Merge branch 'master' into pair_drip

cmake/CMakeLists.txt

@@ -1220,8 +1220,7 @@ if(PKG_USER-INTEL)
                          ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
                          ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
                          ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
-                         ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
-                         ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
 
   set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
 
@@ -1230,9 +1229,12 @@ if(PKG_USER-INTEL)
   RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
   RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
   RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
-  RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 
   get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
+  if(PKG_KSPACE)
+    list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
+    RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
+  endif()
 
   list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
   include_directories(${USER-INTEL_SOURCES_DIR})
@@ -1370,7 +1372,15 @@ if(PKG_GPU)
       set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
 
       file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
-      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
+      list(REMOVE_ITEM GPU_LIB_CU
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
+      )
 
       foreach(GPU_KERNEL ${GPU_LIB_CU})
           get_filename_component(basename ${GPU_KERNEL} NAME_WE)
@@ -1381,7 +1391,21 @@ if(PKG_GPU)
 
       GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
       GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
-      list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h)
+      GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
+      GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
+      GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
+      GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
+      GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
+
+      list(APPEND GPU_LIB_SOURCES
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
+      )
 
       add_library(gpu STATIC ${GPU_LIB_SOURCES})
       target_link_libraries(gpu ${OpenCL_LIBRARIES})

cmake/Modules/OpenCLUtils.cmake

@@ -6,7 +6,7 @@ function(GenerateOpenCLHeader varname outfile files)
     foreach(IDX RANGE 2 ${ARG_END})
         list(GET ARGV ${IDX} filename)
         file(READ ${filename} content)
-        string(REGEX REPLACE "\\s*//[^\n]*\n" "" content "${content}")
+        string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
         string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
         string(REGEX REPLACE "\"" "\\\\\"" content "${content}")
         string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}")

cmake/README.md

@@ -211,7 +211,7 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </td>
 </tr>
 <tr>
-  <td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
+  <td><code>CMAKE_VERBOSE_MAKEFILE</code></td>
   <td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
   <td>
   <dl>

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "11 April 2019" "2019-04-11"
+.TH LAMMPS "30 April 2019" "2019-04-30"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_extras.txt

@@ -247,7 +247,10 @@ Maxwell50 = NVIDIA Maxwell generation CC 5.0
 Maxwell52 = NVIDIA Maxwell generation CC 5.2
 Maxwell53 = NVIDIA Maxwell generation CC 5.3
 Pascal60 = NVIDIA Pascal generation CC 6.0
-Pascal61 = NVIDIA Pascal generation CC 6.1 :ul
+Pascal61 = NVIDIA Pascal generation CC 6.1
+Volta70 = NVIDIA Volta generation CC 7.0
+Volta72 = NVIDIA Volta generation CC 7.2
+Turing75 = NVIDIA Turing generation CC 7.5 :ul
 
 [CMake build]:
 

doc/src/Commands_all.txt

@@ -83,6 +83,7 @@ An alphabetic list of all general LAMMPS commands.
 "molecule"_molecule.html,
 "ndx2group"_group2ndx.html,
 "neb"_neb.html,
+"neb_spin"_neb_spin.html,
 "neigh_modify"_neigh_modify.html,
 "neighbor"_neighbor.html,
 "newton"_newton.html,

doc/src/Commands_category.txt

@@ -116,6 +116,7 @@ Actions:
 
 "minimize"_minimize.html,
 "neb"_neb.html,
+"neb_spin"_neb_spin.html,
 "prd"_prd.html,
 "rerun"_rerun.html,
 "run"_run.html,

doc/src/Commands_fix.txt

@@ -107,6 +107,7 @@ OPT.
 "mvv/edpd"_fix_mvv_dpd.html,
 "mvv/tdpd"_fix_mvv_dpd.html,
 "neb"_fix_neb.html,
+"neb_spin"_fix_neb_spin.html,
 "nph (ko)"_fix_nh.html,
 "nph/asphere (o)"_fix_nph_asphere.html,
 "nph/body"_fix_nph_body.html,

doc/src/Eqs/neb_spin_angle.tex

@@ -0,0 +1,15 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \omega_i^{\nu} = 
+    (\nu - 1) \Delta \omega_i
+    {\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
+  , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/neb_spin_k.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{k}_i =  
+    \frac{\vec{m}_i^I \times \vec{m}_i^F}{\left|\vec{m}_i^I 
+    \times \vec{m}_i^F\right|} 
+    %&{\rm ~if~}& \vec{m}_i^I \times \vec{m}_i^F  
+  , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/neb_spin_rodrigues_formula.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{m}_i^{\nu} = \vec{m}_i^{I} \cos(\omega_i^{\nu})
+    + (\vec{k}_i \times \vec{m}_i^{I}) \sin(\omega_i^{\nu})
+    + (1.0-\cos(\omega_i^{\nu})) \vec{k}_i (\vec{k}_i\cdot
+    \vec{m}_i^{I})
+  , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_mdf-6.tex

@@ -1,9 +1,9 @@
 \documentclass[12pt]{article}
-
+\pagestyle{empty}
 \begin{document}
 
 $$
-   E(r) = \frac{A}{r^{12}} - \frac{A}{r^{6}}
+   E(r) = \frac{A}{r^{12}} - \frac{B}{r^{6}}
 $$
 
 \end{document}

doc/src/Howto_replica.txt

@@ -17,6 +17,7 @@ periodically.
 These are the relevant commands:
 
 "neb"_neb.html for nudged elastic band calculations
+"neb_spin"_neb_spin.html for magnetic nudged elastic band calculations
 "prd"_prd.html for parallel replica dynamics
 "tad"_tad.html for temperature accelerated dynamics
 "temper"_temper.html for parallel tempering

doc/src/Howto_spins.txt

@@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 Magnetic spins :h3
 
 The magnetic spin simulations are enabled by the SPIN package, whose
-implementation is detailed in "Tranchida"_#Tranchida7.
+implementation is detailed in "Tranchida"_#Tranchida.
 
 The model represents the simulation of atomic magnetic spins coupled
 to lattice vibrations. The dynamics of those magnetic spins can be used
@@ -36,13 +36,28 @@ A Langevin thermostat can be applied to those magnetic spins using
 "fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
 can be coupled to another Langevin thermostat applied to the atoms
 using "fix langevin"_fix_langevin.html in order to simulate
-thermostatted spin-lattice system.
+thermostatted spin-lattice systems.
 
 The magnetic Gilbert damping can also be applied using "fix
 langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
 the thermal energy of the Langevin thermostat, or to perform a
 relaxation of the magnetic configuration toward an equilibrium state.
 
+The command "fix setforce/spin"_fix_setforce.html allows to set the 
+components of the magnetic precession vectors (while erasing and 
+replacing the previously computed magnetic precession vectors on 
+the atom). 
+This command can be used to freeze the magnetic moment of certain 
+atoms in the simulation by zeroing their precession vector. 
+
+The command "fix nve/spin"_fix_nve_spin.html can be used to
+perform a symplectic integration of the combined dynamics of spins 
+and atomic motions.
+
+The minimization style "min/spin"_min_spin.html can be applied
+to the spins to perform a minimization of the spin configuration. 
+
+
 All the computed magnetic properties can be output by two main
 commands. The first one is "compute spin"_compute_spin.html, that
 enables to evaluate magnetic averaged quantities, such as the total
@@ -54,6 +69,6 @@ magnetic spin, or the magnetic force acting on this spin.
 
 :line
 
-:link(Tranchida7)
+:link(Tranchida)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="29 Mar 2019 version">
+<META NAME="docnumber" CONTENT="30 Apr 2019 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 @@
 :line
 
 LAMMPS Documentation :c,h1
-29 Mar 2019 version :c,h2
+30 Apr 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -918,6 +918,7 @@ src/SPIN: filenames -> commands
 "fix nve/spin"_fix_nve_spin.html
 "fix precession/spin"_fix_precession_spin.html
 "compute spin"_compute_spin.html
+"neb/spin"_neb_spin.html
 examples/SPIN :ul
 
 :line

doc/src/Speed_kokkos.txt

@@ -111,16 +111,10 @@ Makefile.kokkos_mpi_only) will give better performance than the OpenMP
 back end (i.e. Makefile.kokkos_omp) because some of the overhead to make
 the code thread-safe is removed.
 
-NOTE: The default for the "package kokkos"_package.html command is to
+NOTE: Use the "-pk kokkos" "command-line switch"_Run_options.html to 
-use "full" neighbor lists and set the Newton flag to "off" for both
+change the default "package kokkos"_package.html options. See its doc 
-pairwise and bonded interactions. However, when running on CPUs, it
+page for details and default settings. Experimenting with its options 
-will typically be faster to use "half" neighbor lists and set the
+can provide a speed-up for specific calculations. For example: 
-Newton flag to "on", just as is the case for non-accelerated pair
-styles. It can also be faster to use non-threaded communication.  Use
-the "-pk kokkos" "command-line switch"_Run_options.html to change the
-default "package kokkos"_package.html options. See its doc page for
-details and default settings. Experimenting with its options can
-provide a speed-up for specific calculations. For example:
 
 mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm :pre
 
@@ -190,19 +184,18 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of
 threads/task as Nt. The product of these two values should be N, i.e.
 256 or 264.
 
-NOTE: The default for the "package kokkos"_package.html command is to
+NOTE: The default for the "package kokkos"_package.html command when 
-use "full" neighbor lists and set the Newton flag to "off" for both
+running on KNL is to use "half" neighbor lists and set the Newton flag 
-pairwise and bonded interactions. When running on KNL, this will
+to "on" for both pairwise and bonded interactions. This will typically 
-typically be best for pair-wise potentials. For many-body potentials,
+be best for many-body potentials. For simpler pair-wise potentials, it 
-using "half" neighbor lists and setting the Newton flag to "on" may be
+may be faster to use a "full" neighbor list with Newton flag to "off". 
-faster. It can also be faster to use non-threaded communication.  Use
+Use the "-pk kokkos" "command-line switch"_Run_options.html to change 
-the "-pk kokkos" "command-line switch"_Run_options.html to change the
+the default "package kokkos"_package.html options. See its doc page for 
-default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can provide 
-details and default settings. Experimenting with its options can
+a speed-up for specific calculations. For example: 
-provide a speed-up for specific calculations. For example:
 
-mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj      #  Newton off, full neighbor list, non-threaded comm
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm host -in in.reax      #  Newton on, half neighbor list, threaded comm
-mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax      # Newton on, half neighbor list, non-threaded comm :pre
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton off neigh full comm no -in in.lj      # Newton off, full neighbor list, non-threaded comm :pre
 
 NOTE: MPI tasks and threads should be bound to cores as described
 above for CPUs.
@@ -236,19 +229,19 @@ one or more nodes, each with two GPUs:
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node
 mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
 
-NOTE: The default for the "package kokkos"_package.html command is to
+NOTE: The default for the "package kokkos"_package.html command when 
-use "full" neighbor lists and set the Newton flag to "off" for both
+running on GPUs is to use "full" neighbor lists and set the Newton flag 
-pairwise and bonded interactions, along with threaded communication.
+to "off" for both pairwise and bonded interactions, along with threaded 
-When running on Maxwell or Kepler GPUs, this will typically be
+communication. When running on Maxwell or Kepler GPUs, this will 
-best. For Pascal GPUs, using "half" neighbor lists and setting the
+typically be best. For Pascal GPUs, using "half" neighbor lists and 
-Newton flag to "on" may be faster. For many pair styles, setting the
+setting the Newton flag to "on" may be faster. For many pair styles, 
-neighbor binsize equal to the ghost atom cutoff will give speedup.
+setting the neighbor binsize equal to twice the CPU default value will 
-Use the "-pk kokkos" "command-line switch"_Run_options.html to change
+give speedup, which is the default when running on GPUs. Use the "-pk 
-the default "package kokkos"_package.html options. See its doc page
+kokkos" "command-line switch"_Run_options.html to change the default 
-for details and default settings. Experimenting with its options can
+"package kokkos"_package.html options. See its doc page for details and 
-provide a speed-up for specific calculations. For example:
+default settings. Experimenting with its options can provide a speed-up 
+for specific calculations. For example: 
 
-mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj      # Set binsize = neighbor ghost cutoff
 mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighbor list, set binsize = neighbor ghost cutoff :pre
 
 NOTE: For good performance of the KOKKOS package on GPUs, you must

doc/src/commands_list.txt

@@ -67,6 +67,7 @@ Commands :h1
    minimize
    molecule
    neb
+   neb_spin
    neigh_modify
    neighbor
    newton

doc/src/fix_colvars.txt

@@ -98,6 +98,16 @@ fix to add the energy change from the biasing force added by the fix
 to the system's potential energy as part of "thermodynamic
 output"_thermo_style.html.
 
+The {fix_modify configfile <config file>} option allows to add settings
+from an additional config file to the colvars module. This option can
+only be used, after the system has been initialized with a "run"_run.html
+command.
+
+The {fix_modify config <quoted string>} option allows to add settings
+from inline strings. Those have to fit on a single line when enclosed
+in a pair of double quotes ("), or can span multiple lines when bracketed
+by a pair of triple double quotes (""", like python embedded documentation).
+
 This fix computes a global scalar which can be accessed by various
 "output commands"_Howto_output.html.  The scalar is the cumulative
 energy change due to this fix.  The scalar value calculated by this

doc/src/fix_langevin_spin.txt

@@ -99,4 +99,4 @@ integration fix (e.g. {fix nve/spin}).
 
 :link(Tranchida2)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/fix_neb.txt

@@ -97,7 +97,7 @@ Note that in this case the specified {Kspring} is in force/distance
 units.
 
 With a value of {ideal}, the spring force is computed as suggested in
-"(WeinenE)"_#WeinenE :
+"(WeinanE)"_#WeinanE :
 
 Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
 
@@ -224,8 +224,8 @@ specified (no inter-replica force on the end replicas).
 [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).
 
-:link(WeinenE)
+:link(WeinanE)
-[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
+[(WeinanE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
 
 :link(Jonsson)
 [(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum

doc/src/fix_neb_spin.txt

@@ -0,0 +1,76 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix neb/spin command :h3
+
+[Syntax:]
+
+fix ID group-ID neb/spin Kspring :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+neb/spin = style name of this fix command :l
+Kspring = spring constant for parallel nudging force
+(force/distance units or force units, see parallel keyword) :pre,ule
+
+[Examples:]
+
+fix 1 active neb/spin 1.0
+
+[Description:]
+
+Add nudging forces to spins in the group for a multi-replica
+simulation run via the "neb/spin"_neb_spin.html command to perform a 
+geodesic nudged elastic band (GNEB) calculation for finding the 
+transition state.
+Hi-level explanations of GNEB are given with the 
+"neb/spin"_neb_spin.html command and on the 
+"Howto replica"_Howto_replica.html doc page.  
+The fix neb/spin command must be used with the "neb/spin" command and 
+defines how inter-replica nudging forces are computed.  A GNEB 
+calculation is divided in two stages. In the first stage n replicas 
+are relaxed toward a MEP until convergence.  In the second stage, the 
+climbing image scheme is enabled, so that the replica having the highest 
+energy relaxes toward the saddle point (i.e. the point of highest energy 
+along the MEP), and a second relaxation is performed.
+
+The nudging forces are calculated as explained in
+"(BessarabB)"_#BessarabB).
+See this reference for more explanation about their expression.
+
+[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"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+as invoked by the "minimize"_minimize.html command via the
+"neb/spin"_neb_spin.html command.
+
+[Restrictions:]
+
+This command can only be used if LAMMPS was built with the SPIN
+package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"neb_spin"_neb_spin.html
+
+[Default:]
+
+none
+
+:line
+
+:link(BessarabB)
+[(BessarabB)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
+335-347 (2015).

doc/src/fix_nve_spin.txt

@@ -73,4 +73,4 @@ instead of "array" is also valid.
 
 :link(Tranchida1)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/fix_precession_spin.txt

@@ -31,7 +31,7 @@ fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :p
 
 [Description:]
 
-Impose a force torque to each magnetic spin in the group.
+This fix applies a precession torque to each magnetic spin in the group.
 
 Style {zeeman} is used for the simulation of the interaction
 between the magnetic spins in the defined group and an external

doc/src/fix_print.txt

@@ -14,7 +14,7 @@ fix ID group-ID print N string keyword value ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 print = style name of this fix command :l
-N = print every N steps :l
+N = print every N steps; N can be a variable (see below) :l
 string = text string to print with optional variable names :l
 zero or more keyword/value pairs may be appended :l
 keyword = {file} or {append} or {screen} or {title} :l
@@ -40,6 +40,21 @@ If it contains variables it must be enclosed in double quotes to
 insure they are not evaluated when the input script line is read, but
 will instead be evaluated each time the string is printed.
 
+Instead of a numeric value, N can be specified as an "equal-style
+variable"_variable.html, which should be specified as v_name, where
+name is the variable name.  In this case, the variable is evaluated at
+the beginning of a run to determine the [next] timestep at which the
+string will be written out.  On that timestep, the variable will be
+evaluated again to determine the next timestep, etc.
+Thus the variable should return timestep values.  See the stagger()
+and logfreq() and stride() math functions for "equal-style
+variables"_variable.html, as examples of useful functions to use in
+this context. For example, the following commands will print output at
+timesteps 10,20,30,100,200,300,1000,2000,etc:
+
+variable        s equal logfreq(10,3,10)
+fix extra all print v_s "Coords of marker atom = $x $y $z" :pre
+
 The specified group-ID is ignored by this fix.
 
 See the "variable"_variable.html command for a description of {equal}

doc/src/fix_setforce.txt

@@ -8,6 +8,7 @@
 
 fix setforce command :h3
 fix setforce/kk command :h3
+fix setforce/spin command :h3
 
 [Syntax:]
 
@@ -27,6 +28,7 @@ keyword = {region}  :l
 
 fix freeze indenter setforce 0.0 0.0 0.0
 fix 2 edge setforce NULL 0.0 0.0
+fix 1 edge setforce/spin 0.0 0.0 0.0
 fix 2 edge setforce NULL 0.0 v_oscillate :pre
 
 [Description:]
@@ -65,6 +67,19 @@ to it.
 
 :line
 
+Style {spin} suffix sets the components of the magnetic precession 
+vectors instead of the mechanical forces. This also erases all 
+previously computed magnetic precession vectors on the atom, though 
+additional magnetic fixes could add new forces.
+
+This command can be used to freeze the magnetic moment of certain 
+atoms in the simulation by zeroing their precession vector. 
+
+All options defined above remain valid, they just apply to the magnetic 
+precession vectors instead of the forces.
+
+: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
@@ -117,7 +132,10 @@ forces to any value besides zero when performing a minimization.  Use
 the "fix addforce"_fix_addforce.html command if you want to apply a
 non-zero force to atoms during a minimization.
 
-[Restrictions:] none
+[Restrictions:] 
+
+The fix {setforce/spin} only makes sense when LAMMPS was built with the
+SPIN package.
 
 [Related commands:]
 

doc/src/fix_wall_gran.txt

@@ -17,13 +17,13 @@ wall/gran = style name of this fix command :l
 fstyle = style of force interactions between particles and wall :l
   possible choices: hooke, hooke/history, hertz/history, granular :pre
 fstyle_params = parameters associated with force interaction style :l
-  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
+  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
-	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
+        Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
-	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
+        Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
-	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
+        gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
-	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  
+        gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
-	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 
+        xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
-	dampflag = 0 or 1 if tangential damping force is excluded or included :pre
+        dampflag = 0 or 1 if tangential damping force is excluded or included :pre
   For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
 wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l
 args = list of arguments for a particular style :l
@@ -46,10 +46,10 @@ keyword = {wiggle} or {shear} :l
 
 fix 1 all wall/gran hooke  200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
 fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
-fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 
+fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0
-fix 3 all wall/gran granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 zplane 0.0 NULL
+fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
-fix 4 all wall/gran granular jkr 1000.0 50.0 0.3 5.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall zcylinder 15.0 wiggle z 3.0 2.0
+fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
-fix 5 all wall/gran granular dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall zplane 0.0 NULL :pre
+fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre
 
 [Description:]
 

doc/src/fix_wall_gran_region.txt

@@ -17,23 +17,23 @@ wall/region = style name of this fix command :l
 fstyle = style of force interactions between particles and wall :l
   possible choices: hooke, hooke/history, hertz/history, granular :pre
 fstyle_params = parameters associated with force interaction style :l
-  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
+  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
-	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
+        Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
-	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
+        Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
-	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
+        gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
-	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  
+        gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)
-	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 
+        xmu = static yield criterion (unitless value between 0.0 and 1.0e4)
-	dampflag = 0 or 1 if tangential damping force is excluded or included :pre
+        dampflag = 0 or 1 if tangential damping force is excluded or included :pre
   For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
 wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l
 region-ID = region whose boundary will act as wall :l,ule
 
 [Examples:]
 
-fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone 
+fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone
-fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 region myBox
+fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
-fix 4 all wall/gran/region granular jkr 1000.0 50.0 tangential linear_history 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
+fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
-fix 5 all wall/gran/region granular dmt 1000.0 50.0 0.3 10.0 tangential linear_history 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall region myCone :pre
+fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre
 
 [Description:]
 

doc/src/fixes.txt

@@ -84,6 +84,7 @@ Fixes :h1
    fix_msst
    fix_mvv_dpd
    fix_neb
+   fix_neb_spin
    fix_nh
    fix_nh_eff
    fix_nh_uef

doc/src/lammps.book

@@ -179,6 +179,7 @@ min_spin.html
 minimize.html
 molecule.html
 neb.html
+neb_spin.html
 neigh_modify.html
 neighbor.html
 newton.html
@@ -309,6 +310,7 @@ fix_mscg.html
 fix_msst.html
 fix_mvv_dpd.html
 fix_neb.html
+fix_neb_spin.html
 fix_nh.html
 fix_nh_eff.html
 fix_nph_asphere.html

doc/src/neb_spin.txt

@@ -0,0 +1,375 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+neb command :h3
+
+[Syntax:]
+
+neb/spin etol ttol N1 N2 Nevery file-style arg keyword :pre
+
+etol = stopping tolerance for energy (energy units) :ulb,l
+ttol = stopping tolerance for torque ( units) :l
+N1 = max # of iterations (timesteps) to run initial NEB :l
+N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
+Nevery = print replica energies and reaction coordinates every this many timesteps :l
+file-style = {final} or {each} or {none} :l
+  {final} arg = filename
+    filename = file with initial coords for final replica
+      coords for intermediate replicas are linearly interpolated
+      between first and last replica
+  {each} arg = filename
+    filename = unique filename for each replica (except first)
+      with its initial coords
+  {none} arg = no argument all replicas assumed to already have
+      their initial coords :pre
+keyword = {verbose}
+:ule
+
+[Examples:]
+
+neb/spin 0.1 0.0 1000 500 50 final coords.final
+neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i
+neb/spin 0.0 0.001 1000 500 50 none verbose :pre
+
+[Description:]
+
+Perform a geodesic nudged elastic band (GNEB) calculation using multiple
+replicas of a system.  Two or more replicas must be used; the first
+and last are the end points of the transition path.
+
+GNEB is a method for finding both the spin configurations and height
+of the energy barrier associated with a transition state, e.g.
+spins to perform a collective rotation from one energy basin to
+another. 
+The implementation in LAMMPS follows the discussion in the
+following paper: "(BessarabA)"_#BessarabA.
+
+Each replica runs on a partition of one or more processors.  Processor
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html.  Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on just one or two processors.  You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica.  See the "Howto replica"_Howto_replica.html
+doc page for further discussion.
+
+NOTE: As explained below, a GNEB calculation performs a damped dynamics
+minimization across all the replicas.  The "spin"_min_spin.html
+style minimizer has to be defined in your input script. 
+
+When a GNEB calculation is performed, it is assumed that each replica
+is running the same system, though LAMMPS does not check for this.
+I.e. the simulation domain, the number of magnetic atoms, the 
+interaction potentials, and the starting configuration when the neb 
+command is issued should be the same for every replica.
+
+In a GNEB calculation each replica is connected to other replicas by
+inter-replica nudging forces.  These forces are imposed by the "fix
+neb/spin"_fix_neb_spin.html command, which must be used in conjunction 
+with the neb command.  
+The group used to define the fix neb/spin command defines the
+GNEB magnetic atoms which are the only ones that inter-replica springs 
+are applied to.  
+If the group does not include all magnetic atoms, then non-GNEB
+magnetic atoms have no inter-replica springs and the torques they feel 
+and their precession motion is computed in the usual way due only 
+to other magnetic atoms within their replica.  
+Conceptually, the non-GNEB atoms provide a background force field for 
+the GNEB atoms.  
+Their magnetic spins can be allowed to evolve during the GNEB 
+minimization procedure.
+
+The initial spin configuration for each of the replicas can be
+specified in different manners via the {file-style} setting, as
+discussed below.  Only atomic spins whose initial coordinates should 
+differ from the current configuration need to be specified.
+
+Conceptually, the initial and final configurations for the first
+replica should be states on either side of an energy barrier.
+
+As explained below, the initial configurations of intermediate
+replicas can be spin coordinates interpolated in a linear fashion
+between the first and last replicas.  This is often adequate for
+simple transitions.  For more complex transitions, it may lead to slow
+convergence or even bad results if the minimum energy path (MEP, see
+below) of states over the barrier cannot be correctly converged to
+from such an initial path.  In this case, you will want to generate
+initial states for the intermediate replicas that are geometrically
+closer to the MEP and read them in.
+
+:line
+
+For a {file-style} setting of {final}, a filename is specified which
+contains atomic and spin coordinates for zero or more atoms, in the 
+format described below.  
+For each atom that appears in the file, the new coordinates are 
+assigned to that atom in the final replica.  Each intermediate replica 
+also assigns a new spin to that atom in an interpolated manner.  
+This is done by using the current direction of the spin at the starting 
+point and the read-in direction as the final point.  
+The "angular distance" between them is calculated, and the new direction 
+is assigned to be a fraction of the angular distance.
+
+NOTE: The "angular distance" between the starting and final point is 
+evaluated in the geodesic sense, as described in 
+"(BessarabA)"_#BessarabA. 
+
+NOTE: The angular interpolation between the starting and final point 
+is achieved using Rodrigues formula:
+
+:c,image(Eqs/neb_spin_rodrigues_formula.jpg)
+
+where m_i^I is the initial spin configuration for the spin i,
+omega_i^nu is a rotation angle defined as:
+
+:c,image(Eqs/neb_spin_angle.jpg)
+
+with nu the image number, Q the total number of images, and 
+omega_i the total rotation between the initial and final spins.
+k_i defines a rotation axis such as:
+
+:c,image(Eqs/neb_spin_k.jpg)
+
+if the initial and final spins are not aligned.
+If the initial and final spins are aligned, then their cross
+product is null, and the expression above does not apply.
+If they point toward the same direction, the intermediate images 
+conserve the same orientation.
+If the initial and final spins are aligned, but point toward
+opposite directions, an arbitrary rotation vector belonging to
+the plane perpendicular to initial and final spins is chosen. 
+In this case, a warning message is displayed.
+
+For a {file-style} setting of {each}, a filename is specified which is
+assumed to be unique to each replica. 
+See the "neb"_neb.html documentation page for more information about this 
+option.
+
+For a {file-style} setting of {none}, no filename is specified.  Each
+replica is assumed to already be in its initial configuration at the
+time the neb command is issued.  This allows each replica to define
+its own configuration by reading a replica-specific data or restart or
+dump file, via the "read_data"_read_data.html,
+"read_restart"_read_restart.html, or "read_dump"_read_dump.html
+commands.  The replica-specific names of these files can be specified
+as in the discussion above for the {each} file-style.  Also see the
+section below for how a NEB calculation can produce restart files, so
+that a long calculation can be restarted if needed.
+
+NOTE: None of the {file-style} settings change the initial
+configuration of any atom in the first replica.  The first replica
+must thus be in the correct initial configuration at the time the neb
+command is issued.
+
+:line
+
+A NEB calculation proceeds in two stages, each of which is a
+minimization procedure, performed via damped dynamics.  To enable
+this, you must first define a damped spin dynamics
+"min_style"_min_style.html, using the {spin} style (see
+"min_spin"_min_spin.html for more information).  
+The other styles cannot be used, since they relax the lattice
+degrees of freedom instead of the spins.
+
+The minimizer tolerances for energy and force are set by {etol} and
+{ttol}, the same as for the "minimize"_minimize.html command.
+
+A non-zero {etol} means that the GNEB calculation will terminate if the
+energy criterion is met by every replica.  The energies being compared
+to {etol} do not include any contribution from the inter-replica
+nudging forces, since these are non-conservative.  A non-zero {ttol}
+means that the GNEB calculation will terminate if the torque criterion
+is met by every replica.  The torques being compared to {ttol} include
+the inter-replica nudging forces.
+
+The maximum number of iterations in each stage is set by {N1} and
+{N2}.  These are effectively timestep counts since each iteration of
+damped dynamics is like a single timestep in a dynamics
+"run"_run.html.  During both stages, the potential energy of each
+replica and its normalized distance along the reaction path (reaction
+coordinate RD) will be printed to the screen and log file every
+{Nevery} timesteps.  The RD is 0 and 1 for the first and last replica.
+For intermediate replicas, it is the cumulative angular distance 
+(normalized by the total cumulative angular distance) between adjacent 
+replicas, where "distance" is defined as the length of the 3N-vector of 
+the geodesic distances in spin coordinates, with N the number of
+GNEB spins involved (see equation (13) in "(BessarabA)"_#BessarabA).
+These outputs allow you to monitor NEB's progress in
+finding a good energy barrier.  {N1} and {N2} must both be multiples
+of {Nevery}.
+
+In the first stage of GNEB, the set of replicas should converge toward
+a minimum energy path (MEP) of conformational states that transition
+over a barrier.  The MEP for a transition is defined as a sequence of
+3N-dimensional spin states, each of which has a potential energy 
+gradient parallel to the MEP itself.  
+The configuration of highest energy along a MEP corresponds to a saddle 
+point.  The replica states will also be roughly equally spaced along 
+the MEP due to the inter-replica nudging force added by the 
+"fix neb"_fix_neb.html command.
+
+In the second stage of GNEB, the replica with the highest energy is
+selected and the inter-replica forces on it are converted to a force
+that drives its spin coordinates to the top or saddle point of the
+barrier, via the barrier-climbing calculation described in
+"(BessarabA)"_#BessarabA.  As before, the other replicas rearrange
+themselves along the MEP so as to be roughly equally spaced.
+
+When both stages are complete, if the GNEB calculation was successful,
+the configurations of the replicas should be along (close to) the MEP
+and the replica with the highest energy should be a spin
+configuration at (close to) the saddle point of the transition. The
+potential energies for the set of replicas represents the energy
+profile of the transition along the MEP.
+
+:line
+
+An atom map must be defined which it is not by default for "atom_style
+atomic"_atom_style.html problems.  The "atom_modify
+map"_atom_modify.html command can be used to do this.
+
+An initial value can be defined for the timestep. Although, the {spin} 
+minimization algorithm is an adaptive timestep methodology, so that 
+this timestep is likely to evolve during the calculation.  
+
+The minimizers in LAMMPS operate on all spins in your system, even
+non-GNEB atoms, as defined above.  
+
+:line
+
+Each file read by the neb/spin command containing spin coordinates used
+to initialize one or more replicas must be formatted as follows.
+
+The file can be ASCII text or a gzipped text file (detected by a .gz
+suffix).  The file can contain initial blank lines or comment lines
+starting with "#" which are ignored.  The first non-blank, non-comment
+line should list N = the number of lines to follow.  The N successive
+lines contain the following information:
+
+ID1 g1 x1 y1 z1 sx1 sy1 sz1
+ID2 g2 x2 y2 z2 sx2 sy2 sz2
+...
+IDN gN yN zN sxN syN szN :pre
+
+The fields are the atom ID, the norm of the associated magnetic spin, 
+followed by the {x,y,z} coordinates and the {sx,sy,sz} spin coordinates.
+The lines can be listed in any order.  Additional trailing information on
+the line is OK, such as a comment.
+
+Note that for a typical GNEB calculation you do not need to specify
+initial spin coordinates for very many atoms to produce differing starting
+and final replicas whose intermediate replicas will converge to the
+energy barrier.  Typically only new spin coordinates for atoms
+geometrically near the barrier need be specified.
+
+Also note there is no requirement that the atoms in the file
+correspond to the GNEB atoms in the group defined by the "fix
+neb"_fix_neb.html command.  Not every GNEB atom need be in the file,
+and non-GNEB atoms can be listed in the file.
+
+:line
+
+Four kinds of output can be generated during a GNEB calculation: energy
+barrier statistics, thermodynamic output by each replica, dump files,
+and restart files.
+
+When running with multiple partitions (each of which is a replica in
+this case), the print-out to the screen and master log.lammps file
+contains a line of output, printed once every {Nevery} timesteps.  It
+contains the timestep, the maximum torque per replica, the maximum
+torque per atom (in any replica), potential gradients in the initial,
+final, and climbing replicas, the forward and backward energy
+barriers, the total reaction coordinate (RDT), and the normalized
+reaction coordinate and potential energy of each replica.
+
+The "maximum torque per replica" is the two-norm of the
+3N-length vector given by the cross product of a spin by its
+precession vector omega, in each replica, maximized across replicas, 
+which is what the {ttol} setting is checking against.  In this case, N is
+all the atoms in each replica.  The "maximum torque per atom" is the
+maximum torque component of any atom in any replica.  The potential
+gradients are the two-norm of the 3N-length magnetic precession vector 
+solely due to the interaction potential i.e. without adding in 
+inter-replica forces, and projected along the path tangent (as detailed 
+in Appendix D of "(BessarabA)"_#BessarabA).
+
+The "reaction coordinate" (RD) for each replica is the two-norm of the
+3N-length vector of geodesic distances between its spins and the preceding
+replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to 
+the RD of the preceding replica. The RD of the first replica RD1 = 0.0; 
+the RD of the final replica RDN = RDT, the total reaction coordinate.  
+The normalized RDs are divided by RDT, so that they form a monotonically 
+increasing sequence from zero to one. When computing RD, N only includes 
+the spins being operated on by the fix neb/spin command.
+
+The forward (reverse) energy barrier is the potential energy of the
+highest replica minus the energy of the first (last) replica.
+
+Supplementary information for all replicas can be printed out to the
+screen and master log.lammps file by adding the verbose keyword. This
+information include the following. 
+The "GradVidottan" are the projections of the potential gradient for 
+the replica i on its tangent vector (as detailed in Appendix D of 
+"(BessarabA)"_#BessarabA).
+The "DNi" are the non normalized geodesic distances (see equation (13) 
+of "(BessarabA)"_#BessarabA), between a replica i and the next replica 
+i+1. For the last replica, this distance is not defined and a "NAN"
+value is the corresponding output. 
+
+When a NEB calculation does not converge properly, the supplementary
+information can help understanding what is going wrong. 
+
+When running on multiple partitions, LAMMPS produces additional log
+files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a
+GNEB calculation, these contain the thermodynamic output for each
+replica.
+
+If "dump"_dump.html commands in the input script define a filename
+that includes a {universe} or {uloop} style "variable"_variable.html,
+then one dump file (per dump command) will be created for each
+replica.  At the end of the GNEB calculation, the final snapshot in
+each file will contain the sequence of snapshots that transition the
+system over the energy barrier.  Earlier snapshots will show the
+convergence of the replicas to the MEP.
+
+Likewise, "restart"_restart.html filenames can be specified with a
+{universe} or {uloop} style "variable"_variable.html, to generate
+restart files for each replica.  These may be useful if the GNEB
+calculation fails to converge properly to the MEP, and you wish to
+restart the calculation from an intermediate point with altered
+parameters.
+
+A c file script in provided in the tool/spin/interpolate_gneb
+directory, that interpolates the MEP given the information provided 
+by the verbose output option (as detailed in Appendix D of
+"(BessarabA)"_#BessarabA). 
+
+:line
+
+[Restrictions:]
+
+This command can only be used if LAMMPS was built with the SPIN
+package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+:line
+
+[Related commands:]
+
+"min/spin"_min_spin.html, "fix neb/spin"_fix_neb_spin.html
+
+[Default:]
+
+none
+
+:line
+
+:link(BessarabA)
+[(BessarabA)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
+335-347 (2015).

doc/src/package.txt

@@ -64,7 +64,7 @@ args = arguments specific to the style :l
       {no_affinity} values = none
   {kokkos} args = keyword value ...
     zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse}
+    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {gpu/direct}
       {neigh} value = {full} or {half}
         full = full neighbor list
         half = half neighbor list built in thread-safe manner
@@ -72,7 +72,7 @@ args = arguments specific to the style :l
         full = full neighbor list
         half = half neighbor list built in thread-safe manner
       {newton} = {off} or {on}
-        off = set Newton pairwise and bonded flags off (default)
+        off = set Newton pairwise and bonded flags off
         on = set Newton pairwise and bonded flags on
       {binsize} value = size
         size = bin size for neighbor list construction (distance units)
@@ -422,101 +422,103 @@ processes/threads used for LAMMPS.
 
