;
      ix[n]++; wrap(ix);
      A1 = data[address(ix)];
-    } else {
-      factor = 0.;
-      ix = ix0;
-      if (ix[n] > 0) { // not left edge
-        ix[n]--;
-        factor += 1.;
+      if (A0 * A1 == 0) {
+        return 0.; // can't handle empty bins
+      } else {
+        return (std::log((cvm::real)A1) - std::log((cvm::real)A0))
+          / (widths[n] * 2.);
      }
+    } else if (ix[n] > 0 && ix[n] < nx[n]-1) { // not an edge
+      ix[n]--;
      A0 = data[address(ix)];
      ix = ix0;
-      if (ix[n]+1 < nx[n]) { // not right edge
-        ix[n]++;
-        factor += 1.;
-      }
+      ix[n]++;
      A1 = data[address(ix)];
-    }
-    if (A0 == 0 || A1 == 0) {
-      // can't handle empty bins
-      return 0.;
+      if (A0 * A1 == 0) {
+        return 0.; // can't handle empty bins
+      } else {
+        return (std::log((cvm::real)A1) - std::log((cvm::real)A0))
+          / (widths[n] * 2.);
+      }
    } else {
-      return (std::log((cvm::real)A1) - std::log((cvm::real)A0))
-        / (widths[n] * factor);
+      // edge: use 2nd order derivative
+      int increment = (ix[n] == 0 ? 1 : -1);
+      // move right from left edge, or the other way around
+      A0 = data[address(ix)];
+      ix[n] += increment; A1 = data[address(ix)];
+      ix[n] += increment; A2 = data[address(ix)];
+      if (A0 * A1 * A2 == 0) {
+        return 0.; // can't handle empty bins
+      } else {
+        return (-1.5 * std::log((cvm::real)A0) + 2. * std::log((cvm::real)A1)
+          - 0.5 * std::log((cvm::real)A2)) * increment / widths[n];
+      }
    }
  }
 };
@ -1322,6 +1368,9 @@ public:
  /// \brief Return the lowest value
  cvm::real minimum_value() const;

+  /// \brief Return the lowest positive value
+  cvm::real minimum_pos_value() const;
+
  /// \brief Calculates the integral of the map (uses widths if they are defined)
  cvm::real integral() const;

--- a/lib/colvars/colvarmodule.cpp
+++ b/lib/colvars/colvarmodule.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 <sstream>
 #include <string.h>

@ -296,6 +303,9 @@ int colvarmodule::parse_biases(std::string const &conf)
  /// initialize harmonic restraints
  parse_biases_type<colvarbias_restraint_harmonic>(conf, "harmonic", n_rest_biases);

+  /// initialize harmonic walls restraints
+  parse_biases_type<colvarbias_restraint_harmonic_walls>(conf, "harmonicWalls", n_rest_biases);
+
  /// initialize histograms
  parse_biases_type<colvarbias_histogram>(conf, "histogram", n_histo_biases);

@ -562,7 +572,6 @@ int colvarmodule::calc_colvars()
    colvars_smp_items.reserve(colvars.size());

    // set up a vector containing all components
-    size_t num_colvar_items = 0;
    cvm::increase_depth();
    for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {

@ -576,8 +585,6 @@ int colvarmodule::calc_colvars()
        colvars_smp.push_back(*cvi);
        colvars_smp_items.push_back(icvc);
      }
-
-      num_colvar_items += num_items;
    }
    cvm::decrease_depth();

@ -641,7 +648,7 @@ int colvarmodule::calc_biases()
    for (bi = biases.begin(); bi != biases.end(); bi++) {
      error_code |= (*bi)->update();
      if (cvm::get_error()) {
-        return COLVARS_ERROR;
+        return error_code;
      }
    }
    cvm::decrease_depth();
@ -1007,7 +1014,7 @@ std::istream & colvarmodule::read_restart(std::istream &is)
  for (std::vector<colvarbias *>::iterator bi = biases.begin();
       bi != biases.end();
       bi++) {
-    if (!((*bi)->read_restart(is))) {
+    if (!((*bi)->read_state(is))) {
      cvm::error("Error: in reading restart configuration for bias \""+
                 (*bi)->name+"\".\n",
                 INPUT_ERROR);
@ -1070,15 +1077,15 @@ continue the previous simulation.\n\n");
    cvm::log(cvm::line_marker);

    // update this ahead of time in this special case
-    output_prefix = proxy->output_prefix();
+    output_prefix = proxy->input_prefix();
    cvm::log("All output files will now be saved with the prefix \""+output_prefix+".tmp.*\".\n");
-    output_prefix = output_prefix+".tmp";
-    write_output_files();
    cvm::log(cvm::line_marker);
    cvm::log("Please review the important warning above. After that, you may rename:\n\
 \""+output_prefix+".tmp.colvars.state\"\n\
 to:\n\
-\""+output_prefix+".colvars.state\"\n");
+\""+ proxy->input_prefix()+".colvars.state\"\n");
+    output_prefix = output_prefix+".tmp";
+    write_output_files();
    cvm::error("Exiting with error until issue is addressed.\n", FATAL_ERROR);
  }

@ -1120,6 +1127,7 @@ int colvarmodule::write_output_files()
       bi != biases.end();
       bi++) {
    (*bi)->write_output_files();
+    (*bi)->write_state_to_replicas();
  }
  cvm::decrease_depth();

@ -1212,20 +1220,30 @@ std::ostream & colvarmodule::write_restart(std::ostream &os)
     << "  version " << std::string(COLVARS_VERSION) << "\n"
     << "}\n\n";

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

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

+  if (error_code != COLVARS_OK) {
+    // TODO make this function return an int instead
+    os.setstate(std::ios::failbit);
+  }
+
  return os;
 }

--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@ -1,10 +1,17 @@
 // -*- 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 COLVARMODULE_H
 #define COLVARMODULE_H

 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2016-10-21"
+#define COLVARS_VERSION "2016-12-27"
 #endif

 #ifndef COLVARS_DEBUG
@ -198,7 +205,7 @@ public:
  }

  /// \brief How many objects are configured yet?
-  inline size_t const size() const
+  inline size_t size() const
  {
    return colvars.size() + biases.size();
  }
--- a/lib/colvars/colvarparse.cpp
+++ b/lib/colvars/colvarparse.cpp
@ -1,3 +1,11 @@
+// -*- 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 <sstream>
--- a/lib/colvars/colvarparse.h
+++ b/lib/colvars/colvarparse.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 COLVARPARSE_H
 #define COLVARPARSE_H

--- a/lib/colvars/colvarproxy.h
+++ b/lib/colvars/colvarproxy.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 COLVARPROXY_H
 #define COLVARPROXY_H

@ -24,11 +31,18 @@ public:
  /// Pointer to the main object
  colvarmodule *colvars;

-  /// Default constructor
-  inline colvarproxy() : script(NULL), b_smp_active(true) {}
+  /// Constructor
+  colvarproxy()
+  {
+    colvars = NULL;
+    b_simulation_running = true;
+    b_smp_active = true;
+    script = NULL;
+  }

-  /// Default destructor
-  virtual ~colvarproxy() {}
+  /// Destructor
+  virtual ~colvarproxy()
+  {}

  /// (Re)initialize required member data after construction
  virtual int setup()
@ -104,6 +118,19 @@ public:
    return 0;
  }

+protected:
+
+  /// Whether a simulation is running (and try to prevent irrecovarable errors)
+  bool b_simulation_running;
+
+public:
+
+  /// Whether a simulation is running (and try to prevent irrecovarable errors)
+  virtual bool simulation_running() const
+  {
+    return b_simulation_running;
+  }
+
 protected:

  /// \brief Currently opened output files: by default, these are ofstream objects.
--- a/lib/colvars/colvarscript.cpp
+++ b/lib/colvars/colvarscript.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 <cstdlib>
 #include <stdlib.h>
 #include <string.h>
--- a/lib/colvars/colvarscript.h
+++ b/lib/colvars/colvarscript.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 COLVARSCRIPT_H
 #define COLVARSCRIPT_H

--- a/lib/colvars/colvartypes.cpp
+++ b/lib/colvars/colvartypes.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 <stdlib.h>
 #include <string.h>

--- a/lib/colvars/colvartypes.h
+++ b/lib/colvars/colvartypes.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 COLVARTYPES_H
 #define COLVARTYPES_H

--- a/lib/colvars/colvarvalue.cpp
+++ b/lib/colvars/colvarvalue.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 <vector>
 #include <sstream>
 #include <iostream>
@ -70,45 +77,30 @@ void colvarvalue::set_elem(int const icv, colvarvalue const &x)
 }


-colvarvalue colvarvalue::inverse() const
+void colvarvalue::set_random()
 {
-  switch (value_type) {
+  size_t ic;
+  switch (this->type()) {
  case colvarvalue::type_scalar:
-    return colvarvalue(1.0/real_value);
+    this->real_value = cvm::rand_gaussian();
    break;
  case colvarvalue::type_3vector:
  case colvarvalue::type_unit3vector:
  case colvarvalue::type_unit3vectorderiv:
-    return colvarvalue(cvm::rvector(1.0/rvector_value.x,
-                                    1.0/rvector_value.y,
-                                    1.0/rvector_value.z));
+    this->rvector_value.x = cvm::rand_gaussian();
+    this->rvector_value.y = cvm::rand_gaussian();
+    this->rvector_value.z = cvm::rand_gaussian();
    break;
  case colvarvalue::type_quaternion:
  case colvarvalue::type_quaternionderiv:
-    return colvarvalue(cvm::quaternion(1.0/quaternion_value.q0,
-                                       1.0/quaternion_value.q1,
-                                       1.0/quaternion_value.q2,
-                                       1.0/quaternion_value.q3));
+    this->quaternion_value.q0 = cvm::rand_gaussian();
+    this->quaternion_value.q1 = cvm::rand_gaussian();
+    this->quaternion_value.q2 = cvm::rand_gaussian();
+    this->quaternion_value.q3 = cvm::rand_gaussian();
    break;
  case colvarvalue::type_vector:
-    {
-      cvm::vector1d<cvm::real> result(vector1d_value);
-      if (elem_types.size() > 0) {
-        // if we have information about non-scalar types, use it
-        size_t i;
-        for (i = 0; i < elem_types.size(); i++) {
-          result.sliceassign(elem_indices[i], elem_indices[i]+elem_sizes[i],
-                             cvm::vector1d<cvm::real>((this->get_elem(i)).inverse()));
-        }
-      } else {
-        size_t i;
-        for (i = 0; i < result.size(); i++) {
-          if (result[i] != 0.0) {
-            result = 1.0/result[i];
-          }
-        }
-      }
-      return colvarvalue(result, type_vector);
+    for (ic = 0; ic < this->vector1d_value.size(); ic++) {
+      this->vector1d_value[ic] = cvm::rand_gaussian();
    }
    break;
  case colvarvalue::type_notset:
@ -116,7 +108,6 @@ colvarvalue colvarvalue::inverse() const
    undef_op();
    break;
  }
-  return colvarvalue();
 }