 :line
 
-The {kokkos} style invokes settings associated with the use of the
+The {kokkos} style invokes settings associated with the use of the 
-KOKKOS package.
+KOKKOS package. 
 
-All of the settings are optional keyword/value pairs.  Each has a
+All of the settings are optional keyword/value pairs. Each has a default 
-default value as listed below.
+value as listed below. 
 
-The {neigh} keyword determines how neighbor lists are built.  A value
+The {neigh} keyword determines how neighbor lists are built. A value of 
-of {half} uses a thread-safe variant of half-neighbor lists,
+{half} uses a thread-safe variant of half-neighbor lists, the same as 
-the same as used by most pair styles in LAMMPS.
+used by most pair styles in LAMMPS, which is the default when running on 
+CPUs (i.e. the Kokkos CUDA back end is not enabled). 
 
-A value of {full} uses a full neighbor lists and is the default.  This
+A value of {full} uses a full neighbor lists and is the default when 
-performs twice as much computation as the {half} option, however that
+running on GPUs. This performs twice as much computation as the {half} 
-is often a win because it is thread-safe and doesn't require atomic
+option, however that is often a win because it is thread-safe and 
-operations in the calculation of pair forces.  For that reason, {full}
+doesn't require atomic operations in the calculation of pair forces. For 
-is the default setting.  However, when running in MPI-only mode with 1
+that reason, {full} is the default setting for GPUs. However, when 
-thread per MPI task, {half} neighbor lists will typically be faster,
+running on CPUs, a {half} neighbor list is the default because it are 
-just as it is for non-accelerated pair styles. Similarly, the {neigh/qeq}
+often faster, just as it is for non-accelerated pair styles. Similarly, 
-keyword determines how neighbor lists are built for "fix qeq/reax/kk"_fix_qeq_reax.html.
+the {neigh/qeq} keyword determines how neighbor lists are built for "fix 
-If not explicitly set, the value of {neigh/qeq} will match {neigh}.
+qeq/reax/kk"_fix_qeq_reax.html. If not explicitly set, the value of 
+{neigh/qeq} will match {neigh}. 
 
-The {newton} keyword sets the Newton flags for pairwise and bonded
+The {newton} keyword sets the Newton flags for pairwise and bonded 
-interactions to {off} or {on}, the same as the "newton"_newton.html
+interactions to {off} or {on}, the same as the "newton"_newton.html 
-command allows.  The default is {off} because this will almost always
+command allows. The default for GPUs is {off} because this will almost 
-give better performance for the KOKKOS package.  This means more
+always give better performance for the KOKKOS package. This means more 
-computation is done, but less communication.  However, when running in
+computation is done, but less communication. However, when running on 
-MPI-only mode with 1 thread per MPI task, a value of {on} will
+CPUs a value of {on} is the default since it can often be faster, just 
-typically be faster, just as it is for non-accelerated pair styles.
+as it is for non-accelerated pair styles 
 
-The {binsize} keyword sets the size of bins used to bin atoms in
+The {binsize} keyword sets the size of bins used to bin atoms in 
-neighbor list builds.  The same value can be set by the "neigh_modify
+neighbor list builds. The same value can be set by the "neigh_modify 
-binsize"_neigh_modify.html command.  Making it an option in the
+binsize"_neigh_modify.html command. Making it an option in the package 
-package kokkos command allows it to be set from the command line.  The
+kokkos command allows it to be set from the command line. The default 
-default value is 0.0, which means the LAMMPS default will be used,
+value for CPUs is 0.0, which means the LAMMPS default will be used, 
-which is bins = 1/2 the size of the pairwise cutoff + neighbor skin
+which is bins = 1/2 the size of the pairwise cutoff + neighbor skin 
-distance.  This is fine when neighbor lists are built on the CPU.  For
+distance. This is fine when neighbor lists are built on the CPU. For GPU 
-GPU builds, a 2x larger binsize equal to the pairwise cutoff +
+builds, a 2x larger binsize equal to the pairwise cutoff + neighbor skin 
-neighbor skin, is often faster, which can be set by this keyword.
+is often faster, which is the default. Note that if you use a 
-Note that if you use a longer-than-usual pairwise cutoff, e.g. to
+longer-than-usual pairwise cutoff, e.g. to allow for a smaller fraction 
-allow for a smaller fraction of KSpace work with a "long-range
+of KSpace work with a "long-range Coulombic solver"_kspace_style.html 
-Coulombic solver"_kspace_style.html because the GPU is faster at
+because the GPU is faster at performing pairwise interactions, then this 
-performing pairwise interactions, then this rule of thumb may give too
+rule of thumb may give too large a binsize and the default should be 
-large a binsize.
+overridden with a smaller value. 
 
-The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} keywords determine
+The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} 
-whether the host or device performs the packing and unpacking of data
+keywords determine whether the host or device performs the packing and 
-when communicating per-atom data between processors.  "Exchange"
+unpacking of data when communicating per-atom data between processors. 
-communication happens only on timesteps that neighbor lists are
+"Exchange" communication happens only on timesteps that neighbor lists 
-rebuilt.  The data is only for atoms that migrate to new processors.
+are rebuilt. The data is only for atoms that migrate to new processors. 
-"Forward" communication happens every timestep. "Reverse" communication
+"Forward" communication happens every timestep. "Reverse" communication 
-happens every timestep if the {newton} option is on.  The data is for atom
+happens every timestep if the {newton} option is on. The data is for 
-coordinates and any other atom properties that needs to be updated for
+atom coordinates and any other atom properties that needs to be updated 
-ghost atoms owned by each processor.
+for ghost atoms owned by each processor. 
 
-The {comm} keyword is simply a short-cut to set the same value
+The {comm} keyword is simply a short-cut to set the same value for both 
-for both the {comm/exchange} and {comm/forward} and {comm/reverse} keywords.
+the {comm/exchange} and {comm/forward} and {comm/reverse} keywords. 
 
-The value options for all 3 keywords are {no} or {host} or {device}.
+The value options for all 3 keywords are {no} or {host} or {device}. A 
-A value of {no} means to use the standard non-KOKKOS method of
+value of {no} means to use the standard non-KOKKOS method of 
-packing/unpacking data for the communication.  A value of {host} means
+packing/unpacking data for the communication. A value of {host} means to 
-to use the host, typically a multi-core CPU, and perform the
+use the host, typically a multi-core CPU, and perform the 
-packing/unpacking in parallel with threads.  A value of {device}
+packing/unpacking in parallel with threads. A value of {device} means to 
-means to use the device, typically a GPU, to perform the
+use the device, typically a GPU, to perform the packing/unpacking 
-packing/unpacking operation.
+operation. 
 
-The optimal choice for these keywords depends on the input script and
+The optimal choice for these keywords depends on the input script and 
-the hardware used.  The {no} value is useful for verifying that the
+the hardware used. The {no} value is useful for verifying that the 
-Kokkos-based {host} and {device} values are working correctly.
+Kokkos-based {host} and {device} values are working correctly. It is the 
-It may also be the fastest choice when using Kokkos styles in
+default when running on CPUs since it is usually the fastest. 
-MPI-only mode (i.e. with a thread count of 1).
 
-When running on CPUs or Xeon Phi, the {host} and {device} values work
+When running on CPUs or Xeon Phi, the {host} and {device} values work 
-identically.  When using GPUs, the {device} value will typically be
+identically. When using GPUs, the {device} value is the default since it 
-optimal if all of your styles used in your input script are supported
+will typically be optimal if all of your styles used in your input 
-by the KOKKOS package.  In this case data can stay on the GPU for many
+script are supported by the KOKKOS package. In this case data can stay 
-timesteps without being moved between the host and GPU, if you use the
+on the GPU for many timesteps without being moved between the host and 
-{device} value.  This requires that your MPI is able to access GPU
+GPU, if you use the {device} value. This requires that your MPI is able 
-memory directly.  Currently that is true for OpenMPI 1.8 (or later
+to access GPU memory directly. Currently that is true for OpenMPI 1.8 
-versions), Mvapich2 1.9 (or later), and CrayMPI.  If your script uses
+(or later versions), Mvapich2 1.9 (or later), and CrayMPI. If your 
-styles (e.g. fixes) which are not yet supported by the KOKKOS package,
+script uses styles (e.g. fixes) which are not yet supported by the 
-then data has to be move between the host and device anyway, so it is
+KOKKOS package, then data has to be move between the host and device 
-typically faster to let the host handle communication, by using the
+anyway, so it is typically faster to let the host handle communication, 
-{host} value.  Using {host} instead of {no} will enable use of
+by using the {host} value. Using {host} instead of {no} will enable use 
-multiple threads to pack/unpack communicated data.
+of multiple threads to pack/unpack communicated data. 
 
-The {gpu/direct} keyword chooses whether GPU-direct will be used. When
+The {gpu/direct} keyword chooses whether GPU-direct will be used. When 
-this keyword is set to {on}, buffers in GPU memory are passed directly
+this keyword is set to {on}, buffers in GPU memory are passed directly 
-through MPI send/receive calls. This reduces overhead of first copying
+through MPI send/receive calls. This reduces overhead of first copying 
-the data to the host CPU. However GPU-direct is not supported on all
+the data to the host CPU. However GPU-direct is not supported on all 
-systems, which can lead to segmentation faults and would require
+systems, which can lead to segmentation faults and would require using a 
-using a value of {off}. If LAMMPS can safely detect that GPU-direct is
+value of {off}. If LAMMPS can safely detect that GPU-direct is not 
-not available (currently only possible with OpenMPI v2.0.0 or later),
+available (currently only possible with OpenMPI v2.0.0 or later), then 
-then the {gpu/direct} keyword is automatically set to {off} by default.
+the {gpu/direct} keyword is automatically set to {off} by default. When 
-When the {gpu/direct} keyword is set to {off} while any of the {comm}
+the {gpu/direct} keyword is set to {off} while any of the {comm} 
-keywords are set to {device}, the value for these {comm} keywords will
+keywords are set to {device}, the value for these {comm} keywords will 
-be automatically changed to {host}.
+be automatically changed to {host}. This setting has no effect if not 
+running on GPUs.
 
 :line
 
@@ -623,14 +625,16 @@ not used, you must invoke the package intel command in your input
 script or or via the "-pk intel" "command-line
 switch"_Run_options.html.
 
-For the KOKKOS package, the option defaults neigh = full, neigh/qeq =
+For the KOKKOS package, the option defaults for GPUs are neigh = full, 
-full, newton = off, binsize = 0.0, and comm = device, gpu/direct = on.
+neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default 
-When LAMMPS can safely detect, that GPU-direct is not available, the
+value, comm = device, gpu/direct = on. When LAMMPS can safely detect 
-default value of gpu/direct becomes "off".
+that GPU-direct is not available, the default value of gpu/direct 
-These settings are made automatically by the required "-k on"
+becomes "off". For CPUs or Xeon Phis, the option defaults are neigh = 
-"command-line switch"_Run_options.html. You can change them by
+half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. These 
-using the package kokkos command in your input script or via the
+settings are made automatically by the required "-k on" "command-line 
-"-pk kokkos command-line switch"_Run_options.html.
+switch"_Run_options.html. You can change them by using the package 
+kokkos command in your input script or via the "-pk kokkos command-line 
+switch"_Run_options.html.
 
 For the OMP package, the default is Nthreads = 0 and the option
 defaults are neigh = yes.  These settings are made automatically if

doc/src/pair_airebo.txt

@@ -36,7 +36,7 @@ pair_style airebo/morse 3.0
 pair_coeff * * ../potentials/CH.airebo-m H C :pre
 
 pair_style rebo
-pair_coeff * * ../potentials/CH.airebo H C :pre
+pair_coeff * * ../potentials/CH.rebo H C :pre
 
 [Description:]
 
@@ -57,7 +57,8 @@ The {rebo} pair style computes the Reactive Empirical Bond Order (REBO)
 Potential of "(Brenner)"_#Brenner. Note that this is the so-called
 2nd generation REBO from 2002, not the original REBO from 1990.
 As discussed below, 2nd generation REBO is closely related to the
-initial AIREBO; it is just a subset of the potential energy terms.
+initial AIREBO; it is just a subset of the potential energy terms
+with a few slightly different parameters
 
 The AIREBO potential consists of three terms:
 
@@ -113,12 +114,12 @@ various dihedral angle preferences in hydrocarbon configurations.
 :line
 
 Only a single pair_coeff command is used with the {airebo}, {airebo}
-or {rebo} style which specifies an AIREBO or AIREBO-M potential file
+or {rebo} style which specifies an AIREBO, REBO, or AIREBO-M potential
-with parameters for C and H.  Note that the {rebo} style in LAMMPS
+file with parameters for C and H.  Note that as of LAMMPS version
-uses the same AIREBO-formatted potential file.  These are mapped to
+15 May 2019 the {rebo} style in LAMMPS uses its own potential
-LAMMPS atom types by specifying N additional arguments after the
+file (CH.rebo).  These are mapped to LAMMPS atom types by specifying
-filename in the pair_coeff command, where N is the number of LAMMPS
+N additional arguments after the filename in the pair_coeff command,
-atom types:
+where N is the number of LAMMPS atom types:
 
 filename
 N element names = mapping of AIREBO elements to atom types :ul

doc/src/pair_granular.txt

@@ -24,22 +24,24 @@ cutoff = global cutoff (optional).  See discussion below. :ul
 [Examples:]
 
 pair_style granular
-pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 :pre
+pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping mass_velocity :pre
 
 pair_style granular
-pair_coeff * * hertz 1000.0 50.0 tangential mindlin NULL 1.0 0.4 :pre
+pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity :pre
 
 pair_style granular
-pair_coeff * * hertz/material 1e8 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :pre
+pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 :pre
 
 pair_style granular
-pair_coeff 1 1 jkr 1000.0 50.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :pre
-pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall :pre
 
 pair_style granular
-pair_coeff 1 1 hertz 1000.0 50.0 tangential mindlin 800.0 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff 1 * jkr 1000.0 500.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
-pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall
+pair_coeff 2 2 hertz 200.0 100.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall :pre
-pair_coeff 1 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall :pre
+
+pair_style granular
+pair_coeff 1 1 dmt 1000.0 50.0 0.3 0.0 tangential mindlin NULL 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin NULL 0.5 0.1 rolling sds 500.0 200.0 0.1 twisting marshall :pre
 
 [Description:]
 
@@ -57,18 +59,18 @@ global, but can be set to different values for different combinations
 of particle types, as determined by the "pair_coeff"_pair_coeff.html
 command.  If the contact model choice is the same for two particle
 types, the mixing for the cross-coefficients can be carried out
-automatically. This is shown in the second example, where model
+automatically. This is shown in the last example, where model
 choices are the same for type 1 - type 1 as for type 2 - type2
 interactions, but coefficients are different. In this case, the
-coefficients for type 2 - type interactions can be determined from
+mixed coefficients for type 1 - type 2 interactions can be determined from
 mixing rules discussed below.  For additional flexibility,
 coefficients as well as model forms can vary between particle types,
-as shown in the third example: type 1- type 1 interactions are based
+as shown in the fourth example: type 1 - type 1 interactions are based
-on a Hertzian normal contact model and 2-2 interactions are based on a
+on a Johnson-Kendall-Roberts normal contact model and 2-2 interactions
-DMT cohesive model (see below).  In that example, 1-1 and 2-2
+are based on a DMT cohesive model (see below).  In that example, 1-1
-interactions have different model forms, in which case mixing of
+and 2-2 interactions have different model forms, in which case mixing of
 coefficients cannot be determined, so 1-2 interactions must be
-explicitly defined via the {pair_coeff 1 2} command, otherwise an
+explicitly defined via the {pair_coeff 1 *} command, otherwise an
 error would result.
 
 :line
@@ -189,6 +191,7 @@ other settings, potentially also the twisting damping).  The options
 for the damping model currently supported are:
 
 {velocity}
+{mass_velocity}
 {viscoelastic}
 {tsuji} :ol
 
@@ -199,11 +202,23 @@ For {damping velocity}, the normal damping is simply equal to the
 user-specified damping coefficient in the {normal} model:
 
 \begin\{equation\}
-\eta_n = \eta_\{n0\}\
+\eta_n = \eta_\{n0\}
 \end\{equation\}
 
-Here, \(\gamma_n\) is the damping coefficient specified for the normal
+Here, \(\eta_\{n0\}\) is the damping coefficient specified for the normal
-contact model, in units of {mass}/{time},
+contact model, in units of {mass}/{time}.
+
+For {damping mass_velocity}, the normal damping is given by:
+
+\begin\{equation\}
+\eta_n = \eta_\{n0\} m_\{eff\}
+\end\{equation\}
+
+Here, \(\eta_\{n0\}\) is the damping coefficient specified for the normal
+contact model, in units of {mass}/{time} and
+\(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass.
+Use {damping mass_velocity} to reproduce the damping behavior of
+{pair gran/hooke/*}.
 
 The {damping viscoelastic} model is based on the viscoelastic
 treatment of "(Brilliantov et al)"_#Brill1996, where the normal
@@ -213,11 +228,10 @@ damping is given by:
 \eta_n = \eta_\{n0\}\ a m_\{eff\}
 \end\{equation\}
 
-Here, \(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass, {a}
+Here, {a} is the contact radius, given by \(a =\sqrt\{R\delta\}\)
-is the contact radius, given by \(a =\sqrt\{R\delta\}\) for all models
+for all models except {jkr}, for which it is given implicitly according
-except {jkr}, for which it is given implicitly according to \(delta =
+to \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\).  For {damping viscoelastic},
-a^2/R - 2\sqrt\{\pi \gamma a/E\}\).  In this case, \eta_\{n0\}\ is in
+\(\eta_\{n0\}\) is in units of 1/({time}*{distance}).
-units of 1/({time}*{distance}).
 
 The {tsuji} model is based on the work of "(Tsuji et
 al)"_#Tsuji1992. Here, the damping coefficient specified as part of
@@ -564,6 +578,20 @@ Finally, the twisting torque on each particle is given by:
 
 :line
 
+The {granular} pair style can reproduce the behavior of the
+{pair gran/*} styles with the appropriate settings (some very
+minor differences can be expected due to corrections in
+displacement history frame-of-reference, and the application
+of the torque at the center of the contact rather than
+at each particle). The first example above
+is equivalent to {pair gran/hooke 1000.0 NULL 50.0 50.0 0.4 1}.
+The second example is equivalent to
+{pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1}.
+The third example is equivalent to
+{pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1}.
+
+:line
+
 LAMMPS automatically sets pairwise cutoff values for {pair_style
 granular} based on particle radii (and in the case of {jkr} pull-off
 distances). In the vast majority of situations, this is adequate.
@@ -619,7 +647,7 @@ interactions is set to \(\mu_1\), and friction coefficient for type
 2-type 2 interactions is set to \(\mu_2\), the friction coefficient
 for type1-type2 interactions is computed as \(\sqrt\{\mu_1\mu_2\}\)
 (unless explicitly specified to a different value by a {pair_coeff 1 2
-...} command. The exception to this is elastic modulus, only
+...} command). The exception to this is elastic modulus, only
 applicable to {hertz/material}, {dmt} and {jkr} normal contact
 models. In that case, the effective elastic modulus is computed as:
 
@@ -706,7 +734,7 @@ For the {pair_coeff} settings: {damping viscoelastic}, {rolling none},
 J. M., & Poschel, T. (1996).  Model for collisions in granular
 gases. Physical review E, 53(5), 5382.
 
-:link(Tsuji1992) 
+:link(Tsuji1992)
 [(Tsuji et al, 1992)] Tsuji, Y., Tanaka, T., & Ishida,
 T. (1992). Lagrangian numerical simulation of plug flow of
 cohesionless particles in a horizontal pipe. Powder technology, 71(3),

doc/src/pair_mdf.txt

@@ -30,16 +30,16 @@ args = list of arguments for a particular style :l
 [Examples:]
 
 pair_style lj/mdf 2.5 3.0
-pair_coeff * * 1 1
+pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1 1.1 2.8 3.0 3.2 :pre
+pair_coeff 1 1 1.1 2.8 3.0 3.2 :pre
 
 pair_style buck 2.5 3.0
 pair_coeff * * 100.0 1.5 200.0
 pair_coeff * * 100.0 1.5 200.0 3.0 3.5 :pre
 
 pair_style lennard/mdf 2.5 3.0
-pair_coeff * * 1 1
+pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1 1.1 2.8 3.0 3.2 :pre
+pair_coeff 1 1 1021760.3664 2120.317338 3.0 3.2 :pre
 
 [Description:]
 
@@ -69,11 +69,12 @@ standard 12-6 Lennard-Jones written in the epsilon/sigma form:
 
 :c,image(Eqs/pair_mdf-4.jpg)
 
-The following coefficients must be defined for each pair of atoms
+Either the first two or all of the following coefficients must be
-types via the pair_coeff command as in the examples above, or in the
+defined for each pair of atoms types via the pair_coeff command as
-data file or restart files read by the "read_data"_read_data.html or
+in the examples above, or in the data file read by the
-"read_restart commands"_read_restart.html, or by mixing as described
+"read_data"_read_data.html. The two cutoffs default to the global
-below:
+values and epsilon and sigma can also be determined by mixing as
+described below:
 
 epsilon (energy units)
 sigma (distance units)
@@ -83,7 +84,9 @@ r_{cut} (distance units) :ul
 :line
 
 For the {buck/mdf} pair_style, the potential energy, {E(r)}, is the
-standard Buckingham potential:
+standard Buckingham potential with three required coefficients.
+The two cutoffs can be omitted and default to the corresponding
+global values:
 
 :c,image(Eqs/pair_mdf-5.jpg)
 
@@ -91,19 +94,20 @@ A (energy units)
 \rho (distance units)
 C (energy-distance^6 units)
 r_m (distance units)
-r_{cut}$ (distance units) :ul
+r_{cut} (distance units) :ul
 
 :line
 
 For the {lennard/mdf} pair_style, the potential energy, {E(r)}, is the
-standard 12-6 Lennard-Jones written in the $A/B$ form:
+standard 12-6 Lennard-Jones written in the A/B form:
 
 :c,image(Eqs/pair_mdf-6.jpg)
 
 The following coefficients must be defined for each pair of atoms
 types via the pair_coeff command as in the examples above, or in the
-data file or restart files read by the read_data or read_restart
+data file read by the read_data commands, or by mixing as described below.
-commands, or by mixing as described below:
+The two cutoffs default to their global values and must be either both
+given or both left out:
 
 A (energy-distance^12 units)
 B (energy-distance^6 units)
@@ -115,33 +119,23 @@ r_{cut} (distance units) :ul
 [Mixing, shift, table, tail correction, restart, rRESPA info]:
 
 For atom type pairs I,J and I != J, the epsilon and sigma coefficients
-and cutoff distance for all of the lj/cut pair styles can be mixed.
+and cutoff distances for the lj/mdf pair style can be mixed.
 The default mix value is {geometric}.  See the "pair_modify" command
-for details.
+for details. The other two pair styles buck/mdf and lennard/mdf do not
+support mixing, so all I,J pairs of coefficients must be specified
+explicitly.
 
-All of the {lj/cut} pair styles support the
+None of the lj/mdf, buck/mdf, or lennard/mdf pair styles supports
-"pair_modify"_pair_modify.html shift option for the energy of the
+the "pair_modify"_pair_modify.html shift option or long-range
-Lennard-Jones portion of the pair interaction.
+tail corrections to pressure and energy.
 
-The {lj/cut/coul/long} and {lj/cut/tip4p/long} pair styles support the
+These styles write their information to "binary restart
-"pair_modify"_pair_modify.html table option since they can tabulate
+files"_restart.html, so pair_style and pair_coeff commands do not need
-the short-range portion of the long-range Coulombic interaction.
+to be specified in an input script that reads a restart file.
 
-All of the {lj/cut} pair styles support the
+These styles can only be used via the {pair} keyword of the "run_style
-"pair_modify"_pair_modify.html tail option for adding a long-range
+respa"_run_style.html command.  They do not support the {inner},
-tail correction to the energy and pressure for the Lennard-Jones
+{middle}, {outer} keywords.
-portion of the pair interaction.
-
-All of the {lj/cut} pair styles write their information to "binary
-restart files"_restart.html, so pair_style and pair_coeff commands do
-not need to be specified in an input script that reads a restart file.
-
-The {lj/cut} and {lj/cut/coul/long} pair styles support the use of the
-{inner}, {middle}, and {outer} keywords of the "run_style
-respa"_run_style.html command, meaning the pairwise forces can be
-partitioned by distance at different levels of the rRESPA hierarchy.
-The other styles only support the {pair} keyword of run_style respa.
-See the "run_style"_run_style.html command for details.
 
 :line
 

doc/src/pair_spin_dmi.txt

@@ -88,4 +88,4 @@ package"_Build_package.html doc page for more info.
 Physical Review B, 88(18), 184422. (2013).
 :link(Tranchida5)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/pair_spin_exchange.txt

@@ -95,4 +95,4 @@ package"_Build_package.html doc page for more info.
 
 :link(Tranchida3)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/pair_spin_magelec.txt

@@ -70,4 +70,4 @@ package"_Build_package.html doc page for more info.
 
 :link(Tranchida4)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/pair_spin_neel.txt

@@ -80,4 +80,4 @@ package"_Build_package.html doc page for more info.
 
 :link(Tranchida6)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/write_coeff.txt

@@ -26,11 +26,9 @@ coefficients in a way, that it can be read by LAMMPS with the
 option of "write_data"_write_data.html this can be used to move
 the Coeffs sections from a data file into a separate file.
 
-NOTE: The write_coeff command is not yet fully implemented in two
+NOTE: The write_coeff command is not yet fully implemented as
-respects.  First, some pair styles do not yet write their coefficient
+some pair styles do not output their coefficient information.
-information into the coeff file.  This means you will need to specify
+This means you will need to add/copy this information manually.
-that information in your input script that reads the data file, via
-the "pair_coeff"_pair_coeff.html command.
 
 :line
 

doc/utils/sphinx-config/false_positives.txt

@@ -200,6 +200,7 @@ Berkowitz
 berlin
 Berne
 Bertotti
+Bessarab
 Beutler
 bgq
 Bh
@@ -592,6 +593,7 @@ Dmax
 dmg
 dmi
 dnf
+DNi
 Dobson
 Dodds
 dodgerblue
@@ -963,6 +965,8 @@ gmail
 gmake
 gmask
 Gmask
+gneb
+GNEB
 googlemail
 Gordan
 GPa
@@ -2370,6 +2374,7 @@ rNEMD
 ro
 Rochus
 Rockett
+Rodrigues
 Rohart
 Ronchetti
 Rosati
@@ -2774,6 +2779,7 @@ tt
 Tt
 TThis
 ttm
+ttol
 tu
 Tuckerman
 tue
@@ -2846,6 +2852,7 @@ utsa
 Uttormark
 uvm
 uwo
+Uzdin
 vacf
 valent
 Valeriu
@@ -2945,7 +2952,7 @@ wB
 Wbody
 webpage
 Weckner
-WeinenE
+WeinanE
 Wennberg
 Westview
 wget

examples/SPIN/gneb/README

@@ -0,0 +1,13 @@
+Perform geodesic NEB calculations for spin configurations.
+The two examples are:
+- the magnetic switching of an iron nanoisland
+- the collapse of a magnetic skyrmion
+
+Run those examples as:
+
+mpirun -np 3 lmp_mpi -in in.gneb.iron -partition 3x1
+
+You should be able to use any number of replicas >= 3.
+
+In the interpolate/ directory, a c routine is provided to
+interpolate the MEP. 

examples/SPIN/gneb/iron/final.iron_spin

@@ -0,0 +1,68 @@
+32
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+3 2.2000000000000002e+00 2.8664999999999998e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+

examples/SPIN/gneb/iron/in.gneb.iron

@@ -0,0 +1,50 @@
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+# setting mass, mag. moments, and interactions for bcc iron
+# (mass not necessary for fixed lattice calculation)
+
+read_data       initial.iron_spin
+mass		1 55.845
+
+pair_style 	spin/exchange 3.5
+pair_coeff 	* * exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.0001 1.0 0.0 0.0 
+fix_modify	1 energy yes
+fix		3 all neb/spin 1.0  
+
+timestep	0.0001
+thermo		100
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+variable	u universe 1 2 3 4
+dump 		1 all custom 200 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+neb/spin	1.0e-12 1.0e-12 200000 100000 1000 final final.iron_spin verbose

examples/SPIN/gneb/iron/initial.iron_spin

@@ -0,0 +1,82 @@
+LAMMPS data file via write_data, version 4 Jan 2019, timestep = 0
+
+32 atoms
+1 atom types
+
+0.0000000000000000e+00 1.1465999999999999e+01 xlo xhi
+0.0000000000000000e+00 1.1465999999999999e+01 ylo yhi
+0.0000000000000000e+00 2.8664999999999998e+00 zlo zhi
+
+Masses
+
+1 55.845
+
+Atoms # spin
+
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examples/SPIN/gneb/skyrmion/final.skyrmion

@@ -0,0 +1,401 @@
+400
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examples/SPIN/gneb/skyrmion/in.gneb.skyrmion

@@ -0,0 +1,47 @@
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+# setting mass, mag. moments, and interactions for bcc iron
+# (mass not necessary for fixed lattice calculation)
+
+read_data       initial.skyrmion
+mass		1 55.845
+
+pair_style 	hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
+pair_coeff 	* * spin/exchange exchange 3.1 0.01593 0.06626915552 1.211
+pair_coeff 	* * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0 
+fix_modify	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+fix		3 all neb/spin 1.0  
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+variable	u universe 1 2 3 4
+dump 		1 all custom 1 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+neb/spin	1.0e-9 1.0e-9 10000 10000 10 final final.skyrmion

examples/SPIN/gneb/skyrmion/initial.skyrmion

@@ -0,0 +1,818 @@
+LAMMPS data file via write_data, version 28 Feb 2019, timestep = 6
+
+400 atoms
+1 atom types
+
+0.0000000000000000e+00 6.0000000000000000e+01 xlo xhi
+0.0000000000000000e+00 6.0000000000000000e+01 ylo yhi
+0.0000000000000000e+00 3.0000000000000000e+00 zlo zhi
+
+Masses
+
+1 55.845
+
+Atoms # spin
+
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+140 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+160 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+180 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+200 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+220 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+240 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+260 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+280 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+300 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+320 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+340 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+360 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+380 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
+400 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00

examples/SPIN/read_restart/in.spin.read_data

@@ -40,6 +40,6 @@ thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
 thermo_modify   format float %20.15g
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
 run 		100

examples/SPIN/setforce_spin/in.spinmin.setforce

@@ -0,0 +1,59 @@
+
+units 		metal
+dimension 	3
+boundary 	f f f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	sc 3.0
+region 		box block 0.0 10.0 0.0 10.0 0.0 1.0
+create_box 	2 box
+region		reg1 block 0.0 10.0 	0.0 5.0 	0.0 1.0
+region		reg2 block 0.0 10.0 	6.0 10.0 	0.0 1.0
+create_atoms 	1 region reg1 
+create_atoms 	2 region reg2
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+mass		2 55.845
+set 		region reg1 spin 2.2 0.0 0.0 1.0
+set 		region reg2 spin/random 31 2.2
+
+group 		fixed_spin region reg1
+
+pair_style 	hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
+pair_coeff 	* * spin/exchange exchange 3.1 -0.01593 0.06626915552 1.211
+pair_coeff	* * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0 
+fix_modify	1 energy yes
+fix 		2 fixed_spin setforce/spin 0.0 0.0 0.0
+fix 		3 all langevin/spin 0.0 0.1 21
+fix		4 all nve/spin lattice no 
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          1000
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 1000 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 20.0
+minimize        1.0e-16 1.0e-16 50000 1000

examples/USER/misc/kolmogorov_crespi_z/CH.airebo

@@ -1 +0,0 @@
-../../../../potentials/CH.airebo

examples/USER/misc/kolmogorov_crespi_z/CH.rebo

@@ -0,0 +1 @@
+../../../../potentials/CH.rebo

examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene

@@ -22,7 +22,7 @@ group adsorbant type 2
 ######################## Potential defition ########################
 pair_style  hybrid/overlay  rebo  kolmogorov/crespi/z 14.0
 ####################################################################
-pair_coeff * * rebo                 CH.airebo  C C  # chemical
+pair_coeff * * rebo                 CH.rebo  C C  # chemical
 pair_coeff 1 2 kolmogorov/crespi/z  CC.KC      C C  # long-range
 ####################################################################
 

examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1

@@ -1,208 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      atomic
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       data.bilayer-graphene # read lammps data file
-  orthogonal box = (0 0 -20) to (17.04 19.6761 40)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  256 atoms
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-# Separate atom groups
-group membrane  type 1
-128 atoms in group membrane
-group adsorbant type 2
-128 atoms in group adsorbant
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  kolmogorov/crespi/z 14.0
-####################################################################
-pair_coeff * * rebo                 CH.airebo  C C  # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff 1 2 kolmogorov/crespi/z  CC.KC      C C  # long-range
-####################################################################
-
-#### Simulation settings ####
-timestep  0.0001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-compute   COM1 membrane  com
-compute   COM2 adsorbant com
-############################
-
-# Output
-#dump            1 all xyz 100 trajec.xyz
-#dump_modify     1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
-thermo          10
-thermo_style    custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
-thermo_modify   line one format float %14.8f
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 16
-  ghost atom cutoff = 16
-  binsize = 8, bins = 3 3 8
-  3 neighbor lists, perpetual/occasional/extra = 3 0 0
-  (1) pair rebo, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (2) pair kolmogorov/crespi/z, perpetual, skip from (3)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) neighbor class addition, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes
-Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] 
-       0     0.00000000 -1888.67041214 -1898.55881323   300.00000000     0.00000000     3.30000000 
-      10     0.00100000 -1888.67037221 -1898.21029897   289.42778520    -0.00020126     3.30020126 
-      20     0.00200000 -1888.67021541 -1897.22943612   259.67456089    -0.00041357     3.30041357 
-      30     0.00300000 -1888.66999308 -1895.86681311   218.34126559    -0.00063673     3.30063673 
-      40     0.00400000 -1888.66978354 -1894.47163830   176.02000692    -0.00087055     3.30087055 
-      50     0.00500000 -1888.66966068 -1893.37123377   142.63902862    -0.00111486     3.30111486 
-      60     0.00600000 -1888.66966132 -1892.75822749   124.04127205    -0.00136952     3.30136952 
-      70     0.00700000 -1888.66976974 -1892.63445751   120.28297808    -0.00163441     3.30163441 
-      80     0.00800000 -1888.66992867 -1892.83467462   126.35245792    -0.00190946     3.30190946 
-      90     0.00900000 -1888.67006868 -1893.11387069   134.81862145    -0.00219458     3.30219458 
-     100     0.01000000 -1888.67013621 -1893.25481851   139.09272853    -0.00248973     3.30248973 
-     110     0.01100000 -1888.67011201 -1893.15155790   135.96068294    -0.00279489     3.30279489 
-     120     0.01200000 -1888.67001496 -1892.84002960   126.51230266    -0.00311004     3.30311004 
-     130     0.01300000 -1888.66988997 -1892.47004238   115.29120968    -0.00343519     3.30343519 
-     140     0.01400000 -1888.66979230 -1892.23503116   108.16426723    -0.00377038     3.30377038 
-     150     0.01500000 -1888.66976478 -1892.28630583   109.72070257    -0.00411562     3.30411562 
-     160     0.01600000 -1888.66982054 -1892.66640611   121.25071190    -0.00447099     3.30447099 
-     170     0.01700000 -1888.66993790 -1893.28862637   140.12442721    -0.00483654     3.30483654 
-     180     0.01800000 -1888.67007017 -1893.97029258   160.80119589    -0.00521235     3.30521235 
-     190     0.01900000 -1888.67016712 -1894.50458787   177.00801243    -0.00559851     3.30559851 
-     200     0.02000000 -1888.67019459 -1894.73890106   184.11590729    -0.00599512     3.30599512 
-     210     0.02100000 -1888.67014420 -1894.62906014   180.78501932    -0.00640230     3.30640230 
-     220     0.02200000 -1888.67003680 -1894.25249103   169.36370738    -0.00682016     3.30682016 
-     230     0.02300000 -1888.66991386 -1893.77601613   154.91186767    -0.00724883     3.30724883 
-     240     0.02400000 -1888.66982525 -1893.38995084   143.20188490    -0.00768845     3.30768845 
-     250     0.02500000 -1888.66980630 -1893.23138936   138.39193056    -0.00813913     3.30813913 
-     260     0.02600000 -1888.66986130 -1893.32993923   141.38012476    -0.00860097     3.30860097 
-     270     0.02700000 -1888.66996305 -1893.60070606   149.59171763    -0.00907408     3.30907408 
-     280     0.02800000 -1888.67006686 -1893.88587226   158.24010433    -0.00955849     3.30955849 
-     290     0.02900000 -1888.67012981 -1894.02402669   162.42960292    -0.01005424     3.31005424 
-     300     0.03000000 -1888.67012722 -1893.91715234   159.18726627    -0.01056129     3.31056129 
-     310     0.03100000 -1888.67005731 -1893.57037242   148.66857852    -0.01107957     3.31107957 
-     320     0.03200000 -1888.66994573 -1893.09358619   134.20694883    -0.01160898     3.31160898 
-     330     0.03300000 -1888.66983589 -1892.66132663   121.09614207    -0.01214935     3.31214935 
-     340     0.03400000 -1888.66977410 -1892.44446345   114.51869676    -0.01270046     3.31270046 
-     350     0.03500000 -1888.66978826 -1892.53901235   117.38674604    -0.01326207     3.31326207 
-     360     0.03600000 -1888.66987439 -1892.92337288   129.04508371    -0.01383390     3.31383390 
-     370     0.03700000 -1888.66999800 -1893.46445570   145.45701555    -0.01441561     3.31441561 
-     380     0.03800000 -1888.67010960 -1893.97065516   160.81100020    -0.01500688     3.31500688 
-     390     0.03900000 -1888.67016540 -1894.26835818   169.84119247    -0.01560734     3.31560734 
-     400     0.04000000 -1888.67014667 -1894.26967975   169.88185546    -0.01621664     3.31621664 
-     410     0.04100000 -1888.67006166 -1894.00321069   161.80014280    -0.01683442     3.31683442 
-     420     0.04200000 -1888.66994367 -1893.60086324   149.59707418    -0.01746033     3.31746033 
-     430     0.04300000 -1888.66984058 -1893.24559841   138.82197275    -0.01809405     3.31809405 
-     440     0.04400000 -1888.66979399 -1893.09727874   134.32357877    -0.01873527     3.31873527 
-     450     0.04500000 -1888.66982139 -1893.22837442   138.30000378    -0.01938373     3.31938373 
-     460     0.04600000 -1888.66990972 -1893.59670383   149.47191354    -0.02003918     3.32003918 
-     470     0.04700000 -1888.67002173 -1894.06542598   163.68887743    -0.02070143     3.32070143 
-     480     0.04800000 -1888.67011389 -1894.46010842   175.66018439    -0.02137030     3.32137030 
-     490     0.04900000 -1888.67015175 -1894.63688098   181.02206322    -0.02204565     3.32204565 
-     500     0.05000000 -1888.67012158 -1894.53632221   177.97216882    -0.02272740     3.32272740 
-     510     0.05100000 -1888.67003762 -1894.20444731   167.90610436    -0.02341547     3.32341547 
-     520     0.05200000 -1888.66993151 -1893.77231066   154.79891353    -0.02410981     3.32410981 
-     530     0.05300000 -1888.66984505 -1893.40525927   143.66572038    -0.02481040     3.32481040 
-     540     0.05400000 -1888.66981408 -1893.23762083   138.58074854    -0.02551724     3.32551724 
-     550     0.05500000 -1888.66985005 -1893.31793594   141.01630317    -0.02623032     3.32623032 
-     560     0.05600000 -1888.66993737 -1893.59069013   149.28862751    -0.02694963     3.32694963 
-     570     0.05700000 -1888.67003852 -1893.92089571   159.30352588    -0.02767517     3.32767517 
-     580     0.05800000 -1888.67011322 -1894.15124753   166.28980524    -0.02840691     3.32840691 
-     590     0.05900000 -1888.67013192 -1894.16548041   166.72104345    -0.02914478     3.32914478 
-     600     0.06000000 -1888.67008713 -1893.93443318   159.71275856    -0.02988871     3.32988871 
-     610     0.06100000 -1888.66999438 -1893.52841656   147.39760646    -0.03063856     3.33063856 
-     620     0.06200000 -1888.66988809 -1893.09235021   134.17119963    -0.03139416     3.33139416 
-     630     0.06300000 -1888.66980996 -1892.79172016   125.05288240    -0.03215531     3.33215531 
-     640     0.06400000 -1888.66979261 -1892.74755390   123.71346730    -0.03292176     3.33292176 
-     650     0.06500000 -1888.66984332 -1892.98665459   130.96590324    -0.03369323     3.33369323 
-     660     0.06600000 -1888.66994245 -1893.42999868   144.41332389    -0.03446937     3.33446937 
-     670     0.06700000 -1888.67005233 -1893.92310681   159.37018806    -0.03524986     3.33524986 
-     680     0.06800000 -1888.67013309 -1894.29451581   170.63575808    -0.03603430     3.33603430 
-     690     0.06900000 -1888.67015452 -1894.41878117   174.40514192    -0.03682229     3.33682229 
-     700     0.07000000 -1888.67010897 -1894.26288036   169.67671530    -0.03761343     3.33761343 
-     710     0.07100000 -1888.67001367 -1893.89812904   158.61357114    -0.03840729     3.33840729 
-     720     0.07200000 -1888.66990378 -1893.47348746   145.73388454    -0.03920344     3.33920344 
-     730     0.07300000 -1888.66982212 -1893.15984839   136.22099960    -0.04000148     3.34000148 
-     740     0.07400000 -1888.66980109 -1893.08373746   133.91254029    -0.04080098     3.34080098 
-     750     0.07500000 -1888.66984794 -1893.27755511   139.79127024    -0.04160156     3.34160156 
-     760     0.07600000 -1888.66994215 -1893.66837365   151.64528967    -0.04240282     3.34240282 
-     770     0.07700000 -1888.67004554 -1894.10941206   165.02263027    -0.04320441     3.34320441 
-     780     0.07800000 -1888.67011702 -1894.43947545   175.03411436    -0.04400599     3.34400599 
-     790     0.07900000 -1888.67013297 -1894.54590471   178.26254255    -0.04480726     3.34480726 
-     800     0.08000000 -1888.67008751 -1894.40384142   173.95392406    -0.04560792     3.34560792 
-     810     0.08100000 -1888.66999923 -1894.08389003   164.24973321    -0.04640773     3.34640773 
-     820     0.08200000 -1888.66990447 -1893.72313979   153.30795965    -0.04720647     3.34720647 
-     830     0.08300000 -1888.66984367 -1893.46839190   145.58111626    -0.04800393     3.34800393 
-     840     0.08400000 -1888.66984156 -1893.41412536   143.93481093    -0.04879995     3.34879995 
-     850     0.08500000 -1888.66989670 -1893.56426154   148.48805553    -0.04959439     3.34959439 
-     860     0.08600000 -1888.66998222 -1893.83463719   156.68827294    -0.05038713     3.35038713 
-     870     0.08700000 -1888.67006171 -1894.09325045   164.53181920    -0.05117805     3.35117805 
-     880     0.08800000 -1888.67010273 -1894.21712661   168.28880100    -0.05196706     3.35196706 
-     890     0.08900000 -1888.67008993 -1894.14263950   166.02935656    -0.05275408     3.35275408 
-     900     0.09000000 -1888.67002891 -1893.89014571   158.37090587    -0.05353904     3.35353904 
-     910     0.09100000 -1888.66994326 -1893.55535709   148.21649469    -0.05432186     3.35432186 
-     920     0.09200000 -1888.66986526 -1893.27257949   139.63979178    -0.05510247     3.35510247 
-     930     0.09300000 -1888.66982730 -1893.16330891   136.32582949    -0.05588078     3.35588078 
-     940     0.09400000 -1888.66984631 -1893.28643285   140.06065785    -0.05665670     3.35665670 
-     950     0.09500000 -1888.66991503 -1893.61245342   149.94957268    -0.05743015     3.35743015 
-     960     0.09600000 -1888.67000691 -1894.03423922   162.74316516    -0.05820101     3.35820101 
-     970     0.09700000 -1888.67008649 -1894.40848025   174.09469037    -0.05896915     3.35896915 
-     980     0.09800000 -1888.67012436 -1894.61056767   180.22458605    -0.05973444     3.35973444 
-     990     0.09900000 -1888.67010608 -1894.58107659   179.33042338    -0.06049672     3.36049672 
-    1000     0.10000000 -1888.67003981 -1894.34773305   172.25312330    -0.06125581     3.36125581 
-Loop time of 3.90147 on 1 procs for 1000 steps with 256 atoms
-
-Performance: 2.215 ns/day, 10.837 hours/ns, 256.314 timesteps/s
-99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 3.8786     | 3.8786     | 3.8786     |   0.0 | 99.41
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.010816   | 0.010816   | 0.010816   |   0.0 |  0.28
-Output  | 0.002461   | 0.002461   | 0.002461   |   0.0 |  0.06
-Modify  | 0.0051703  | 0.0051703  | 0.0051703  |   0.0 |  0.13
-Other   |            | 0.004447   |            |       |  0.11
-
-Nlocal:    256 ave 256 max 256 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1721 ave 1721 max 1721 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    37312 ave 37312 max 37312 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  94592 ave 94592 max 94592 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 94592
-Ave neighs/atom = 369.5
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:03

examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4

@@ -1,208 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      atomic
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       data.bilayer-graphene # read lammps data file
-  orthogonal box = (0 0 -20) to (17.04 19.6761 40)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  256 atoms
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-# Separate atom groups
-group membrane  type 1
-128 atoms in group membrane
-group adsorbant type 2
-128 atoms in group adsorbant
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  kolmogorov/crespi/z 14.0
-####################################################################
-pair_coeff * * rebo                 CH.airebo  C C  # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff 1 2 kolmogorov/crespi/z  CC.KC      C C  # long-range
-####################################################################
-
-#### Simulation settings ####
-timestep  0.0001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-compute   COM1 membrane  com
-compute   COM2 adsorbant com
-############################
-
-# Output
-#dump            1 all xyz 100 trajec.xyz
-#dump_modify     1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
-thermo          10
-thermo_style    custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
-thermo_modify   line one format float %14.8f
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 16
-  ghost atom cutoff = 16
-  binsize = 8, bins = 3 3 8
-  3 neighbor lists, perpetual/occasional/extra = 3 0 0
-  (1) pair rebo, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (2) pair kolmogorov/crespi/z, perpetual, skip from (3)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) neighbor class addition, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes
-Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] 
-       0     0.00000000 -1888.67041214 -1898.55881323   300.00000000     0.00000000     3.30000000 
-      10     0.00100000 -1888.67037221 -1898.21029897   289.42778520    -0.00020126     3.30020126 
-      20     0.00200000 -1888.67021541 -1897.22943612   259.67456089    -0.00041357     3.30041357 
-      30     0.00300000 -1888.66999308 -1895.86681311   218.34126559    -0.00063673     3.30063673 
-      40     0.00400000 -1888.66978354 -1894.47163830   176.02000692    -0.00087055     3.30087055 
-      50     0.00500000 -1888.66966068 -1893.37123377   142.63902862    -0.00111486     3.30111486 
-      60     0.00600000 -1888.66966132 -1892.75822749   124.04127205    -0.00136952     3.30136952 
-      70     0.00700000 -1888.66976974 -1892.63445751   120.28297808    -0.00163441     3.30163441 
-      80     0.00800000 -1888.66992867 -1892.83467462   126.35245792    -0.00190946     3.30190946 
-      90     0.00900000 -1888.67006868 -1893.11387069   134.81862145    -0.00219458     3.30219458 
-     100     0.01000000 -1888.67013621 -1893.25481851   139.09272853    -0.00248973     3.30248973 
-     110     0.01100000 -1888.67011201 -1893.15155790   135.96068294    -0.00279489     3.30279489 
-     120     0.01200000 -1888.67001496 -1892.84002960   126.51230266    -0.00311004     3.30311004 
-     130     0.01300000 -1888.66988997 -1892.47004238   115.29120968    -0.00343519     3.30343519 
-     140     0.01400000 -1888.66979230 -1892.23503116   108.16426723    -0.00377038     3.30377038 
-     150     0.01500000 -1888.66976478 -1892.28630583   109.72070257    -0.00411562     3.30411562 
-     160     0.01600000 -1888.66982054 -1892.66640611   121.25071190    -0.00447099     3.30447099 
-     170     0.01700000 -1888.66993790 -1893.28862637   140.12442721    -0.00483654     3.30483654 
-     180     0.01800000 -1888.67007017 -1893.97029258   160.80119589    -0.00521235     3.30521235 
-     190     0.01900000 -1888.67016712 -1894.50458787   177.00801243    -0.00559851     3.30559851 
-     200     0.02000000 -1888.67019459 -1894.73890106   184.11590729    -0.00599512     3.30599512 
-     210     0.02100000 -1888.67014420 -1894.62906014   180.78501932    -0.00640230     3.30640230 
-     220     0.02200000 -1888.67003680 -1894.25249103   169.36370738    -0.00682016     3.30682016 
-     230     0.02300000 -1888.66991386 -1893.77601613   154.91186767    -0.00724883     3.30724883 
-     240     0.02400000 -1888.66982525 -1893.38995084   143.20188490    -0.00768845     3.30768845 
-     250     0.02500000 -1888.66980630 -1893.23138936   138.39193056    -0.00813913     3.30813913 
-     260     0.02600000 -1888.66986130 -1893.32993923   141.38012476    -0.00860097     3.30860097 
-     270     0.02700000 -1888.66996305 -1893.60070606   149.59171763    -0.00907408     3.30907408 
-     280     0.02800000 -1888.67006686 -1893.88587226   158.24010433    -0.00955849     3.30955849 
-     290     0.02900000 -1888.67012981 -1894.02402669   162.42960292    -0.01005424     3.31005424 
-     300     0.03000000 -1888.67012722 -1893.91715234   159.18726627    -0.01056129     3.31056129 
-     310     0.03100000 -1888.67005731 -1893.57037242   148.66857852    -0.01107957     3.31107957 
-     320     0.03200000 -1888.66994573 -1893.09358619   134.20694883    -0.01160898     3.31160898 
-     330     0.03300000 -1888.66983589 -1892.66132663   121.09614207    -0.01214935     3.31214935 
-     340     0.03400000 -1888.66977410 -1892.44446345   114.51869676    -0.01270046     3.31270046 
-     350     0.03500000 -1888.66978826 -1892.53901235   117.38674604    -0.01326207     3.31326207 
-     360     0.03600000 -1888.66987439 -1892.92337288   129.04508371    -0.01383390     3.31383390 
-     370     0.03700000 -1888.66999800 -1893.46445570   145.45701555    -0.01441561     3.31441561 
-     380     0.03800000 -1888.67010960 -1893.97065516   160.81100020    -0.01500688     3.31500688 
-     390     0.03900000 -1888.67016540 -1894.26835818   169.84119247    -0.01560734     3.31560734 
-     400     0.04000000 -1888.67014667 -1894.26967975   169.88185546    -0.01621664     3.31621664 
-     410     0.04100000 -1888.67006166 -1894.00321069   161.80014280    -0.01683442     3.31683442 
-     420     0.04200000 -1888.66994367 -1893.60086324   149.59707418    -0.01746033     3.31746033 
-     430     0.04300000 -1888.66984058 -1893.24559841   138.82197275    -0.01809405     3.31809405 
-     440     0.04400000 -1888.66979399 -1893.09727874   134.32357877    -0.01873527     3.31873527 
-     450     0.04500000 -1888.66982139 -1893.22837442   138.30000378    -0.01938373     3.31938373 
-     460     0.04600000 -1888.66990972 -1893.59670383   149.47191354    -0.02003918     3.32003918 
-     470     0.04700000 -1888.67002173 -1894.06542598   163.68887743    -0.02070143     3.32070143 
-     480     0.04800000 -1888.67011389 -1894.46010842   175.66018439    -0.02137030     3.32137030 
-     490     0.04900000 -1888.67015175 -1894.63688098   181.02206322    -0.02204565     3.32204565 
-     500     0.05000000 -1888.67012158 -1894.53632221   177.97216882    -0.02272740     3.32272740 
-     510     0.05100000 -1888.67003762 -1894.20444731   167.90610436    -0.02341547     3.32341547 
-     520     0.05200000 -1888.66993151 -1893.77231066   154.79891353    -0.02410981     3.32410981 
-     530     0.05300000 -1888.66984505 -1893.40525927   143.66572038    -0.02481040     3.32481040 
-     540     0.05400000 -1888.66981408 -1893.23762083   138.58074854    -0.02551724     3.32551724 
-     550     0.05500000 -1888.66985005 -1893.31793594   141.01630317    -0.02623032     3.32623032 
-     560     0.05600000 -1888.66993737 -1893.59069013   149.28862751    -0.02694963     3.32694963 
-     570     0.05700000 -1888.67003852 -1893.92089571   159.30352588    -0.02767517     3.32767517 
-     580     0.05800000 -1888.67011322 -1894.15124753   166.28980524    -0.02840691     3.32840691 
-     590     0.05900000 -1888.67013192 -1894.16548041   166.72104345    -0.02914478     3.32914478 
-     600     0.06000000 -1888.67008713 -1893.93443318   159.71275856    -0.02988871     3.32988871 
-     610     0.06100000 -1888.66999438 -1893.52841656   147.39760646    -0.03063856     3.33063856 
-     620     0.06200000 -1888.66988809 -1893.09235021   134.17119963    -0.03139416     3.33139416 
-     630     0.06300000 -1888.66980996 -1892.79172016   125.05288240    -0.03215531     3.33215531 
-     640     0.06400000 -1888.66979261 -1892.74755390   123.71346730    -0.03292176     3.33292176 
-     650     0.06500000 -1888.66984332 -1892.98665459   130.96590324    -0.03369323     3.33369323 
-     660     0.06600000 -1888.66994245 -1893.42999868   144.41332389    -0.03446937     3.33446937 
-     670     0.06700000 -1888.67005233 -1893.92310681   159.37018806    -0.03524986     3.33524986 
-     680     0.06800000 -1888.67013309 -1894.29451581   170.63575808    -0.03603430     3.33603430 
-     690     0.06900000 -1888.67015452 -1894.41878117   174.40514192    -0.03682229     3.33682229 
-     700     0.07000000 -1888.67010897 -1894.26288036   169.67671530    -0.03761343     3.33761343 
-     710     0.07100000 -1888.67001367 -1893.89812904   158.61357114    -0.03840729     3.33840729 
-     720     0.07200000 -1888.66990378 -1893.47348746   145.73388454    -0.03920344     3.33920344 
-     730     0.07300000 -1888.66982212 -1893.15984839   136.22099960    -0.04000148     3.34000148 
-     740     0.07400000 -1888.66980109 -1893.08373746   133.91254029    -0.04080098     3.34080098 
-     750     0.07500000 -1888.66984794 -1893.27755511   139.79127024    -0.04160156     3.34160156 
-     760     0.07600000 -1888.66994215 -1893.66837365   151.64528967    -0.04240282     3.34240282 
-     770     0.07700000 -1888.67004554 -1894.10941206   165.02263027    -0.04320441     3.34320441 
-     780     0.07800000 -1888.67011702 -1894.43947545   175.03411436    -0.04400599     3.34400599 
-     790     0.07900000 -1888.67013297 -1894.54590471   178.26254255    -0.04480726     3.34480726 
-     800     0.08000000 -1888.67008751 -1894.40384142   173.95392406    -0.04560792     3.34560792 
-     810     0.08100000 -1888.66999923 -1894.08389003   164.24973321    -0.04640773     3.34640773 
-     820     0.08200000 -1888.66990447 -1893.72313979   153.30795965    -0.04720647     3.34720647 
-     830     0.08300000 -1888.66984367 -1893.46839190   145.58111626    -0.04800393     3.34800393 
-     840     0.08400000 -1888.66984156 -1893.41412536   143.93481093    -0.04879995     3.34879995 
-     850     0.08500000 -1888.66989670 -1893.56426154   148.48805553    -0.04959439     3.34959439 
-     860     0.08600000 -1888.66998222 -1893.83463719   156.68827294    -0.05038713     3.35038713 
-     870     0.08700000 -1888.67006171 -1894.09325045   164.53181920    -0.05117805     3.35117805 
-     880     0.08800000 -1888.67010273 -1894.21712661   168.28880100    -0.05196706     3.35196706 
-     890     0.08900000 -1888.67008993 -1894.14263950   166.02935656    -0.05275408     3.35275408 
-     900     0.09000000 -1888.67002891 -1893.89014571   158.37090587    -0.05353904     3.35353904 
-     910     0.09100000 -1888.66994326 -1893.55535709   148.21649469    -0.05432186     3.35432186 
-     920     0.09200000 -1888.66986526 -1893.27257949   139.63979178    -0.05510247     3.35510247 
-     930     0.09300000 -1888.66982730 -1893.16330891   136.32582949    -0.05588078     3.35588078 
-     940     0.09400000 -1888.66984631 -1893.28643285   140.06065785    -0.05665670     3.35665670 
-     950     0.09500000 -1888.66991503 -1893.61245342   149.94957268    -0.05743015     3.35743015 
-     960     0.09600000 -1888.67000691 -1894.03423922   162.74316516    -0.05820101     3.35820101 
-     970     0.09700000 -1888.67008649 -1894.40848025   174.09469037    -0.05896915     3.35896915 
-     980     0.09800000 -1888.67012436 -1894.61056767   180.22458605    -0.05973444     3.35973444 
-     990     0.09900000 -1888.67010608 -1894.58107659   179.33042338    -0.06049672     3.36049672 
-    1000     0.10000000 -1888.67003981 -1894.34773305   172.25312330    -0.06125581     3.36125581 
-Loop time of 1.32192 on 4 procs for 1000 steps with 256 atoms
-
-Performance: 6.536 ns/day, 3.672 hours/ns, 756.476 timesteps/s
-98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.1157     | 1.172      | 1.2369     |   4.0 | 88.66
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.071678   | 0.13667    | 0.19304    |  11.8 | 10.34
-Output  | 0.0029244  | 0.0031272  | 0.0035112  |   0.4 |  0.24
-Modify  | 0.0016961  | 0.0017477  | 0.0017846  |   0.1 |  0.13
-Other   |            | 0.008334   |            |       |  0.63
-
-Nlocal:    64 ave 64 max 64 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    1265 ave 1265 max 1265 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    9328 ave 9328 max 9328 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  23648 ave 23648 max 23648 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 94592
-Ave neighs/atom = 369.5
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:01

examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1

@@ -0,0 +1,210 @@
+LAMMPS (30 Apr 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      atomic
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data       data.bilayer-graphene # read lammps data file
+  orthogonal box = (0 0 -20) to (17.04 19.6761 40)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  256 atoms
+  read_data CPU = 0.000291348 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+# Separate atom groups
+group membrane  type 1
+128 atoms in group membrane
+group adsorbant type 2
+128 atoms in group adsorbant
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  kolmogorov/crespi/z 14.0
+####################################################################
+pair_coeff * * rebo                 CH.rebo  C C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff 1 2 kolmogorov/crespi/z  CC.KC      C C  # long-range
+####################################################################
+
+#### Simulation settings ####
+timestep  0.0001
+velocity  all create 300.0 12345
+fix       thermostat all nve
+compute   COM1 membrane  com
+compute   COM2 adsorbant com
+############################
+
+# Output
+#dump            1 all xyz 100 trajec.xyz
+#dump_modify     1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
+thermo          10
+thermo_style    custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
+thermo_modify   line one format float %14.8f
+
+###### Run molecular dynamics ######
+run 1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 16
+  ghost atom cutoff = 16
+  binsize = 8, bins = 3 3 8
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair kolmogorov/crespi/z, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes
+Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] 
+       0     0.00000000 -1888.67041233 -1898.55881343   300.00000000     0.00000000     3.30000000 
+      10     0.00100000 -1888.67037240 -1898.21029916   289.42778520    -0.00020126     3.30020126 
+      20     0.00200000 -1888.67021561 -1897.22943631   259.67456089    -0.00041357     3.30041357 
+      30     0.00300000 -1888.66999327 -1895.86681330   218.34126559    -0.00063673     3.30063673 
+      40     0.00400000 -1888.66978373 -1894.47163849   176.02000692    -0.00087055     3.30087055 
+      50     0.00500000 -1888.66966087 -1893.37123396   142.63902861    -0.00111486     3.30111486 
+      60     0.00600000 -1888.66966151 -1892.75822768   124.04127204    -0.00136952     3.30136952 
+      70     0.00700000 -1888.66976993 -1892.63445770   120.28297806    -0.00163441     3.30163441 
+      80     0.00800000 -1888.66992887 -1892.83467481   126.35245790    -0.00190946     3.30190946 
+      90     0.00900000 -1888.67006887 -1893.11387088   134.81862143    -0.00219458     3.30219458 
+     100     0.01000000 -1888.67013641 -1893.25481870   139.09272852    -0.00248973     3.30248973 
+     110     0.01100000 -1888.67011221 -1893.15155809   135.96068294    -0.00279489     3.30279489 
+     120     0.01200000 -1888.67001516 -1892.84002980   126.51230266    -0.00311004     3.30311004 
+     130     0.01300000 -1888.66989017 -1892.47004258   115.29120969    -0.00343519     3.30343519 
+     140     0.01400000 -1888.66979250 -1892.23503136   108.16426724    -0.00377038     3.30377038 
+     150     0.01500000 -1888.66976498 -1892.28630603   109.72070258    -0.00411562     3.30411562 
+     160     0.01600000 -1888.66982073 -1892.66640631   121.25071190    -0.00447099     3.30447099 
+     170     0.01700000 -1888.66993810 -1893.28862656   140.12442720    -0.00483654     3.30483654 
+     180     0.01800000 -1888.67007037 -1893.97029277   160.80119589    -0.00521235     3.30521235 
+     190     0.01900000 -1888.67016732 -1894.50458806   177.00801243    -0.00559851     3.30559851 
+     200     0.02000000 -1888.67019479 -1894.73890125   184.11590729    -0.00599512     3.30599512 
+     210     0.02100000 -1888.67014440 -1894.62906034   180.78501933    -0.00640230     3.30640230 
+     220     0.02200000 -1888.67003699 -1894.25249122   169.36370739    -0.00682016     3.30682016 
+     230     0.02300000 -1888.66991405 -1893.77601632   154.91186768    -0.00724883     3.30724883 
+     240     0.02400000 -1888.66982545 -1893.38995103   143.20188490    -0.00768845     3.30768845 
+     250     0.02500000 -1888.66980650 -1893.23138955   138.39193054    -0.00813913     3.30813913 
+     260     0.02600000 -1888.66986149 -1893.32993943   141.38012473    -0.00860097     3.30860097 
+     270     0.02700000 -1888.66996324 -1893.60070625   149.59171759    -0.00907408     3.30907408 
+     280     0.02800000 -1888.67006705 -1893.88587245   158.24010430    -0.00955849     3.30955849 
+     290     0.02900000 -1888.67013001 -1894.02402688   162.42960290    -0.01005424     3.31005424 
+     300     0.03000000 -1888.67012741 -1893.91715254   159.18726627    -0.01056129     3.31056129 
+     310     0.03100000 -1888.67005750 -1893.57037262   148.66857854    -0.01107957     3.31107957 
+     320     0.03200000 -1888.66994592 -1893.09358639   134.20694885    -0.01160898     3.31160898 
+     330     0.03300000 -1888.66983608 -1892.66132683   121.09614209    -0.01214935     3.31214935 
+     340     0.03400000 -1888.66977429 -1892.44446364   114.51869677    -0.01270046     3.31270046 
+     350     0.03500000 -1888.66978845 -1892.53901254   117.38674604    -0.01326207     3.31326207 
+     360     0.03600000 -1888.66987459 -1892.92337308   129.04508370    -0.01383390     3.31383390 
+     370     0.03700000 -1888.66999819 -1893.46445589   145.45701553    -0.01441561     3.31441561 
+     380     0.03800000 -1888.67010979 -1893.97065536   160.81100019    -0.01500688     3.31500688 
+     390     0.03900000 -1888.67016559 -1894.26835837   169.84119248    -0.01560734     3.31560734 
+     400     0.04000000 -1888.67014686 -1894.26967995   169.88185548    -0.01621664     3.31621664 
+     410     0.04100000 -1888.67006186 -1894.00321089   161.80014284    -0.01683442     3.31683442 
+     420     0.04200000 -1888.66994386 -1893.60086344   149.59707422    -0.01746033     3.31746033 
+     430     0.04300000 -1888.66984078 -1893.24559860   138.82197278    -0.01809405     3.31809405 
+     440     0.04400000 -1888.66979419 -1893.09727893   134.32357877    -0.01873527     3.31873527 
+     450     0.04500000 -1888.66982159 -1893.22837461   138.30000376    -0.01938373     3.31938373 
+     460     0.04600000 -1888.66990991 -1893.59670402   149.47191350    -0.02003918     3.32003918 
+     470     0.04700000 -1888.67002193 -1894.06542618   163.68887740    -0.02070143     3.32070143 
+     480     0.04800000 -1888.67011408 -1894.46010861   175.66018436    -0.02137030     3.32137030 
+     490     0.04900000 -1888.67015195 -1894.63688117   181.02206322    -0.02204565     3.32204565 
+     500     0.05000000 -1888.67012178 -1894.53632241   177.97216884    -0.02272740     3.32272740 
+     510     0.05100000 -1888.67003782 -1894.20444750   167.90610440    -0.02341547     3.32341547 
+     520     0.05200000 -1888.66993171 -1893.77231086   154.79891357    -0.02410981     3.32410981 
+     530     0.05300000 -1888.66984524 -1893.40525947   143.66572040    -0.02481040     3.32481040 
+     540     0.05400000 -1888.66981428 -1893.23762103   138.58074854    -0.02551724     3.32551724 
+     550     0.05500000 -1888.66985024 -1893.31793613   141.01630314    -0.02623032     3.32623032 
+     560     0.05600000 -1888.66993756 -1893.59069032   149.28862746    -0.02694963     3.32694963 
+     570     0.05700000 -1888.67003871 -1893.92089591   159.30352583    -0.02767517     3.32767517 
+     580     0.05800000 -1888.67011342 -1894.15124772   166.28980520    -0.02840691     3.32840691 
+     590     0.05900000 -1888.67013211 -1894.16548061   166.72104344    -0.02914478     3.32914478 
+     600     0.06000000 -1888.67008732 -1893.93443338   159.71275857    -0.02988871     3.32988871 
+     610     0.06100000 -1888.66999458 -1893.52841675   147.39760649    -0.03063856     3.33063856 
+     620     0.06200000 -1888.66988829 -1893.09235041   134.17119966    -0.03139416     3.33139416 
+     630     0.06300000 -1888.66981016 -1892.79172036   125.05288241    -0.03215531     3.33215531 
+     640     0.06400000 -1888.66979281 -1892.74755409   123.71346729    -0.03292176     3.33292176 
+     650     0.06500000 -1888.66984352 -1892.98665478   130.96590321    -0.03369323     3.33369323 
+     660     0.06600000 -1888.66994264 -1893.42999887   144.41332385    -0.03446937     3.33446937 
+     670     0.06700000 -1888.67005253 -1893.92310700   159.37018803    -0.03524986     3.33524986 
+     680     0.06800000 -1888.67013328 -1894.29451600   170.63575807    -0.03603430     3.33603430 
+     690     0.06900000 -1888.67015472 -1894.41878137   174.40514195    -0.03682229     3.33682229 
+     700     0.07000000 -1888.67010916 -1894.26288055   169.67671536    -0.03761343     3.33761343 
+     710     0.07100000 -1888.67001386 -1893.89812923   158.61357122    -0.03840729     3.33840729 
+     720     0.07200000 -1888.66990397 -1893.47348765   145.73388461    -0.03920344     3.33920344 
+     730     0.07300000 -1888.66982231 -1893.15984859   136.22099965    -0.04000148     3.34000148 
+     740     0.07400000 -1888.66980129 -1893.08373765   133.91254030    -0.04080098     3.34080098 
+     750     0.07500000 -1888.66984814 -1893.27755530   139.79127022    -0.04160156     3.34160156 
+     760     0.07600000 -1888.66994235 -1893.66837384   151.64528962    -0.04240282     3.34240282 
+     770     0.07700000 -1888.67004573 -1894.10941225   165.02263022    -0.04320441     3.34320441 
+     780     0.07800000 -1888.67011722 -1894.43947564   175.03411433    -0.04400599     3.34400599 
+     790     0.07900000 -1888.67013317 -1894.54590490   178.26254255    -0.04480726     3.34480726 
+     800     0.08000000 -1888.67008771 -1894.40384162   173.95392409    -0.04560792     3.34560792 
+     810     0.08100000 -1888.66999942 -1894.08389023   164.24973325    -0.04640773     3.34640773 
+     820     0.08200000 -1888.66990467 -1893.72313999   153.30795968    -0.04720647     3.34720647 
+     830     0.08300000 -1888.66984387 -1893.46839210   145.58111627    -0.04800393     3.34800393 
+     840     0.08400000 -1888.66984175 -1893.41412556   143.93481091    -0.04879995     3.34879995 
+     850     0.08500000 -1888.66989690 -1893.56426173   148.48805548    -0.04959439     3.34959439 
+     860     0.08600000 -1888.66998242 -1893.83463738   156.68827289    -0.05038713     3.35038713 
+     870     0.08700000 -1888.67006191 -1894.09325064   164.53181916    -0.05117805     3.35117805 
+     880     0.08800000 -1888.67010292 -1894.21712680   168.28880099    -0.05196706     3.35196706 
+     890     0.08900000 -1888.67009013 -1894.14263970   166.02935659    -0.05275408     3.35275408 
+     900     0.09000000 -1888.67002911 -1893.89014590   158.37090593    -0.05353904     3.35353904 
+     910     0.09100000 -1888.66994346 -1893.55535729   148.21649476    -0.05432186     3.35432186 
+     920     0.09200000 -1888.66986545 -1893.27257968   139.63979183    -0.05510247     3.35510247 
+     930     0.09300000 -1888.66982750 -1893.16330910   136.32582951    -0.05588078     3.35588078 
+     940     0.09400000 -1888.66984650 -1893.28643304   140.06065783    -0.05665670     3.35665670 
+     950     0.09500000 -1888.66991522 -1893.61245361   149.94957262    -0.05743015     3.35743015 
+     960     0.09600000 -1888.67000710 -1894.03423941   162.74316510    -0.05820101     3.35820101 
+     970     0.09700000 -1888.67008668 -1894.40848044   174.09469033    -0.05896915     3.35896915 
+     980     0.09800000 -1888.67012456 -1894.61056787   180.22458605    -0.05973444     3.35973444 
+     990     0.09900000 -1888.67010627 -1894.58107679   179.33042341    -0.06049672     3.36049672 
+    1000     0.10000000 -1888.67004000 -1894.34773324   172.25312335    -0.06125581     3.36125581 
+Loop time of 2.60456 on 1 procs for 1000 steps with 256 atoms
+
+Performance: 3.317 ns/day, 7.235 hours/ns, 383.942 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.5864     | 2.5864     | 2.5864     |   0.0 | 99.30
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0079134  | 0.0079134  | 0.0079134  |   0.0 |  0.30
+Output  | 0.0027175  | 0.0027175  | 0.0027175  |   0.0 |  0.10
+Modify  | 0.00419    | 0.00419    | 0.00419    |   0.0 |  0.16
+Other   |            | 0.00331    |            |       |  0.13
+
+Nlocal:    256 ave 256 max 256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1721 ave 1721 max 1721 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    37312 ave 37312 max 37312 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  94592 ave 94592 max 94592 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 94592
+Ave neighs/atom = 369.5
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4