@ -288,7 +279,7 @@ colvarvalue colvarvalue::dist2_grad(colvarvalue const &x2) const
                                       (-1.0) * sin_t * v2.z +
                                       cos_t/sin_t * (v1.z - cos_t*v2.z)
                                       ),
-                          colvarvalue::type_unit3vector );
+                          colvarvalue::type_unit3vectorderiv );
    }
  case colvarvalue::type_quaternion:
  case colvarvalue::type_quaternionderiv:
--- a/lib/colvars/colvarvalue.h
+++ b/lib/colvars/colvarvalue.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 COLVARVALUE_H
 #define COLVARVALUE_H

@ -128,30 +135,23 @@ public:
  {}

  /// \brief Copy constructor from rvector base type (Note: this sets
-  /// automatically a type \link type_3vector \endlink , if you want a
+  /// by default a type \link type_3vector \endlink , if you want a
  /// \link type_unit3vector \endlink you must set it explicitly)
-  inline colvarvalue(cvm::rvector const &v)
-    : value_type(type_3vector), rvector_value(v)
-  {}
-
-  /// \brief Copy constructor from rvector base type (additional
-  /// argument to make possible to choose a \link type_unit3vector
-  /// \endlink
-  inline colvarvalue(cvm::rvector const &v, Type const &vti)
+  inline colvarvalue(cvm::rvector const &v, Type vti = type_3vector)
    : value_type(vti), rvector_value(v)
  {}

  /// \brief Copy constructor from quaternion base type
-  inline colvarvalue(cvm::quaternion const &q)
-    : value_type(type_quaternion), quaternion_value(q)
+  inline colvarvalue(cvm::quaternion const &q, Type vti = type_quaternion)
+    : value_type(vti), quaternion_value(q)
  {}

+  /// Copy constructor from vector1d base type
+  colvarvalue(cvm::vector1d<cvm::real> const &v, Type vti = type_vector);
+
  /// Copy constructor from another \link colvarvalue \endlink
  colvarvalue(colvarvalue const &x);

-  /// Copy constructor from vector1d base type
-  colvarvalue(cvm::vector1d<cvm::real> const &v, Type const &vti);
-

  /// Set to the null value for the data type currently defined
  void reset();
@ -211,10 +211,6 @@ public:
    return std::sqrt(this->norm2());
  }

-  /// \brief Return the value whose scalar product with this value is
-  /// 1
-  inline colvarvalue inverse() const;
-
  /// Square distance between this \link colvarvalue \endlink and another
  cvm::real dist2(colvarvalue const &x2) const;

@ -297,6 +293,9 @@ public:
  /// Set elements of the vector from a single colvarvalue
  void set_elem(int const i_begin, int const i_end, colvarvalue const &x);

+  /// Make each element a random number in N(0,1)
+  void set_random();
+
  /// Get a single colvarvalue out of elements of the vector
  colvarvalue const get_elem(int const icv) const;

@ -533,7 +532,7 @@ inline colvarvalue::colvarvalue(colvarvalue const &x)
  }
 }

-inline colvarvalue::colvarvalue(cvm::vector1d<cvm::real> const &v, Type const &vti)
+inline colvarvalue::colvarvalue(cvm::vector1d<cvm::real> const &v, Type vti)
 {
  if ((vti != type_vector) && (v.size() != num_dimensions(vti))) {
    cvm::error("Error: trying to initialize a variable of type \""+type_desc(vti)+
@ -617,11 +616,22 @@ inline int colvarvalue::check_types_assign(colvarvalue::Type const &vt1,
  }

  if (vt1 != type_notset) {
-    if (vt1 != vt2) {
-      cvm::error("Trying to assign a colvar value with type \""+
-                 type_desc(vt2)+"\" to one with type \""+
-                 type_desc(vt1)+"\".\n");
-      return COLVARS_ERROR;
+    if (((vt1 == type_unit3vector) &&
+         (vt2 == type_unit3vectorderiv)) ||
+        ((vt2 == type_unit3vector) &&
+         (vt1 == type_unit3vectorderiv)) ||
+        ((vt1 == type_quaternion) &&
+         (vt2 == type_quaternionderiv)) ||
+        ((vt2 == type_quaternion) &&
+         (vt1 == type_quaternionderiv))) {
+      return COLVARS_OK;
+    } else {
+      if (vt1 != vt2) {
+        cvm::error("Trying to assign a colvar value with type \""+
+                   type_desc(vt2)+"\" to one with type \""+
+                   type_desc(vt1)+"\".\n");
+        return COLVARS_ERROR;
+      }
    }
  }
  return COLVARS_OK;
--- a/src/.gitignore
+++ b/src/.gitignore
@ -18,10 +18,13 @@
 /*_tally.cpp
 /*_rx.h
 /*_rx.cpp
+/*_ssa.h
+/*_ssa.cpp

 /kokkos.cpp
 /kokkos.h
 /kokkos_type.h
+/kokkos_few.h

 /manifold*.cpp
 /manifold*.h
--- a/src/KOKKOS/Install.sh
+++ b/src/KOKKOS/Install.sh
@ -91,6 +91,8 @@ action fix_reaxc_species_kokkos.cpp fix_reaxc_species.cpp
 action fix_reaxc_species_kokkos.h fix_reaxc_species.h
 action fix_setforce_kokkos.cpp
 action fix_setforce_kokkos.h
+action fix_momentum_kokkos.cpp
+action fix_momentum_kokkos.h
 action fix_wall_reflect_kokkos.cpp
 action fix_wall_reflect_kokkos.h
 action gridcomm_kokkos.cpp gridcomm.cpp
@ -100,16 +102,22 @@ action improper_harmonic_kokkos.h improper_harmonic.h
 action kokkos.cpp
 action kokkos.h
 action kokkos_type.h
+action kokkos_few.h
 action memory_kokkos.h
 action modify_kokkos.cpp
 action modify_kokkos.h
 action neigh_bond_kokkos.cpp
 action neigh_bond_kokkos.h
-action neigh_full_kokkos.h
 action neigh_list_kokkos.cpp
 action neigh_list_kokkos.h
 action neighbor_kokkos.cpp
 action neighbor_kokkos.h
+action npair_copy_kokkos.cpp
+action npair_copy_kokkos.h
+action npair_kokkos.cpp
+action npair_kokkos.h
+action nbin_kokkos.cpp
+action nbin_kokkos.h
 action math_special_kokkos.cpp
 action math_special_kokkos.h
 action pair_buck_coul_cut_kokkos.cpp
--- a/src/KOKKOS/atom_vec_angle_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp
@ -1593,7 +1593,7 @@ int AtomVecAngleKokkos::unpack_restart(double *buf)

  double **extra = atom->extra;
  if (atom->nextra_store) {
-    int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+    int size = static_cast<int> (buf[0]) - m;
    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
  }

--- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
@ -1232,7 +1232,7 @@ int AtomVecAtomicKokkos::unpack_restart(double *buf)

  double **extra = atom->extra;
  if (atom->nextra_store) {
-    int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+    int size = static_cast<int> (buf[0]) - m;
    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
  }

--- a/src/KOKKOS/atom_vec_bond_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp
@ -1460,7 +1460,7 @@ int AtomVecBondKokkos::unpack_restart(double *buf)

  double **extra = atom->extra;
  if (atom->nextra_store) {
-    int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+    int size = static_cast<int> (buf[0]) - m;
    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
  }

--- a/src/KOKKOS/atom_vec_charge_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp
@ -1314,7 +1314,7 @@ int AtomVecChargeKokkos::unpack_restart(double *buf)

  double **extra = atom->extra;
  if (atom->nextra_store) {
-    int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+    int size = static_cast<int> (buf[0]) - m;
    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
  }

--- a/src/KOKKOS/atom_vec_full_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_full_kokkos.cpp
@ -1936,7 +1936,7 @@ int AtomVecFullKokkos::unpack_restart(double *buf)

  double **extra = atom->extra;
  if (atom->nextra_store) {
-    int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+    int size = static_cast<int> (buf[0]) - m;
    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
  }

--- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
@ -1850,7 +1850,7 @@ int AtomVecMolecularKokkos::unpack_restart(double *buf)

  double **extra = atom->extra;
  if (atom->nextra_store) {
-    int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+    int size = static_cast<int> (buf[0]) - m;
    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
  }

--- a/src/KOKKOS/comm_tiled_kokkos.cpp
+++ b/src/KOKKOS/comm_tiled_kokkos.cpp
@ -262,5 +262,5 @@ void CommTiledKokkos::forward_comm_array(int nsize, double **array)

 int CommTiledKokkos::exchange_variable(int n, double *inbuf, double *&outbuf)
 {
-  CommTiled::exchange_variable(n,inbuf,outbuf);
-}
+  return CommTiled::exchange_variable(n,inbuf,outbuf);
+}
--- a/src/KOKKOS/compute_temp_kokkos.h
+++ b/src/KOKKOS/compute_temp_kokkos.h
@ -45,14 +45,13 @@ namespace LAMMPS_NS {
    }

    KOKKOS_INLINE_FUNCTION
-    volatile s_CTEMP& operator+=(const volatile s_CTEMP &rhs) volatile {
+    void operator+=(const volatile s_CTEMP &rhs) volatile {
      t0 += rhs.t0;
      t1 += rhs.t1;
      t2 += rhs.t2;
      t3 += rhs.t3;
      t4 += rhs.t4;
      t5 += rhs.t5;
-      return *this;
    }
  };
  typedef s_CTEMP CTEMP;
--- a/src/KOKKOS/domain_kokkos.h
+++ b/src/KOKKOS/domain_kokkos.h
@ -16,6 +16,7 @@