@@ -0,0 +1,210 @@
+LAMMPS (30 Apr 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      atomic
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data       data.bilayer-graphene # read lammps data file
+  orthogonal box = (0 0 -20) to (17.04 19.6761 40)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  256 atoms
+  read_data CPU = 0.0488505 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+# Separate atom groups
+group membrane  type 1
+128 atoms in group membrane
+group adsorbant type 2
+128 atoms in group adsorbant
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  kolmogorov/crespi/z 14.0
+####################################################################
+pair_coeff * * rebo                 CH.rebo  C C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff 1 2 kolmogorov/crespi/z  CC.KC      C C  # long-range
+####################################################################
+
+#### Simulation settings ####
+timestep  0.0001
+velocity  all create 300.0 12345
+fix       thermostat all nve
+compute   COM1 membrane  com
+compute   COM2 adsorbant com
+############################
+
+# Output
+#dump            1 all xyz 100 trajec.xyz
+#dump_modify     1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
+thermo          10
+thermo_style    custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
+thermo_modify   line one format float %14.8f
+
+###### Run molecular dynamics ######
+run 1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 16
+  ghost atom cutoff = 16
+  binsize = 8, bins = 3 3 8
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair kolmogorov/crespi/z, perpetual, skip from (3)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) neighbor class addition, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes
+Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3] 
+       0     0.00000000 -1888.67041233 -1898.55881343   300.00000000     0.00000000     3.30000000 
+      10     0.00100000 -1888.67037240 -1898.21029916   289.42778520    -0.00020126     3.30020126 
+      20     0.00200000 -1888.67021561 -1897.22943631   259.67456089    -0.00041357     3.30041357 
+      30     0.00300000 -1888.66999327 -1895.86681330   218.34126559    -0.00063673     3.30063673 
+      40     0.00400000 -1888.66978373 -1894.47163849   176.02000692    -0.00087055     3.30087055 
+      50     0.00500000 -1888.66966087 -1893.37123396   142.63902861    -0.00111486     3.30111486 
+      60     0.00600000 -1888.66966151 -1892.75822768   124.04127204    -0.00136952     3.30136952 
+      70     0.00700000 -1888.66976993 -1892.63445770   120.28297806    -0.00163441     3.30163441 
+      80     0.00800000 -1888.66992887 -1892.83467481   126.35245790    -0.00190946     3.30190946 
+      90     0.00900000 -1888.67006887 -1893.11387088   134.81862143    -0.00219458     3.30219458 
+     100     0.01000000 -1888.67013641 -1893.25481870   139.09272852    -0.00248973     3.30248973 
+     110     0.01100000 -1888.67011221 -1893.15155809   135.96068294    -0.00279489     3.30279489 
+     120     0.01200000 -1888.67001516 -1892.84002980   126.51230266    -0.00311004     3.30311004 
+     130     0.01300000 -1888.66989017 -1892.47004258   115.29120969    -0.00343519     3.30343519 
+     140     0.01400000 -1888.66979250 -1892.23503136   108.16426724    -0.00377038     3.30377038 
+     150     0.01500000 -1888.66976498 -1892.28630603   109.72070258    -0.00411562     3.30411562 
+     160     0.01600000 -1888.66982073 -1892.66640631   121.25071190    -0.00447099     3.30447099 
+     170     0.01700000 -1888.66993810 -1893.28862656   140.12442720    -0.00483654     3.30483654 
+     180     0.01800000 -1888.67007037 -1893.97029277   160.80119589    -0.00521235     3.30521235 
+     190     0.01900000 -1888.67016732 -1894.50458806   177.00801243    -0.00559851     3.30559851 
+     200     0.02000000 -1888.67019479 -1894.73890125   184.11590729    -0.00599512     3.30599512 
+     210     0.02100000 -1888.67014440 -1894.62906034   180.78501933    -0.00640230     3.30640230 
+     220     0.02200000 -1888.67003699 -1894.25249122   169.36370739    -0.00682016     3.30682016 
+     230     0.02300000 -1888.66991405 -1893.77601632   154.91186768    -0.00724883     3.30724883 
+     240     0.02400000 -1888.66982545 -1893.38995103   143.20188490    -0.00768845     3.30768845 
+     250     0.02500000 -1888.66980650 -1893.23138955   138.39193054    -0.00813913     3.30813913 
+     260     0.02600000 -1888.66986149 -1893.32993943   141.38012473    -0.00860097     3.30860097 
+     270     0.02700000 -1888.66996324 -1893.60070625   149.59171759    -0.00907408     3.30907408 
+     280     0.02800000 -1888.67006705 -1893.88587245   158.24010430    -0.00955849     3.30955849 
+     290     0.02900000 -1888.67013001 -1894.02402688   162.42960290    -0.01005424     3.31005424 
+     300     0.03000000 -1888.67012741 -1893.91715254   159.18726627    -0.01056129     3.31056129 
+     310     0.03100000 -1888.67005750 -1893.57037262   148.66857854    -0.01107957     3.31107957 
+     320     0.03200000 -1888.66994592 -1893.09358639   134.20694885    -0.01160898     3.31160898 
+     330     0.03300000 -1888.66983608 -1892.66132683   121.09614209    -0.01214935     3.31214935 
+     340     0.03400000 -1888.66977429 -1892.44446364   114.51869677    -0.01270046     3.31270046 
+     350     0.03500000 -1888.66978845 -1892.53901254   117.38674604    -0.01326207     3.31326207 
+     360     0.03600000 -1888.66987459 -1892.92337308   129.04508370    -0.01383390     3.31383390 
+     370     0.03700000 -1888.66999819 -1893.46445589   145.45701553    -0.01441561     3.31441561 
+     380     0.03800000 -1888.67010979 -1893.97065536   160.81100019    -0.01500688     3.31500688 
+     390     0.03900000 -1888.67016559 -1894.26835837   169.84119248    -0.01560734     3.31560734 
+     400     0.04000000 -1888.67014686 -1894.26967995   169.88185548    -0.01621664     3.31621664 
+     410     0.04100000 -1888.67006186 -1894.00321089   161.80014284    -0.01683442     3.31683442 
+     420     0.04200000 -1888.66994386 -1893.60086344   149.59707422    -0.01746033     3.31746033 
+     430     0.04300000 -1888.66984078 -1893.24559860   138.82197278    -0.01809405     3.31809405 
+     440     0.04400000 -1888.66979419 -1893.09727893   134.32357877    -0.01873527     3.31873527 
+     450     0.04500000 -1888.66982159 -1893.22837461   138.30000376    -0.01938373     3.31938373 
+     460     0.04600000 -1888.66990991 -1893.59670402   149.47191350    -0.02003918     3.32003918 
+     470     0.04700000 -1888.67002193 -1894.06542618   163.68887740    -0.02070143     3.32070143 
+     480     0.04800000 -1888.67011408 -1894.46010861   175.66018436    -0.02137030     3.32137030 
+     490     0.04900000 -1888.67015195 -1894.63688117   181.02206322    -0.02204565     3.32204565 
+     500     0.05000000 -1888.67012178 -1894.53632241   177.97216884    -0.02272740     3.32272740 
+     510     0.05100000 -1888.67003782 -1894.20444750   167.90610440    -0.02341547     3.32341547 
+     520     0.05200000 -1888.66993171 -1893.77231086   154.79891357    -0.02410981     3.32410981 
+     530     0.05300000 -1888.66984524 -1893.40525947   143.66572040    -0.02481040     3.32481040 
+     540     0.05400000 -1888.66981428 -1893.23762103   138.58074854    -0.02551724     3.32551724 
+     550     0.05500000 -1888.66985024 -1893.31793613   141.01630314    -0.02623032     3.32623032 
+     560     0.05600000 -1888.66993756 -1893.59069032   149.28862746    -0.02694963     3.32694963 
+     570     0.05700000 -1888.67003871 -1893.92089591   159.30352583    -0.02767517     3.32767517 
+     580     0.05800000 -1888.67011342 -1894.15124772   166.28980520    -0.02840691     3.32840691 
+     590     0.05900000 -1888.67013211 -1894.16548061   166.72104344    -0.02914478     3.32914478 
+     600     0.06000000 -1888.67008732 -1893.93443338   159.71275857    -0.02988871     3.32988871 
+     610     0.06100000 -1888.66999458 -1893.52841675   147.39760649    -0.03063856     3.33063856 
+     620     0.06200000 -1888.66988829 -1893.09235041   134.17119966    -0.03139416     3.33139416 
+     630     0.06300000 -1888.66981016 -1892.79172036   125.05288241    -0.03215531     3.33215531 
+     640     0.06400000 -1888.66979281 -1892.74755409   123.71346729    -0.03292176     3.33292176 
+     650     0.06500000 -1888.66984352 -1892.98665478   130.96590321    -0.03369323     3.33369323 
+     660     0.06600000 -1888.66994264 -1893.42999887   144.41332385    -0.03446937     3.33446937 
+     670     0.06700000 -1888.67005253 -1893.92310700   159.37018803    -0.03524986     3.33524986 
+     680     0.06800000 -1888.67013328 -1894.29451600   170.63575807    -0.03603430     3.33603430 
+     690     0.06900000 -1888.67015472 -1894.41878137   174.40514195    -0.03682229     3.33682229 
+     700     0.07000000 -1888.67010916 -1894.26288055   169.67671536    -0.03761343     3.33761343 
+     710     0.07100000 -1888.67001386 -1893.89812923   158.61357122    -0.03840729     3.33840729 
+     720     0.07200000 -1888.66990397 -1893.47348765   145.73388461    -0.03920344     3.33920344 
+     730     0.07300000 -1888.66982231 -1893.15984859   136.22099965    -0.04000148     3.34000148 
+     740     0.07400000 -1888.66980129 -1893.08373765   133.91254030    -0.04080098     3.34080098 
+     750     0.07500000 -1888.66984814 -1893.27755530   139.79127022    -0.04160156     3.34160156 
+     760     0.07600000 -1888.66994235 -1893.66837384   151.64528962    -0.04240282     3.34240282 
+     770     0.07700000 -1888.67004573 -1894.10941225   165.02263022    -0.04320441     3.34320441 
+     780     0.07800000 -1888.67011722 -1894.43947564   175.03411433    -0.04400599     3.34400599 
+     790     0.07900000 -1888.67013317 -1894.54590490   178.26254255    -0.04480726     3.34480726 
+     800     0.08000000 -1888.67008771 -1894.40384162   173.95392409    -0.04560792     3.34560792 
+     810     0.08100000 -1888.66999942 -1894.08389023   164.24973325    -0.04640773     3.34640773 
+     820     0.08200000 -1888.66990467 -1893.72313999   153.30795968    -0.04720647     3.34720647 
+     830     0.08300000 -1888.66984387 -1893.46839210   145.58111627    -0.04800393     3.34800393 
+     840     0.08400000 -1888.66984175 -1893.41412556   143.93481091    -0.04879995     3.34879995 
+     850     0.08500000 -1888.66989690 -1893.56426173   148.48805548    -0.04959439     3.34959439 
+     860     0.08600000 -1888.66998242 -1893.83463738   156.68827289    -0.05038713     3.35038713 
+     870     0.08700000 -1888.67006191 -1894.09325064   164.53181916    -0.05117805     3.35117805 
+     880     0.08800000 -1888.67010292 -1894.21712680   168.28880099    -0.05196706     3.35196706 
+     890     0.08900000 -1888.67009013 -1894.14263970   166.02935659    -0.05275408     3.35275408 
+     900     0.09000000 -1888.67002911 -1893.89014590   158.37090593    -0.05353904     3.35353904 
+     910     0.09100000 -1888.66994346 -1893.55535729   148.21649476    -0.05432186     3.35432186 
+     920     0.09200000 -1888.66986545 -1893.27257968   139.63979183    -0.05510247     3.35510247 
+     930     0.09300000 -1888.66982750 -1893.16330910   136.32582951    -0.05588078     3.35588078 
+     940     0.09400000 -1888.66984650 -1893.28643304   140.06065783    -0.05665670     3.35665670 
+     950     0.09500000 -1888.66991522 -1893.61245361   149.94957262    -0.05743015     3.35743015 
+     960     0.09600000 -1888.67000710 -1894.03423941   162.74316510    -0.05820101     3.35820101 
+     970     0.09700000 -1888.67008668 -1894.40848044   174.09469033    -0.05896915     3.35896915 
+     980     0.09800000 -1888.67012456 -1894.61056787   180.22458605    -0.05973444     3.35973444 
+     990     0.09900000 -1888.67010627 -1894.58107679   179.33042341    -0.06049672     3.36049672 
+    1000     0.10000000 -1888.67004000 -1894.34773324   172.25312335    -0.06125581     3.36125581 
+Loop time of 1.55992 on 4 procs for 1000 steps with 256 atoms
+
+Performance: 5.539 ns/day, 4.333 hours/ns, 641.059 timesteps/s
+96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.3161     | 1.3724     | 1.4128     |   3.0 | 87.98
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.11734    | 0.16017    | 0.21617    |   8.9 | 10.27
+Output  | 0.0032182  | 0.0051764  | 0.010916   |   4.6 |  0.33
+Modify  | 0.0020187  | 0.0022321  | 0.0026002  |   0.5 |  0.14
+Other   |            | 0.0199     |            |       |  1.28
+
+Nlocal:    64 ave 64 max 64 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    1265 ave 1265 max 1265 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    9328 ave 9328 max 9328 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  23648 ave 23648 max 23648 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 94592
+Ave neighs/atom = 369.5
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:01

examples/airebo/CH.rebo

@@ -0,0 +1 @@
+../../potentials/CH.rebo

examples/airebo/in.airebo-0-0

@@ -0,0 +1,22 @@
+# AIREBO polyethelene benchmark
+
+units		    metal
+atom_style	    atomic
+
+read_data	    data.airebo
+
+replicate	    17 16 2
+
+neighbor	    0.5 bin
+neigh_modify	    delay 5 every 1
+
+pair_style	    airebo 3.0 0 0
+pair_coeff	    * * CH.airebo C H
+
+velocity	    all create 300.0 761341
+
+fix		    1 all nve
+timestep	    0.0005
+
+thermo		    10
+run		    100

examples/airebo/in.rebo2

@@ -0,0 +1,22 @@
+# REBO polyethelene benchmark
+
+units		    metal
+atom_style	    atomic
+
+read_data	    data.airebo
+
+replicate	    17 16 2
+
+neighbor	    0.5 bin
+neigh_modify	    delay 5 every 1
+
+pair_style	    rebo
+pair_coeff	    * * CH.rebo C H
+
+velocity	    all create 300.0 761341
+
+fix		    1 all nve
+timestep	    0.0005
+
+thermo		    10
+run		    100

examples/airebo/log.30Apr2019.airebo-0-0.g++.1

@@ -0,0 +1,89 @@
+LAMMPS (30 Apr 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# AIREBO polyethelene benchmark
+
+units		    metal
+atom_style	    atomic
+
+read_data	    data.airebo
+  orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  60 atoms
+  read_data CPU = 0.000232458 secs
+
+replicate	    17 16 2
+  orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
+  1 by 1 by 1 MPI processor grid
+  32640 atoms
+  replicate CPU = 0.00206327 secs
+
+neighbor	    0.5 bin
+neigh_modify	    delay 5 every 1
+
+pair_style	    airebo 3.0 0 0
+pair_coeff	    * * CH.airebo C H
+Reading potential file CH.airebo with DATE: 2011-10-25
+
+velocity	    all create 300.0 761341
+
+fix		    1 all nve
+timestep	    0.0005
+
+thermo		    10
+run		    100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.5
+  ghost atom cutoff = 6.5
+  binsize = 3.25, bins = 22 21 16
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair airebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -138442.83            0   -137177.16    2463.0755 
+      10    179.38448   -137931.29            0   -137174.48     15656.69 
+      20    206.89283   -138047.06            0   -137174.19   -24047.407 
+      30    150.81289   -137807.48            0   -137171.21   -16524.191 
+      40    173.24289   -137902.32            0   -137171.42   -5721.7187 
+      50    151.80722   -137812.37            0   -137171.91    3489.8954 
+      60    199.06038    -138013.7            0   -137173.88    17887.025 
+      70    217.84848   -138093.82            0   -137174.73    -12266.16 
+      80    202.34667   -138029.28            0   -137175.59   -7623.6634 
+      90    194.92367   -137997.12            0   -137174.75   -32277.173 
+     100     185.2078   -137954.64            0   -137173.26   -6888.5104 
+Loop time of 9.70367 on 1 procs for 100 steps with 32640 atoms
+
+Performance: 0.445 ns/day, 53.909 hours/ns, 10.305 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.2508     | 7.2508     | 7.2508     |   0.0 | 74.72
+Neigh   | 2.3573     | 2.3573     | 2.3573     |   0.0 | 24.29
+Comm    | 0.03116    | 0.03116    | 0.03116    |   0.0 |  0.32
+Output  | 0.0014739  | 0.0014739  | 0.0014739  |   0.0 |  0.02
+Modify  | 0.0447     | 0.0447     | 0.0447     |   0.0 |  0.46
+Other   |            | 0.01819    |            |       |  0.19
+
+Nlocal:    32640 ave 32640 max 32640 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    26460 ave 26460 max 26460 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4902134
+Ave neighs/atom = 150.188
+Neighbor list builds = 9
+Dangerous builds = 0
+Total wall time: 0:00:10

examples/airebo/log.30Apr2019.airebo-0-0.g++.4

@@ -0,0 +1,89 @@
+LAMMPS (30 Apr 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# AIREBO polyethelene benchmark
+
+units		    metal
+atom_style	    atomic
+
+read_data	    data.airebo
+  orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  60 atoms
+  read_data CPU = 0.000363827 secs
+
+replicate	    17 16 2
+  orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
+  2 by 2 by 1 MPI processor grid
+  32640 atoms
+  replicate CPU = 0.00244427 secs
+
+neighbor	    0.5 bin
+neigh_modify	    delay 5 every 1
+
+pair_style	    airebo 3.0 0 0
+pair_coeff	    * * CH.airebo C H
+Reading potential file CH.airebo with DATE: 2011-10-25
+
+velocity	    all create 300.0 761341
+
+fix		    1 all nve
+timestep	    0.0005
+
+thermo		    10
+run		    100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.5
+  ghost atom cutoff = 6.5
+  binsize = 3.25, bins = 22 21 16
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair airebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -138442.83            0   -137177.16    2463.0755 
+      10    179.38448   -137931.29            0   -137174.48     15656.69 
+      20    206.89283   -138047.06            0   -137174.19   -24047.407 
+      30    150.81289   -137807.48            0   -137171.21   -16524.191 
+      40    173.24289   -137902.32            0   -137171.42   -5721.7187 
+      50    151.80722   -137812.37            0   -137171.91    3489.8954 
+      60    199.06038    -138013.7            0   -137173.88    17887.025 
+      70    217.84848   -138093.82            0   -137174.73    -12266.16 
+      80    202.34667   -138029.28            0   -137175.59   -7623.6634 
+      90    194.92367   -137997.12            0   -137174.75   -32277.173 
+     100     185.2078   -137954.64            0   -137173.26   -6888.5104 
+Loop time of 6.71962 on 4 procs for 100 steps with 32640 atoms
+
+Performance: 0.643 ns/day, 37.331 hours/ns, 14.882 timesteps/s
+96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.4598     | 4.6375     | 4.7708     |   5.5 | 69.01
+Neigh   | 1.5903     | 1.6452     | 1.7207     |   3.8 | 24.48
+Comm    | 0.16708    | 0.37041    | 0.56709    |  25.1 |  5.51
+Output  | 0.001061   | 0.0059808  | 0.0090635  |   4.3 |  0.09
+Modify  | 0.030086   | 0.03154    | 0.032522   |   0.5 |  0.47
+Other   |            | 0.02897    |            |       |  0.43
+
+Nlocal:    8160 ave 8163 max 8157 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    11605.8 ave 11615 max 11593 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1.22553e+06 ave 1.22734e+06 max 1.22455e+06 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 4902134
+Ave neighs/atom = 150.188
+Neighbor list builds = 9
+Dangerous builds = 0
+Total wall time: 0:00:07

examples/airebo/log.30Apr2019.airebo-m.g++.1

@@ -1,36 +1,38 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (30 Apr 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
   using 1 OpenMP thread(s) per MPI task
 # AIREBO polyethelene benchmark
 
-units		    metal
+units               metal
-atom_style	    atomic
+atom_style          atomic
 
-read_data	    data.airebo
+read_data           data.airebo
   orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
   1 by 1 by 1 MPI processor grid
   reading atoms ...
   60 atoms
+  read_data CPU = 0.000225067 secs
 
-replicate	    17 16 2
+replicate           17 16 2
   orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
   1 by 1 by 1 MPI processor grid
   32640 atoms
-  Time spent = 0.00141144 secs
+  replicate CPU = 0.00226521 secs
 
-neighbor	    0.5 bin
+neighbor            0.5 bin
-neigh_modify	    delay 5 every 1
+neigh_modify        delay 5 every 1
 
-pair_style	    airebo/morse 3.0 1 1
+pair_style          airebo/morse 3.0 1 1
-pair_coeff	    * * ../../potentials/CH.airebo-m C H
+pair_coeff          * * CH.airebo-m C H
-Reading potential file ../../potentials/CH.airebo-m with DATE: 2016-03-15
+Reading potential file CH.airebo-m with DATE: 2016-03-15
 
-velocity	    all create 300.0 761341
+velocity            all create 300.0 761341
 
-fix		    1 all nve
+fix                 1 all nve
-timestep	    0.0005
+timestep            0.0005
 
-thermo		    10
+thermo              10
-run		    100
+run                 100
 Neighbor list info ...
   update every 1 steps, delay 5 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -45,7 +47,7 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes
 Step Temp E_pair E_mol TotEng Press 
-       0          300   -139283.82            0   -138018.14    152.25271 
+       0          300   -139283.82            0   -138018.14    152.25266 
       10    166.76148   -138718.75            0   -138015.19    17412.343 
       20     207.7293   -138891.79            0    -138015.4   -19395.339 
       30    138.54469   -138596.42            0   -138011.92   -11909.248 
@@ -55,21 +57,21 @@ Step Temp E_pair E_mol TotEng Press
       70    185.72779   -138799.18            0   -138015.61   -10803.744 
       80    164.28396    -138709.5            0    -138016.4   -1524.7353 
       90    180.26403   -138776.42            0    -138015.9   -27143.467 
-     100    164.05694   -138706.58            0   -138014.44    5157.5516 
+     100    164.05694   -138706.58            0   -138014.44    5157.5517 
-Loop time of 64.6107 on 1 procs for 100 steps with 32640 atoms
+Loop time of 111.537 on 1 procs for 100 steps with 32640 atoms
 
-Performance: 0.067 ns/day, 358.948 hours/ns, 1.548 timesteps/s
+Performance: 0.039 ns/day, 619.650 hours/ns, 0.897 timesteps/s
 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 59.916     | 59.916     | 59.916     |   0.0 | 92.73
+Pair    | 103.58     | 103.58     | 103.58     |   0.0 | 92.87
-Neigh   | 4.6347     | 4.6347     | 4.6347     |   0.0 |  7.17
+Neigh   | 7.8371     | 7.8371     | 7.8371     |   0.0 |  7.03
-Comm    | 0.025572   | 0.025572   | 0.025572   |   0.0 |  0.04
+Comm    | 0.046259   | 0.046259   | 0.046259   |   0.0 |  0.04
-Output  | 0.00098896 | 0.00098896 | 0.00098896 |   0.0 |  0.00
+Output  | 0.001497   | 0.001497   | 0.001497   |   0.0 |  0.00
-Modify  | 0.022327   | 0.022327   | 0.022327   |   0.0 |  0.03
+Modify  | 0.047151   | 0.047151   | 0.047151   |   0.0 |  0.04
-Other   |            | 0.01076    |            |       |  0.02
+Other   |            | 0.02204    |            |       |  0.02
 
 Nlocal:    32640 ave 32640 max 32640 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -84,4 +86,4 @@ Total # of neighbors = 22210922
 Ave neighs/atom = 680.482
 Neighbor list builds = 8
 Dangerous builds = 0
-Total wall time: 0:01:05
+Total wall time: 0:01:53

examples/airebo/log.30Apr2019.airebo-m.g++.4

@@ -1,36 +1,38 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (30 Apr 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
   using 1 OpenMP thread(s) per MPI task
 # AIREBO polyethelene benchmark
 
-units		    metal
+units               metal
-atom_style	    atomic
+atom_style          atomic
 
-read_data	    data.airebo
+read_data           data.airebo
   orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
   1 by 1 by 4 MPI processor grid
   reading atoms ...
   60 atoms
+  read_data CPU = 0.000880957 secs
 
-replicate	    17 16 2
+replicate           17 16 2
   orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
   2 by 2 by 1 MPI processor grid
   32640 atoms
-  Time spent = 0.000637531 secs
+  replicate CPU = 0.00271702 secs
 
-neighbor	    0.5 bin
+neighbor            0.5 bin
-neigh_modify	    delay 5 every 1
+neigh_modify        delay 5 every 1
 
-pair_style	    airebo/morse 3.0 1 1
+pair_style          airebo/morse 3.0 1 1
-pair_coeff	    * * ../../potentials/CH.airebo-m C H
+pair_coeff          * * CH.airebo-m C H
-Reading potential file ../../potentials/CH.airebo-m with DATE: 2016-03-15
+Reading potential file CH.airebo-m with DATE: 2016-03-15
 
-velocity	    all create 300.0 761341
+velocity            all create 300.0 761341
 
-fix		    1 all nve
+fix                 1 all nve
-timestep	    0.0005
+timestep            0.0005
 
-thermo		    10
+thermo              10
-run		    100
+run                 100
 Neighbor list info ...
   update every 1 steps, delay 5 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -45,7 +47,7 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 29.37 | 29.75 | 30.13 Mbytes
 Step Temp E_pair E_mol TotEng Press 
-       0          300   -139283.82            0   -138018.14    152.25271 
+       0          300   -139283.82            0   -138018.14    152.25266 
       10    166.76148   -138718.75            0   -138015.19    17412.343 
       20     207.7293   -138891.79            0    -138015.4   -19395.339 
       30    138.54469   -138596.42            0   -138011.92   -11909.248 
@@ -55,21 +57,21 @@ Step Temp E_pair E_mol TotEng Press
       70    185.72779   -138799.18            0   -138015.61   -10803.744 
       80    164.28396    -138709.5            0    -138016.4   -1524.7353 
       90    180.26403   -138776.42            0    -138015.9   -27143.467 
-     100    164.05694   -138706.58            0   -138014.44    5157.5516 
+     100    164.05694   -138706.58            0   -138014.44    5157.5517 
-Loop time of 18.1922 on 4 procs for 100 steps with 32640 atoms
+Loop time of 68.9923 on 4 procs for 100 steps with 32640 atoms
 
-Performance: 0.237 ns/day, 101.068 hours/ns, 5.497 timesteps/s
+Performance: 0.063 ns/day, 383.290 hours/ns, 1.449 timesteps/s
-98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 15.968     | 16.084     | 16.308     |   3.4 | 88.41
+Pair    | 60.09      | 60.276     | 60.515     |   2.1 | 87.37
-Neigh   | 1.6017     | 1.6334     | 1.7006     |   3.1 |  8.98
+Neigh   | 6.7521     | 6.8996     | 7.0678     |   4.3 | 10.00
-Comm    | 0.1603     | 0.45122    | 0.59951    |  26.0 |  2.48
+Comm    | 1.5441     | 1.7514     | 2.0838     |  16.9 |  2.54
-Output  | 0.00042605 | 0.00073195 | 0.0016003  |   0.0 |  0.00
+Output  | 0.0010803  | 0.001972   | 0.0043106  |   3.0 |  0.00
-Modify  | 0.0092106  | 0.010544   | 0.014411   |   2.2 |  0.06
+Modify  | 0.031365   | 0.032539   | 0.034404   |   0.7 |  0.05
-Other   |            | 0.01193    |            |       |  0.07
+Other   |            | 0.03104    |            |       |  0.04
 
 Nlocal:    8160 ave 8167 max 8153 min
 Histogram: 1 0 1 0 0 0 0 1 0 1
@@ -84,4 +86,4 @@ Total # of neighbors = 22210922
 Ave neighs/atom = 680.482
 Neighbor list builds = 8
 Dangerous builds = 0
-Total wall time: 0:00:18
+Total wall time: 0:01:10

examples/airebo/log.30Apr2019.airebo.g++.1

@@ -1,36 +1,38 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (30 Apr 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
   using 1 OpenMP thread(s) per MPI task
 # AIREBO polyethelene benchmark
 
-units		    metal
+units               metal
-atom_style	    atomic
+atom_style          atomic
 
-read_data	    data.airebo
+read_data           data.airebo
   orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
   1 by 1 by 1 MPI processor grid
   reading atoms ...
   60 atoms
+  read_data CPU = 0.000217438 secs
 
-replicate	    17 16 2
+replicate           17 16 2
   orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
   1 by 1 by 1 MPI processor grid
   32640 atoms
-  Time spent = 0.00144172 secs
+  replicate CPU = 0.00204968 secs
 
-neighbor	    0.5 bin
+neighbor            0.5 bin
-neigh_modify	    delay 5 every 1
+neigh_modify        delay 5 every 1
 
-pair_style	    airebo 3.0 1 1
+pair_style          airebo 3.0 1 1
-pair_coeff	    * * ../../potentials/CH.airebo C H
+pair_coeff          * * CH.airebo C H
-Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25
+Reading potential file CH.airebo with DATE: 2011-10-25
 
-velocity	    all create 300.0 761341
+velocity            all create 300.0 761341
 
-fix		    1 all nve
+fix                 1 all nve
-timestep	    0.0005
+timestep            0.0005
 
-thermo		    10
+thermo              10
-run		    100
+run                 100
 Neighbor list info ...
   update every 1 steps, delay 5 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -45,31 +47,31 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 106.4 | 106.4 | 106.4 Mbytes
 Step Temp E_pair E_mol TotEng Press 
-       0          300   -139300.72            0   -138035.04    7988.6647 
+       0          300   -139300.72            0   -138035.04    7988.6646 
       10    161.34683    -138712.9            0   -138032.19    33228.921 
       20    208.59504   -138912.79            0   -138032.74   -3211.8806 
       30     139.7513   -138618.85            0   -138029.25    10878.143 
       40    142.14562   -138629.02            0   -138029.32    14601.302 
-      50    114.23401   -138510.95            0      -138029    24691.125 
+      50    114.23401   -138510.95            0      -138029    24691.124 
       60    164.92002      -138726            0   -138030.21    35125.541 
       70    162.15256    -138715.9            0   -138031.79    5658.7946 
       80    157.16184   -138695.77            0   -138032.72    19824.698 
-      90    196.15907   -138860.65            0   -138033.07   -7950.8462 
+      90    196.15907   -138860.65            0   -138033.07   -7950.8463 
      100    178.31875   -138784.89            0   -138032.57    30997.671 
-Loop time of 57.9914 on 1 procs for 100 steps with 32640 atoms
+Loop time of 98.1502 on 1 procs for 100 steps with 32640 atoms
 
-Performance: 0.074 ns/day, 322.174 hours/ns, 1.724 timesteps/s
+Performance: 0.044 ns/day, 545.279 hours/ns, 1.019 timesteps/s
-99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 53.275     | 53.275     | 53.275     |   0.0 | 91.87
+Pair    | 90.237     | 90.237     | 90.237     |   0.0 | 91.94
-Neigh   | 4.6548     | 4.6548     | 4.6548     |   0.0 |  8.03
+Neigh   | 7.796      | 7.796      | 7.796      |   0.0 |  7.94
-Comm    | 0.026622   | 0.026622   | 0.026622   |   0.0 |  0.05
+Comm    | 0.048884   | 0.048884   | 0.048884   |   0.0 |  0.05
-Output  | 0.00097251 | 0.00097251 | 0.00097251 |   0.0 |  0.00
+Output  | 0.0016053  | 0.0016053  | 0.0016053  |   0.0 |  0.00
-Modify  | 0.022773   | 0.022773   | 0.022773   |   0.0 |  0.04
+Modify  | 0.045511   | 0.045511   | 0.045511   |   0.0 |  0.05
-Other   |            | 0.01089    |            |       |  0.02
+Other   |            | 0.0217     |            |       |  0.02
 
 Nlocal:    32640 ave 32640 max 32640 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -84,4 +86,4 @@ Total # of neighbors = 22217840
 Ave neighs/atom = 680.694
 Neighbor list builds = 8
 Dangerous builds = 0
-Total wall time: 0:00:59
+Total wall time: 0:01:39

examples/airebo/log.30Apr2019.airebo.g++.4

@@ -1,36 +1,38 @@
-LAMMPS (27 Nov 2018)
+LAMMPS (30 Apr 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
   using 1 OpenMP thread(s) per MPI task
 # AIREBO polyethelene benchmark
 
-units		    metal
+units               metal
-atom_style	    atomic
+atom_style          atomic
 
-read_data	    data.airebo
+read_data           data.airebo
   orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
   1 by 1 by 4 MPI processor grid
   reading atoms ...
   60 atoms
+  read_data CPU = 0.000266314 secs
 
-replicate	    17 16 2
+replicate           17 16 2
   orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
   2 by 2 by 1 MPI processor grid
   32640 atoms
-  Time spent = 0.00262594 secs
+  replicate CPU = 0.00146151 secs
 
-neighbor	    0.5 bin
+neighbor            0.5 bin
-neigh_modify	    delay 5 every 1
+neigh_modify        delay 5 every 1
 
-pair_style	    airebo 3.0 1 1
+pair_style          airebo 3.0 1 1
-pair_coeff	    * * ../../potentials/CH.airebo C H
+pair_coeff          * * CH.airebo C H
-Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25
+Reading potential file CH.airebo with DATE: 2011-10-25
 
-velocity	    all create 300.0 761341
+velocity            all create 300.0 761341
 
-fix		    1 all nve
+fix                 1 all nve
-timestep	    0.0005
+timestep            0.0005
 
-thermo		    10
+thermo              10
-run		    100
+run                 100
 Neighbor list info ...
   update every 1 steps, delay 5 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -45,31 +47,31 @@ Neighbor list info ...
       bin: standard
 Per MPI rank memory allocation (min/avg/max) = 29.37 | 29.75 | 30.13 Mbytes
 Step Temp E_pair E_mol TotEng Press 
-       0          300   -139300.72            0   -138035.04    7988.6647 
+       0          300   -139300.72            0   -138035.04    7988.6646 
       10    161.34683    -138712.9            0   -138032.19    33228.921 
       20    208.59504   -138912.79            0   -138032.74   -3211.8806 
       30     139.7513   -138618.85            0   -138029.25    10878.143 
       40    142.14562   -138629.02            0   -138029.32    14601.302 
-      50    114.23401   -138510.95            0      -138029    24691.125 
+      50    114.23401   -138510.95            0      -138029    24691.124 
       60    164.92002      -138726            0   -138030.21    35125.541 
       70    162.15256    -138715.9            0   -138031.79    5658.7946 
       80    157.16184   -138695.77            0   -138032.72    19824.698 
-      90    196.15907   -138860.65            0   -138033.07   -7950.8462 
+      90    196.15907   -138860.65            0   -138033.07   -7950.8463 
      100    178.31875   -138784.89            0   -138032.57    30997.671 
-Loop time of 16.4395 on 4 procs for 100 steps with 32640 atoms
+Loop time of 60.4943 on 4 procs for 100 steps with 32640 atoms
 
-Performance: 0.263 ns/day, 91.331 hours/ns, 6.083 timesteps/s
+Performance: 0.071 ns/day, 336.080 hours/ns, 1.653 timesteps/s
-98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 14.263     | 14.349     | 14.483     |   2.3 | 87.28
+Pair    | 51.737     | 52.46      | 52.86      |   6.2 | 86.72
-Neigh   | 1.6071     | 1.6283     | 1.6636     |   1.7 |  9.90
+Neigh   | 6.5823     | 6.6605     | 6.726      |   2.0 | 11.01
-Comm    | 0.26261    | 0.43435    | 0.52323    |  16.1 |  2.64
+Comm    | 0.92426    | 1.3125     | 2.0111     |  37.0 |  2.17
-Output  | 0.00042105 | 0.0007121  | 0.001538   |   0.0 |  0.00
+Output  | 0.0010669  | 0.0019811  | 0.0043974  |   3.1 |  0.00
-Modify  | 0.00898    | 0.009112   | 0.0093675  |   0.2 |  0.06
+Modify  | 0.030364   | 0.031523   | 0.032495   |   0.5 |  0.05
-Other   |            | 0.0184     |            |       |  0.11
+Other   |            | 0.028      |            |       |  0.05
 