 #include "domain.h"
 #include "kokkos_type.h"
+#include "kokkos_few.h"

 namespace LAMMPS_NS {

@ -35,6 +36,10 @@ class DomainKokkos : public Domain {
  void image_flip(int, int, int);
  void x2lamda(int);
  void lamda2x(int);
+  // these lines bring in the x2lamda signatures from Domain
+  // that are not overloaded here
+  using Domain::x2lamda;
+  using Domain::lamda2x;

  int closest_image(const int, int) const;

@ -50,6 +55,10 @@ class DomainKokkos : public Domain {
  KOKKOS_INLINE_FUNCTION
  void operator()(TagDomain_x2lamda, const int&) const;

+  static KOKKOS_INLINE_FUNCTION
+  Few<double,3> unmap(Few<double,3> prd, Few<double,6> h, int triclinic,
+      Few<double,3> x, imageint image);
+
 private:
  double lo[3],hi[3],period[3];
  int n_flip, m_flip, p_flip;
@ -57,6 +66,26 @@ class DomainKokkos : public Domain {
  ArrayTypes<LMPDeviceType>::t_imageint_1d image;
 };

+KOKKOS_INLINE_FUNCTION
+Few<double,3> DomainKokkos::unmap(Few<double,3> prd, Few<double,6> h,
+    int triclinic, Few<double,3> x, imageint image)
+{
+  int xbox = (image & IMGMASK) - IMGMAX;
+  int ybox = (image >> IMGBITS & IMGMASK) - IMGMAX;
+  int zbox = (image >> IMG2BITS) - IMGMAX;
+  Few<double,3> y;
+  if (triclinic == 0) {
+    y[0] = x[0] + xbox*prd[0];
+    y[1] = x[1] + ybox*prd[1];
+    y[2] = x[2] + zbox*prd[2];
+  } else {
+    y[0] = x[0] + h[0]*xbox + h[5]*ybox + h[4]*zbox;
+    y[1] = x[1] + h[1]*ybox + h[3]*zbox;
+    y[2] = x[2] + h[2]*zbox;
+  }
+  return y;
+}
+
 }

 #endif
--- a/src/KOKKOS/fix_momentum_kokkos.cpp
+++ b/src/KOKKOS/fix_momentum_kokkos.cpp
@ -0,0 +1,204 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include <stdlib.h>
+#include <string.h>
+#include "fix_momentum_kokkos.h"
+#include "atom_kokkos.h"
+#include "atom_masks.h"
+#include "domain.h"
+#include "domain_kokkos.h"
+#include "group.h"
+#include "error.h"
+#include "force.h"
+#include "kokkos_few.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ----------------------------------------------------------------------
+   Contributing author: Dan Ibanez (SNL)
+------------------------------------------------------------------------- */
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+FixMomentumKokkos<DeviceType>::FixMomentumKokkos(LAMMPS *lmp, int narg, char **arg) :
+  FixMomentum(lmp, narg, arg)
+{
+  kokkosable = 1;
+  atomKK = (AtomKokkos *) atom;
+  execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
+  datamask_read = EMPTY_MASK;
+  datamask_modify = EMPTY_MASK;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+static double get_kinetic_energy(
+    AtomKokkos* atomKK,
+    MPI_Comm world,
+    int groupbit,
+    int nlocal,
+    typename ArrayTypes<DeviceType>::t_v_array_randomread v,
+    typename ArrayTypes<DeviceType>::t_int_1d_randomread mask)
+{
+  using AT = ArrayTypes<DeviceType>;
+  auto execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
+  double ke=0.0;
+  if (atomKK->rmass) {
+    atomKK->sync(execution_space, RMASS_MASK);
+    typename AT::t_float_1d_randomread rmass = atomKK->k_rmass.view<DeviceType>();
+    Kokkos::parallel_reduce(nlocal, LAMMPS_LAMBDA(int i, double& update) {
+      if (mask(i) & groupbit)
+        update += rmass(i) *
+          (v(i,0)*v(i,0) + v(i,1)*v(i,1) + v(i,2)*v(i,2));
+    }, ke);
+  } else {
+    // D.I. : why is there no MASS_MASK ?
+    atomKK->sync(execution_space, TYPE_MASK);
+    typename AT::t_int_1d_randomread type = atomKK->k_type.view<DeviceType>();
+    typename AT::t_float_1d_randomread mass = atomKK->k_mass.view<DeviceType>();
+    Kokkos::parallel_reduce(nlocal, LAMMPS_LAMBDA(int i, double& update) {
+      if (mask(i) & groupbit)
+        update += mass(type(i)) *
+          (v(i,0)*v(i,0) + v(i,1)*v(i,1) + v(i,2)*v(i,2));
+    }, ke);
+  }
+  double ke_total;
+  MPI_Allreduce(&ke,&ke_total,1,MPI_DOUBLE,MPI_SUM,world);
+  return ke_total;
+}
+
+template<class DeviceType>
+void FixMomentumKokkos<DeviceType>::end_of_step()
+{
+  atomKK->sync(execution_space, V_MASK | MASK_MASK);
+
+  typename AT::t_v_array v = atomKK->k_v.view<DeviceType>();
+  typename AT::t_int_1d_randomread mask = atomKK->k_mask.view<DeviceType>();
+
+  const int nlocal = atom->nlocal;
+  double ekin_old,ekin_new;
+  ekin_old = ekin_new = 0.0;
+
+  if (dynamic)
+    masstotal = group->mass(igroup); // change once Group is ported to Kokkos
+
+  // do nothing if group is empty, i.e. mass is zero;
+
+  if (masstotal == 0.0) return;
+
+  // compute kinetic energy before momentum removal, if needed
+
+  if (rescale) {
+    ekin_old = get_kinetic_energy<DeviceType>(atomKK, world, groupbit, nlocal, v, mask);
+  }
+
+  auto groupbit2 = groupbit;
+  if (linear) {
+    /* this is needed because Group is not Kokkos-aware ! */
+    atomKK->sync(ExecutionSpaceFromDevice<LMPHostType>::space,
+        V_MASK | MASK_MASK | TYPE_MASK | RMASS_MASK);
+    Few<double, 3> vcm;
+    group->vcm(igroup,masstotal,&vcm[0]);
+
+    // adjust velocities by vcm to zero linear momentum
+    // only adjust a component if flag is set
+    
+    auto xflag2 = xflag;
+    auto yflag2 = yflag;
+    auto zflag2 = zflag;
+
+    Kokkos::parallel_for(nlocal, LAMMPS_LAMBDA(int i) {
+      if (mask(i) & groupbit2) {
+        if (xflag2) v(i,0) -= vcm[0];
+        if (yflag2) v(i,1) -= vcm[1];
+        if (zflag2) v(i,2) -= vcm[2];
+      }
+    });
+    atomKK->modified(execution_space, V_MASK);
+  }
+
+  if (angular) {
+    Few<double, 3> xcm, angmom, omega;
+    double inertia[3][3];
+    /* syncs for each Kokkos-unaware Group method */
+    atomKK->sync(ExecutionSpaceFromDevice<LMPHostType>::space,
+        X_MASK | MASK_MASK | TYPE_MASK | IMAGE_MASK | RMASS_MASK);
+    group->xcm(igroup,masstotal,&xcm[0]);
+    atomKK->sync(ExecutionSpaceFromDevice<LMPHostType>::space,
+        X_MASK | V_MASK | MASK_MASK | TYPE_MASK | IMAGE_MASK | RMASS_MASK);
+    group->angmom(igroup,&xcm[0],&angmom[0]);
+    atomKK->sync(ExecutionSpaceFromDevice<LMPHostType>::space,
+        X_MASK | MASK_MASK | TYPE_MASK | IMAGE_MASK | RMASS_MASK);
+    group->inertia(igroup,&xcm[0],inertia);
+    group->omega(&angmom[0],inertia,&omega[0]);
+
+    // adjust velocities to zero omega
+    // vnew_i = v_i - w x r_i
+    // must use unwrapped coords to compute r_i correctly
+
+    atomKK->sync(execution_space, X_MASK | IMAGE_MASK);
+    typename AT::t_x_array_randomread x = atomKK->k_x.view<DeviceType>();
+    typename AT::t_imageint_1d_randomread image = atomKK->k_image.view<DeviceType>();
+    int nlocal = atom->nlocal;
+
+    auto prd = Few<double,3>(domain->prd);
+    auto h = Few<double,6>(domain->h);
+    auto triclinic = domain->triclinic;
+    Kokkos::parallel_for(nlocal, LAMMPS_LAMBDA(int i) {
+      if (mask[i] & groupbit2) {
+        Few<double,3> x_i;
+        x_i[0] = x(i,0);
+        x_i[1] = x(i,1);
+        x_i[2] = x(i,2);
+        auto unwrap = DomainKokkos::unmap(prd,h,triclinic,x_i,image(i));
+        auto dx = unwrap[0] - xcm[0];
+        auto dy = unwrap[1] - xcm[1];
+        auto dz = unwrap[2] - xcm[2];
+        v(i,0) -= omega[1]*dz - omega[2]*dy;
+        v(i,1) -= omega[2]*dx - omega[0]*dz;
+        v(i,2) -= omega[0]*dy - omega[1]*dx;
+      }
+    });
+    atomKK->modified(execution_space, V_MASK);
+  }
+
+  // compute kinetic energy after momentum removal, if needed
+
+  if (rescale) {
+
+    ekin_new = get_kinetic_energy<DeviceType>(atomKK, world, groupbit, nlocal, v, mask);
+
+    double factor = 1.0;
+    if (ekin_new != 0.0) factor = sqrt(ekin_old/ekin_new);
+    Kokkos::parallel_for(nlocal, LAMMPS_LAMBDA(int i) {
+      if (mask(i) & groupbit2) {
+        v(i,0) *= factor;
+        v(i,1) *= factor;
+        v(i,2) *= factor;
+      }
+    });
+    atomKK->modified(execution_space, V_MASK);
+  }
+}
+
+namespace LAMMPS_NS {
+template class FixMomentumKokkos<LMPDeviceType>;
+#ifdef KOKKOS_HAVE_CUDA
+template class FixMomentumKokkos<LMPHostType>;
+#endif
+}
+
--- a/src/KOKKOS/fix_momentum_kokkos.h
+++ b/src/KOKKOS/fix_momentum_kokkos.h
@ -0,0 +1,46 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(momentum/kk,FixMomentumKokkos<LMPDeviceType>)
+FixStyle(momentum/kk/device,FixMomentumKokkos<LMPDeviceType>)
+FixStyle(momentum/kk/host,FixMomentumKokkos<LMPHostType>)
+
+#else
+
+#ifndef LMP_FIX_MOMENTUM_KOKKOS_H
+#define LMP_FIX_MOMENTUM_KOKKOS_H
+
+#include "fix_momentum.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class FixMomentumKokkos : public FixMomentum {
+ public:
+  typedef ArrayTypes<DeviceType> AT;
+
+  FixMomentumKokkos(class LAMMPS *, int, char **);
+  void end_of_step();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@ -125,12 +125,10 @@ void FixQEqReaxKokkos<DeviceType>::init()
      neighbor->requests[irequest]->pair = 0;
      neighbor->requests[irequest]->full = 1;
      neighbor->requests[irequest]->half = 0;
-      neighbor->requests[irequest]->full_cluster = 0;
    } else { //if (neighflag == HALF || neighflag == HALFTHREAD)
      neighbor->requests[irequest]->fix = 1;
      neighbor->requests[irequest]->full = 0;
      neighbor->requests[irequest]->half = 1;
-      neighbor->requests[irequest]->full_cluster = 0;
      neighbor->requests[irequest]->ghost = 1;
    }
  }
--- a/src/KOKKOS/fix_setforce_kokkos.h
+++ b/src/KOKKOS/fix_setforce_kokkos.h
@ -43,11 +43,10 @@ struct s_double_3 {
  }