 Nlocal:    8160 ave 8174 max 8146 min
 Histogram: 1 0 1 0 0 0 0 1 0 1
@@ -84,4 +86,4 @@ Total # of neighbors = 22217840
 Ave neighs/atom = 680.694
 Neighbor list builds = 8
 Dangerous builds = 0
-Total wall time: 0:00:16
+Total wall time: 0:01:01

examples/airebo/log.30Apr2019.rebo2.g++.1

@@ -0,0 +1,89 @@
+LAMMPS (30 Apr 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# REBO polyethelene benchmark
+
+units		    metal
+atom_style	    atomic
+
+read_data	    data.airebo
+  orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  60 atoms
+  read_data CPU = 0.000190735 secs
+
+replicate	    17 16 2
+  orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
+  1 by 1 by 1 MPI processor grid
+  32640 atoms
+  replicate CPU = 0.00197148 secs
+
+neighbor	    0.5 bin
+neigh_modify	    delay 5 every 1
+
+pair_style	    rebo
+pair_coeff	    * * CH.rebo C H
+Reading potential file CH.rebo with DATE: 2018-7-3
+
+velocity	    all create 300.0 761341
+
+fix		    1 all nve
+timestep	    0.0005
+
+thermo		    10
+run		    100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.5
+  ghost atom cutoff = 6.5
+  binsize = 3.25, bins = 22 21 16
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 34.21 | 34.21 | 34.21 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -138442.83            0   -137177.16    2463.0748 
+      10    179.37985   -137931.27            0   -137174.48    15655.936 
+      20    206.87654   -138046.99            0   -137174.19   -24042.627 
+      30    150.80122   -137807.43            0   -137171.21   -16524.118 
+      40    173.24945   -137902.35            0   -137171.42   -5716.9119 
+      50    151.80455   -137812.36            0   -137171.91    3480.4584 
+      60    199.08777   -138013.82            0   -137173.88    17881.372 
+      70    217.85748   -138093.86            0   -137174.73   -12270.999 
+      80    202.37482   -138029.39            0   -137175.59   -7622.7319 
+      90    194.90628   -137997.05            0   -137174.75   -32267.471 
+     100    185.17818   -137954.51            0   -137173.26   -6901.7499 
+Loop time of 9.44819 on 1 procs for 100 steps with 32640 atoms
+
+Performance: 0.457 ns/day, 52.490 hours/ns, 10.584 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.037      | 7.037      | 7.037      |   0.0 | 74.48
+Neigh   | 2.3182     | 2.3182     | 2.3182     |   0.0 | 24.54
+Comm    | 0.029898   | 0.029898   | 0.029898   |   0.0 |  0.32
+Output  | 0.0014331  | 0.0014331  | 0.0014331  |   0.0 |  0.02
+Modify  | 0.043851   | 0.043851   | 0.043851   |   0.0 |  0.46
+Other   |            | 0.01774    |            |       |  0.19
+
+Nlocal:    32640 ave 32640 max 32640 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    26460 ave 26460 max 26460 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4902134
+Ave neighs/atom = 150.188
+Neighbor list builds = 9
+Dangerous builds = 0
+Total wall time: 0:00:09

examples/airebo/log.30Apr2019.rebo2.g++.4

@@ -0,0 +1,89 @@
+LAMMPS (30 Apr 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# REBO polyethelene benchmark
+
+units		    metal
+atom_style	    atomic
+
+read_data	    data.airebo
+  orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  60 atoms
+  read_data CPU = 0.000682831 secs
+
+replicate	    17 16 2
+  orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
+  2 by 2 by 1 MPI processor grid
+  32640 atoms
+  replicate CPU = 0.00221777 secs
+
+neighbor	    0.5 bin
+neigh_modify	    delay 5 every 1
+
+pair_style	    rebo
+pair_coeff	    * * CH.rebo C H
+Reading potential file CH.rebo with DATE: 2018-7-3
+
+velocity	    all create 300.0 761341
+
+fix		    1 all nve
+timestep	    0.0005
+
+thermo		    10
+run		    100
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.5
+  ghost atom cutoff = 6.5
+  binsize = 3.25, bins = 22 21 16
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.75 | 11.94 | 12.13 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          300   -138442.83            0   -137177.16    2463.0748 
+      10    179.37985   -137931.27            0   -137174.48    15655.936 
+      20    206.87654   -138046.99            0   -137174.19   -24042.627 
+      30    150.80122   -137807.43            0   -137171.21   -16524.118 
+      40    173.24945   -137902.35            0   -137171.42   -5716.9119 
+      50    151.80455   -137812.36            0   -137171.91    3480.4584 
+      60    199.08777   -138013.82            0   -137173.88    17881.372 
+      70    217.85748   -138093.86            0   -137174.73   -12270.999 
+      80    202.37482   -138029.39            0   -137175.59   -7622.7319 
+      90    194.90628   -137997.05            0   -137174.75   -32267.471 
+     100    185.17818   -137954.51            0   -137173.26   -6901.7499 
+Loop time of 6.35645 on 4 procs for 100 steps with 32640 atoms
+
+Performance: 0.680 ns/day, 35.314 hours/ns, 15.732 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.4335     | 4.5041     | 4.56       |   2.1 | 70.86
+Neigh   | 1.5332     | 1.5919     | 1.6466     |   3.6 | 25.04
+Comm    | 0.098299   | 0.20854    | 0.26277    |  14.2 |  3.28
+Output  | 0.0011072  | 0.0018047  | 0.0037503  |   2.6 |  0.03
+Modify  | 0.028811   | 0.030358   | 0.031516   |   0.6 |  0.48
+Other   |            | 0.01977    |            |       |  0.31
+
+Nlocal:    8160 ave 8163 max 8157 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    11605.8 ave 11615 max 11593 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1.22553e+06 ave 1.22735e+06 max 1.22455e+06 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 4902134
+Ave neighs/atom = 150.188
+Neighbor list builds = 9
+Dangerous builds = 0
+Total wall time: 0:00:06

examples/granular/in.pour.drum

@@ -0,0 +1,98 @@
+# pour two types of particles (cohesive and non-cohesive) into cylinder
+# 'turn' cylinder by changing direction of gravity, then rotate it.
+# This simulates a rotating drum powder characterization experiment.
+
+variable	name string rotating_drum_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 30
+variable	boxy equal 30
+variable	boxz equal 50
+
+variable	drum_rad equal ${boxx}*0.5
+variable	drum_height equal 20
+
+variable	xc equal 0.5*${boxx}
+variable	yc equal 0.5*${boxx}
+variable	zc equal 0.5*${boxz}
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dhi equal 2.0*${rhi}
+
+variable	cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+
+variable	dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+
+#############
+processors * * 1
+region		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+create_box	2 boxreg
+change_box	all boundary p p f
+comm_modify	vel yes
+
+variable	theta equal 0
+
+region		curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+
+region		insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+
+fix		0 all balance 100 1.0 shift xy 5 1.1
+fix		1 all nve/sphere
+fix		grav all gravity 10 vector 0 0 -1
+fix		ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular 
+pair_coeff	1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
+pair_coeff	2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
+
+fix		3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall 
+fix		4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
+
+thermo_style	custom step atoms ke v_theta
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+#dump		1 all custom 100 ${name}.dump id type radius mass x y z 
+
+#For removal later
+compute		1 all property/atom radius
+variable	zmax atom z+c_1>0.5*${drum_height}
+group		delgroup dynamic all var zmax every 10000
+
+run		2000
+
+#Remove any particles that are above z > 0.5*drum_height
+delete_atoms	group delgroup
+
+#Add top lid
+region		top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+fix		5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
+
+# 'Turn' drum by switching the direction of gravity
+unfix		grav
+fix		grav all gravity 10 vector 0 -1 0
+
+variable	theta equal 2*PI*elapsed/20000.0
+run		3000

examples/granular/in.pour.flatwall

@@ -0,0 +1,67 @@
+# pour two types of particles (cohesive and non-cohesive) on flat wall
+
+variable   	name string pour_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 20
+variable	boxy equal 20
+variable	boxz equal 30
+
+variable	xc1 equal 0.3*${boxx}
+variable	xc2 equal 0.7*${boxx}
+variable	yc equal 0.5*${boxy}
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dhi equal 2.0*${rhi}
+
+variable	dens equal 1.0
+
+variable skin equal 0.3*${rhi}
+
+#############
+processors	* * 1
+region 		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+create_box	2 boxreg
+change_box	all boundary p p f
+
+comm_modify 	vel yes
+
+region		insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
+region		insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
+
+fix		1 all nve/sphere
+fix		grav all gravity 10.0 vector 0 0 -1
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular 
+pair_coeff 	1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff 	2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall 
+
+fix		3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL 
+
+thermo_style	custom step cpu atoms ke
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+#dump		1 all custom 100 ${name}.dump id type radius mass x y z 
+
+run		5000

examples/granular/log.29Mar19.pour.drum.g++.1

@@ -0,0 +1,271 @@
+LAMMPS (29 Mar 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# pour two types of particles (cohesive and non-cohesive) into cylinder
+# 'turn' cylinder by changing direction of gravity, then rotate it.
+# This simulates a rotating drum powder characterization experiment.
+
+variable	name string rotating_drum_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 30
+variable	boxy equal 30
+variable	boxz equal 50
+
+variable	drum_rad equal ${boxx}*0.5
+variable	drum_rad equal 30*0.5
+variable	drum_height equal 20
+
+variable	xc equal 0.5*${boxx}
+variable	xc equal 0.5*30
+variable	yc equal 0.5*${boxx}
+variable	yc equal 0.5*30
+variable	zc equal 0.5*${boxz}
+variable	zc equal 0.5*50
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable	cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+variable	cyl_rad_inner equal 15-1.1*${rhi}
+variable	cyl_rad_inner equal 15-1.1*0.5
+
+variable	dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+variable skin equal 0.4*0.5
+
+#############
+processors * * 1
+region		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region		boxreg block 0 30 0 ${boxy} 0 ${boxz}
+region		boxreg block 0 30 0 30 0 ${boxz}
+region		boxreg block 0 30 0 30 0 50
+create_box	2 boxreg
+Created orthogonal box = (0 0 0) to (30 30 50)
+  1 by 1 by 1 MPI processor grid
+change_box	all boundary p p f
+comm_modify	vel yes
+
+variable	theta equal 0
+
+region		curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
+region		bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
+
+region		insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 14.45 20 ${boxz}
+region		insreg cylinder z 15 15 14.45 20 50
+
+fix		0 all balance 100 1.0 shift xy 5 1.1
+fix		1 all nve/sphere
+fix		grav all gravity 10 vector 0 0 -1
+fix		ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+fix		ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neighbor	0.2 bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular
+pair_coeff	1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
+pair_coeff	2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
+
+fix		3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
+fix		4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
+
+thermo_style	custom step atoms ke v_theta
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+dump		1 all custom 100 ${name}.dump id type radius mass x y z
+dump		1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z
+
+#For removal later
+compute		1 all property/atom radius
+variable	zmax atom z+c_1>0.5*${drum_height}
+variable	zmax atom z+c_1>0.5*20
+group		delgroup dynamic all var zmax every 10000
+dynamic group delgroup defined
+
+run		2000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 50 50 84
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.02 | 13.02 | 13.02 Mbytes
+Step Atoms KinEng v_theta 
+       0        0           -0            0 
+     100     4000           -0            0 
+     200     4000           -0            0 
+     300     4000           -0            0 
+     400     4000           -0            0 
+     500     4000           -0            0 
+     600     4000           -0            0 
+     700     4000           -0            0 
+     800     4000           -0            0 
+     900     4000           -0            0 
+    1000     4000           -0            0 
+    1100     4000           -0            0 
+    1200     4000           -0            0 
+    1300     4000           -0            0 
+    1400     4000           -0            0 
+    1500     4000           -0            0 
+    1600     4000           -0            0 
+    1700     4000           -0            0 
+    1800     4000           -0            0 
+    1900     4000           -0            0 
+    2000     4000           -0            0 
+Loop time of 3.54461 on 1 procs for 2000 steps with 4000 atoms
+
+Performance: 48750.057 tau/day, 564.237 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.61949    | 0.61949    | 0.61949    |   0.0 | 17.48
+Neigh   | 1.2492     | 1.2492     | 1.2492     |   0.0 | 35.24
+Comm    | 0.046404   | 0.046404   | 0.046404   |   0.0 |  1.31
+Output  | 0.15901    | 0.15901    | 0.15901    |   0.0 |  4.49
+Modify  | 1.4165     | 1.4165     | 1.4165     |   0.0 | 39.96
+Other   |            | 0.05391    |            |       |  1.52
+
+Nlocal:    4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    166 ave 166 max 166 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    8195 ave 8195 max 8195 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 8195
+Ave neighs/atom = 2.04875
+Neighbor list builds = 1004
+Dangerous builds = 3
+
+#Remove any particles that are above z > 0.5*drum_height
+delete_atoms	group delgroup
+Deleted 0 atoms, new total = 4000
+
+#Add top lid
+region		top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
+fix		5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
+
+# 'Turn' drum by switching the direction of gravity
+unfix		grav
+fix		grav all gravity 10 vector 0 -1 0
+
+variable	theta equal 2*PI*elapsed/20000.0
+run		3000
+Per MPI rank memory allocation (min/avg/max) = 24.81 | 24.81 | 24.81 Mbytes
+Step Atoms KinEng v_theta 
+    2000     4000    64.333531            0 
+    2100     4000    106.69182  0.031415927 
+    2200     4000     121.8461  0.062831853 
+    2300     4000    88.767952   0.09424778 
+    2400     4000    82.850721   0.12566371 
+    2500     4000    91.683284   0.15707963 
+    2600     4000     31.56344   0.18849556 
+    2700     4000    4.5697672   0.21991149 
+    2800     4000    3.9879051   0.25132741 
+    2900     4000    4.4394235   0.28274334 
+    3000     4000    5.1212931   0.31415927 
+    3100     4000    5.8608892   0.34557519 
+    3200     4000     6.600714   0.37699112 
+    3300     4000    7.3497851   0.40840704 
+    3400     4000    8.0490988   0.43982297 
+    3500     4000    8.6712396    0.4712389 
+    3600     4000    9.1328667   0.50265482 
+    3700     4000    9.4683561   0.53407075 
+    3800     4000    9.5878145   0.56548668 
+    3900     4000     9.387745    0.5969026 
+    4000     4000    8.9117631   0.62831853 
+    4100     4000    8.2344368   0.65973446 
+    4200     4000    7.5335088   0.69115038 
+    4300     4000    6.8426179   0.72256631 
+    4400     4000    6.0567247   0.75398224 
+    4500     4000    5.4166132   0.78539816 
+    4600     4000    4.6012409   0.81681409 
+    4700     4000    3.8314982   0.84823002 
+    4800     4000    3.1916415   0.87964594 
+    4900     4000    2.7833964   0.91106187 
+    5000     4000    2.5051362    0.9424778 
+Loop time of 11.9545 on 1 procs for 3000 steps with 4000 atoms
+
+Performance: 21682.142 tau/day, 250.951 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.8291     | 4.8291     | 4.8291     |   0.0 | 40.40
+Neigh   | 2.7489     | 2.7489     | 2.7489     |   0.0 | 22.99
+Comm    | 0.071249   | 0.071249   | 0.071249   |   0.0 |  0.60
+Output  | 0.20547    | 0.20547    | 0.20547    |   0.0 |  1.72
+Modify  | 4.0179     | 4.0179     | 4.0179     |   0.0 | 33.61
+Other   |            | 0.0819     |            |       |  0.69
+
+Nlocal:    4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    322 ave 322 max 322 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    14849 ave 14849 max 14849 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 14849
+Ave neighs/atom = 3.71225
+Neighbor list builds = 1290
+Dangerous builds = 672
+Total wall time: 0:00:15

examples/granular/log.29Mar19.pour.drum.g++.4

@@ -0,0 +1,271 @@
+LAMMPS (29 Mar 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# pour two types of particles (cohesive and non-cohesive) into cylinder
+# 'turn' cylinder by changing direction of gravity, then rotate it.
+# This simulates a rotating drum powder characterization experiment.
+
+variable	name string rotating_drum_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 30
+variable	boxy equal 30
+variable	boxz equal 50
+
+variable	drum_rad equal ${boxx}*0.5
+variable	drum_rad equal 30*0.5
+variable	drum_height equal 20
+
+variable	xc equal 0.5*${boxx}
+variable	xc equal 0.5*30
+variable	yc equal 0.5*${boxx}
+variable	yc equal 0.5*30
+variable	zc equal 0.5*${boxz}
+variable	zc equal 0.5*50
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable	cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+variable	cyl_rad_inner equal 15-1.1*${rhi}
+variable	cyl_rad_inner equal 15-1.1*0.5
+
+variable	dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+variable skin equal 0.4*0.5
+
+#############
+processors * * 1
+region		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region		boxreg block 0 30 0 ${boxy} 0 ${boxz}
+region		boxreg block 0 30 0 30 0 ${boxz}
+region		boxreg block 0 30 0 30 0 50
+create_box	2 boxreg
+Created orthogonal box = (0 0 0) to (30 30 50)
+  2 by 2 by 1 MPI processor grid
+change_box	all boundary p p f
+comm_modify	vel yes
+
+variable	theta equal 0
+
+region		curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
+region		bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
+
+region		insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 14.45 20 ${boxz}
+region		insreg cylinder z 15 15 14.45 20 50
+
+fix		0 all balance 100 1.0 shift xy 5 1.1
+fix		1 all nve/sphere
+fix		grav all gravity 10 vector 0 0 -1
+fix		ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+fix		ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neighbor	0.2 bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular
+pair_coeff	1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
+pair_coeff	2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
+
+fix		3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
+fix		4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
+
+thermo_style	custom step atoms ke v_theta
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+dump		1 all custom 100 ${name}.dump id type radius mass x y z
+dump		1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z
+
+#For removal later
+compute		1 all property/atom radius
+variable	zmax atom z+c_1>0.5*${drum_height}
+variable	zmax atom z+c_1>0.5*20
+group		delgroup dynamic all var zmax every 10000
+dynamic group delgroup defined
+
+run		2000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 50 50 84
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.25 | 12.25 | 12.25 Mbytes
+Step Atoms KinEng v_theta 
+       0        0           -0            0 
+     100     4000           -0            0 
+     200     4000           -0            0 
+     300     4000           -0            0 
+     400     4000           -0            0 
+     500     4000           -0            0 
+     600     4000           -0            0 
+     700     4000           -0            0 
+     800     4000           -0            0 
+     900     4000           -0            0 
+    1000     4000           -0            0 
+    1100     4000           -0            0 
+    1200     4000           -0            0 
+    1300     4000           -0            0 
+    1400     4000           -0            0 
+    1500     4000           -0            0 
+    1600     4000           -0            0 
+    1700     4000           -0            0 
+    1800     4000           -0            0 
+    1900     4000           -0            0 
+    2000     4000           -0            0 
+Loop time of 2.0709 on 4 procs for 2000 steps with 4000 atoms
+
+Performance: 83442.024 tau/day, 965.764 timesteps/s
+97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.24679    | 0.26336    | 0.28853    |   3.0 | 12.72
+Neigh   | 0.52279    | 0.5332     | 0.53858    |   0.9 | 25.75
+Comm    | 0.17418    | 0.20253    | 0.23266    |   4.7 |  9.78
+Output  | 0.092897   | 0.093531   | 0.09515    |   0.3 |  4.52
+Modify  | 0.88151    | 0.89571    | 0.90582    |   0.9 | 43.25
+Other   |            | 0.08257    |            |       |  3.99
+
+Nlocal:    1000 ave 1001 max 999 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    267.75 ave 276 max 262 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:    2031.5 ave 2091 max 1958 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+
+Total # of neighbors = 8126
+Ave neighs/atom = 2.0315
+Neighbor list builds = 1004
+Dangerous builds = 3
+
+#Remove any particles that are above z > 0.5*drum_height
+delete_atoms	group delgroup
+Deleted 0 atoms, new total = 4000
+
+#Add top lid
+region		top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
+fix		5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
+
+# 'Turn' drum by switching the direction of gravity
+unfix		grav
+fix		grav all gravity 10 vector 0 -1 0
+
+variable	theta equal 2*PI*elapsed/20000.0
+run		3000
+Per MPI rank memory allocation (min/avg/max) = 21.6 | 22.6 | 23.82 Mbytes
+Step Atoms KinEng v_theta 
+    2000     4000    64.255821            0 
+    2100     4000    106.47082  0.031415927 
+    2200     4000    121.52634  0.062831853 
+    2300     4000    87.748818   0.09424778 
+    2400     4000    82.712784   0.12566371 
+    2500     4000    90.618713   0.15707963 
+    2600     4000    30.096031   0.18849556 
+    2700     4000    4.0838611   0.21991149 
+    2800     4000    3.7485959   0.25132741 
+    2900     4000    4.2159774   0.28274334 
+    3000     4000    4.8730048   0.31415927 
+    3100     4000    5.6109465   0.34557519 
+    3200     4000    6.4290528   0.37699112 
+    3300     4000    7.2699677   0.40840704 
+    3400     4000    8.0895944   0.43982297 
+    3500     4000    8.7222781    0.4712389 
+    3600     4000     9.133205   0.50265482 
+    3700     4000    9.3404584   0.53407075 
+    3800     4000    9.3359844   0.56548668 
+    3900     4000    9.0916854    0.5969026 
+    4000     4000    8.5596424   0.62831853 
+    4100     4000    7.9734883   0.65973446 
+    4200     4000    7.2154383   0.69115038 
+    4300     4000    6.7039232   0.72256631 
+    4400     4000    6.1542738   0.75398224 
+    4500     4000    5.4049454   0.78539816 
+    4600     4000    4.4603192   0.81681409 
+    4700     4000    3.6197985   0.84823002 
+    4800     4000    2.9895571   0.87964594 
+    4900     4000    2.5314553   0.91106187 
+    5000     4000    2.2645533    0.9424778 
+Loop time of 6.64209 on 4 procs for 3000 steps with 4000 atoms
+
+Performance: 39023.861 tau/day, 451.665 timesteps/s
+96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.8376     | 2.126      | 2.3131     |  12.6 | 32.01
+Neigh   | 0.97762    | 1.0518     | 1.1337     |   5.4 | 15.84
+Comm    | 0.53699    | 0.84265    | 1.2325     |  27.6 | 12.69
+Output  | 0.13922    | 0.14159    | 0.14388    |   0.4 |  2.13
+Modify  | 1.8815     | 2.1026     | 2.3368     |  11.2 | 31.66
+Other   |            | 0.3774     |            |       |  5.68
+
+Nlocal:    1000 ave 1256 max 744 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    579.5 ave 789 max 498 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Neighs:    3696.25 ave 4853 max 2590 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 14785
+Ave neighs/atom = 3.69625
+Neighbor list builds = 1230
+Dangerous builds = 676
+Total wall time: 0:00:08

examples/granular/log.29Mar19.pour.flatwall.g++.1

@@ -0,0 +1,134 @@
+LAMMPS (29 Mar 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# pour two types of particles (cohesive and non-cohesive) on flat wall
+
+variable   	name string pour_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 20
+variable	boxy equal 20
+variable	boxz equal 30
+
+variable	xc1 equal 0.3*${boxx}
+variable	xc1 equal 0.3*20
+variable	xc2 equal 0.7*${boxx}
+variable	xc2 equal 0.7*20
+variable	yc equal 0.5*${boxy}
+variable	yc equal 0.5*20
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable	dens equal 1.0
+
+variable skin equal 0.3*${rhi}
+variable skin equal 0.3*0.5
+
+#############
+processors	* * 1
+region 		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region 		boxreg block 0 20 0 ${boxy} 0 ${boxz}
+region 		boxreg block 0 20 0 20 0 ${boxz}
+region 		boxreg block 0 20 0 20 0 30
+create_box	2 boxreg
+Created orthogonal box = (0 0 0) to (20 20 30)
+  1 by 1 by 1 MPI processor grid
+change_box	all boundary p p f
+
+comm_modify 	vel yes
+
+region		insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
+region		insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
+region		insreg1 cylinder z 6 10 5 15 ${boxz}
+region		insreg1 cylinder z 6 10 5 15 30
+region		insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
+region		insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
+region		insreg2 cylinder z 14 10 5 15 ${boxz}
+region		insreg2 cylinder z 14 10 5 15 30
+
+fix		1 all nve/sphere
+fix		grav all gravity 10.0 vector 0 0 -1
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neighbor	0.15 bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular
+pair_coeff 	1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff 	2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
+
+fix		3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
+
+thermo_style	custom step cpu atoms ke
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+#dump		1 all custom 100 ${name}.dump id type radius mass x y z
+
+run		5000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.15
+  ghost atom cutoff = 1.15
+  binsize = 0.575, bins = 35 35 53
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.22 | 12.22 | 12.22 Mbytes
+Step CPU Atoms KinEng 
+       0            0        0           -0 
+     100    3.8153191      855           -0 
+     200     4.195287      855           -0 
+     300    4.5890362      855           -0 
+     400    10.636087     1500           -0 
+     500    11.306909     1500           -0 
+     600    11.968198     1500           -0 
+     700    22.631892     2288           -0 
+     800    23.711387     2288           -0 
+     900    24.754344     2288           -0 
+    1000    25.811778     2288           -0 
+    1100    35.368869     2845           -0 
+    1200    37.149843     2845           -0 
+    1300    39.026458     2845           -0 
+    1400    41.757583     3000           -0 
+    1500    45.155503     3000           -0 
+    1600    48.570241     3000           -0 
+    1700    52.839322     3000           -0 
+    1800    59.772697     3000           -0 
+    1900    69.493305     3000           -0 
+    2000    114.61886     3000           -0 
+    2100    152.89232     3000           -0 

examples/granular/log.29Mar19.pour.flatwall.g++.4

@@ -0,0 +1,191 @@
+LAMMPS (29 Mar 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# pour two types of particles (cohesive and non-cohesive) on flat wall
+
+variable   	name string pour_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 20
+variable	boxy equal 20
+variable	boxz equal 30
+
+variable	xc1 equal 0.3*${boxx}
+variable	xc1 equal 0.3*20
+variable	xc2 equal 0.7*${boxx}
+variable	xc2 equal 0.7*20
+variable	yc equal 0.5*${boxy}
+variable	yc equal 0.5*20
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable	dens equal 1.0
+
+variable skin equal 0.3*${rhi}
+variable skin equal 0.3*0.5
+
+#############
+processors	* * 1
+region 		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region 		boxreg block 0 20 0 ${boxy} 0 ${boxz}
+region 		boxreg block 0 20 0 20 0 ${boxz}
+region 		boxreg block 0 20 0 20 0 30
+create_box	2 boxreg
+Created orthogonal box = (0 0 0) to (20 20 30)
+  2 by 2 by 1 MPI processor grid
+change_box	all boundary p p f
+
+comm_modify 	vel yes
+
+region		insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
+region		insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
+region		insreg1 cylinder z 6 10 5 15 ${boxz}
+region		insreg1 cylinder z 6 10 5 15 30
+region		insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
+region		insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
+region		insreg2 cylinder z 14 10 5 15 ${boxz}
+region		insreg2 cylinder z 14 10 5 15 30
+
+fix		1 all nve/sphere
+fix		grav all gravity 10.0 vector 0 0 -1
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neighbor	0.15 bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular
+pair_coeff 	1 * jkr 1000.0 50.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff 	2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall
+
+fix		3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
+
+thermo_style	custom step cpu atoms ke
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+dump		1 all custom 100 ${name}.dump id type radius mass x y z
+dump		1 all custom 100 pour_two_types.dump id type radius mass x y z
+
+run		5000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.15
+  ghost atom cutoff = 1.15
+  binsize = 0.575, bins = 35 35 53
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.98 | 11.98 | 11.98 Mbytes
+Step CPU Atoms KinEng 
+       0            0        0           -0 
+     100   0.11584234      855           -0 
+     200   0.12743592      855           -0 
+     300   0.13925815      855           -0 
+     400   0.35203671     1500           -0 
+     500   0.37055922     1500           -0 
+     600   0.38671875     1500           -0 
+     700   0.71736908     2288           -0 
+     800   0.74506783     2288           -0 
+     900   0.77112222     2288           -0 
+    1000   0.79632139     2288           -0 
+    1100    1.0384252     2845           -0 
+    1200      1.08093     2845           -0 
+    1300    1.1224561     2845           -0 
+    1400    1.1811485     3000           -0 
+    1500    1.2414908     3000           -0 
+    1600    1.3105879     3000           -0 
+    1700     1.390928     3000           -0 
+    1800    1.4869275     3000           -0 
+    1900    1.5958266     3000           -0 
+    2000    1.7172487     3000           -0 
+    2100     1.851155     3000           -0 
+    2200    1.9957182     3000           -0 
+    2300    2.1593764     3000           -0 
+    2400    2.3433132     3000           -0 
+    2500     2.532742     3000           -0 
+    2600    2.7376895     3000           -0 
+    2700    2.9463468     3000           -0 
+    2800    3.1645725     3000           -0 
+    2900    3.3879526     3000           -0 
+    3000    3.6152103     3000           -0 
+    3100    3.8467371     3000           -0 
+    3200    4.0787683     3000           -0 
+    3300    4.3097105     3000           -0 
+    3400    4.5423617     3000           -0 
+    3500    4.7773693     3000           -0 
+    3600    5.0127218     3000           -0 
+    3700    5.2519271     3000           -0 
+    3800    5.4951298     3000           -0 
+    3900    5.7210469     3000           -0 
+    4000    5.9432652     3000           -0 
+    4100    6.1687591     3000           -0 
+    4200    6.3942792     3000           -0 
+    4300    6.6331475     3000           -0 
+    4400    6.8632154     3000           -0 
+    4500    7.0979366     3000           -0 
+    4600    7.3305347     3000           -0 
+    4700    7.5670528     3000           -0 
+    4800    7.8086057     3000           -0 
+    4900    8.0407174     3000           -0 
+    5000    8.2765219     3000           -0 
+Loop time of 8.27669 on 4 procs for 5000 steps with 3000 atoms
+
+Performance: 52194.788 tau/day, 604.106 timesteps/s
+97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.6106     | 3.4073     | 5.4191     |  95.7 | 41.17
+Neigh   | 0.51456    | 0.64572    | 0.81542    |  16.6 |  7.80
+Comm    | 0.2808     | 2.5222     | 4.4998     | 121.9 | 30.47
+Output  | 0.15695    | 0.15919    | 0.16502    |   0.8 |  1.92
+Modify  | 1.3517     | 1.4192     | 1.4904     |   4.9 | 17.15
+Other   |            | 0.123      |            |       |  1.49
+
+Nlocal:    750 ave 1036 max 482 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    429.75 ave 475 max 386 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    4051.75 ave 6274 max 2057 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 16207
+Ave neighs/atom = 5.40233
+Neighbor list builds = 1165
+Dangerous builds = 0
+Total wall time: 0:00:08

lib/colvars/colvar.cpp

@@ -24,12 +24,13 @@ colvar::colvar()
 {
   runave_os = NULL;
 
-  prev_timestep = -1;
+  prev_timestep = -1L;
   after_restart = false;
   kinetic_energy = 0.0;
   potential_energy = 0.0;
 
-  init_cv_requires();
+  description = "uninitialized colvar";
+  init_dependencies();
 }
 
 
@@ -193,7 +194,7 @@ int colvar::init(std::string const &conf)
   {
     bool homogeneous = is_enabled(f_cv_linear);
     for (i = 0; i < cvcs.size(); i++) {
-      if ((std::fabs(cvcs[i]->sup_coeff) - 1.0) > 1.0e-10) {
+      if ((cvm::fabs(cvcs[i]->sup_coeff) - 1.0) > 1.0e-10) {
         homogeneous = false;
       }
     }
@@ -224,7 +225,7 @@ int colvar::init(std::string const &conf)
   // Allow scripted/custom functions to be defined as periodic
   if ( (is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function)) && is_enabled(f_cv_scalar) ) {
     if (get_keyval(conf, "period", period, 0.)) {
-      set_enabled(f_cv_periodic, true);
+      enable(f_cv_periodic);
       get_keyval(conf, "wrapAround", wrap_center, 0.);
     }
   }
@@ -471,7 +472,7 @@ int colvar::init_grid_parameters(std::string const &conf)
     if (get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0,
                    parse_silent)) {
       cvm::log("Reading legacy options lowerWall and lowerWallConstant: "
-               "consider using a harmonicWalls restraint.\n");
+               "consider using a harmonicWalls restraint\n(caution: force constant would then be scaled by width^2).\n");
       lower_wall.type(value());
       if (!get_keyval(conf, "lowerWall", lower_wall, lower_boundary)) {
         cvm::log("Warning: lowerWall will need to be "
@@ -485,7 +486,7 @@ int colvar::init_grid_parameters(std::string const &conf)
     if (get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0,
                    parse_silent)) {
       cvm::log("Reading legacy options upperWall and upperWallConstant: "
-               "consider using a harmonicWalls restraint.\n");
+               "consider using a harmonicWalls restraint\n(caution: force constant would then be scaled by width^2).\n");
       upper_wall.type(value());
       if (!get_keyval(conf, "upperWall", upper_wall, upper_boundary)) {
         cvm::log("Warning: upperWall will need to be "
@@ -562,13 +563,13 @@ int colvar::init_extended_Lagrangian(std::string const &conf)
   get_keyval_feature(this, conf, "extendedLagrangian", f_cv_extended_Lagrangian, false);
 
   if (is_enabled(f_cv_extended_Lagrangian)) {
-    cvm::real temp, tolerance, period;
+    cvm::real temp, tolerance, extended_period;
 
     cvm::log("Enabling the extended Lagrangian term for colvar \""+
              this->name+"\".\n");
 
-    xr.type(value());
+    x_ext.type(value());
-    vr.type(value());
+    v_ext.type(value());
     fr.type(value());
 
     const bool found = get_keyval(conf, "extendedTemp", temp, cvm::temperature());
@@ -590,11 +591,11 @@ int colvar::init_extended_Lagrangian(std::string const &conf)
     ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance);
     cvm::log("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " [E]/U^2");
 
-    get_keyval(conf, "extendedTimeConstant", period, 200.0);
+    get_keyval(conf, "extendedTimeConstant", extended_period, 200.0);
-    if (period <= 0.0) {
+    if (extended_period <= 0.0) {
       cvm::error("Error: \"extendedTimeConstant\" must be positive.\n", INPUT_ERROR);
     }
-    ext_mass = (cvm::boltzmann() * temp * period * period)
+    ext_mass = (cvm::boltzmann() * temp * extended_period * extended_period)
       / (4.0 * PI * PI * tolerance * tolerance);
     cvm::log("Computed fictitious mass: " + cvm::to_str(ext_mass) + " [E]/(U/fs)^2   (U: colvar unit)");
 
@@ -615,7 +616,7 @@ int colvar::init_extended_Lagrangian(std::string const &conf)
       enable(f_cv_Langevin);
       ext_gamma *= 1.0e-3; // correct as long as input is required in ps-1 and cvm::dt() is in fs
       // Adjust Langevin sigma for slow time step if time_step_factor != 1
-      ext_sigma = std::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor)));
+      ext_sigma = cvm::sqrt(2.0 * cvm::boltzmann() * temp * ext_gamma * ext_mass / (cvm::dt() * cvm::real(time_step_factor)));
     }
   }
 
@@ -761,6 +762,8 @@ int colvar::init_components(std::string const &conf)
     "weighted by inverse power", "distanceInv");
   error_code |= init_components_type<distance_pairs>(conf, "N1xN2-long vector "
     "of pairwise distances", "distancePairs");
+  error_code |= init_components_type<dipole_magnitude>(conf, "dipole magnitude",
+    "dipoleMagnitude");
   error_code |= init_components_type<coordnum>(conf, "coordination "
     "number", "coordNum");
   error_code |= init_components_type<selfcoordnum>(conf, "self-coordination "
@@ -831,22 +834,25 @@ void colvar::build_atom_list(void)
 
   for (size_t i = 0; i < cvcs.size(); i++) {
     for (size_t j = 0; j < cvcs[i]->atom_groups.size(); j++) {
-      cvm::atom_group &ag = *(cvcs[i]->atom_groups[j]);
+      cvm::atom_group const &ag = *(cvcs[i]->atom_groups[j]);
       for (size_t k = 0; k < ag.size(); k++) {
         temp_id_list.push_back(ag[k].id);
       }
+      if (ag.is_enabled(f_ag_fitting_group) && ag.is_enabled(f_ag_fit_gradients)) {
+        cvm::atom_group const &fg = *(ag.fitting_group);
+        for (size_t k = 0; k < fg.size(); k++) {
+          temp_id_list.push_back(fg[k].id);
+        }
+      }
     }
   }
 
   temp_id_list.sort();
   temp_id_list.unique();
 
-  // atom_ids = std::vector<int> (temp_id_list.begin(), temp_id_list.end());
-  unsigned int id_i = 0;
   std::list<int>::iterator li;
   for (li = temp_id_list.begin(); li != temp_id_list.end(); ++li) {
-    atom_ids[id_i] = *li;
+    atom_ids.push_back(*li);
-    id_i++;
   }
 
   temp_id_list.clear();
@@ -934,16 +940,153 @@ int colvar::parse_analysis(std::string const &conf)
 }
 