  KOKKOS_INLINE_FUNCTION
-  volatile s_double_3& operator+=(const volatile s_double_3 &rhs) volatile {
+  void operator+=(const volatile s_double_3 &rhs) volatile {
    d0 += rhs.d0;
    d1 += rhs.d1;
    d2 += rhs.d2;
-    return *this;
  }
 };
 typedef s_double_3 double_3;
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@ -168,7 +168,6 @@ void KokkosLMP::accelerator(int narg, char **arg)
        else 
          neighflag = HALF;
      } else if (strcmp(arg[iarg+1],"n2") == 0) neighflag = N2;
-      else if (strcmp(arg[iarg+1],"full/cluster") == 0) neighflag = FULLCLUSTER;
      else error->all(FLERR,"Illegal package kokkos command");
      iarg += 2;
    } else if (strcmp(arg[iarg],"binsize") == 0) {
@ -232,20 +231,6 @@ void KokkosLMP::accelerator(int narg, char **arg)
   called by Finish
 ------------------------------------------------------------------------- */

-int KokkosLMP::neigh_list_kokkos(int m)
-{
-  NeighborKokkos *nk = (NeighborKokkos *) neighbor;
-  if (nk->lists_host[m] && nk->lists_host[m]->d_numneigh.dimension_0())
-    return 1;
-  if (nk->lists_device[m] && nk->lists_device[m]->d_numneigh.dimension_0())
-    return 1;
-  return 0;
-}
-
-/* ----------------------------------------------------------------------
-   called by Finish
------------------------------------------------------------------------- */
-
 int KokkosLMP::neigh_count(int m)
 {
  int inum;
@ -255,28 +240,30 @@ int KokkosLMP::neigh_count(int m)
  ArrayTypes<LMPHostType>::t_int_1d h_numneigh;

  NeighborKokkos *nk = (NeighborKokkos *) neighbor;
-  if (nk->lists_host[m]) {
-    inum = nk->lists_host[m]->inum;
+  if (nk->lists[m]->execution_space == Host) {
+    NeighListKokkos<LMPHostType>* nlistKK = (NeighListKokkos<LMPHostType>*) nk->lists[m];
+    inum = nlistKK->inum;
 #ifndef KOKKOS_USE_CUDA_UVM
-    h_ilist = Kokkos::create_mirror_view(nk->lists_host[m]->d_ilist);
-    h_numneigh = Kokkos::create_mirror_view(nk->lists_host[m]->d_numneigh);
+    h_ilist = Kokkos::create_mirror_view(nlistKK->d_ilist);
+    h_numneigh = Kokkos::create_mirror_view(nlistKK->d_numneigh);
 #else
-    h_ilist = nk->lists_host[m]->d_ilist;
-    h_numneigh = nk->lists_host[m]->d_numneigh;
+    h_ilist = nlistKK->d_ilist;
+    h_numneigh = nlistKK->d_numneigh;
 #endif
-    Kokkos::deep_copy(h_ilist,nk->lists_host[m]->d_ilist);
-    Kokkos::deep_copy(h_numneigh,nk->lists_host[m]->d_numneigh);
-  } else if (nk->lists_device[m]) {
-    inum = nk->lists_device[m]->inum;
+    Kokkos::deep_copy(h_ilist,nlistKK->d_ilist);
+    Kokkos::deep_copy(h_numneigh,nlistKK->d_numneigh);
+  } else if (nk->lists[m]->execution_space == Device) {
+    NeighListKokkos<LMPDeviceType>* nlistKK = (NeighListKokkos<LMPDeviceType>*) nk->lists[m];
+    inum = nlistKK->inum;
 #ifndef KOKKOS_USE_CUDA_UVM
-    h_ilist = Kokkos::create_mirror_view(nk->lists_device[m]->d_ilist);
-    h_numneigh = Kokkos::create_mirror_view(nk->lists_device[m]->d_numneigh);
+    h_ilist = Kokkos::create_mirror_view(nlistKK->d_ilist);
+    h_numneigh = Kokkos::create_mirror_view(nlistKK->d_numneigh);
 #else
-    h_ilist = nk->lists_device[m]->d_ilist;
-    h_numneigh = nk->lists_device[m]->d_numneigh;
+    h_ilist = nlistKK->d_ilist;
+    h_numneigh = nlistKK->d_numneigh;
 #endif
-    Kokkos::deep_copy(h_ilist,nk->lists_device[m]->d_ilist);
-    Kokkos::deep_copy(h_numneigh,nk->lists_device[m]->d_numneigh);
+    Kokkos::deep_copy(h_ilist,nlistKK->d_ilist);
+    Kokkos::deep_copy(h_numneigh,nlistKK->d_numneigh);
  }

  for (int i = 0; i < inum; i++) nneigh += h_numneigh[h_ilist[i]];
--- a/src/KOKKOS/kokkos.h
+++ b/src/KOKKOS/kokkos.h
@ -34,7 +34,6 @@ class KokkosLMP : protected Pointers {
  KokkosLMP(class LAMMPS *, int, char **);
  ~KokkosLMP();
  void accelerator(int, char **);
-  int neigh_list_kokkos(int);
  int neigh_count(int);
 private:
  static void my_signal_handler(int);
--- a/src/KOKKOS/kokkos_few.h
+++ b/src/KOKKOS/kokkos_few.h
@ -0,0 +1,68 @@
+#ifndef KOKKOS_FEW_H
+#define KOKKOS_FEW_H
+
+#include <Kokkos_Core.hpp>
+
+template <typename T, std::size_t n>
+class Few {
+  alignas(T) char array_[n * sizeof(T)];
+
+ public:
+  enum { size = n };
+  Few(std::initializer_list<T> l) {
+    std::size_t i = 0;
+    for (auto it = l.begin(); it != l.end(); ++it) {
+      new (data() + (i++)) T(*it);
+    }
+  }
+  KOKKOS_INLINE_FUNCTION Few(T const a[]) {
+    for (std::size_t i = 0; i < n; ++i) new (data() + i) T(a[i]);
+  }
+  KOKKOS_INLINE_FUNCTION Few() {
+    for (std::size_t i = 0; i < n; ++i) new (data() + i) T();
+  }
+  KOKKOS_INLINE_FUNCTION ~Few() {
+    for (std::size_t i = 0; i < n; ++i) (data()[i]).~T();
+  }
+  KOKKOS_INLINE_FUNCTION Few(Few<T, n> const& rhs) {
+    for (std::size_t i = 0; i < n; ++i) new (data() + i) T(rhs[i]);
+  }
+  KOKKOS_INLINE_FUNCTION Few(Few<T, n> const volatile& rhs) {
+    for (std::size_t i = 0; i < n; ++i) new (data() + i) T(rhs[i]);
+  }
+  KOKKOS_INLINE_FUNCTION void operator=(Few<T, n> const& rhs) volatile {
+    for (std::size_t i = 0; i < n; ++i) data()[i] = rhs[i];
+  }
+  KOKKOS_INLINE_FUNCTION void operator=(Few<T, n> const& rhs) {
+    for (std::size_t i = 0; i < n; ++i) data()[i] = rhs[i];
+  }
+  KOKKOS_INLINE_FUNCTION void operator=(Few<T, n> const volatile& rhs) {
+    for (std::size_t i = 0; i < n; ++i) data()[i] = rhs[i];
+  }
+  KOKKOS_INLINE_FUNCTION T* data() {
+    return reinterpret_cast<T*>(array_);
+  }
+  KOKKOS_INLINE_FUNCTION T const* data() const {
+    return reinterpret_cast<T const*>(array_);
+  }
+  KOKKOS_INLINE_FUNCTION T volatile* data() volatile {
+    return reinterpret_cast<T volatile*>(array_);
+  }
+  KOKKOS_INLINE_FUNCTION T const volatile* data() const volatile {
+    return reinterpret_cast<T const volatile*>(array_);
+  }
+  KOKKOS_INLINE_FUNCTION T& operator[](std::size_t i) {
+    return data()[i];
+  }
+  KOKKOS_INLINE_FUNCTION T const& operator[](std::size_t i) const {
+    return data()[i];
+  }
+  KOKKOS_INLINE_FUNCTION T volatile& operator[](std::size_t i) volatile {
+    return data()[i];
+  }
+  KOKKOS_INLINE_FUNCTION T const volatile& operator[](std::size_t i) const volatile {
+    return data()[i];
+  }
+};
+
+#endif
--- a/src/KOKKOS/kokkos_type.h
+++ b/src/KOKKOS/kokkos_type.h
@ -920,4 +920,10 @@ void memset_kokkos (ViewType &view) {
 #define ISFINITE(x) std::isfinite(x)
 #endif