 
-void colvar::setup() {
+int colvar::init_dependencies() {
-  // loop over all components to reset masses of all groups
+  size_t i;
-  for (size_t i = 0; i < cvcs.size(); i++) {
+  if (features().size() == 0) {
-    for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
+    for (i = 0; i < f_cv_ntot; i++) {
-      cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
+      modify_features().push_back(new feature);
-      atoms.setup();
+    }
-      atoms.reset_mass(name,i,ig);
+
-      atoms.read_positions();
+    init_feature(f_cv_active, "active", f_type_dynamic);
+    // Do not require f_cvc_active in children, as some components may be disabled
+    // Colvars must be either a linear combination, or scalar (and polynomial) or scripted/custom
+    require_feature_alt(f_cv_active, f_cv_scalar, f_cv_linear, f_cv_scripted, f_cv_custom_function);
+
+    init_feature(f_cv_awake, "awake", f_type_static);
+    require_feature_self(f_cv_awake, f_cv_active);
+
+    init_feature(f_cv_gradient, "gradient", f_type_dynamic);
+    require_feature_children(f_cv_gradient, f_cvc_gradient);
+
+    init_feature(f_cv_collect_gradient, "collect gradient", f_type_dynamic);
+    require_feature_self(f_cv_collect_gradient, f_cv_gradient);
+    require_feature_self(f_cv_collect_gradient, f_cv_scalar);
+    // The following exlusion could be lifted by implementing the feature
+    exclude_feature_self(f_cv_collect_gradient, f_cv_scripted);
+    require_feature_children(f_cv_collect_gradient, f_cvc_explicit_gradient);
+
+    init_feature(f_cv_fdiff_velocity, "velocity from finite differences", f_type_dynamic);
+
+    // System force: either trivial (spring force); through extended Lagrangian, or calculated explicitly
+    init_feature(f_cv_total_force, "total force", f_type_dynamic);
+    require_feature_alt(f_cv_total_force, f_cv_extended_Lagrangian, f_cv_total_force_calc);
+
+    // Deps for explicit total force calculation
+    init_feature(f_cv_total_force_calc, "total force calculation", f_type_dynamic);
+    require_feature_self(f_cv_total_force_calc, f_cv_scalar);
+    require_feature_self(f_cv_total_force_calc, f_cv_linear);
+    require_feature_children(f_cv_total_force_calc, f_cvc_inv_gradient);
+    require_feature_self(f_cv_total_force_calc, f_cv_Jacobian);
+
+    init_feature(f_cv_Jacobian, "Jacobian derivative", f_type_dynamic);
+    require_feature_self(f_cv_Jacobian, f_cv_scalar);
+    require_feature_self(f_cv_Jacobian, f_cv_linear);
+    require_feature_children(f_cv_Jacobian, f_cvc_Jacobian);
+
+    init_feature(f_cv_hide_Jacobian, "hide Jacobian force", f_type_user);
+    require_feature_self(f_cv_hide_Jacobian, f_cv_Jacobian); // can only hide if calculated
+
+    init_feature(f_cv_extended_Lagrangian, "extended Lagrangian", f_type_user);
+    require_feature_self(f_cv_extended_Lagrangian, f_cv_scalar);
+    require_feature_self(f_cv_extended_Lagrangian, f_cv_gradient);
+
+    init_feature(f_cv_Langevin, "Langevin dynamics", f_type_user);
+    require_feature_self(f_cv_Langevin, f_cv_extended_Lagrangian);
+
+    init_feature(f_cv_linear, "linear", f_type_static);
+
+    init_feature(f_cv_scalar, "scalar", f_type_static);
+
+    init_feature(f_cv_output_energy, "output energy", f_type_user);
+
+    init_feature(f_cv_output_value, "output value", f_type_user);
+
+    init_feature(f_cv_output_velocity, "output velocity", f_type_user);
+    require_feature_self(f_cv_output_velocity, f_cv_fdiff_velocity);
+
+    init_feature(f_cv_output_applied_force, "output applied force", f_type_user);
+
+    init_feature(f_cv_output_total_force, "output total force", f_type_user);
+    require_feature_self(f_cv_output_total_force, f_cv_total_force);
+
+    init_feature(f_cv_subtract_applied_force, "subtract applied force from total force", f_type_user);
+    require_feature_self(f_cv_subtract_applied_force, f_cv_total_force);
+
+    init_feature(f_cv_lower_boundary, "lower boundary", f_type_user);
+    require_feature_self(f_cv_lower_boundary, f_cv_scalar);
+
+    init_feature(f_cv_upper_boundary, "upper boundary", f_type_user);
+    require_feature_self(f_cv_upper_boundary, f_cv_scalar);
+
+    init_feature(f_cv_grid, "grid", f_type_dynamic);
+    require_feature_self(f_cv_grid, f_cv_lower_boundary);
+    require_feature_self(f_cv_grid, f_cv_upper_boundary);
+
+    init_feature(f_cv_runave, "running average", f_type_user);
+
+    init_feature(f_cv_corrfunc, "correlation function", f_type_user);
+
+    init_feature(f_cv_scripted, "scripted", f_type_user);
+
+    init_feature(f_cv_custom_function, "custom function", f_type_user);
+    exclude_feature_self(f_cv_custom_function, f_cv_scripted);
+
+    init_feature(f_cv_periodic, "periodic", f_type_static);
+    require_feature_self(f_cv_periodic, f_cv_scalar);
+    init_feature(f_cv_scalar, "scalar", f_type_static);
+    init_feature(f_cv_linear, "linear", f_type_static);
+    init_feature(f_cv_homogeneous, "homogeneous", f_type_static);
+
+    // because total forces are obtained from the previous time step,
+    // we cannot (currently) have colvar values and total forces for the same timestep
+    init_feature(f_cv_multiple_ts, "multiple timestep colvar", f_type_static);
+    exclude_feature_self(f_cv_multiple_ts, f_cv_total_force_calc);
+
+    // check that everything is initialized
+    for (i = 0; i < colvardeps::f_cv_ntot; i++) {
+      if (is_not_set(i)) {
+        cvm::error("Uninitialized feature " + cvm::to_str(i) + " in " + description);
+      }
     }
   }
+
+  // Initialize feature_states for each instance
+  feature_states.reserve(f_cv_ntot);
+  for (i = 0; i < f_cv_ntot; i++) {
+    feature_states.push_back(feature_state(true, false));
+    // Most features are available, so we set them so
+    // and list exceptions below
+   }
+
+  feature_states[f_cv_fdiff_velocity].available =
+    cvm::main()->proxy->simulation_running();
+
+  return COLVARS_OK;
+}
+
+
+void colvar::setup()
+{
+  // loop over all components to update masses and charges of all groups
+  for (size_t i = 0; i < cvcs.size(); i++) {
+    for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
+      cvm::atom_group *atoms = cvcs[i]->atom_groups[ig];
+      atoms->setup();
+      atoms->print_properties(name, i, ig);
+      atoms->read_positions();
+    }
+  }
+}
+
+
+std::vector<std::vector<int> > colvar::get_atom_lists()
+{
+  std::vector<std::vector<int> > lists;
+  for (size_t i = 0; i < cvcs.size(); i++) {
+    std::vector<std::vector<int> > li = cvcs[i]->get_atom_lists();
+    lists.insert(lists.end(), li.begin(), li.end());
+  }
+  return lists;
 }
 
 
@@ -953,8 +1096,8 @@ colvar::~colvar()
   // because the children are cvcs and will be deleted
   // just below
 
-//   Clear references to this colvar's cvcs as children
+  // Clear references to this colvar's cvcs as children
-//   for dependency purposes
+  // for dependency purposes
   remove_all_children();
 
   for (std::vector<cvc *>::reverse_iterator ci = cvcs.rbegin();
@@ -1231,7 +1374,6 @@ int colvar::calc_cvc_gradients(int first_cvc, size_t num_cvcs)
 int colvar::collect_cvc_gradients()
 {
   size_t i;
-
   if (is_enabled(f_cv_collect_gradient)) {
     // Collect the atomic gradients inside colvar object
     for (unsigned int a = 0; a < atomic_gradients.size(); a++) {
@@ -1239,34 +1381,7 @@ int colvar::collect_cvc_gradients()
     }
     for (i = 0; i < cvcs.size(); i++) {
       if (!cvcs[i]->is_enabled()) continue;
-      // Coefficient: d(a * x^n) = a * n * x^(n-1) * dx
+      cvcs[i]->collect_gradients(atom_ids, atomic_gradients);
-      cvm::real coeff = (cvcs[i])->sup_coeff * cvm::real((cvcs[i])->sup_np) *
-        cvm::integer_power((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1);
-
-      for (size_t j = 0; j < cvcs[i]->atom_groups.size(); j++) {
-
-        cvm::atom_group &ag = *(cvcs[i]->atom_groups[j]);
-
-        // If necessary, apply inverse rotation to get atomic
-        // gradient in the laboratory frame
-        if (ag.b_rotate) {
-          cvm::rotation const rot_inv = ag.rot.inverse();
-
-          for (size_t k = 0; k < ag.size(); k++) {
-            size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
-                                        ag[k].id) - atom_ids.begin();
-            atomic_gradients[a] += coeff * rot_inv.rotate(ag[k].grad);
-          }
-
-        } else {
-
-          for (size_t k = 0; k < ag.size(); k++) {
-            size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
-                                        ag[k].id) - atom_ids.begin();
-            atomic_gradients[a] += coeff * ag[k].grad;
-          }
-        }
-      }
     }
   }
   return COLVARS_OK;
@@ -1391,20 +1506,20 @@ int colvar::calc_colvar_properties()
     // initialize the restraint center in the first step to the value
     // just calculated from the cvcs
     if (cvm::step_relative() == 0 && !after_restart) {
-      xr = x;
+      x_ext = x;
-      vr.reset(); // (already 0; added for clarity)
+      v_ext.reset(); // (already 0; added for clarity)
     }
 
     // Special case of a repeated timestep (eg. multiple NAMD "run" statements)
     // revert values of the extended coordinate and velocity prior to latest integration
-    if (cvm::step_relative() == prev_timestep) {
+    if (cvm::proxy->simulation_running() && cvm::step_relative() == prev_timestep) {
-      xr = prev_xr;
+      x_ext = prev_x_ext;
-      vr = prev_vr;
+      v_ext = prev_v_ext;
     }
 
     // report the restraint center as "value"
-    x_reported = xr;
+    x_reported = x_ext;
-    v_reported = vr;
+    v_reported = v_ext;
     // the "total force" with the extended Lagrangian is
     // calculated in update_forces_energy() below
 
@@ -1458,77 +1573,86 @@ cvm::real colvar::update_forces_energy()
   // extended variable if there is one
 
   if (is_enabled(f_cv_extended_Lagrangian)) {
-    if (cvm::debug()) {
+    if (cvm::proxy->simulation_running()) {
-      cvm::log("Updating extended-Lagrangian degree of freedom.\n");
+      // Only integrate the extended equations of motion in running MD simulations
-    }
+      if (cvm::debug()) {
-
+        cvm::log("Updating extended-Lagrangian degree of freedom.\n");
-    if (prev_timestep > -1) {
-      // Keep track of slow timestep to integrate MTS colvars
-      // the colvar checks the interval after waking up twice
-      int n_timesteps = cvm::step_relative() - prev_timestep;
-      if (n_timesteps != 0 && n_timesteps != time_step_factor) {
-        cvm::error("Error: extended-Lagrangian " + description + " has timeStepFactor " +
-          cvm::to_str(time_step_factor) + ", but was activated after " + cvm::to_str(n_timesteps) +
-          " steps at timestep " + cvm::to_str(cvm::step_absolute()) + " (relative step: " +
-          cvm::to_str(cvm::step_relative()) + ").\n" +
-          "Make sure that this colvar is requested by biases at multiples of timeStepFactor.\n");
-        return 0.;
       }
-    }
 
-    // Integrate with slow timestep (if time_step_factor != 1)
+      if (prev_timestep > -1) {
-    cvm::real dt = cvm::dt() * cvm::real(time_step_factor);
+        // Keep track of slow timestep to integrate MTS colvars
+        // the colvar checks the interval after waking up twice
+        int n_timesteps = cvm::step_relative() - prev_timestep;
+        if (n_timesteps != 0 && n_timesteps != time_step_factor) {
+          cvm::error("Error: extended-Lagrangian " + description + " has timeStepFactor " +
+            cvm::to_str(time_step_factor) + ", but was activated after " + cvm::to_str(n_timesteps) +
+            " steps at timestep " + cvm::to_str(cvm::step_absolute()) + " (relative step: " +
+            cvm::to_str(cvm::step_relative()) + ").\n" +
+            "Make sure that this colvar is requested by biases at multiples of timeStepFactor.\n");
+          return 0.;
+        }
+      }
 
-    colvarvalue f_ext(fr.type()); // force acting on the extended variable
+      // Integrate with slow timestep (if time_step_factor != 1)
-    f_ext.reset();
+      cvm::real dt = cvm::dt() * cvm::real(time_step_factor);
 
-    // the total force is applied to the fictitious mass, while the
+      colvarvalue f_ext(fr.type()); // force acting on the extended variable
-    // atoms only feel the harmonic force + wall force
+      f_ext.reset();
-    // 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
-    //    - after this code block, colvar force to be applied to atomic coordinates
-    //      ie. spring force (fb_actual will be added just below)
-    fr    = f;
-    // External force has been scaled for a 1-timestep impulse, scale it back because we will
-    // integrate it with the colvar's own timestep factor
-    f_ext = f / cvm::real(time_step_factor);
-    f_ext += (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
-    f      = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
-    // Coupling force is a slow force, to be applied to atomic coords impulse-style
-    f *= cvm::real(time_step_factor);
 
-    if (is_enabled(f_cv_subtract_applied_force)) {
+      // the total force is applied to the fictitious mass, while the
-      // Report a "system" force without the biases on this colvar
+      // atoms only feel the harmonic force + wall force
-      // that is, just the spring force
+      // fr: bias force on extended variable (without harmonic spring), for output in trajectory
-      ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
+      // f_ext: total force on extended variable (including harmonic spring)
+      // f: - initially, external biasing force
+      //    - after this code block, colvar force to be applied to atomic coordinates
+      //      ie. spring force (fb_actual will be added just below)
+      fr    = f;
+      // External force has been scaled for a 1-timestep impulse, scale it back because we will
+      // integrate it with the colvar's own timestep factor
+      f_ext = f / cvm::real(time_step_factor);
+      f_ext += (-0.5 * ext_force_k) * this->dist2_lgrad(x_ext, x);
+      f      = (-0.5 * ext_force_k) * this->dist2_rgrad(x_ext, x);
+      // Coupling force is a slow force, to be applied to atomic coords impulse-style
+      f *= cvm::real(time_step_factor);
+
+      if (is_enabled(f_cv_subtract_applied_force)) {
+        // Report a "system" force without the biases on this colvar
+        // that is, just the spring force
+        ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(x_ext, x);
+      } else {
+        // The total force acting on the extended variable is f_ext
+        // This will be used in the next timestep
+        ft_reported = f_ext;
+      }
+
+      // backup in case we need to revert this integration timestep
+      // if the same MD timestep is re-run
+      prev_x_ext = x_ext;
+      prev_v_ext = v_ext;
+
+      // leapfrog: starting from x_i, f_i, v_(i-1/2)
+      v_ext  += (0.5 * dt) * f_ext / ext_mass;
+      // Because of leapfrog, kinetic energy at time i is approximate
+      kinetic_energy = 0.5 * ext_mass * v_ext * v_ext;
+      potential_energy = 0.5 * ext_force_k * this->dist2(x_ext, x);
+      // leap to v_(i+1/2)
+      if (is_enabled(f_cv_Langevin)) {
+        v_ext -= dt * ext_gamma * v_ext;
+        colvarvalue rnd(x);
+        rnd.set_random();
+        v_ext += dt * ext_sigma * rnd / ext_mass;
+      }
+      v_ext  += (0.5 * dt) * f_ext / ext_mass;
+      x_ext  += dt * v_ext;
+      x_ext.apply_constraints();
+      this->wrap(x_ext);
     } else {
-      // The total force acting on the extended variable is f_ext
+      // If this is a postprocessing run (eg. in VMD), the extended DOF
-      // This will be used in the next timestep
+      // is equal to the actual coordinate
-      ft_reported = f_ext;
+      x_ext = x;
     }
-
+    // Report extended value
-    // backup in case we need to revert this integration timestep
+    x_reported = x_ext;
-    // if the same MD timestep is re-run
-    prev_xr = xr;
-    prev_vr = vr;
-
-    // leapfrog: starting from x_i, f_i, v_(i-1/2)
-    vr  += (0.5 * dt) * f_ext / ext_mass;
-    // Because of leapfrog, kinetic energy at time i is approximate
-    kinetic_energy = 0.5 * ext_mass * vr * vr;
-    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;
-      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();
-    this->wrap(xr);
   }
 
   // Now adding the force on the actual colvar (for those biases that
@@ -1730,7 +1854,7 @@ int colvar::update_cvc_config(std::vector<std::string> const &confs)
 
 
 // ******************** METRIC FUNCTIONS ********************
-// Use the metrics defined by \link cvc \endlink objects
+// Use the metrics defined by \link colvar::cvc \endlink objects
 
 
 bool colvar::periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) const
@@ -1742,7 +1866,7 @@ bool colvar::periodic_boundaries(colvarvalue const &lb, colvarvalue const &ub) c
   }
 
   if (period > 0.0) {
-    if ( ((std::sqrt(this->dist2(lb, ub))) / this->width)
+    if ( ((cvm::sqrt(this->dist2(lb, ub))) / this->width)
          < 1.0E-10 ) {
       return true;
     }
@@ -1792,21 +1916,21 @@ colvarvalue colvar::dist2_rgrad(colvarvalue const &x1,
   }
 }
 
-void colvar::wrap(colvarvalue &x) const
+
+void colvar::wrap(colvarvalue &x_unwrapped) const
 {
-  if ( !is_enabled(f_cv_periodic) ) {
+  if (!is_enabled(f_cv_periodic)) {
     return;
   }
 
   if ( is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function) ) {
     // Scripted functions do their own wrapping, as cvcs might not be periodic
-    cvm::real shift = std::floor((x.real_value - wrap_center) / period + 0.5);
+    cvm::real shift = cvm::floor((x_unwrapped.real_value - wrap_center) /
-    x.real_value -= shift * period;
+                                 period + 0.5);
+    x_unwrapped.real_value -= shift * period;
   } else {
-    cvcs[0]->wrap(x);
+    cvcs[0]->wrap(x_unwrapped);
   }
-
-  return;
 }
 
 
@@ -1852,15 +1976,15 @@ std::istream & colvar::read_restart(std::istream &is)
 
   if (is_enabled(f_cv_extended_Lagrangian)) {
 
-    if ( !(get_keyval(conf, "extended_x", xr,
+    if ( !(get_keyval(conf, "extended_x", x_ext,
                       colvarvalue(x.type()), colvarparse::parse_silent)) &&
-         !(get_keyval(conf, "extended_v", vr,
+         !(get_keyval(conf, "extended_v", v_ext,
                       colvarvalue(x.type()), colvarparse::parse_silent)) ) {
       cvm::log("Error: restart file does not contain "
                "\"extended_x\" or \"extended_v\" for the colvar \""+
                name+"\", but you requested \"extendedLagrangian\".\n");
     }
-    x_reported = xr;
+    x_reported = x_ext;
   } else {
     x_reported = x;
   }
@@ -1875,7 +1999,7 @@ std::istream & colvar::read_restart(std::istream &is)
     }
 
     if (is_enabled(f_cv_extended_Lagrangian)) {
-      v_reported = vr;
+      v_reported = v_ext;
     } else {
       v_reported = v_fdiff;
     }
@@ -1901,8 +2025,8 @@ std::istream & colvar::read_traj(std::istream &is)
     }
 
     if (is_enabled(f_cv_extended_Lagrangian)) {
-      is >> xr;
+      is >> x_ext;
-      x_reported = xr;
+      x_reported = x_ext;
     } else {
       x_reported = x;
     }
@@ -1913,8 +2037,8 @@ std::istream & colvar::read_traj(std::istream &is)
     is >> v_fdiff;
 
     if (is_enabled(f_cv_extended_Lagrangian)) {
-      is >> vr;
+      is >> v_ext;
-      v_reported = vr;
+      v_reported = v_ext;
     } else {
       v_reported = v_fdiff;
     }
@@ -1955,11 +2079,11 @@ std::ostream & colvar::write_restart(std::ostream &os) {
     os << "  extended_x "
        << std::setprecision(cvm::cv_prec)
        << std::setw(cvm::cv_width)
-       << xr << "\n"
+       << x_ext << "\n"
        << "  extended_v "
        << std::setprecision(cvm::cv_prec)
        << std::setw(cvm::cv_width)
-       << vr << "\n";
+       << v_ext << "\n";
   }
 
   os << "}\n\n";
@@ -2190,6 +2314,7 @@ int colvar::calc_acf()
       acf_x_history_p = acf_x_history.begin();
       break;
 
+    case acf_notset:
     default:
       break;
     }
@@ -2222,6 +2347,7 @@ int colvar::calc_acf()
       history_incr(acf_x_history, acf_x_history_p);
       break;
 
+    case acf_notset:
     default:
       break;
     }
@@ -2257,7 +2383,7 @@ void colvar::calc_vel_acf(std::list<colvarvalue> &v_list,
 
 
 void colvar::calc_coor_acf(std::list<colvarvalue> &x_list,
-                            colvarvalue const      &x)
+                           colvarvalue const &x_now)
 {
   // same as above but for coordinates
   if (x_list.size() >= acf_length+acf_offset) {
@@ -2269,7 +2395,7 @@ void colvar::calc_coor_acf(std::list<colvarvalue> &x_list,
 
     *(acf_i++) += x.norm2();
 
-    colvarvalue::inner_opt(x, xs_i, x_list.end(), acf_i);
+    colvarvalue::inner_opt(x_now, xs_i, x_list.end(), acf_i);
 
     acf_nframes++;
   }
@@ -2277,7 +2403,7 @@ void colvar::calc_coor_acf(std::list<colvarvalue> &x_list,
 
 
 void colvar::calc_p2coor_acf(std::list<colvarvalue> &x_list,
-                             colvarvalue const      &x)
+                             colvarvalue const &x_now)
 {
   // same as above but with second order Legendre polynomial instead
   // of just the scalar product
@@ -2291,7 +2417,7 @@ void colvar::calc_p2coor_acf(std::list<colvarvalue> &x_list,
     // value of P2(0) = 1
     *(acf_i++) += 1.0;
 
-    colvarvalue::p2leg_opt(x, xs_i, x_list.end(), acf_i);
+    colvarvalue::p2leg_opt(x_now, xs_i, x_list.end(), acf_i);
 
     acf_nframes++;
   }
@@ -2316,6 +2442,9 @@ int colvar::write_acf(std::ostream &os)
   case acf_p2coor:
     os << "Coordinate (2nd Legendre poly)";
     break;
+  case acf_notset:
+  default:
+    break;
   }
 
   if (acf_colvar_name == name) {
@@ -2420,7 +2549,7 @@ int colvar::calc_runave()
                    << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
                    << runave << " "
                    << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
-                   << std::sqrt(runave_variance) << "\n";
+                   << cvm::sqrt(runave_variance) << "\n";
       }
 
       history_add_value(runave_length, *x_history_p, x);

lib/colvars/colvar.h

@@ -92,7 +92,7 @@ public:
   static std::vector<feature *> cv_features;
 
   /// \brief Implementation of the feature list accessor for colvar
-  virtual const std::vector<feature *> &features()
+  virtual const std::vector<feature *> &features() const
   {
     return cv_features;
   }
@@ -133,7 +133,7 @@ protected:
 
     Here:
     S(x(t)) = x
-    s(t)    = xr
+    s(t)    = x_ext
     DS = Ds = delta
   */
 
@@ -170,13 +170,13 @@ protected:
 
   // Options for extended_lagrangian
   /// Restraint center
-  colvarvalue xr;
+  colvarvalue x_ext;
   /// Previous value of the restraint center;
-  colvarvalue prev_xr;
+  colvarvalue prev_x_ext;
   /// Velocity of the restraint center
-  colvarvalue vr;
+  colvarvalue v_ext;
   /// Previous velocity of the restraint center
-  colvarvalue prev_vr;
+  colvarvalue prev_v_ext;
   /// Mass of the restraint center
   cvm::real ext_mass;
   /// Restraint force constant
@@ -273,6 +273,9 @@ public:
   /// Init output flags
   int init_output_flags(std::string const &conf);
 
+  /// \brief Initialize dependency tree
+  virtual int init_dependencies();
+
 private:
   /// Parse the CVC configuration for all components of a certain type
   template<typename def_class_name> int init_components_type(std::string const &conf,
@@ -373,7 +376,7 @@ protected:
   void update_active_cvc_square_norm();
 
   /// \brief Absolute timestep number when this colvar was last updated
-  int prev_timestep;
+  cvm::step_number prev_timestep;
 
 public:
 
@@ -383,32 +386,32 @@ public:
   /// \brief Return the number of CVC objects with an active flag (as set by update_cvc_flags)
   inline size_t num_active_cvcs() const { return n_active_cvcs; }
 
-  /// \brief Use the internal metrics (as from \link cvc
+  /// \brief Use the internal metrics (as from \link colvar::cvc
   /// \endlink objects) to calculate square distances and gradients
   ///
   /// Handles correctly symmetries and periodic boundary conditions
   cvm::real dist2(colvarvalue const &x1,
                   colvarvalue const &x2) const;
 
-  /// \brief Use the internal metrics (as from \link cvc
+  /// \brief Use the internal metrics (as from \link colvar::cvc
   /// \endlink objects) to calculate square distances and gradients
   ///
   /// Handles correctly symmetries and periodic boundary conditions
   colvarvalue dist2_lgrad(colvarvalue const &x1,
                           colvarvalue const &x2) const;
 
-  /// \brief Use the internal metrics (as from \link cvc
+  /// \brief Use the internal metrics (as from \link colvar::cvc
   /// \endlink objects) to calculate square distances and gradients
   ///
   /// Handles correctly symmetries and periodic boundary conditions
   colvarvalue dist2_rgrad(colvarvalue const &x1,
                           colvarvalue const &x2) const;
 
-  /// \brief Use the internal metrics (as from \link cvc
+  /// \brief Use the internal metrics (as from \link colvar::cvc
   /// \endlink objects) to wrap a value into a standard interval
   ///
   /// Handles correctly symmetries and periodic boundary conditions
-  void wrap(colvarvalue &x) const;
+  void wrap(colvarvalue &x_unwrapped) const;
 
 
   /// Read the analysis tasks
@@ -546,6 +549,7 @@ public:
   class polar_phi;
   class distance_inv;
   class distance_pairs;
+  class dipole_magnitude;
   class angle;
   class dipole_angle;
   class dihedral;
@@ -574,7 +578,7 @@ public:
 
 protected:
 
-  /// \brief Array of \link cvc \endlink objects
+  /// \brief Array of \link colvar::cvc \endlink objects
   std::vector<cvc *> cvcs;
 
   /// \brief Flags to enable or disable cvcs at next colvar evaluation
@@ -619,6 +623,9 @@ public:
   inline size_t n_components() const {
     return cvcs.size();
   }
+
+  /// \brief Get vector of vectors of atom IDs for all atom groups
+  virtual std::vector<std::vector<int> > get_atom_lists();
 };
 
 inline cvm::real const & colvar::force_constant() const
@@ -655,6 +662,8 @@ inline colvarvalue const & colvar::total_force() const
 
 inline void colvar::add_bias_force(colvarvalue const &force)
 {
+  check_enabled(f_cv_gradient,
+                std::string("applying a force to the variable \""+name+"\""));
   if (cvm::debug()) {
     cvm::log("Adding biasing force "+cvm::to_str(force)+" to colvar \""+name+"\".\n");
   }

lib/colvars/colvar_UIestimator.h

@@ -33,24 +33,24 @@ namespace UIestimator {
 
     public:
         n_matrix() {}
-        n_matrix(const std::vector<double> & lowerboundary,   // lowerboundary of x
+        n_matrix(const std::vector<double> & lowerboundary_input,   // lowerboundary of x
-            const std::vector<double> & upperboundary,   // upperboundary of
+            const std::vector<double> & upperboundary_input,   // upperboundary of
-            const std::vector<double> & width,           // width of x
+            const std::vector<double> & width_input,           // width of x
-            const int y_size) {          // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered
+            const int y_size_input) {          // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered
 
             int i;
 
-            this->lowerboundary = lowerboundary;
+            this->lowerboundary = lowerboundary_input;
-            this->upperboundary = upperboundary;
+            this->upperboundary = upperboundary_input;
-            this->width = width;
+            this->width = width_input;
-            this->dimension = lowerboundary.size();
+            this->dimension = lowerboundary_input.size();
-            this->y_size = y_size;     // keep in mind the internal (spare) matrix is stored in diagonal form
+            this->y_size = y_size_input;     // keep in mind the internal (spare) matrix is stored in diagonal form
-            this->y_total_size = int(std::pow(double(y_size), double(dimension)) + EPSILON);
+            this->y_total_size = int(cvm::pow(double(y_size_input), double(dimension)) + EPSILON);
 
             // the range of the matrix is [lowerboundary, upperboundary]
             x_total_size = 1;
             for (i = 0; i < dimension; i++) {
-                x_size.push_back(int((upperboundary[i] - lowerboundary[i]) / width[i] + EPSILON));
+                x_size.push_back(int((upperboundary_input[i] - lowerboundary_input[i]) / width_input[i] + EPSILON));
                 x_total_size *= x_size[i];
             }
 
@@ -89,9 +89,10 @@ namespace UIestimator {
 
         std::vector<int> temp;         // this vector is used in convert_x and convert_y to save computational resource
 
-        int i, j;
-
         int convert_x(const std::vector<double> & x) {       // convert real x value to its interal index
+
+            int i, j;
+
             for (i = 0; i < dimension; i++) {
                 temp[i] = int((x[i] - lowerboundary[i]) / width[i] + EPSILON);
             }
@@ -121,7 +122,7 @@ namespace UIestimator {
             int index = 0;
             for (i = 0; i < dimension; i++) {
                 if (i + 1 < dimension)
-                    index += temp[i] * int(std::pow(double(y_size), double(dimension - i - 1)) + EPSILON);
+                    index += temp[i] * int(cvm::pow(double(y_size), double(dimension - i - 1)) + EPSILON);
                 else
                     index += temp[i];
             }
@@ -139,19 +140,19 @@ namespace UIestimator {
 
     public:
         n_vector() {}
-        n_vector(const std::vector<double> & lowerboundary,   // lowerboundary of x
+        n_vector(const std::vector<double> & lowerboundary_input,   // lowerboundary of x
-            const std::vector<double> & upperboundary,   // upperboundary of
+            const std::vector<double> & upperboundary_input,   // upperboundary of
-            const std::vector<double> & width,                // width of x
+            const std::vector<double> & width_input,                // width of x
-            const int y_size,           // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered
+            const int y_size_input,           // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered
             const T & default_value) {         //   the default value of T
 
-            this->width = width;
+            this->width = width_input;
-            this->dimension = lowerboundary.size();
+            this->dimension = lowerboundary_input.size();
 
             x_total_size = 1;
             for (int i = 0; i < dimension; i++) {
-                this->lowerboundary.push_back(lowerboundary[i] - (y_size - 1) / 2 * width[i] - EPSILON);
+                this->lowerboundary.push_back(lowerboundary_input[i] - (y_size_input - 1) / 2 * width_input[i] - EPSILON);
-                this->upperboundary.push_back(upperboundary[i] + (y_size - 1) / 2 * width[i] + EPSILON);
+                this->upperboundary.push_back(upperboundary_input[i] + (y_size_input - 1) / 2 * width_input[i] + EPSILON);
 
                 x_size.push_back(int((this->upperboundary[i] - this->lowerboundary[i]) / this->width[i] + EPSILON));
                 x_total_size *= x_size[i];
@@ -215,26 +216,26 @@ namespace UIestimator {
         UIestimator() {}
 
         //called when (re)start an eabf simulation
-        UIestimator(const std::vector<double> & lowerboundary,
+        UIestimator(const std::vector<double> & lowerboundary_input,
-            const std::vector<double> & upperboundary,
+            const std::vector<double> & upperboundary_input,
-            const std::vector<double> & width,
+            const std::vector<double> & width_input,
-            const std::vector<double> & krestr,                // force constant in eABF
+            const std::vector<double> & krestr_input,                // force constant in eABF
-            const std::string & output_filename,              // the prefix of output files
+            const std::string & output_filename_input,              // the prefix of output files
-            const int output_freq,
+            const int output_freq_input,
-            const bool restart,                              // whether restart from a .count and a .grad file
+            const bool restart_input,                              // whether restart from a .count and a .grad file
-            const std::vector<std::string> & input_filename,   // the prefixes of input files
+            const std::vector<std::string> & input_filename_input,   // the prefixes of input files
-            const double temperature) {
+            const double temperature_input) {
 
             // initialize variables
-            this->lowerboundary = lowerboundary;
+            this->lowerboundary = lowerboundary_input;
-            this->upperboundary = upperboundary;
+            this->upperboundary = upperboundary_input;
-            this->width = width;
+            this->width = width_input;
-            this->krestr = krestr;
+            this->krestr = krestr_input;
-            this->output_filename = output_filename;
+            this->output_filename = output_filename_input;
-            this->output_freq = output_freq;
+            this->output_freq = output_freq_input;
-            this->restart = restart;
+            this->restart = restart_input;
-            this->input_filename = input_filename;
+            this->input_filename = input_filename_input;
-            this->temperature = temperature;
+            this->temperature = temperature_input;
 
             int i, j;
 
@@ -300,7 +301,7 @@ namespace UIestimator {
         ~UIestimator() {}
 
         // called from MD engine every step
-        bool update(const int step, std::vector<double> x, std::vector<double> y) {
+        bool update(cvm::step_number step, std::vector<double> x, std::vector<double> y) {
 
             int i;
 
@@ -431,7 +432,7 @@ namespace UIestimator {
                     loop_flag_y[k] = loop_flag_x[k] - HALF_Y_SIZE * width[k];
                 }
 
-                int j = 0;
+                j = 0;
                 while (j >= 0) {
                     norm += distribution_x_y.get_value(loop_flag_x, loop_flag_y);
                     for (k = 0; k < dimension; k++) {
@@ -672,7 +673,7 @@ namespace UIestimator {
         }
 
         // read input files
-        void read_inputfiles(const std::vector<std::string> input_filename)
+        void read_inputfiles(const std::vector<std::string> filename)
         {
             char sharp;
             double nothing;
@@ -683,11 +684,11 @@ namespace UIestimator {
             std::vector<double> position_temp(dimension, 0);
             std::vector<double> grad_temp(dimension, 0);
             int count_temp = 0;
-            for (i = 0; i < int(input_filename.size()); i++) {
+            for (i = 0; i < int(filename.size()); i++) {
                 int size = 1 , size_temp = 0;
 
-                std::string count_filename = input_filename[i] + ".UI.count";
+                std::string count_filename = filename[i] + ".UI.count";
-                std::string grad_filename = input_filename[i] + ".UI.grad";
+                std::string grad_filename = filename[i] + ".UI.grad";
 
                 std::ifstream count_file(count_filename.c_str(), std::ios::in);
                 std::ifstream grad_file(grad_filename.c_str(), std::ios::in);

lib/colvars/colvaratoms.cpp

@@ -22,7 +22,7 @@ cvm::atom::atom()
   index = -1;
   id = -1;
   mass = 1.0;
-  charge = 1.0;
+  charge = 0.0;
   reset_data();
 }
 
@@ -107,6 +107,8 @@ cvm::atom_group::~atom_group()
     delete fitting_group;
     fitting_group = NULL;
   }
+
+  cvm::main()->unregister_named_atom_group(this);
 }
 