+#ifdef KOKKOS_HAVE_CUDA
+#define LAMMPS_LAMBDA [=] __device__
+#else
+#define LAMMPS_LAMBDA [=]
+#endif
+
 #endif
--- a/src/KOKKOS/modify_kokkos.cpp
+++ b/src/KOKKOS/modify_kokkos.cpp
@ -81,7 +81,7 @@ void ModifyKokkos::setup_pre_exchange()
      atomKK->sync(fix[list_min_pre_exchange[i]]->execution_space,
                   fix[list_min_pre_exchange[i]]->datamask_read);
      if (!fix[list_min_pre_exchange[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
-      fix[list_min_pre_exchange[i]]->min_setup_pre_exchange();
+      fix[list_min_pre_exchange[i]]->setup_pre_exchange();
      lmp->kokkos->auto_sync = 0;
      atomKK->modified(fix[list_min_pre_exchange[i]]->execution_space,
                       fix[list_min_pre_exchange[i]]->datamask_modify);
@ -110,7 +110,7 @@ void ModifyKokkos::setup_pre_neighbor()
      atomKK->sync(fix[list_min_pre_neighbor[i]]->execution_space,
                   fix[list_min_pre_neighbor[i]]->datamask_read);
      if (!fix[list_min_pre_neighbor[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
-      fix[list_min_pre_neighbor[i]]->min_setup_pre_neighbor();
+      fix[list_min_pre_neighbor[i]]->setup_pre_neighbor();
      lmp->kokkos->auto_sync = 0;
      atomKK->modified(fix[list_min_pre_neighbor[i]]->execution_space,
                       fix[list_min_pre_neighbor[i]]->datamask_modify);
@ -139,13 +139,42 @@ void ModifyKokkos::setup_pre_force(int vflag)
      atomKK->sync(fix[list_min_pre_force[i]]->execution_space,
                   fix[list_min_pre_force[i]]->datamask_read);
      if (!fix[list_min_pre_force[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
-      fix[list_min_pre_force[i]]->min_setup_pre_force(vflag);
+      fix[list_min_pre_force[i]]->setup_pre_force(vflag);
      lmp->kokkos->auto_sync = 0;
      atomKK->modified(fix[list_min_pre_force[i]]->execution_space,
                       fix[list_min_pre_force[i]]->datamask_modify);
    }
 }

+/* ----------------------------------------------------------------------
+   setup pre_reverse call, only for fixes that define pre_reverse
+   called from Verlet, RESPA, Min
+------------------------------------------------------------------------- */
+
+void ModifyKokkos::setup_pre_reverse(int eflag, int vflag)
+{
+  if (update->whichflag == 1)
+    for (int i = 0; i < n_pre_reverse; i++) {
+      atomKK->sync(fix[list_pre_reverse[i]]->execution_space,
+                   fix[list_pre_reverse[i]]->datamask_read);
+      if (!fix[list_pre_reverse[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
+      fix[list_pre_reverse[i]]->setup_pre_reverse(eflag,vflag);
+      lmp->kokkos->auto_sync = 0;
+      atomKK->modified(fix[list_pre_reverse[i]]->execution_space,
+                       fix[list_pre_reverse[i]]->datamask_modify);
+    }
+  else if (update->whichflag == 2)
+    for (int i = 0; i < n_min_pre_reverse; i++) {
+      atomKK->sync(fix[list_min_pre_reverse[i]]->execution_space,
+                   fix[list_min_pre_reverse[i]]->datamask_read);
+      if (!fix[list_min_pre_reverse[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
+      fix[list_min_pre_reverse[i]]->setup_pre_reverse(eflag,vflag);
+      lmp->kokkos->auto_sync = 0;
+      atomKK->modified(fix[list_min_pre_reverse[i]]->execution_space,
+                       fix[list_min_pre_reverse[i]]->datamask_modify);
+    }
+}
+
 /* ----------------------------------------------------------------------
   1st half of integrate call, only for relevant fixes
 ------------------------------------------------------------------------- */
@ -231,6 +260,23 @@ void ModifyKokkos::pre_force(int vflag)
  }
 }

+/* ----------------------------------------------------------------------
+   pre_reverse call, only for relevant fixes
+------------------------------------------------------------------------- */
+
+void ModifyKokkos::pre_reverse(int eflag, int vflag)
+{
+  for (int i = 0; i < n_pre_reverse; i++) {
+    atomKK->sync(fix[list_pre_reverse[i]]->execution_space,
+                 fix[list_pre_reverse[i]]->datamask_read);
+    if (!fix[list_pre_reverse[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
+    fix[list_pre_reverse[i]]->pre_reverse(eflag,vflag);
+    lmp->kokkos->auto_sync = 0;
+    atomKK->modified(fix[list_pre_reverse[i]]->execution_space,
+                     fix[list_pre_reverse[i]]->datamask_modify);
+  }
+}
+
 /* ----------------------------------------------------------------------
   post_force call, only for relevant fixes
 ------------------------------------------------------------------------- */
@ -476,6 +522,23 @@ void ModifyKokkos::min_pre_force(int vflag)
  }
 }

+/* ----------------------------------------------------------------------
+   minimizer pre-reverse call, only for relevant fixes
+------------------------------------------------------------------------- */
+
+void ModifyKokkos::min_pre_reverse(int eflag, int vflag)
+{
+  for (int i = 0; i < n_min_pre_reverse; i++) {
+    atomKK->sync(fix[list_min_pre_reverse[i]]->execution_space,
+                 fix[list_min_pre_reverse[i]]->datamask_read);
+    if (!fix[list_min_pre_reverse[i]]->kokkosable) lmp->kokkos->auto_sync = 1;
+    fix[list_min_pre_reverse[i]]->min_pre_reverse(eflag,vflag);
+    lmp->kokkos->auto_sync = 0;
+    atomKK->modified(fix[list_min_pre_reverse[i]]->execution_space,
+                     fix[list_min_pre_reverse[i]]->datamask_modify);
+  }
+}
+
 /* ----------------------------------------------------------------------
   minimizer force adjustment call, only for relevant fixes
 ------------------------------------------------------------------------- */
@ -658,4 +721,3 @@ int ModifyKokkos::min_reset_ref()
  }
  return itmpall;
 }
-
--- a/src/KOKKOS/modify_kokkos.h
+++ b/src/KOKKOS/modify_kokkos.h
@ -26,12 +26,14 @@ class ModifyKokkos : public Modify {
  void setup_pre_exchange();
  void setup_pre_neighbor();
  void setup_pre_force(int);
+  void setup_pre_reverse(int, int);
  void initial_integrate(int);
  void post_integrate();
  void pre_decide();
  void pre_exchange();
  void pre_neighbor();
  void pre_force(int);
+  void pre_reverse(int,int);
  void post_force(int);
  void final_integrate();
  void end_of_step();
@ -48,6 +50,7 @@ class ModifyKokkos : public Modify {
  void min_pre_exchange();
  void min_pre_neighbor();
  void min_pre_force(int);
+  void min_pre_reverse(int,int);
  void min_post_force(int);