 
@@ -183,10 +185,7 @@ int cvm::atom_group::init()
   // These may be overwritten by parse(), if a name is provided
 
   atoms.clear();
-
+  init_dependencies();
-  // TODO: check with proxy whether atom forces etc are available
-  init_ag_requires();
-
   index = -1;
 
   b_dummy = false;
@@ -207,8 +206,67 @@ int cvm::atom_group::init()
 }
 
 
+int cvm::atom_group::init_dependencies() {
+  size_t i;
+  // Initialize static array once and for all
+  if (features().size() == 0) {
+    for (i = 0; i < f_ag_ntot; i++) {
+      modify_features().push_back(new feature);
+    }
+
+    init_feature(f_ag_active, "active", f_type_dynamic);
+    init_feature(f_ag_center, "translational fit", f_type_static);
+    init_feature(f_ag_rotate, "rotational fit", f_type_static);
+    init_feature(f_ag_fitting_group, "fitting group", f_type_static);
+    init_feature(f_ag_explicit_gradient, "explicit atom gradient", f_type_dynamic);
+    init_feature(f_ag_fit_gradients, "fit gradients", f_type_user);
+    require_feature_self(f_ag_fit_gradients, f_ag_explicit_gradient);
+
+    init_feature(f_ag_atom_forces, "atomic forces", f_type_dynamic);
+
+    // parallel calculation implies that we have at least a scalable center of mass,
+    // but f_ag_scalable is kept as a separate feature to deal with future dependencies
+    init_feature(f_ag_scalable, "scalable group calculation", f_type_static);
+    init_feature(f_ag_scalable_com, "scalable group center of mass calculation", f_type_static);
+    require_feature_self(f_ag_scalable, f_ag_scalable_com);
+
+    // check that everything is initialized
+    for (i = 0; i < colvardeps::f_ag_ntot; i++) {
+      if (is_not_set(i)) {
+        cvm::error("Uninitialized feature " + cvm::to_str(i) + " in " + description);
+      }
+    }
+  }
+
+  // Initialize feature_states for each instance
+  // default as unavailable, not enabled
+  feature_states.reserve(f_ag_ntot);
+  for (i = 0; i < colvardeps::f_ag_ntot; i++) {
+    feature_states.push_back(feature_state(false, false));
+  }
+
+  // Features that are implemented (or not) by all atom groups
+  feature_states[f_ag_active].available = true;
+  // f_ag_scalable_com is provided by the CVC iff it is COM-based
+  feature_states[f_ag_scalable_com].available = false;
+  // TODO make f_ag_scalable depend on f_ag_scalable_com (or something else)
+  feature_states[f_ag_scalable].available = true;
+  feature_states[f_ag_fit_gradients].available = true;
+  feature_states[f_ag_fitting_group].available = true;
+  feature_states[f_ag_explicit_gradient].available = true;
+
+  return COLVARS_OK;
+}
+
+
 int cvm::atom_group::setup()
 {
+  if (atoms_ids.size() == 0) {
+    atoms_ids.reserve(atoms.size());
+    for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
+      atoms_ids.push_back(ai->id);
+    }
+  }
   for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
     ai->update_mass();
     ai->update_charge();
@@ -237,15 +295,6 @@ void cvm::atom_group::update_total_mass()
 }
 
 
-void cvm::atom_group::reset_mass(std::string &name, int i, int j)
-{
-  update_total_mass();
-  cvm::log("Re-initialized atom group "+name+":"+cvm::to_str(i)+"/"+
-           cvm::to_str(j)+". "+ cvm::to_str(atoms_ids.size())+
-           " atoms: total mass = "+cvm::to_str(total_mass)+".\n");
-}
-
-
 void cvm::atom_group::update_total_charge()
 {
   if (b_dummy) {
@@ -264,6 +313,19 @@ void cvm::atom_group::update_total_charge()
 }
 
 
+void cvm::atom_group::print_properties(std::string const &colvar_name,
+                                       int i, int j)
+{
+  if (cvm::proxy->updated_masses() && cvm::proxy->updated_charges()) {
+    cvm::log("Re-initialized atom group for variable \""+colvar_name+"\":"+
+             cvm::to_str(i)+"/"+
+             cvm::to_str(j)+". "+ cvm::to_str(atoms_ids.size())+
+             " atoms: total mass = "+cvm::to_str(total_mass)+
+             ", total charge = "+cvm::to_str(total_charge)+".\n");
+  }
+}
+
+
 int cvm::atom_group::parse(std::string const &group_conf)
 {
   cvm::log("Initializing atom group \""+key+"\".\n");
@@ -450,10 +512,21 @@ int cvm::atom_group::parse(std::string const &group_conf)
   if (cvm::debug())
     cvm::log("Done initializing atom group \""+key+"\".\n");
 
-  cvm::log("Atom group \""+key+"\" defined, "+
+  {
-            cvm::to_str(atoms_ids.size())+" atoms initialized: total mass = "+
+    std::string init_msg;
-            cvm::to_str(total_mass)+", total charge = "+
+    init_msg.append("Atom group \""+key+"\" defined with "+
-            cvm::to_str(total_charge)+".\n");
+                    cvm::to_str(atoms_ids.size())+" atoms requested");
+    if ((cvm::proxy)->updated_masses()) {
+      init_msg.append(": total mass = "+
+                      cvm::to_str(total_mass));
+      if ((cvm::proxy)->updated_charges()) {
+        init_msg.append(", total charge = "+
+                        cvm::to_str(total_charge));
+      }
+    }
+    init_msg.append(".\n");
+    cvm::log(init_msg);
+  }
 
   if (b_print_atom_ids) {
     cvm::log("Internal definition of the atom group:\n");
@@ -464,7 +537,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
 }
 
 
-int cvm::atom_group::add_atoms_of_group(atom_group const * ag)
+int cvm::atom_group::add_atoms_of_group(atom_group const *ag)
 {
   std::vector<int> const &source_ids = ag->atoms_ids;
 
@@ -696,6 +769,7 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf)
           return INPUT_ERROR;
         }
       }
+      enable(f_ag_fitting_group);
     }
 
     atom_group *group_for_fit = fitting_group ? fitting_group : this;
@@ -800,24 +874,24 @@ int cvm::atom_group::create_sorted_ids()
 
   // Sort the internal IDs
   std::list<int> sorted_atoms_ids_list;
-  for (size_t i = 0; i < this->size(); i++) {
+  for (size_t i = 0; i < atoms_ids.size(); i++) {
     sorted_atoms_ids_list.push_back(atoms_ids[i]);
   }
   sorted_atoms_ids_list.sort();
   sorted_atoms_ids_list.unique();
-  if (sorted_atoms_ids_list.size() != this->size()) {
+  if (sorted_atoms_ids_list.size() != atoms_ids.size()) {
     return cvm::error("Error: duplicate atom IDs in atom group? (found " +
                       cvm::to_str(sorted_atoms_ids_list.size()) +
                       " unique atom IDs instead of " +
-                      cvm::to_str(this->size()) + ").\n", BUG_ERROR);
+                      cvm::to_str(atoms_ids.size()) + ").\n", BUG_ERROR);
   }
 
   // Compute map between sorted and unsorted elements
-  sorted_atoms_ids.resize(this->size());
+  sorted_atoms_ids.resize(atoms_ids.size());
-  sorted_atoms_ids_map.resize(this->size());
+  sorted_atoms_ids_map.resize(atoms_ids.size());
   std::list<int>::iterator lsii = sorted_atoms_ids_list.begin();
   size_t ii = 0;
-  for ( ; ii < this->size(); lsii++, ii++) {
+  for ( ; ii < atoms_ids.size(); lsii++, ii++) {
     sorted_atoms_ids[ii] = *lsii;
     size_t const pos = std::find(atoms_ids.begin(), atoms_ids.end(), *lsii) -
       atoms_ids.begin();
@@ -1038,15 +1112,15 @@ int cvm::atom_group::calc_center_of_mass()
 }
 
 
-int cvm::atom_group::calc_dipole(cvm::atom_pos const &com)
+int cvm::atom_group::calc_dipole(cvm::atom_pos const &dipole_center)
 {
   if (b_dummy) {
-    cvm::error("Error: trying to compute the dipole of an empty group.\n", INPUT_ERROR);
+    return cvm::error("Error: trying to compute the dipole "
-    return COLVARS_ERROR;
+                      "of a dummy group.\n", INPUT_ERROR);
   }
   dip.reset();
   for (cvm::atom_const_iter ai = this->begin(); ai != this->end(); ai++) {
-    dip += ai->charge * (ai->pos - com);
+    dip += ai->charge * (ai->pos - dipole_center);
   }
   return COLVARS_OK;
 }
@@ -1056,13 +1130,12 @@ void cvm::atom_group::set_weighted_gradient(cvm::rvector const &grad)
 {
   if (b_dummy) return;
 
-  if (is_enabled(f_ag_scalable)) {
+  scalar_com_gradient = grad;
-    scalar_com_gradient = grad;
-    return;
-  }
 
-  for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
+  if (!is_enabled(f_ag_scalable)) {
-    ai->grad = (ai->mass/total_mass) * grad;
+    for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
+      ai->grad = (ai->mass/total_mass) * grad;
+    }
   }
 }
 

lib/colvars/colvaratoms.h

@@ -17,7 +17,7 @@
 
 
 /// \brief Stores numeric id, mass and all mutable data for an atom,
-/// mostly used by a \link cvc \endlink
+/// mostly used by a \link colvar::cvc \endlink
 ///
 /// This class may be used to keep atomic data such as id, mass,
 /// position and collective variable derivatives) altogether.
@@ -63,7 +63,7 @@ public:
   /// from the \link colvarvalue \endlink class), which is also the
   /// most frequent case. For more complex types of \link
   /// colvarvalue \endlink objects, atomic gradients should be
-  /// defined within the specific \link cvc \endlink
+  /// defined within the specific \link colvar::cvc \endlink
   /// implementation
   cvm::rvector   grad;
 
@@ -100,13 +100,19 @@ public:
   /// Get the latest value of the mass
   inline void update_mass()
   {
-    mass = (cvm::proxy)->get_atom_mass(index);
+    colvarproxy *p = cvm::proxy;
+    if (p->updated_masses()) {
+      mass = p->get_atom_mass(index);
+    }
   }
 
   /// Get the latest value of the charge
   inline void update_charge()
   {
-    charge = (cvm::proxy)->get_atom_charge(index);
+    colvarproxy *p = cvm::proxy;
+    if (p->updated_charges()) {
+      charge = p->get_atom_charge(index);
+    }
   }
 
   /// Get the current position
@@ -145,7 +151,7 @@ public:
 
 
 /// \brief Group of \link atom \endlink objects, mostly used by a
-/// \link cvc \endlink object to gather all atomic data
+/// \link colvar::cvc \endlink object to gather all atomic data
 class colvarmodule::atom_group
   : public colvarparse, public colvardeps
 {
@@ -174,6 +180,9 @@ public:
   /// \brief Set default values for common flags
   int init();
 
+  /// \brief Initialize dependency tree
+  virtual int init_dependencies();
+
   /// \brief Update data required to calculate cvc's
   int setup();
 
@@ -198,16 +207,16 @@ public:
   /// \brief Remove an atom object from this group
   int remove_atom(cvm::atom_iter ai);
 
-  /// \brief Re-initialize the total mass of a group.
+  /// \brief Print the updated the total mass and charge of a group.
   /// This is needed in case the hosting MD code has an option to
   /// change atom masses after their initialization.
-  void reset_mass(std::string &name, int i, int j);
+  void print_properties(std::string const &colvar_name, int i, int j);
 
   /// \brief Implementation of the feature list for atom group
   static std::vector<feature *> ag_features;
 
   /// \brief Implementation of the feature list accessor for atom group
-  virtual const std::vector<feature *> &features()
+  virtual const std::vector<feature *> &features() const
   {
     return ag_features;
   }
@@ -347,15 +356,19 @@ public:
 
   /// Total mass of the atom group
   cvm::real total_mass;
+
+  /// Update the total mass of the atom group
   void update_total_mass();
 
   /// Total charge of the atom group
   cvm::real total_charge;
+
+  /// Update the total mass of the group
   void update_total_charge();
 
   /// \brief Don't apply any force on this group (use its coordinates
   /// only to calculate a colvar)
-  bool        noforce;
+  bool noforce;
 
   /// \brief Get the current positions
   void read_positions();
@@ -423,20 +436,32 @@ public:
   /// \brief Calculate the center of mass of the atomic positions, assuming that
   /// they are already pbc-wrapped
   int calc_center_of_mass();
+
 private:
+
   /// \brief Center of mass
   cvm::atom_pos com;
+
   /// \brief The derivative of a scalar variable with respect to the COM
   // TODO for scalable calculations of more complex variables (e.g. rotation),
   // use a colvarvalue of vectors to hold the entire derivative
   cvm::rvector scalar_com_gradient;
+
 public:
-  /// \brief Return the center of mass of the atomic positions
+
+  /// \brief Return the center of mass (COM) of the atomic positions
   inline cvm::atom_pos center_of_mass() const
   {
     return com;
   }
 
+  /// \brief Return previously gradient of scalar variable with respect to the
+  /// COM
+  inline cvm::rvector center_of_mass_scalar_gradient() const
+  {
+    return scalar_com_gradient;
+  }
+
   /// \brief Return a copy of the current atom positions, shifted by a constant vector
   std::vector<cvm::atom_pos> positions_shifted(cvm::rvector const &shift) const;
 
@@ -444,10 +469,15 @@ public:
   std::vector<cvm::rvector> velocities() const;
 
   ///\brief Calculate the dipole of the atom group around the specified center
-  int calc_dipole(cvm::atom_pos const &com);
+  int calc_dipole(cvm::atom_pos const &dipole_center);
+
 private:
+
+  /// Dipole moment of the atom group
   cvm::rvector dip;
+
 public:
+
   ///\brief Return the (previously calculated) dipole of the atom group
   inline cvm::rvector dipole() const
   {

lib/colvars/colvarbias.cpp

@@ -17,15 +17,14 @@
 colvarbias::colvarbias(char const *key)
   : bias_type(to_lower_cppstr(key))
 {
-  init_cvb_requires();
+  description = "uninitialized " + cvm::to_str(key) + " bias";
-
+  init_dependencies();
   rank = 1;
 
   has_data = false;
   b_output_energy = false;
   reset();
-  state_file_step = 0;
+  state_file_step = 0L;
-  description = "uninitialized " + cvm::to_str(key) + " bias";
 }
 
 
@@ -76,6 +75,7 @@ int colvarbias::init(std::string const &conf)
       cvm::error("Error: no collective variables specified.\n", INPUT_ERROR);
       return INPUT_ERROR;
     }
+
   } else {
     cvm::log("Reinitializing bias \""+name+"\".\n");
   }
@@ -98,6 +98,70 @@ int colvarbias::init(std::string const &conf)
 }
 
 
+int colvarbias::init_dependencies() {
+  int i;
+  if (features().size() == 0) {
+    for (i = 0; i < f_cvb_ntot; i++) {
+      modify_features().push_back(new feature);
+    }
+
+    init_feature(f_cvb_active, "active", f_type_dynamic);
+    require_feature_children(f_cvb_active, f_cv_active);
+
+    init_feature(f_cvb_awake, "awake", f_type_static);
+    require_feature_self(f_cvb_awake, f_cvb_active);
+
+    init_feature(f_cvb_apply_force, "apply force", f_type_user);
+    require_feature_children(f_cvb_apply_force, f_cv_gradient);
+
+    init_feature(f_cvb_get_total_force, "obtain total force", f_type_dynamic);
+    require_feature_children(f_cvb_get_total_force, f_cv_total_force);
+
+    init_feature(f_cvb_output_acc_work, "output accumulated work", f_type_user);
+    require_feature_self(f_cvb_output_acc_work, f_cvb_apply_force);
+
+    init_feature(f_cvb_history_dependent, "history-dependent", f_type_static);
+
+    init_feature(f_cvb_time_dependent, "time-dependent", f_type_static);
+
+    init_feature(f_cvb_scalar_variables, "require scalar variables", f_type_static);
+    require_feature_children(f_cvb_scalar_variables, f_cv_scalar);
+
+    init_feature(f_cvb_calc_pmf, "calculate a PMF", f_type_static);
+
+    init_feature(f_cvb_calc_ti_samples, "calculate TI samples", f_type_dynamic);
+    require_feature_self(f_cvb_calc_ti_samples, f_cvb_get_total_force);
+    require_feature_children(f_cvb_calc_ti_samples, f_cv_grid);
+
+    init_feature(f_cvb_write_ti_samples, "write TI samples ", f_type_user);
+    require_feature_self(f_cvb_write_ti_samples, f_cvb_calc_ti_samples);
+
+    init_feature(f_cvb_write_ti_pmf, "write TI PMF", f_type_user);
+    require_feature_self(f_cvb_write_ti_pmf, f_cvb_calc_ti_samples);
+
+    // check that everything is initialized
+    for (i = 0; i < colvardeps::f_cvb_ntot; i++) {
+      if (is_not_set(i)) {
+        cvm::error("Uninitialized feature " + cvm::to_str(i) + " in " + description);
+      }
+    }
+  }
+
+  // Initialize feature_states for each instance
+  feature_states.reserve(f_cvb_ntot);
+  for (i = 0; i < f_cvb_ntot; i++) {
+    feature_states.push_back(feature_state(true, false));
+    // Most features are available, so we set them so
+    // and list exceptions below
+  }
+
+  // only compute TI samples when deriving from colvarbias_ti
+  feature_states[f_cvb_calc_ti_samples].available = false;
+
+  return COLVARS_OK;
+}
+
+
 int colvarbias::reset()
 {
   bias_energy = 0.0;
@@ -217,6 +281,9 @@ int colvarbias::update()
 
 void colvarbias::communicate_forces()
 {
+  if (! is_enabled(f_cvb_apply_force)) {
+    return;
+  }
   size_t i = 0;
   for (i = 0; i < num_variables(); i++) {
     if (cvm::debug()) {
@@ -345,7 +412,8 @@ std::istream & colvarbias::read_state(std::istream &is)
        (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);
+               cvm::to_str(static_cast<size_t>(is.tellg()))+
+               " in stream.\n", INPUT_ERROR);
     is.clear();
     is.seekg(start_pos, std::ios::beg);
     is.setstate(std::ios::failbit);
@@ -355,7 +423,8 @@ std::istream & colvarbias::read_state(std::istream &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);
+               cvm::to_str(static_cast<size_t>(is.tellg()))+
+               " in stream.\n", INPUT_ERROR);
     is.clear();
     is.seekg(start_pos, std::ios::beg);
     is.setstate(std::ios::failbit);
@@ -365,7 +434,8 @@ std::istream & colvarbias::read_state(std::istream &is)
   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");
+               cvm::to_str(static_cast<size_t>(is.tellg()))+
+               " in stream.\n");
     is.setstate(std::ios::failbit);
   }
 
@@ -381,7 +451,8 @@ std::istream & colvarbias::read_state_data_key(std::istream &is, char const *key
        !(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);
+               cvm::to_str(static_cast<size_t>(is.tellg()))+
+               " in stream.\n", INPUT_ERROR);
     is.clear();
     is.seekg(start_pos, std::ios::beg);
     is.setstate(std::ios::failbit);
@@ -640,7 +711,7 @@ int colvarbias_ti::write_output_files()
       cvm::proxy->close_output_stream(ti_count_file_name);
     }
 
-    std::string const ti_grad_file_name(ti_output_prefix+".ti.grad");
+    std::string const ti_grad_file_name(ti_output_prefix+".ti.force");
     os = cvm::proxy->output_stream(ti_grad_file_name);
     if (os) {
       ti_avg_forces->write_multicol(*os);

lib/colvars/colvarbias.h

@@ -96,6 +96,9 @@ public:
   /// \brief Parse config string and (re)initialize
   virtual int init(std::string const &conf);
 
+  /// \brief Initialize dependency tree
+  virtual int init_dependencies();
+
   /// \brief Set to zero all mutable data
   virtual int reset();
 
@@ -181,7 +184,7 @@ public:
   static std::vector<feature *> cvb_features;
 
   /// \brief Implementation of the feature list accessor for colvarbias
-  virtual const std::vector<feature *> &features()
+  virtual const std::vector<feature *> &features() const
   {
     return cvb_features;
   }
@@ -220,7 +223,7 @@ protected:
   bool                     has_data;
 
   /// \brief Step number read from the last state file
-  size_t                   state_file_step;
+  cvm::step_number         state_file_step;
 
 };
 

lib/colvars/colvarbias_abf.cpp

@@ -191,10 +191,10 @@ int colvarbias_abf::init(std::string const &conf)
       // Projected ABF
       get_keyval(conf, "pABFintegrateFreq", pabf_freq, 0);
       // Parameters for integrating initial (and final) gradient data
-      get_keyval(conf, "integrateInitSteps", integrate_initial_steps, 1e4);
+      get_keyval(conf, "integrateInitMaxIterations", integrate_initial_iterations, 1e4);
       get_keyval(conf, "integrateInitTol", integrate_initial_tol, 1e-6);
       // for updating the integrated PMF on the fly
-      get_keyval(conf, "integrateSteps", integrate_steps, 100);
+      get_keyval(conf, "integrateMaxIterations", integrate_iterations, 100);
       get_keyval(conf, "integrateTol", integrate_tol, 1e-4);
     }
   } else {
@@ -366,10 +366,10 @@ int colvarbias_abf::update()
     if ( b_integrate ) {
       if ( pabf_freq && cvm::step_relative() % pabf_freq == 0 ) {
         cvm::real err;
-        int iter = pmf->integrate(integrate_steps, integrate_tol, err);
+        int iter = pmf->integrate(integrate_iterations, integrate_tol, err);
-        if ( iter == integrate_steps ) {
+        if ( iter == integrate_iterations ) {
           cvm::log("Warning: PMF integration did not converge to " + cvm::to_str(integrate_tol)
-            + " in " + cvm::to_str(integrate_steps)
+            + " in " + cvm::to_str(integrate_iterations)
             + " steps. Residual error: " +  cvm::to_str(err));
         }
         pmf->set_zero_minimum(); // TODO: do this only when necessary
@@ -597,7 +597,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
   if (b_integrate) {
     // Do numerical integration (to high precision) and output a PMF
     cvm::real err;
-    pmf->integrate(integrate_initial_steps, integrate_initial_tol, err);
+    pmf->integrate(integrate_initial_iterations, integrate_initial_tol, err);
     pmf->set_zero_minimum();
 
     std::string  pmf_out_name = prefix + ".pmf";
@@ -661,7 +661,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
       // Do numerical integration (to high precision) and output a PMF
       cvm::real err;
       czar_pmf->set_div();
-      czar_pmf->integrate(integrate_initial_steps, integrate_initial_tol, err);
+      czar_pmf->integrate(integrate_initial_iterations, integrate_initial_tol, err);
       czar_pmf->set_zero_minimum();
 
       std::string  czar_pmf_out_name = prefix + ".czar.pmf";

lib/colvars/colvarbias_abf.h

@@ -27,9 +27,13 @@ class colvarbias_abf : public colvarbias {
 
 public:
 
+  /// Constructor for ABF bias
   colvarbias_abf(char const *key);
+  /// Initializer for ABF bias
   virtual int init(std::string const &conf);
+  /// Default destructor for ABF bias
   virtual ~colvarbias_abf();
+  /// Per-timestep update of ABF bias
   virtual int update();
 
 private:
@@ -40,11 +44,17 @@ private:
   /// Base filename(s) for reading previous gradient data (replaces data from restart file)
   std::vector<std::string> input_prefix;
 
+  /// Adapt the bias at each time step (as opposed to keeping it constant)?
   bool    update_bias;
+  /// Use normalized definition of PMF for distance functions? (flat at long distances)
+  /// by including the Jacobian term separately of the recorded PMF
   bool    hide_Jacobian;
+  /// Integrate gradients into a PMF on output
   bool    b_integrate;
 
+  /// Number of samples per bin before applying the full biasing force
   size_t  full_samples;
+  /// Number of samples per bin before applying a scaled-down biasing force
   size_t  min_samples;
   /// frequency for updating output files
   int     output_freq;
@@ -52,6 +62,7 @@ private:
   bool    b_history_files;
   /// Write CZAR output file for stratified eABF (.zgrad)
   bool    b_czar_window_file;
+  /// Number of timesteps between recording data in history files (if non-zero)
   size_t  history_freq;
   /// Umbrella Integration estimator of free energy from eABF
   UIestimator::UIestimator eabf_UI;
@@ -63,25 +74,30 @@ private:
   /// Frequency for updating pABF PMF (if zero, pABF is not used)
   int   pabf_freq;
   /// Max number of CG iterations for integrating PMF at startup and for file output
-  int       integrate_initial_steps;
+  int       integrate_initial_iterations;
   /// Tolerance for integrating PMF at startup and for file output
   cvm::real integrate_initial_tol;
   /// Max number of CG iterations for integrating PMF at on-the-fly pABF updates
-  int       integrate_steps;
+  int       integrate_iterations;
   /// Tolerance for integrating PMF at on-the-fly pABF updates
   cvm::real integrate_tol;
 
-  /// Cap the biasing force to be applied?
+  /// Cap the biasing force to be applied? (option maxForce)
   bool                    cap_force;
+  /// Maximum force to be applied
   std::vector<cvm::real>  max_force;
 
-  // Frequency for updating 2D gradients
-  int integrate_freq;
-
   // Internal data and methods
 
-  std::vector<int>  bin, force_bin, z_bin;
+  /// Current bin in sample grid
-  gradient_t    system_force, applied_force;
+  std::vector<int>  bin;
+  /// Current bin in force grid
+  std::vector<int> force_bin;
+  /// Cuurent bin in "actual" coordinate, when running extended Lagrangian dynamics
+  std::vector<int> z_bin;
+
+  /// Measured instantaneous system force
+  gradient_t system_force;
 
   /// n-dim grid of free energy gradients
   colvar_grid_gradient  *gradients;
@@ -118,7 +134,7 @@ private:
   // shared ABF
   bool    shared_on;
   size_t  shared_freq;
-  int     shared_last_step;
+  cvm::step_number shared_last_step;
   // Share between replicas -- may be called independently of update
   virtual int replica_share();
 

lib/colvars/colvarbias_histogram.h

@@ -37,7 +37,7 @@ protected:
   std::string out_name, out_name_dx;
   size_t output_freq;
 
-  /// If one or more of the variables are \link type_vector \endlink, treat them as arrays of this length
+  /// If one or more of the variables are \link colvarvalue::type_vector \endlink, treat them as arrays of this length
   size_t colvar_array_size;
   /// If colvar_array_size is larger than 1, weigh each one by this number before accumulating the histogram
   std::vector<cvm::real> weights;

lib/colvars/colvarbias_meta.cpp

@@ -11,7 +11,6 @@
 #include <sstream>
 #include <fstream>
 #include <iomanip>
-#include <cmath>
 #include <algorithm>
 
 // used to set the absolute path of a replica file
@@ -39,6 +38,8 @@ colvarbias_meta::colvarbias_meta(char const *key)
   new_hills_begin = hills.end();
   hills_traj_os = NULL;
   replica_hills_os = NULL;
+
+  ebmeta_equil_steps = 0L;
 }
 
 
@@ -61,7 +62,7 @@ int colvarbias_meta::init(std::string const &conf)
     enable(f_cvb_history_dependent);
   }
 
-  get_keyval(conf, "hillWidth", hill_width, std::sqrt(2.0 * PI) / 2.0);
+  get_keyval(conf, "hillWidth", hill_width, cvm::sqrt(2.0 * PI) / 2.0);
   cvm::log("Half-widths of the Gaussian hills (sigma's):\n");
   for (size_t i = 0; i < num_variables(); i++) {
     cvm::log(variables(i)->name+std::string(": ")+
@@ -201,6 +202,7 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
     }
     target_dist = new colvar_grid_scalar();
     target_dist->init_from_colvars(colvars);
+    std::string target_dist_file;
     get_keyval(conf, "targetdistfile", target_dist_file);
     std::ifstream targetdiststream(target_dist_file.c_str());
     target_dist->read_multicol(targetdiststream);
@@ -221,9 +223,9 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
     }
     // 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());
+    cvm::real volume = cvm::exp(target_dist->entropy());
     target_dist->multiply_constant(volume);
-    get_keyval(conf, "ebMetaEquilSteps", ebmeta_equil_steps, 0);
+    get_keyval(conf, "ebMetaEquilSteps", ebmeta_equil_steps, ebmeta_equil_steps);
   }
 
   return COLVARS_OK;
@@ -291,7 +293,7 @@ colvarbias_meta::create_hill(colvarbias_meta::hill const &h)
     // need to be computed analytically when the colvar returns
     // off-grid
     cvm::real const min_dist = hills_energy->bin_distance_from_boundaries(h.centers, true);
-    if (min_dist < (3.0 * std::floor(hill_width)) + 1.0) {
+    if (min_dist < (3.0 * cvm::floor(hill_width)) + 1.0) {
       hills_off_grid.push_back(h);
     }
   }
@@ -387,7 +389,7 @@ int colvarbias_meta::update_grid_params()
       // first of all, expand the grids, if specified
       bool changed_grids = false;
       int const min_buffer =
-        (3 * (size_t) std::floor(hill_width)) + 1;
+        (3 * (size_t) cvm::floor(hill_width)) + 1;
 
       std::vector<int>         new_sizes(hills_energy->sizes());
       std::vector<colvarvalue> new_lower_boundaries(hills_energy->lower_boundaries);
@@ -492,9 +494,9 @@ int colvarbias_meta::update_bias()
 
     if (ebmeta) {
       hills_scale *= 1.0/target_dist->value(target_dist->get_colvars_index());
-      if(cvm::step_absolute() <= long(ebmeta_equil_steps)) {
+      if(cvm::step_absolute() <= ebmeta_equil_steps) {
         cvm::real const hills_lambda =
-          (cvm::real(long(ebmeta_equil_steps) - cvm::step_absolute())) /
+          (cvm::real(ebmeta_equil_steps - cvm::step_absolute())) /
           (cvm::real(ebmeta_equil_steps));
         hills_scale = hills_lambda + (1-hills_lambda)*hills_scale;
       }
@@ -508,7 +510,7 @@ int colvarbias_meta::update_bias()
       } else {
         calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here);
       }
-      hills_scale *= std::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
+      hills_scale *= cvm::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
     }
 
     switch (comm) {
@@ -710,7 +712,7 @@ void colvarbias_meta::calc_hills(colvarbias_meta::hill_iter      h_first,
       // set it to zero if the exponent is more negative than log(1.0E-05)
       h->value(0.0);
     } else {
-      h->value(std::exp(-0.5*cv_sqdev));
+      h->value(cvm::exp(-0.5*cv_sqdev));
     }
     energy += h->energy();
   }
@@ -904,7 +906,7 @@ void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter  h_first
 
   for (hill_iter h = h_first; h != h_last; h++) {
     cvm::real const min_dist = hills_energy->bin_distance_from_boundaries(h->centers, true);
-    if (min_dist < (3.0 * std::floor(hill_width)) + 1.0) {
+    if (min_dist < (3.0 * cvm::floor(hill_width)) + 1.0) {
       hills_off_grid.push_back(*h);
     }
   }
@@ -1427,8 +1429,8 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
     return is;
   }
 
-  size_t h_it;
+  cvm::step_number h_it;
-  get_keyval(data, "step", h_it, 0, parse_silent);
+  get_keyval(data, "step", h_it, 0L, parse_silent);
   if (h_it <= state_file_step) {
     if (cvm::debug())
       cvm::log("Skipping a hill older than the state file for metadynamics bias \""+
@@ -1457,7 +1459,7 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
 
   std::vector<cvm::real> h_widths(num_variables());
   get_keyval(data, "widths", h_widths,
-             std::vector<cvm::real>(num_variables(), (std::sqrt(2.0 * PI) / 2.0)),
+             std::vector<cvm::real>(num_variables(), (cvm::sqrt(2.0 * PI) / 2.0)),
              parse_silent);
 
   std::string h_replica = "";
@@ -1482,7 +1484,7 @@ std::istream & colvarbias_meta::read_hill(std::istream &is)
     // be computed analytically
     cvm::real const min_dist =
       hills_energy->bin_distance_from_boundaries((hills.back()).centers, true);
-    if (min_dist < (3.0 * std::floor(hill_width)) + 1.0) {
+    if (min_dist < (3.0 * cvm::floor(hill_width)) + 1.0) {
       hills_off_grid.push_back(hills.back());
     }
   }

lib/colvars/colvarbias_meta.h

@@ -19,8 +19,8 @@
 #include "colvargrid.h"
 
 /// Metadynamics bias (implementation of \link colvarbias \endlink)
-class colvarbias_meta 
+class colvarbias_meta
-  : public virtual colvarbias, 
+  : public virtual colvarbias,
     public virtual colvarbias_ti
 {
 
@@ -174,12 +174,14 @@ protected:
   /// \brief Biasing temperature in well-tempered metadynamics
   cvm::real  bias_temperature;
 
-  // EBmeta parameters
+  /// Ensemble-biased metadynamics (EBmeta) flag
   bool       ebmeta;
+
+  /// Target distribution for EBmeta
   colvar_grid_scalar* target_dist;
-  std::string target_dist_file;
+
-  cvm::real target_dist_volume;
+  /// Number of equilibration steps for EBmeta
-  size_t ebmeta_equil_steps;
+  cvm::step_number ebmeta_equil_steps;
 
 
   /// \brief Try to read the restart information by allocating new
@@ -285,7 +287,7 @@ public:
   friend class colvarbias_meta;
 
   /// Time step at which this hill was added
-  size_t      it;
+  cvm::step_number it;
 
   /// Identity of the replica who added this hill (only in multiple replica simulations)
   std::string replica;
@@ -296,9 +298,9 @@ public:
   /// replica (optional) Identity of the replica which creates the
   /// hill
   inline hill(cvm::real             const &W_in,
-               std::vector<colvar *>       &cv,
+              std::vector<colvar *>       &cv,
-               cvm::real             const &hill_width,
+              cvm::real             const &hill_width,
-               std::string           const &replica_in = "")
+              std::string           const &replica_in = "")
     : sW(1.0),
       W(W_in),
       centers(cv.size()),
@@ -325,11 +327,11 @@ public:
   /// weight Weight of the hill \param centers Center of the hill
   /// \param widths Width of the hill around centers \param replica
   /// (optional) Identity of the replica which creates the hill
-  inline hill(size_t                    const &it_in,
+  inline hill(cvm::step_number          const &it_in,
-               cvm::real                 const &W_in,
+              cvm::real                 const &W_in,
-               std::vector<colvarvalue>  const &centers_in,
+              std::vector<colvarvalue>  const &centers_in,
-               std::vector<cvm::real>    const &widths_in,
+              std::vector<cvm::real>    const &widths_in,
-               std::string               const &replica_in = "")
+              std::string               const &replica_in = "")
     : sW(1.0),
       W(W_in),
       centers(centers_in),

lib/colvars/colvarbias_restraint.cpp

@@ -7,8 +7,6 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
-#include <cmath>
-
 #include "colvarmodule.h"
 #include "colvarproxy.h"
 #include "colvarvalue.h"
@@ -179,7 +177,7 @@ int colvarbias_restraint_k::change_configuration(std::string const &conf)
 colvarbias_restraint_moving::colvarbias_restraint_moving(char const *key)
 {
   target_nstages = 0;
-  target_nsteps = 0;
+  target_nsteps = 0L;
   stage = 0;
   acc_work = 0.0;
   b_chg_centers = false;
@@ -241,8 +239,8 @@ int colvarbias_restraint_moving::set_state_params(std::string const &conf)
 {
   if (b_chg_centers || b_chg_force_k) {
     if (target_nstages) {
-      if (!get_keyval(conf, "stage", stage))
+      get_keyval(conf, "stage", stage, stage,
-        cvm::error("Error: current stage is missing from the restart.\n");
+                 colvarparse::parse_restart | colvarparse::parse_required);
     }
   }
   return COLVARS_OK;
@@ -436,13 +434,13 @@ int colvarbias_restraint_centers_moving::set_state_params(std::string const &con
   colvarbias_restraint::set_state_params(conf);
 
   if (b_chg_centers) {
-    //    cvm::log ("Reading the updated restraint centers from the restart.\n");
+    get_keyval(conf, "centers", colvar_centers, colvar_centers,
-    if (!get_keyval(conf, "centers", colvar_centers))
+               colvarparse::parse_restart | colvarparse::parse_required);
-      cvm::error("Error: restraint centers are missing from the restart.\n");
+  }
-    if (is_enabled(f_cvb_output_acc_work)) {
+
-      if (!get_keyval(conf, "accumulatedWork", acc_work))
+  if (is_enabled(f_cvb_output_acc_work)) {
-        cvm::error("Error: accumulatedWork is missing from the restart.\n");
+    get_keyval(conf, "accumulatedWork", acc_work, acc_work,
-    }
+               colvarparse::parse_restart | colvarparse::parse_required);
   }
 
   return COLVARS_OK;
@@ -563,7 +561,7 @@ int colvarbias_restraint_k_moving::update()
           lambda = 0.0;
         }
         force_k = starting_force_k + (target_force_k - starting_force_k)
-          * std::pow(lambda, force_k_exp);
+          * cvm::pow(lambda, force_k_exp);
           cvm::log("Restraint " + this->name + ", stage " + cvm::to_str(stage)
                   + " : lambda = " + cvm::to_str(lambda)
                   + ", k = " + cvm::to_str(force_k));
@@ -585,7 +583,7 @@ int colvarbias_restraint_k_moving::update()
         for (size_t i = 0; i < num_variables(); i++) {
           dU_dk += d_restraint_potential_dk(i);
         }
-        restraint_FE += force_k_exp * std::pow(lambda, force_k_exp - 1.0)
+        restraint_FE += force_k_exp * cvm::pow(lambda, force_k_exp - 1.0)
           * (target_force_k - starting_force_k) * dU_dk;
       }
 