  double min_energy(double *);
--- a/src/KOKKOS/nbin_kokkos.cpp
+++ b/src/KOKKOS/nbin_kokkos.cpp
@ -0,0 +1,145 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "nbin_kokkos.h"
+#include "neighbor.h"
+#include "atom_kokkos.h"
+#include "group.h"
+#include "domain.h"
+#include "comm.h"
+#include "update.h"
+#include "error.h"
+#include "atom_masks.h"
+
+using namespace LAMMPS_NS;
+
+enum{NSQ,BIN,MULTI};       // also in Neighbor
+
+#define SMALL 1.0e-6
+#define CUT2BIN_RATIO 100
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+NBinKokkos<DeviceType>::NBinKokkos(LAMMPS *lmp) : NBinStandard(lmp) {
+  atoms_per_bin = 16;
+
+  d_resize = typename AT::t_int_scalar("NeighborKokkosFunctor::resize");
+#ifndef KOKKOS_USE_CUDA_UVM
+  h_resize = Kokkos::create_mirror_view(d_resize);
+#else
+  h_resize = d_resize;
+#endif
+  h_resize() = 1;
+
+}
+
+/* ----------------------------------------------------------------------
+   setup neighbor binning geometry
+   bin numbering in each dimension is global:
+     0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc
+     nbin-1,nbin,etc = bbox-binsize to bbox, bbox to bbox+binsize, etc
+     -1,-2,etc = -binsize to 0.0, -2*binsize to -binsize, etc
+   code will work for any binsize
+     since next(xyz) and stencil extend as far as necessary
+     binsize = 1/2 of cutoff is roughly optimal
+   for orthogonal boxes:
+     a dim must be filled exactly by integer # of bins
+     in periodic, procs on both sides of PBC must see same bin boundary
+     in non-periodic, coord2bin() still assumes this by use of nbin xyz
+   for triclinic boxes:
+     tilted simulation box cannot contain integer # of bins
+     stencil & neigh list built differently to account for this
+   mbinlo = lowest global bin any of my ghost atoms could fall into
+   mbinhi = highest global bin any of my ghost atoms could fall into
+   mbin = number of bins I need in a dimension
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void NBinKokkos<DeviceType>::bin_atoms_setup(int nall)
+{
+  if (mbins > k_bins.d_view.dimension_0()) {
+    k_bins = DAT::tdual_int_2d("Neighbor::d_bins",mbins,atoms_per_bin);
+    bins = k_bins.view<DeviceType>();
+
+    k_bincount = DAT::tdual_int_1d("Neighbor::d_bincount",mbins);
+    bincount = k_bincount.view<DeviceType>();
+    last_bin_memory = update->ntimestep;
+  }
+
+  last_bin = update->ntimestep;
+}
+
+/* ----------------------------------------------------------------------
+   bin owned and ghost atoms
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void NBinKokkos<DeviceType>::bin_atoms()
+{
+  h_resize() = 1;
+
+  while(h_resize() > 0) {
+    h_resize() = 0;
+    deep_copy(d_resize, h_resize);
+
+    MemsetZeroFunctor<DeviceType> f_zero;
+    f_zero.ptr = (void*) k_bincount.view<DeviceType>().ptr_on_device();
+    Kokkos::parallel_for(mbins, f_zero);
+    DeviceType::fence();
+
+    atomKK->sync(ExecutionSpaceFromDevice<DeviceType>::space,X_MASK);
+    x = atomKK->k_x.view<DeviceType>();
+
+    bboxlo_[0] = bboxlo[0]; bboxlo_[1] = bboxlo[1]; bboxlo_[2] = bboxlo[2];
+    bboxhi_[0] = bboxhi[0]; bboxhi_[1] = bboxhi[1]; bboxhi_[2] = bboxhi[2];
+
+    NPairKokkosBinAtomsFunctor<DeviceType> f(*this);
+
+    Kokkos::parallel_for(atom->nlocal+atom->nghost, f);
+    DeviceType::fence();
+
+    deep_copy(h_resize, d_resize);
+    if(h_resize()) {
+
+      atoms_per_bin += 16;
+      k_bins = DAT::tdual_int_2d("bins", mbins, atoms_per_bin);
+      bins = k_bins.view<DeviceType>();
+      c_bins = bins;
+      last_bin_memory = update->ntimestep;
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+KOKKOS_INLINE_FUNCTION
+void NBinKokkos<DeviceType>::binatomsItem(const int &i) const
+{
+  const int ibin = coord2bin(x(i, 0), x(i, 1), x(i, 2));
+
+  const int ac = Kokkos::atomic_fetch_add(&bincount[ibin], (int)1);
+  if(ac < bins.dimension_1()) {
+    bins(ibin, ac) = i;
+  } else {
+    d_resize() = 1;
+  }
+}
+
+namespace LAMMPS_NS {
+template class NBinKokkos<LMPDeviceType>;
+#ifdef KOKKOS_HAVE_CUDA
+template class NBinKokkos<LMPHostType>;
+#endif
+}
--- a/src/KOKKOS/nbin_kokkos.h
+++ b/src/KOKKOS/nbin_kokkos.h
@ -0,0 +1,153 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef NBIN_CLASS
+
+NBinStyle(kk/host,
+          NBinKokkos<LMPHostType>,
+          NB_KOKKOS_HOST)
+
+NBinStyle(kk/device,
+          NBinKokkos<LMPDeviceType>,
+          NB_KOKKOS_DEVICE)
+
+#else
+
+#ifndef LMP_NBIN_KOKKOS_H
+#define LMP_NBIN_KOKKOS_H
+
+#include "nbin_standard.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class NBinKokkos : public NBinStandard {
+ public:
+  typedef ArrayTypes<DeviceType> AT;
+
+  NBinKokkos(class LAMMPS *);
+  ~NBinKokkos() {}
+  void bin_atoms_setup(int);
+  void bin_atoms();
+
+  int atoms_per_bin;
+  DAT::tdual_int_1d k_bincount;
+  DAT::tdual_int_2d k_bins;
+
+  typename AT::t_int_1d bincount;
+  const typename AT::t_int_1d_const c_bincount;
+  typename AT::t_int_2d bins;
+  typename AT::t_int_2d_const c_bins;
+  typename AT::t_int_scalar d_resize;
+  typename ArrayTypes<LMPHostType>::t_int_scalar h_resize;
+  typename AT::t_x_array_randomread x;
+
+  KOKKOS_INLINE_FUNCTION
+  void binatomsItem(const int &i) const;
+
+  KOKKOS_INLINE_FUNCTION
+  int coord2bin(const X_FLOAT & x,const X_FLOAT & y,const X_FLOAT & z) const
+  {
+    int ix,iy,iz;
+
+    if (x >= bboxhi_[0])
+      ix = static_cast<int> ((x-bboxhi_[0])*bininvx) + nbinx;
+    else if (x >= bboxlo_[0]) {
+      ix = static_cast<int> ((x-bboxlo_[0])*bininvx);
+      ix = MIN(ix,nbinx-1);
+    } else
+      ix = static_cast<int> ((x-bboxlo_[0])*bininvx) - 1;
+
+    if (y >= bboxhi_[1])
+      iy = static_cast<int> ((y-bboxhi_[1])*bininvy) + nbiny;
+    else if (y >= bboxlo_[1]) {
+      iy = static_cast<int> ((y-bboxlo_[1])*bininvy);
+      iy = MIN(iy,nbiny-1);
+    } else
+      iy = static_cast<int> ((y-bboxlo_[1])*bininvy) - 1;
+
+    if (z >= bboxhi_[2])
+      iz = static_cast<int> ((z-bboxhi_[2])*bininvz) + nbinz;
+    else if (z >= bboxlo_[2]) {
+      iz = static_cast<int> ((z-bboxlo_[2])*bininvz);
+      iz = MIN(iz,nbinz-1);
+    } else
+      iz = static_cast<int> ((z-bboxlo_[2])*bininvz) - 1;
+
+    return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
+  }
+
+  KOKKOS_INLINE_FUNCTION
+  int coord2bin(const X_FLOAT & x,const X_FLOAT & y,const X_FLOAT & z, int* i) const
+  {
+    int ix,iy,iz;
+
+    if (x >= bboxhi_[0])
+      ix = static_cast<int> ((x-bboxhi_[0])*bininvx) + nbinx;
+    else if (x >= bboxlo_[0]) {
+      ix = static_cast<int> ((x-bboxlo_[0])*bininvx);
+      ix = MIN(ix,nbinx-1);
+    } else
+      ix = static_cast<int> ((x-bboxlo_[0])*bininvx) - 1;
+
+    if (y >= bboxhi_[1])
+      iy = static_cast<int> ((y-bboxhi_[1])*bininvy) + nbiny;
+    else if (y >= bboxlo_[1]) {
+      iy = static_cast<int> ((y-bboxlo_[1])*bininvy);
+      iy = MIN(iy,nbiny-1);
+    } else
+      iy = static_cast<int> ((y-bboxlo_[1])*bininvy) - 1;
+
+    if (z >= bboxhi_[2])
+      iz = static_cast<int> ((z-bboxhi_[2])*bininvz) + nbinz;
+    else if (z >= bboxlo_[2]) {
+      iz = static_cast<int> ((z-bboxlo_[2])*bininvz);
+      iz = MIN(iz,nbinz-1);
+    } else
+      iz = static_cast<int> ((z-bboxlo_[2])*bininvz) - 1;
+
+    i[0] = ix - mbinxlo;
+    i[1] = iy - mbinylo;
+    i[2] = iz - mbinzlo;
+
+    return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
+  }
+
+ private:
+  double bboxlo_[3],bboxhi_[3];
+};
+
+template<class DeviceType>
+struct NPairKokkosBinAtomsFunctor {
+  typedef DeviceType device_type;
+
+  const NBinKokkos<DeviceType> c;
+
+  NPairKokkosBinAtomsFunctor(const NBinKokkos<DeviceType> &_c):
+    c(_c) {};
+  ~NPairKokkosBinAtomsFunctor() {}
+  KOKKOS_INLINE_FUNCTION
+  void operator() (const int & i) const {
+    c.binatomsItem(i);
+  }
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Steve Plimpton	51fa33a407	patch 6Jan17	2017-01-06 11:14:48 -07:00
Steve Plimpton	142770cb2a	enable pppm/tip4p to work with triclinic	2017-01-06 10:38:32 -07:00
sjplimp	63f202501b	Merge pull request #324 from ibaned/pair-table-kokkos-inherit get PairTableKokkos to inherit from PairTable (also fix GPU)	2017-01-06 10:10:59 -07:00
sjplimp	83da5d3b5d	Merge pull request #323 from akohlmey/pppm-cg-triclinic synchronize pppm/cg with changes in pppm and remove block on triclinic	2017-01-06 10:10:09 -07:00
sjplimp	ebbf60b112	Merge pull request #319 from andeplane/domain_bug Fixed bug in lamda_box_corners function	2017-01-06 10:03:32 -07:00
sjplimp	12c4fa25e8	Merge pull request #318 from andeplane/initialize_pointers Initializing pointers in neighbor.cpp	2017-01-06 10:03:05 -07:00
sjplimp	3ac58452de	Merge pull request #310 from EfremBraun/master Fix nvk implemented	2017-01-06 10:02:22 -07:00
sjplimp	9b348d567b	Merge pull request #315 from Pakketeretet2/github-tutorial-update GitHub tutorial update	2017-01-06 10:01:57 -07:00
sjplimp	467377094a	Merge pull request #314 from stanmoore1/fix-momentum-kokkos Fix momentum kokkos	2017-01-06 10:01:17 -07:00
sjplimp	5656e90b78	Merge pull request #313 from stanmoore1/kokkos_bugfixes Kokkos bugfixes	2017-01-06 10:00:33 -07:00
sjplimp	41a6a3076e	Merge pull request #309 from giacomofiorin/colvars-2016-12-22 Update Colvars library to version 2016-12-22	2017-01-06 09:58:20 -07:00
sjplimp	d4e8d47387	Merge pull request #306 from timattox/USER-DPD_updates USER-DPD updates	2017-01-06 09:58:01 -07:00
Steve Plimpton	f6a819580c	pair TIP4P bug fix for cutoffs >> box size	2017-01-06 09:57:27 -07:00
Axel Kohlmeyer	6af56e686d	polish the introduction, some more clarifications, corrections and formatting improvements	2017-01-06 08:31:02 -05:00
Stefan Paquay	eb1c6a225c	typo fixed	2017-01-06 11:54:30 +01:00
Stefan Paquay	4d0a6d83bd	Merged Axel's suggestions and updated text	2017-01-06 11:51:42 +01:00
Stefan Paquay	958722573f	Merge branch 'github-tutorial-update' of https://github.com/Pakketeretet2/lammps into github-tutorial-update	2017-01-06 11:44:16 +01:00
Stefan Paquay	9d46670972	Updated text and images on reverse pull requests	2017-01-06 11:44:14 +01:00
Stefan Paquay	1a9f2df3d0	Updated text and images on reverse pull requests	2017-01-06 11:44:00 +01:00
Stefan Paquay	1310438c8b	Merge pull request #1 from akohlmey/pull-315 some formatting updates and text rewrites for your pull request	2017-01-06 11:40:32 +01:00
Dan Ibanez	9bf771207d	make PairTable::allocate() virtual forgot to extract this change when separating the commits for PairTableRX and PairTableKokkos.	2017-01-05 20:46:05 -07:00
Dan Ibanez	b9144d6332	Revert "move enum to pair.h" This reverts commit `aebc8ea826`.	2017-01-05 20:22:15 -07:00
Dan Ibanez	267f05e5ca	protect PairTable dtor with copymode	2017-01-05 15:38:45 -07:00
Dan Ibanez	aebc8ea826	move enum to pair.h to avoid having it be replicated in several different locations	2017-01-05 15:38:45 -07:00
Dan Ibanez	53a1de1d40	fix several GPU memory bugs in pair_table_kokkos	2017-01-05 15:38:45 -07:00
Dan Ibanez	d059b5d334	fix crash in create_kokkos_tables the code was crashing when trying to deep_copy or assign views that had not been allocated	2017-01-05 15:38:45 -07:00
Dan Ibanez	7cff343680	fix allocation regressions in PairTableKokkos	2017-01-05 15:38:45 -07:00
Dan Ibanez	a1ac861084	PairTableKokkos : public PairTable	2017-01-05 15:38:45 -07:00
Dan Ibanez	17bdb57bb4	try PairTableKokkos : public PairTable realize that there is a lot of copy-paste in this codebase.	2017-01-05 15:38:45 -07:00
Axel Kohlmeyer	fe14158c10	some formatting updates and text rewrites in the "do not use git add -a" section	2017-01-04 13:13:56 -05:00
Stefan Paquay	0bcbcca140	Highlighted the assignee, maintainer changes, and mentioned LAMMPS collaborator	2017-01-04 17:28:22 +01:00
Dan Ibanez	4cfe122ac6	fix warning about enum comparisons	2017-01-04 08:10:08 -07:00
Stan Moore	b46629ee39	Merge pull request #5 from ibaned/kokkos-fixes prevent implicit dereference of s_CTEMP	2017-01-04 08:06:55 -07:00
Anders Hafreager	42bbeb3f16	NULLing pointers after delete	2017-01-04 16:04:05 +01:00
Stefan Paquay	933b288ce9	Added explaination for assignee, changes pushed by others and collaborator.	2017-01-04 14:31:23 +01:00
Dan Ibanez	a7c5905ca4	prevent implicit dereference of s_CTEMP	2017-01-03 15:17:33 -07:00
Anders Hafreager	37d5567f6d	Fixed bug in lamda_box_corners function	2017-01-03 11:54:14 +01:00
Anders Hafreager	b10d0c17ec	Initializing pointers in neighbor.cpp	2017-01-03 11:24:48 +01:00
Richard Berger	4f45d39ac7	Add warning formatting Any paragraph starting with IMPORTANT NOTE: is transformed into a warning.	2017-01-03 02:34:11 +01:00
Axel Kohlmeyer	7d057d4c83	make it more explicit, that master needs to be updated and feature branches should be created from master	2017-01-02 13:02:48 -05:00
Stefan Paquay	4f096dbad5	Updated some inconsistent text.	2017-01-02 18:53:28 +01:00
Stefan Paquay	18b12efc9f	Small changes to tutorial text.	2017-01-02 18:25:36 +01:00
Stefan Paquay	2c7fea1e0d	Second update round to text and images, a third will follow after succesful merge.	2017-01-02 18:15:08 +01:00
Stefan Paquay	4d98bbdfa5	Almost done with the tutorial now	2017-01-02 18:08:14 +01:00
Stefan Paquay	391ab761a4	Finally updated the github tutorial.	2017-01-02 17:55:02 +01:00
Efrem Braun	b0ebd3ef4e	Merge pull request #1 from akohlmey/pull-310 add authorship attribution to lammps PR #310	2016-12-28 23:12:16 +01:00
Axel Kohlmeyer	94c4f8fe5f	add authorship attribution	2016-12-28 17:03:37 -05:00
Efrem Braun	aa146e9b38	Moved fix_nvk to USER-MISC, updated documentation to reflect move	2016-12-28 19:06:35 +01:00
Stan Moore	eca9539f84	Disallowing full neighborlist for pair_tersoff_kokkos styles until a bugfix is released	2016-12-28 10:59:53 -07:00
Stan Moore	27172c4a55	Fixing Kokkos bug when many atom types	2016-12-28 10:59:42 -07:00
Stan Moore	4f195254af	Fixing bug with Kokkos and reading restart files	2016-12-28 10:59:30 -07:00
Dan Ibanez	9a0007a13f	rename region_block_kokkos inside() this prevents compiler confusion with the inside() function provided by the normal region_block, as the two should be completely separate.	2016-12-28 10:56:16 -07:00
Dan Ibanez	994f36bc6f	silence "implicit dereference" warning see kokkos/kokkos#177 for detailed discussion of the issue and fix	2016-12-28 10:56:06 -07:00
Dan Ibanez	b3557bfbf5	add missing return in comm_tiled_kokkos	2016-12-28 10:55:51 -07:00
Dan Ibanez	371df8ea72	repair sync bugs in fix_momentum_kokkos Since the Group class is completely unaware of Kokkos, the direct calls from FixMomentumKokkos to Group methods need to be preceded by atomKK->sync calls for every atom variable that Group intends to use. fix_momentum_kokkos definitely does not work on GPUs prior to this commit.	2016-12-28 10:51:59 -07:00
Dan Ibanez	06ae2804f6	ensure velocity is marked as modified before syncing it worked before, but this seems more reliable	2016-12-28 10:51:20 -07:00
Efrem Braun	68814d4fc8	Made documentation changes to fix nvk	2016-12-28 16:26:05 +01:00
Efrem Braun	616ca1de03	Fix nvk implemented.	2016-12-28 16:17:07 +01:00
Giacomo Fiorin	b0263e87bb	Fix missing force with extended-Lagrangian mass	2016-12-27 17:16:32 -05:00
Giacomo Fiorin	925f42727f	Fix typo	2016-12-27 14:26:43 -05:00
Giacomo Fiorin	f553e230db	Update Colvars library to version 2016-12-22 Significant code cleanup and several fixes (walls + extended Lagrangian) New harmonicWalls bias to apply confining boundaries with time-dependent force constant & integration	2016-12-27 13:17:34 -05:00
Giacomo Fiorin	6ab716164b	Fix seg fault for gyration collective variable	2016-12-27 13:17:02 -05:00
Giacomo Fiorin	7a45c72b97	Allow extended Lagrangian on non-scalar collective variables	2016-12-27 12:35:30 -05:00
Axel Kohlmeyer	634eb357d2	synchronize pppm/cg with pppm and remove block on triclinic	2016-12-24 16:09:18 -05:00
Tim Mattox	a1036f2d74	USER-DPD: bugfix for new PairExp6rx::polynomialScaling() function.	2016-12-23 11:36:59 -05:00
Tim Mattox	c301d70333	USER-DPD: update example input and output (see commits 3faa57 and `eff7238`)	2016-12-22 17:32:41 -05:00
Tim Mattox	781daad2a0	USER-DPD: update documentation for changes in commit 3faa57	2016-12-22 17:31:17 -05:00
Tim Mattox	3faa57a413	USER-DPD: Several updates to _rx files: 1) Added MY_EPSILON to handle machine precision checks 2) Removed error checks for DPD-RX; enabled use with DPD-E simulations 3) Expanded the EOS functional form to allow corrections in the thermo file or on the command line 4) Updated naming convention from fraction to mixWtSite 5) Changed the name of getParams() method to getMixingWeights() 6) getMixingWeights() now handles fractional and molecular weighting 7) Added optional argument (fractional or molecular) to pair_style command 8) Added argument to specify the exp6 parameter scaling method NOTE: Requires additional arguments in the pair coefficients, thus command line areguments are NOT backward-compatible.	2016-12-22 17:15:09 -05:00
Tim Mattox	fa435fb514	USER-DPD: remove unused variable, and convert some constants to MY_EPSILON	2016-12-22 17:05:49 -05:00
Tim Mattox	ba96fcc15a	USER-DPD: update reference output to reflect changes from commit `eff7238`	2016-12-22 16:21:05 -05:00
stanmoore1	304f65b164	Merge pull request #2 from ibaned/fix-momentum-kokkos Fix momentum kokkos from Dan Ibanez	2016-12-21 12:23:32 -07:00
Dan Ibanez	4c33f31265	Merge branch 'debug-cuda' into fix-momentum-kokkos	2016-12-21 10:57:44 -07:00
Dan Ibanez	ae8d882b03	need to sync new velocities back to host	2016-12-21 10:57:18 -07:00
Dan Ibanez	7559bc9c5f	workaround CUDA View::reference_type it is not an lvalue reference in CUDA. also, the previous code assumed contiguous entries for one atom; now it should be robust in the case of LayoutLeft.	2016-12-21 10:21:55 -07:00
Steve Plimpton	62dea1bb63	21Dec16 patch	2016-12-21 09:53:32 -07:00
sjplimp	800ff43413	Merge pull request #304 from timattox/USER-DPD_whitespace USER-DPD: Whitespace cleanup to pair_dpd_fdt_energy.cpp	2016-12-21 09:51:10 -07:00
Steve Plimpton	9161bd98bf	fixed bug with pair hybrid/overaly and manybody potentials finding the right skip neighbor method	2016-12-21 09:50:29 -07:00
Dan Ibanez	f3327ca214	allow constructing Few from array on device	2016-12-21 09:21:11 -07:00
Dan Ibanez	54963ba7da	allow fix momentum angular with CUDA	2016-12-21 08:55:33 -07:00
Dan Ibanez	ea76041803	CUDA-friendly fix_momentum_kokkos angular	2016-12-21 08:54:40 -07:00
Dan Ibanez	7fb4faa439	draft CUDA-callable version of Domain::unmap	2016-12-21 08:53:57 -07:00
Dan Ibanez	41c9357dde	allow constructing Few from C array	2016-12-21 08:53:27 -07:00
Dan Ibanez	d1a55ad2e0	add kokkos_few.h to .gitignore for /src	2016-12-21 08:07:19 -07:00
Dan Ibanez	d9a0f575f6	get fix_momentum_kokkos to compile on White	2016-12-21 08:01:19 -07:00
Dan Ibanez	01e3a31639	put Few in the global namespace...	2016-12-21 08:01:06 -07:00
Dan Ibanez	992becc75f	silence warning about partial x2lamda overload	2016-12-21 08:00:42 -07:00
Dan Ibanez	8b5e15e979	add a Makefile for the White testbed	2016-12-20 16:30:50 -07:00
Dan Ibanez	b2b33cca16	start working on fix_momentum Kokkos+CUDA it doesn't compile anymore, all in good time...	2016-12-20 16:30:21 -07:00
Dan Ibanez	2ceee6b9be	install kokkos_few, and remove Int	2016-12-20 16:19:17 -07:00
Dan Ibanez	386c12c970	start porting my Few class into this code	2016-12-20 16:09:29 -07:00
Dan Ibanez	590f317550	fix_momentum_kokkos: don't override init()	2016-12-20 11:03:16 -07:00
Tim Mattox	c4e02a5d2b	USER-DPD: more whitespace fixes	2016-12-20 11:17:11 -05:00
Dan Ibanez	c7ac9e79cb	preemptive changes for Kokkos+CUDA I haven't compiled in that mode yet (don't know how), but these are some changes I suspect the compiler will require.	2016-12-19 13:17:22 -07:00
Tim Mattox	2ba424e1a3	USER-DPD: Whitespace cleanup to pair_dpd_fdt_energy.cpp	2016-12-19 15:11:52 -05:00
Dan Ibanez	ca30c1ec88	got fix_momentum_kokkos to compile there are likely still some compile errors for Kokkos+CUDA...	2016-12-19 13:08:09 -07:00
Dan Ibanez	a1b441a71f	draft the parallel_* constructs based on lambdas LAMMPS_LAMBDA was added to kokkos_type.h to facilitate this. some member variables will likely need local copies in the fix_momentum code.	2016-12-19 12:02:12 -07:00
Dan Ibanez	f6f2170369	first draft copied fix_momentum, work on the Kokkos View types for the arrays. the next step is parallel_for and parallel_reduce transformations.	2016-12-19 11:28:24 -07:00
Steve Plimpton	81a2db8a0c	17Dec16 patch	2016-12-16 11:36:54 -07:00
Steve Plimpton	0a176841e7	extra python_wrapper change needed for last patch	2016-12-16 11:35:42 -07:00
Steve Plimpton	3027ac9250	patch 16Dec16	2016-12-16 10:30:57 -07:00
sjplimp	fc54ab5cea	Merge pull request #301 from akohlmey/corrections-and-bugfixes Collected corrections and bugfixes	2016-12-16 10:25:29 -07:00
Steve Plimpton	e364b80724	added length keyword to python command	2016-12-16 10:24:25 -07:00
Axel Kohlmeyer	830c9e8661	Merge branch 'USER-DPD_internal_energy' of https://github.com/timattox/lammps_USER-DPD into corrections-and-bugfixes This closes #303	2016-12-16 11:22:25 -05:00
Axel Kohlmeyer	4907b29ad2	Merge branch 'USER-DPD_bugfixes' of https://github.com/timattox/lammps_USER-DPD into corrections-and-bugfixes This closes #302	2016-12-16 11:21:15 -05:00
Tim Mattox	eff7238ff2	USER-DPD: fix_eos*: partition all internal energy into the uMech term only This makes our results more closely match a vetted serial implementation. NOTE: This does make the output different from any previous versions. Patch by Jim Larentzos. Applied by Tim Mattox.	2016-12-16 10:25:12 -05:00
Tim Mattox	126fb22e93	USER-DPD: Fix #define typo in pair_multi_lucy.h and pair_multi_lucy_rx.h	2016-12-16 10:08:30 -05:00
Tim Mattox	0a90492c44	USER-DPD: Update the header files to properly document all error statements Patch by Jim Larentzos. Applied by Tim Mattox.	2016-12-15 17:39:15 -05:00
Tim Mattox	fed629c23e	USER-DPD: Bugfix for fix_rx and fix_eos_table_rx to handle restart files. Patch by Jim Larentzos. Applied by Tim Mattox.	2016-12-15 17:10:13 -05:00
Tim Mattox	925481c3f4	USER-DPD: Fix hard-wall force interaction bug, and ensure fraction is >= 0 pair_exp6_rx.cpp patch by Jim Larentzos. Applied by Tim Mattox.	2016-12-15 16:46:25 -05:00
Axel Kohlmeyer	da2ad5b6e0	update FixIntel code for new neighbor list code	2016-12-14 15:51:12 -05:00
Axel Kohlmeyer	bfcab72268	restore change to make -DLAMMPS_MEMALIGN=64 default when USER-INTEL package is installed (which requires it)	2016-12-14 15:24:55 -05:00
Steve Plimpton	f509f133af	patch 13Dec16: neighbor refactor, Stan pppm/disp bug fix, M Brown INTEL package updates	2016-12-13 17:14:28 -07:00
sjplimp	624c57e9da	Merge pull request #185 from akohlmey/new-neighbor New neighbor list code with updates for USER-OMP and USER-DPD	2016-12-13 16:24:41 -07:00
sjplimp	f3b355bcbe	Merge pull request #298 from akohlmey/collected-small-fixes Collected small fixes	2016-12-13 16:23:23 -07:00
Steve Plimpton	ae5764beac	added functionity to lib interface	2016-12-13 16:22:17 -07:00
Axel Kohlmeyer	fda43c00fd	add deleted file in package to purge list	2016-12-12 13:22:54 -05:00
Axel Kohlmeyer	b34be30be6	Merge pull request #53 from stanmoore1/new-neighbor New neighbor Kokkos	2016-12-12 13:18:03 -05:00
Stan Moore	13b6196b82	Fixing Kokkos compile error	2016-12-12 10:47:39 -07:00
Stan Moore	baf55c90f4	Whitespace change	2016-12-12 09:25:41 -07:00
Stan Moore	770f5d0bf7	Whitespace change	2016-12-12 09:24:37 -07:00
Stan Moore	a31b00965a	Updating to master	2016-12-12 09:18:20 -07:00
Stan Moore	a5e46e3e6a	Merging	2016-12-09 16:20:42 -07:00
Stan Moore	31be0da590	Merging pull request	2016-12-09 16:17:35 -07:00
stanmoore1	0f3b2544a1	Merge pull request #1 from timattox/new-neighbor USER-DPD workaround for neighbor list issues	2016-12-09 16:08:31 -07:00
stanmoore1	586514e05c	Merge branch 'new-neighbor' into new-neighbor	2016-12-09 16:08:08 -07:00
Stan Moore	43c459ba56	More changes for Kokkos neighbor	2016-12-09 15:56:55 -07:00
Axel Kohlmeyer	b5c3d2f66c	Merge pull request #52 from timattox/new-neighbor USER-DPD workaround for neighbor list issues	2016-12-09 17:51:35 -05:00
Tim Mattox	5187cb97e5	USER-DPD: Make fix_shardlow request its own SSA-specific neighbor list, instead of having pair_dpd_fdt* make the SSA-neighbor list request for it. Forces an "extra" list to be built, but now skip lists work properly. Maybe we can detect if skip lists won't be used, and squash the extra list.	2016-12-09 15:42:27 -06:00
Tim Mattox	eff503e56c	Prevent neighbor list copies between SSA and non-SSA neighbor list requests.	2016-12-09 15:39:46 -06:00
Axel Kohlmeyer	cdcebab3bd	make the output of the %CPU/OpenMP threads line consistent with compiling in OpenMP support, not having USER-OMP installed	2016-12-09 14:43:56 -05:00
Axel Kohlmeyer	ddf678da51	make fix gcmc command overview consistent this closes #296	2016-12-09 14:30:27 -05:00
Stan Moore	435421301b	Small tweaks to Kokkos neighbor	2016-12-09 08:37:01 -07:00
Stan Moore	9b48c49f83	Removing used Kokkos file	2016-12-08 09:18:55 -07:00
Efrem Braun	d3d5ac17bf	Fixed small typos in doc	2016-12-07 19:37:51 -08:00
Stan Moore	8318c67816	Kokkos neighbor refactor	2016-12-07 13:00:27 -07:00
Axel Kohlmeyer	7c61dbf5e2	Merge branch 'new-neighbor' of github.com:akohlmey/lammps into new-neighbor	2016-12-07 13:43:04 -05:00
Axel Kohlmeyer	39a12b15d7	Merge branch 'master' into new-neighbor Resolved Conflicts: src/Purge.list src/neigh_derive.cpp	2016-12-07 13:40:14 -05:00
Axel Kohlmeyer	114926a488	Merge branch 'master' into new-neighbor	2016-10-02 00:26:56 -04:00
Axel Kohlmeyer	5eb9dd0c5d	Merge branch 'master' into new-neighbor	2016-09-29 23:14:28 -04:00
Axel Kohlmeyer	ebabc8f0bc	Merge remote-tracking branch 'lammps-rw/integration' into update-neighbor	2016-09-09 15:46:20 -04:00
Axel Kohlmeyer	232abf8534	restore locale and enforce grep option squashing	2016-09-09 15:42:14 -04:00
Axel Kohlmeyer	d22caf2658	Merge pull request #29 from timattox/new-neighbor USER-DPD: remove several files from src that came from src/USER-DPD/	2016-09-09 15:28:56 -04:00
Axel Kohlmeyer	3842aa6095	forward skip lists /omp neighbor list builds to non-omp implementations	2016-09-09 15:23:40 -04:00
Tim Mattox	32c240978a	USER-DPD: remove several files from src that came from src/USER-DPD/ These were accidentally added to git in `c9c2ae6`.	2016-09-09 15:17:42 -04:00
Axel Kohlmeyer	212c2617f6	delete a couple more files, that don't belong into src/	2016-09-09 14:56:23 -04:00
Axel Kohlmeyer	40f85c93ba	corrected mismatched free() vs. delete[]	2016-09-09 14:10:42 -04:00
Axel Kohlmeyer	2f02d98469	remove USER-DPD files that should not be where they are	2016-09-09 13:53:07 -04:00
Axel Kohlmeyer	4553881fc2	Merge pull request #28 from timattox/new-neighbor New neighbor, USER-DPD updates	2016-09-09 13:11:55 -04:00
Tim Mattox	81fcbcd99c	USER-DPD: move nstencil_ssa out of core LAMMPS into USER-DPD	2016-09-09 12:19:54 -04:00
Tim Mattox	82c6eb4675	USER-DPD: Set missing NP_HALF flag in npair_half_bin_newton_ssa.h	2016-09-09 12:19:36 -04:00
Tim Mattox	8ed3f4226e	USER-DPD: move custom binning stuff to a NBinSSA child class. Removes most SSA specific fields from class NeighList.	2016-09-09 12:19:06 -04:00
Tim Mattox	9b7a0d7e1c	Update gitignore for the new USER-DPD source files.	2016-09-09 12:18:51 -04:00
Steve Plimpton	c9c2ae6c61	new neighbor list changes	2016-09-07 13:42:58 -06:00