@@ -608,7 +606,7 @@ int colvarbias_restraint_k_moving::update()
             lambda = cvm::real(stage) / cvm::real(target_nstages);
           }
           force_k = starting_force_k + (target_force_k - starting_force_k)
-            * std::pow(lambda, force_k_exp);
+            * cvm::pow(lambda, force_k_exp);
           cvm::log("Restraint " + this->name + ", stage " + cvm::to_str(stage)
                   + " : lambda = " + cvm::to_str(lambda)
                   + ", k = " + cvm::to_str(force_k));
@@ -622,7 +620,7 @@ int colvarbias_restraint_k_moving::update()
       lambda = cvm::real(cvm::step_absolute()) / cvm::real(target_nsteps);
       cvm::real const force_k_old = force_k;
       force_k = starting_force_k + (target_force_k - starting_force_k)
-        * std::pow(lambda, force_k_exp);
+        * cvm::pow(lambda, force_k_exp);
       force_k_incr = force_k - force_k_old;
     }
   }
@@ -672,13 +670,13 @@ int colvarbias_restraint_k_moving::set_state_params(std::string const &conf)
   colvarbias_restraint::set_state_params(conf);
 
   if (b_chg_force_k) {
-    //    cvm::log ("Reading the updated force constant from the restart.\n");
+    get_keyval(conf, "forceConstant", force_k, force_k,
-    if (!get_keyval(conf, "forceConstant", force_k, force_k))
+               colvarparse::parse_restart | colvarparse::parse_required);
-      cvm::error("Error: force constant is missing from the restart.\n");
+  }
-    if (is_enabled(f_cvb_output_acc_work)) {
+
-      if (!get_keyval(conf, "accumulatedWork", acc_work))
+  if (is_enabled(f_cvb_output_acc_work)) {
-        cvm::error("Error: accumulatedWork is missing from the restart.\n");
+    get_keyval(conf, "accumulatedWork", acc_work, acc_work,
-    }
+               colvarparse::parse_restart | colvarparse::parse_required);
   }
 
   return COLVARS_OK;
@@ -719,7 +717,8 @@ std::istream & colvarbias_restraint::read_state(std::istream &is)
        (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);
+               cvm::to_str(static_cast<size_t>(is.tellg()))+
+               " in stream.\n", INPUT_ERROR);
     is.clear();
     is.seekg(start_pos, std::ios::beg);
     is.setstate(std::ios::failbit);
@@ -729,7 +728,8 @@ std::istream & colvarbias_restraint::read_state(std::istream &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);
+               cvm::to_str(static_cast<size_t>(is.tellg()))+
+               " in stream.\n", INPUT_ERROR);
     is.clear();
     is.seekg(start_pos, std::ios::beg);
     is.setstate(std::ios::failbit);
@@ -740,7 +740,7 @@ std::istream & colvarbias_restraint::read_state(std::istream &is)
     cvm::log("brace = "+brace+"\n");
     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");
+               cvm::to_str(static_cast<size_t>(is.tellg()))+" in stream.\n");
     is.setstate(std::ios::failbit);
   }
 
@@ -787,11 +787,11 @@ int colvarbias_restraint_harmonic::init(std::string const &conf)
   colvarbias_restraint_k_moving::init(conf);
 
   for (size_t i = 0; i < num_variables(); i++) {
-    if (variables(i)->width != 1.0)
+    cvm::real const w = variables(i)->width;
-      cvm::log("The force constant for colvar \""+variables(i)->name+
+    cvm::log("The force constant for colvar \""+variables(i)->name+
-               "\" will be rescaled to "+
+             "\" will be rescaled to "+
-               cvm::to_str(force_k / (variables(i)->width * variables(i)->width))+
+             cvm::to_str(force_k/(w*w))+
-               " according to the specified width.\n");
+             " according to the specified width ("+cvm::to_str(w)+").\n");
   }
 
   return COLVARS_OK;
@@ -1014,7 +1014,7 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
                  INPUT_ERROR);
       return INPUT_ERROR;
     }
-    force_k = std::sqrt(lower_wall_k * upper_wall_k);
+    force_k = cvm::sqrt(lower_wall_k * upper_wall_k);
     // transform the two constants to relative values using gemetric mean as ref
     // to preserve force_k if provided as single parameter
     // (allow changing both via force_k)
@@ -1037,25 +1037,21 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
 
   if (lower_walls.size() > 0) {
     for (i = 0; i < num_variables(); i++) {
-      if (variables(i)->width != 1.0)
+      cvm::real const w = variables(i)->width;
-        cvm::log("The lower wall force constant for colvar \""+
+      cvm::log("The lower wall force constant for colvar \""+
-                 variables(i)->name+
+               variables(i)->name+"\" will be rescaled to "+
-                 "\" will be rescaled to "+
+               cvm::to_str(lower_wall_k * force_k / (w*w))+
-                 cvm::to_str(lower_wall_k * force_k /
+               " according to the specified width ("+cvm::to_str(w)+").\n");
-                             (variables(i)->width * variables(i)->width))+
-                 " according to the specified width.\n");
     }
   }
 
   if (upper_walls.size() > 0) {
     for (i = 0; i < num_variables(); i++) {
-      if (variables(i)->width != 1.0)
+      cvm::real const w = variables(i)->width;
-        cvm::log("The upper wall force constant for colvar \""+
+      cvm::log("The upper wall force constant for colvar \""+
-                 variables(i)->name+
+               variables(i)->name+"\" will be rescaled to "+
-                 "\" will be rescaled to "+
+               cvm::to_str(upper_wall_k * force_k / (w*w))+
-                 cvm::to_str(upper_wall_k * force_k /
+               " according to the specified width ("+cvm::to_str(w)+").\n");
-                             (variables(i)->width * variables(i)->width))+
-                 " according to the specified width.\n");
     }
   }
 
@@ -1225,11 +1221,11 @@ int colvarbias_restraint_linear::init(std::string const &conf)
                  INPUT_ERROR);
       return INPUT_ERROR;
     }
-    if (variables(i)->width != 1.0)
+    cvm::real const w = variables(i)->width;
-      cvm::log("The force constant for colvar \""+variables(i)->name+
+    cvm::log("The force constant for colvar \""+variables(i)->name+
-               "\" will be rescaled to "+
+             "\" will be rescaled to "+
-               cvm::to_str(force_k / variables(i)->width)+
+             cvm::to_str(force_k / w)+
-               " according to the specified width.\n");
+             " according to the specified width ("+cvm::to_str(w)+").\n");
   }
 
   return COLVARS_OK;
@@ -1367,6 +1363,7 @@ colvarbias_restraint_histogram::colvarbias_restraint_histogram(char const *key)
 int colvarbias_restraint_histogram::init(std::string const &conf)
 {
   colvarbias::init(conf);
+  enable(f_cvb_apply_force);
 
   get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary);
   get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary);
@@ -1390,7 +1387,7 @@ int colvarbias_restraint_histogram::init(std::string const &conf)
   cvm::real const nbins = (upper_boundary - lower_boundary) / width;
   int const nbins_round = (int)(nbins);
 
-  if (std::fabs(nbins - cvm::real(nbins_round)) > 1.0E-10) {
+  if (cvm::fabs(nbins - cvm::real(nbins_round)) > 1.0E-10) {
     cvm::log("Warning: grid interval ("+
              cvm::to_str(lower_boundary, cvm::cv_width, cvm::cv_prec)+" - "+
              cvm::to_str(upper_boundary, cvm::cv_width, cvm::cv_prec)+
@@ -1440,7 +1437,7 @@ int colvarbias_restraint_histogram::init(std::string const &conf)
     }
   }
   cvm::real const ref_integral = ref_p.sum() * width;
-  if (std::fabs(ref_integral - 1.0) > 1.0e-03) {
+  if (cvm::fabs(ref_integral - 1.0) > 1.0e-03) {
     cvm::log("Reference distribution not normalized, normalizing to unity.\n");
     ref_p /= ref_integral;
   }
@@ -1471,7 +1468,7 @@ int colvarbias_restraint_histogram::update()
     vector_size += variables(icv)->value().size();
   }
 
-  cvm::real const norm = 1.0/(std::sqrt(2.0*PI)*gaussian_width*vector_size);
+  cvm::real const norm = 1.0/(cvm::sqrt(2.0*PI)*gaussian_width*vector_size);
 
   // calculate the histogram
   p.reset();
@@ -1482,7 +1479,7 @@ int colvarbias_restraint_histogram::update()
       size_t igrid;
       for (igrid = 0; igrid < p.size(); igrid++) {
         cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
-        p[igrid] += norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
+        p[igrid] += norm * cvm::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
                                     (2.0 * gaussian_width * gaussian_width));
       }
     } else if (cv.type() == colvarvalue::type_vector) {
@@ -1492,7 +1489,7 @@ int colvarbias_restraint_histogram::update()
         size_t igrid;
         for (igrid = 0; igrid < p.size(); igrid++) {
           cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
-          p[igrid] += norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
+          p[igrid] += norm * cvm::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
                                       (2.0 * gaussian_width * gaussian_width));
         }
       }
@@ -1523,7 +1520,7 @@ int colvarbias_restraint_histogram::update()
       for (igrid = 0; igrid < p.size(); igrid++) {
         cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
         force += force_k_cv * p_diff[igrid] *
-          norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
+          norm * cvm::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
                           (2.0 * gaussian_width * gaussian_width)) *
           (-1.0 * (x_grid - cv_value) / (gaussian_width * gaussian_width));
       }
@@ -1536,7 +1533,7 @@ int colvarbias_restraint_histogram::update()
         for (igrid = 0; igrid < p.size(); igrid++) {
           cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
           force += force_k_cv * p_diff[igrid] *
-            norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
+            norm * cvm::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
                             (2.0 * gaussian_width * gaussian_width)) *
             (-1.0 * (x_grid - cv_value) / (gaussian_width * gaussian_width));
         }
@@ -1550,7 +1547,7 @@ int colvarbias_restraint_histogram::update()
 }
 
 
-std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os)
+int colvarbias_restraint_histogram::write_output_files()
 {
   if (b_write_histogram) {
     std::string file_name(cvm::output_prefix()+"."+this->name+".hist.dat");
@@ -1558,6 +1555,9 @@ std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os)
     *os << "# " << cvm::wrap_string(variables(0)->name, cvm::cv_width)
         << "  " << "p(" << cvm::wrap_string(variables(0)->name, cvm::cv_width-3)
         << ")\n";
+
+    os->setf(std::ios::fixed, std::ios::floatfield);
+
     size_t igrid;
     for (igrid = 0; igrid < p.size(); igrid++) {
       cvm::real const x_grid = (lower_boundary + (igrid+1)*width);
@@ -1572,13 +1572,7 @@ std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os)
     }
     cvm::proxy->close_output_stream(file_name);
   }
-  return os;
+  return COLVARS_OK;
-}
-
-
-std::istream & colvarbias_restraint_histogram::read_restart(std::istream &is)
-{
-  return is;
 }
 
 

lib/colvars/colvarbias_restraint.h

@@ -132,7 +132,7 @@ protected:
 
   /// \brief Number of steps required to reach the target force constant
   /// or restraint centers
-  long target_nsteps;
+  cvm::step_number target_nsteps;
 
   /// \brief Accumulated work (computed when outputAccumulatedWork == true)
   cvm::real acc_work;
@@ -328,8 +328,7 @@ public:
 
   virtual int update();
 
-  virtual std::istream & read_restart(std::istream &is);
+  virtual int write_output_files();
-  virtual std::ostream & write_restart(std::ostream &os);
   virtual std::ostream & write_traj_label(std::ostream &os);
   virtual std::ostream & write_traj(std::ostream &os);
 

lib/colvars/colvarcomp.cpp

@@ -20,7 +20,8 @@ colvar::cvc::cvc()
     b_periodic(false),
     b_try_scalable(true)
 {
-  init_cvc_requires();
+  description = "uninitialized colvar component";
+  init_dependencies();
   sup_coeff = 1.0;
   period = 0.0;
   wrap_center = 0.0;
@@ -33,7 +34,8 @@ colvar::cvc::cvc(std::string const &conf)
     b_periodic(false),
     b_try_scalable(true)
 {
-  init_cvc_requires();
+  description = "uninitialized colvar component";
+  init_dependencies();
   sup_coeff = 1.0;
   period = 0.0;
   wrap_center = 0.0;
@@ -176,6 +178,100 @@ cvm::atom_group *colvar::cvc::parse_group(std::string const &conf,
 }
 
 
+int colvar::cvc::init_dependencies() {
+  size_t i;
+  // Initialize static array once and for all
+  if (features().size() == 0) {
+    for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
+      modify_features().push_back(new feature);
+    }
+
+    init_feature(f_cvc_active, "active", f_type_dynamic);
+//     The dependency below may become useful if we use dynamic atom groups
+//     require_feature_children(f_cvc_active, f_ag_active);
+
+    init_feature(f_cvc_scalar, "scalar", f_type_static);
+
+    init_feature(f_cvc_gradient, "gradient", f_type_dynamic);
+
+    init_feature(f_cvc_explicit_gradient, "explicit gradient", f_type_static);
+    require_feature_children(f_cvc_explicit_gradient, f_ag_explicit_gradient);
+
+    init_feature(f_cvc_inv_gradient, "inverse gradient", f_type_dynamic);
+    require_feature_self(f_cvc_inv_gradient, f_cvc_gradient);
+
+    init_feature(f_cvc_debug_gradient, "debug gradient", f_type_user);
+    require_feature_self(f_cvc_debug_gradient, f_cvc_gradient);
+    require_feature_self(f_cvc_debug_gradient, f_cvc_explicit_gradient);
+
+    init_feature(f_cvc_Jacobian, "Jacobian derivative", f_type_dynamic);
+    require_feature_self(f_cvc_Jacobian, f_cvc_inv_gradient);
+
+    init_feature(f_cvc_com_based, "depends on group centers of mass", f_type_static);
+
+    init_feature(f_cvc_pbc_minimum_image, "use minimum-image distances with PBCs", f_type_user);
+
+    // Compute total force on first site only to avoid unwanted
+    // coupling to other colvars (see e.g. Ciccotti et al., 2005)
+    init_feature(f_cvc_one_site_total_force, "compute total force from one group", f_type_user);
+    require_feature_self(f_cvc_one_site_total_force, f_cvc_com_based);
+
+    init_feature(f_cvc_scalable, "scalable calculation", f_type_static);
+    require_feature_self(f_cvc_scalable, f_cvc_scalable_com);
+
+    init_feature(f_cvc_scalable_com, "scalable calculation of centers of mass", f_type_static);
+    require_feature_self(f_cvc_scalable_com, f_cvc_com_based);
+
+
+    // TODO only enable this when f_ag_scalable can be turned on for a pre-initialized group
+    // require_feature_children(f_cvc_scalable, f_ag_scalable);
+    // require_feature_children(f_cvc_scalable_com, f_ag_scalable_com);
+
+    // check that everything is initialized
+    for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
+      if (is_not_set(i)) {
+        cvm::error("Uninitialized feature " + cvm::to_str(i) + " in " + description);
+      }
+    }
+  }
+
+  // Initialize feature_states for each instance
+  // default as available, not enabled
+  // except dynamic features which default as unavailable
+  feature_states.reserve(f_cvc_ntot);
+  for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
+    bool avail = is_dynamic(i) ? false : true;
+    feature_states.push_back(feature_state(avail, false));
+  }
+
+  // Features that are implemented by all cvcs by default
+  // Each cvc specifies what other features are available
+  feature_states[f_cvc_active].available = true;
+  feature_states[f_cvc_gradient].available = true;
+
+  // CVCs are enabled from the start - get disabled based on flags
+  enable(f_cvc_active);
+  // feature_states[f_cvc_active].enabled = true;
+
+  // Explicit gradients are implemented in mosts CVCs. Exceptions must be specified explicitly.
+  // feature_states[f_cvc_explicit_gradient].enabled = true;
+  enable(f_cvc_explicit_gradient);
+
+  // Use minimum-image distances by default
+  // feature_states[f_cvc_pbc_minimum_image].enabled = true;
+  enable(f_cvc_pbc_minimum_image);
+
+  // 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;
+
+  return COLVARS_OK;
+}
+
+
 int colvar::cvc::setup()
 {
   description = "cvc " + name;
@@ -192,6 +288,7 @@ colvar::cvc::~cvc()
   }
 }
 
+
 void colvar::cvc::read_data()
 {
   size_t ig;
@@ -214,6 +311,66 @@ void colvar::cvc::read_data()
 }
 
 
+std::vector<std::vector<int> > colvar::cvc::get_atom_lists()
+{
+  std::vector<std::vector<int> > lists;
+
+  std::vector<cvm::atom_group *>::iterator agi = atom_groups.begin();
+  for ( ; agi != atom_groups.end(); ++agi) {
+    (*agi)->create_sorted_ids();
+    lists.push_back((*agi)->sorted_ids());
+    if ((*agi)->is_enabled(f_ag_fitting_group) && (*agi)->is_enabled(f_ag_fit_gradients)) {
+      cvm::atom_group &fg = *((*agi)->fitting_group);
+      fg.create_sorted_ids();
+      lists.push_back(fg.sorted_ids());
+    }
+  }
+  return lists;
+}
+
+
+void colvar::cvc::collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients)
+{
+  // Coefficient: d(a * x^n) = a * n * x^(n-1) * dx
+  cvm::real coeff = sup_coeff * cvm::real(sup_np) *
+    cvm::integer_power(value().real_value, sup_np-1);
+
+  for (size_t j = 0; j < atom_groups.size(); j++) {
+
+    cvm::atom_group &ag = *(atom_groups[j]);
+
+    // If necessary, apply inverse rotation to get atomic
+    // gradient in the laboratory frame
+    if (ag.b_rotate) {
+      cvm::rotation const rot_inv = ag.rot.inverse();
+
+      for (size_t k = 0; k < ag.size(); k++) {
+        size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
+                                    ag[k].id) - atom_ids.begin();
+        atomic_gradients[a] += coeff * rot_inv.rotate(ag[k].grad);
+      }
+
+    } else {
+
+      for (size_t k = 0; k < ag.size(); k++) {
+        size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
+                                    ag[k].id) - atom_ids.begin();
+        atomic_gradients[a] += coeff * ag[k].grad;
+      }
+    }
+    if (ag.is_enabled(f_ag_fitting_group) && ag.is_enabled(f_ag_fit_gradients)) {
+      cvm::atom_group const &fg = *(ag.fitting_group);
+      for (size_t k = 0; k < fg.size(); k++) {
+        size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
+                                    fg[k].id) - atom_ids.begin();
+        // fit gradients are in the unrotated (simulation) frame
+        atomic_gradients[a] += coeff * fg.fit_gradients[k];
+      }
+    }
+  }
+}
+
+
 void colvar::cvc::calc_force_invgrads()
 {
   cvm::error("Error: calculation of inverse gradients is not implemented "
@@ -306,8 +463,8 @@ void colvar::cvc::debug_gradients()
         cvm::log("dx(interp) = "+cvm::to_str(dx_pred,
                               21, 14)+"\n");
         cvm::log("|dx(actual) - dx(interp)|/|dx(actual)| = "+
-                  cvm::to_str(std::fabs(x_1 - x_0 - dx_pred) /
+                  cvm::to_str(cvm::fabs(x_1 - x_0 - dx_pred) /
-                              std::fabs(x_1 - x_0), 12, 5)+"\n");
+                              cvm::fabs(x_1 - x_0), 12, 5)+"\n");
       }
     }
 
@@ -341,8 +498,8 @@ void colvar::cvc::debug_gradients()
           cvm::log("dx(interp) = "+cvm::to_str (dx_pred,
                                 21, 14)+"\n");
           cvm::log ("|dx(actual) - dx(interp)|/|dx(actual)| = "+
-                    cvm::to_str(std::fabs (x_1 - x_0 - dx_pred) /
+                    cvm::to_str(cvm::fabs (x_1 - x_0 - dx_pred) /
-                                std::fabs (x_1 - x_0),
+                                cvm::fabs (x_1 - x_0),
                                 12, 5)+
                     ".\n");
         }
@@ -378,7 +535,7 @@ colvarvalue colvar::cvc::dist2_rgrad(colvarvalue const &x1,
 }
 
 
-void colvar::cvc::wrap(colvarvalue &x) const
+void colvar::cvc::wrap(colvarvalue &x_unwrapped) const
 {
   return;
 }

lib/colvars/colvarcomp.h

@@ -27,12 +27,12 @@
 
 /// \brief Colvar component (base class for collective variables)
 ///
-/// A \link cvc \endlink object (or an object of a
+/// A \link colvar::cvc \endlink object (or an object of a
 /// cvc-derived class) implements the calculation of a collective
 /// variable, its gradients and any other related physical quantities
 /// that depend on microscopic degrees of freedom.
 ///
-/// No restriction is set to what kind of calculation a \link cvc \endlink
+/// No restriction is set to what kind of calculation a \link colvar::cvc \endlink
 /// object performs (usually an analytical function of atomic coordinates).
 /// The only constraints are that: \par
 ///
@@ -42,9 +42,9 @@
 ///   alike, and allows an automatic selection of the applicable algorithms.
 ///
 /// - The object provides an implementation \link apply_force() \endlink to
-///   apply forces to atoms.  Typically, one or more \link cvm::atom_group
+///   apply forces to atoms.  Typically, one or more \link colvarmodule::atom_group
 ///   \endlink objects are used, but this is not a requirement for as long as
-///   the \link cvc \endlink object communicates with the simulation program.
+///   the \link colvar::cvc \endlink object communicates with the simulation program.
 ///
 /// <b> If you wish to implement a new collective variable component, you
 /// should write your own class by inheriting directly from \link
@@ -75,9 +75,9 @@ public:
   /// \brief Description of the type of collective variable
   ///
   /// Normally this string is set by the parent \link colvar \endlink
-  /// object within its constructor, when all \link cvc \endlink
+  /// object within its constructor, when all \link colvar::cvc \endlink
   /// objects are initialized; therefore the main "config string"
-  /// constructor does not need to define it.  If a \link cvc
+  /// constructor does not need to define it.  If a \link colvar::cvc
   /// \endlink is initialized and/or a different constructor is used,
   /// this variable definition should be set within the constructor.
   std::string function_type;
@@ -109,6 +109,9 @@ public:
   /// cvc \endlink
   virtual int init(std::string const &conf);
 
+  /// \brief Initialize dependency tree
+  virtual int init_dependencies();
+
   /// \brief Within the constructor, make a group parse its own
   /// options from the provided configuration string
   /// Returns reference to new group
@@ -122,7 +125,7 @@ public:
   /// \brief After construction, set data related to dependency handling
   int setup();
 
-  /// \brief Default constructor (used when \link cvc \endlink
+  /// \brief Default constructor (used when \link colvar::cvc \endlink
   /// objects are declared within other ones)
   cvc();
 
@@ -133,7 +136,7 @@ public:
   static std::vector<feature *> cvc_features;
 
   /// \brief Implementation of the feature list accessor for colvar
-  virtual const std::vector<feature *> &features()
+  virtual const std::vector<feature *> &features() const
   {
     return cvc_features;
   }
@@ -148,6 +151,9 @@ public:
     cvc_features.clear();
   }
 
+  /// \brief Get vector of vectors of atom IDs for all atom groups
+  virtual std::vector<std::vector<int> > get_atom_lists();
+
   /// \brief Obtain data needed for the calculation for the backend
   virtual void read_data();
 
@@ -164,6 +170,10 @@ public:
   /// \brief Calculate finite-difference gradients alongside the analytical ones, for each Cartesian component
   virtual void debug_gradients();
 
+  /// \brief Calculate atomic gradients and add them to the corresponding item in gradient vector
+  /// May be overridden by CVCs that do not store their gradients in the classic way, see dihedPC
+  virtual void collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients);
+
   /// \brief Calculate the total force from the system using the
   /// inverse atomic gradients
   virtual void calc_force_invgrads();
@@ -237,7 +247,7 @@ public:
                                   colvarvalue const &x2) const;
 
   /// \brief Wrap value (for periodic/symmetric cvcs)
-  virtual void wrap(colvarvalue &x) const;
+  virtual void wrap(colvarvalue &x_unwrapped) const;
 
   /// \brief Pointers to all atom groups, to let colvars collect info
   /// e.g. atomic gradients
@@ -246,7 +256,7 @@ public:
   /// \brief Store a pointer to new atom group, and list as child for dependencies
   inline void register_atom_group(cvm::atom_group *ag) {
     atom_groups.push_back(ag);
-    add_child((colvardeps *) ag);
+    add_child(ag);
   }
 
   /// \brief Whether or not this CVC will be computed in parallel whenever possible
@@ -415,7 +425,7 @@ public:
   virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
                                   colvarvalue const &x2) const;
   /// \brief Redefined to make use of the user-provided period
-  virtual void wrap(colvarvalue &x) const;
+  virtual void wrap(colvarvalue &x_unwrapped) const;
 };
 
 
@@ -474,7 +484,7 @@ public:
   virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
                                   colvarvalue const &x2) const;
   /// Redefined to handle the 2*PI periodicity
-  virtual void wrap(colvarvalue &x) const;
+  virtual void wrap(colvarvalue &x_unwrapped) const;
 };
 
 
@@ -559,6 +569,35 @@ public:
 
 
 
+/// \brief Colvar component:  dipole magnitude of a molecule
+class colvar::dipole_magnitude
+  : public colvar::cvc
+{
+protected:
+  /// Dipole atom group
+  cvm::atom_group  *atoms;
+  cvm::atom_pos dipoleV;
+public:
+  /// Initialize by parsing the configuration
+  dipole_magnitude (std::string const &conf);
+  dipole_magnitude (cvm::atom const &a1);
+  dipole_magnitude();
+  virtual inline ~dipole_magnitude() {}
+  virtual void calc_value();
+  virtual void calc_gradients();
+  //virtual void calc_force_invgrads();
+  //virtual void calc_Jacobian_derivative();
+  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: Radius of gyration of an atom group
 /// (colvarvalue::type_scalar type, range [0:*))
 class colvar::gyration
@@ -818,7 +857,7 @@ public:
   virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
                                   colvarvalue const &x2) const;
   /// Redefined to handle the 2*PI periodicity
-  virtual void wrap(colvarvalue &x) const;
+  virtual void wrap(colvarvalue &x_unwrapped) const;
 };
 
 
@@ -1002,7 +1041,7 @@ public:
          cvm::atom const &donor,
          cvm::real r0, int en, int ed);
   h_bond();
-  virtual ~h_bond();
+  virtual ~h_bond() {}
   virtual void calc_value();
   virtual void calc_gradients();
   virtual void apply_force(colvarvalue const &force);
@@ -1090,6 +1129,8 @@ public:
   virtual ~alpha_angles();
   void calc_value();
   void calc_gradients();
+  /// Re-implementation of cvc::collect_gradients() to carry over atomic gradients of sub-cvcs
+  void collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients);
   void apply_force(colvarvalue const &force);
   virtual cvm::real dist2(colvarvalue const &x1,
                           colvarvalue const &x2) const;
@@ -1120,6 +1161,8 @@ public:
   virtual  ~dihedPC();
   void calc_value();
   void calc_gradients();
+  /// Re-implementation of cvc::collect_gradients() to carry over atomic gradients of sub-cvcs
+  void collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients);
   void apply_force(colvarvalue const &force);
   virtual cvm::real dist2(colvarvalue const &x1,
                           colvarvalue const &x2) const;
@@ -1159,6 +1202,7 @@ public:
 
   orientation(std::string const &conf);
   orientation();
+  virtual int init(std::string const &conf);
   virtual ~orientation() {}
   virtual void calc_value();
   virtual void calc_gradients();
@@ -1183,6 +1227,7 @@ public:
 
   orientation_angle(std::string const &conf);
   orientation_angle();
+  virtual int init(std::string const &conf);
   virtual ~orientation_angle() {}
   virtual void calc_value();
   virtual void calc_gradients();
@@ -1207,6 +1252,7 @@ public:
 
   orientation_proj(std::string const &conf);
   orientation_proj();
+  virtual int init(std::string const &conf);
   virtual ~orientation_proj() {}
   virtual void calc_value();
   virtual void calc_gradients();
@@ -1234,6 +1280,7 @@ public:
 
   tilt(std::string const &conf);
   tilt();
+  virtual int init(std::string const &conf);
   virtual ~tilt() {}
   virtual void calc_value();
   virtual void calc_gradients();
@@ -1261,6 +1308,7 @@ public:
 
   spin_angle(std::string const &conf);
   spin_angle();
+  virtual int init(std::string const &conf);
   virtual ~spin_angle() {}
   virtual void calc_value();
   virtual void calc_gradients();
@@ -1275,7 +1323,7 @@ public:
   virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
                                   colvarvalue const &x2) const;
   /// Redefined to handle the 2*PI periodicity
-  virtual void wrap(colvarvalue &x) const;
+  virtual void wrap(colvarvalue &x_unwrapped) const;
 };
 
 

lib/colvars/colvarcomp_angles.cpp

@@ -11,9 +11,6 @@
 #include "colvar.h"
 #include "colvarcomp.h"
 
-#include <cmath>
-
-
 
 colvar::angle::angle(std::string const &conf)
   : cvc(conf)
@@ -77,14 +74,14 @@ void colvar::angle::calc_value()
 
   cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
 
-  x.real_value = (180.0/PI) * std::acos(cos_theta);
+  x.real_value = (180.0/PI) * cvm::acos(cos_theta);
 }
 
 
 void colvar::angle::calc_gradients()
 {
   cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
-  cvm::real const dxdcos = -1.0 / std::sqrt(1.0 - cos_theta*cos_theta);
+  cvm::real const dxdcos = -1.0 / cvm::sqrt(1.0 - cos_theta*cos_theta);
 
   dxdr1 = (180.0/PI) * dxdcos *
     (1.0/r21l) * ( r23/r23l + (-1.0) * cos_theta * r21/r21l );
@@ -126,7 +123,7 @@ void colvar::angle::calc_Jacobian_derivative()
   // det(J) = (2 pi) r^2 * sin(theta)
   // hence Jd = cot(theta)
   const cvm::real theta = x.real_value * PI / 180.0;
-  jd = PI / 180.0 * (theta != 0.0 ? std::cos(theta) / std::sin(theta) : 0.0);
+  jd = PI / 180.0 * (theta != 0.0 ? cvm::cos(theta) / cvm::sin(theta) : 0.0);
 }
 
 
@@ -202,7 +199,7 @@ void colvar::dipole_angle::calc_value()
 
   cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
 
-  x.real_value = (180.0/PI) * std::acos(cos_theta);
+  x.real_value = (180.0/PI) * cvm::acos(cos_theta);
 }
 
 //to be implemented
@@ -212,7 +209,7 @@ void colvar::dipole_angle::calc_value()
 void colvar::dipole_angle::calc_gradients()
 {
   cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
-  cvm::real const dxdcos = -1.0 / std::sqrt(1.0 - cos_theta*cos_theta);
+  cvm::real const dxdcos = -1.0 / cvm::sqrt(1.0 - cos_theta*cos_theta);
 
   dxdr1 = (180.0/PI) * dxdcos *
   (1.0/r21l)* (r23/r23l + (-1.0) * cos_theta * r21/r21l );
@@ -346,7 +343,7 @@ void colvar::dihedral::calc_value()
   cvm::real const cos_phi = n1 * n2;
   cvm::real const sin_phi = n1 * r34 * r23.norm();
 
-  x.real_value = (180.0/PI) * std::atan2(sin_phi, cos_phi);
+  x.real_value = (180.0/PI) * cvm::atan2(sin_phi, cos_phi);
   this->wrap(x);
 }
 
@@ -368,7 +365,7 @@ void colvar::dihedral::calc_gradients()
   rB = 1.0/rB;
   B *= rB;
 
-  if (std::fabs(sin_phi) > 0.1) {
+  if (cvm::fabs(sin_phi) > 0.1) {
     rA = 1.0/rA;
     A *= rA;
     cvm::rvector const dcosdA = rA*(cos_phi*A-B);
@@ -440,8 +437,8 @@ void colvar::dihedral::calc_force_invgrads()
   cvm::real const dot1 = u23 * u12;
   cvm::real const dot4 = u23 * u34;
 
-  cvm::real const fact1 = d12 * std::sqrt(1.0 - dot1 * dot1);
+  cvm::real const fact1 = d12 * cvm::sqrt(1.0 - dot1 * dot1);
-  cvm::real const fact4 = d34 * std::sqrt(1.0 - dot4 * dot4);
+  cvm::real const fact4 = d34 * cvm::sqrt(1.0 - dot4 * dot4);
 
   group1->read_total_forces();
   if (is_enabled(f_cvc_one_site_total_force)) {
@@ -508,19 +505,17 @@ colvarvalue colvar::dihedral::dist2_rgrad(colvarvalue const &x1,
 }
 
 
-void colvar::dihedral::wrap(colvarvalue &x) const
+void colvar::dihedral::wrap(colvarvalue &x_unwrapped) const
 {
-  if ((x.real_value - wrap_center) >= 180.0) {
+  if ((x_unwrapped.real_value - wrap_center) >= 180.0) {
-    x.real_value -= 360.0;
+    x_unwrapped.real_value -= 360.0;
     return;
   }
 
-  if ((x.real_value - wrap_center) < -180.0) {
+  if ((x_unwrapped.real_value - wrap_center) < -180.0) {
-    x.real_value += 360.0;
+    x_unwrapped.real_value += 360.0;
     return;
   }
-
-  return;
 }
 
 
@@ -548,8 +543,8 @@ void colvar::polar_theta::calc_value()
   cvm::rvector pos = atoms->center_of_mass();
   r = atoms->center_of_mass().norm();
   // Internal values of theta and phi are radians
-  theta = (r > 0.) ? std::acos(pos.z / r) : 0.;
+  theta = (r > 0.) ? cvm::acos(pos.z / r) : 0.;
-  phi = std::atan2(pos.y, pos.x);
+  phi = cvm::atan2(pos.y, pos.x);
   x.real_value = (180.0/PI) * theta;
 }
 
@@ -560,9 +555,9 @@ void colvar::polar_theta::calc_gradients()
     atoms->set_weighted_gradient(cvm::rvector(0., 0., 0.));
   else
     atoms->set_weighted_gradient(cvm::rvector(
-      (180.0/PI) *  std::cos(theta) * std::cos(phi) / r,
+      (180.0/PI) *  cvm::cos(theta) * cvm::cos(phi) / r,
-      (180.0/PI) *  std::cos(theta) * std::sin(phi) / r,
+      (180.0/PI) *  cvm::cos(theta) * cvm::sin(phi) / r,
-      (180.0/PI) * -std::sin(theta) / r));
+      (180.0/PI) * -cvm::sin(theta) / r));
 }
 
 
@@ -602,8 +597,8 @@ void colvar::polar_phi::calc_value()
   cvm::rvector pos = atoms->center_of_mass();
   r = atoms->center_of_mass().norm();
   // Internal values of theta and phi are radians
-  theta = (r > 0.) ? std::acos(pos.z / r) : 0.;
+  theta = (r > 0.) ? cvm::acos(pos.z / r) : 0.;
-  phi = std::atan2(pos.y, pos.x);
+  phi = cvm::atan2(pos.y, pos.x);
   x.real_value = (180.0/PI) * phi;
 }
 
@@ -611,8 +606,8 @@ void colvar::polar_phi::calc_value()
 void colvar::polar_phi::calc_gradients()
 {
   atoms->set_weighted_gradient(cvm::rvector(
-    (180.0/PI) * -std::sin(phi) / (r*std::sin(theta)),
+    (180.0/PI) * -cvm::sin(phi) / (r*cvm::sin(theta)),
-    (180.0/PI) *  std::cos(phi) / (r*std::sin(theta)),
+    (180.0/PI) *  cvm::cos(phi) / (r*cvm::sin(theta)),
     0.));
 }
 
@@ -653,15 +648,15 @@ colvarvalue colvar::polar_phi::dist2_rgrad(colvarvalue const &x1,
 }
 
 
-void colvar::polar_phi::wrap(colvarvalue &x) const
+void colvar::polar_phi::wrap(colvarvalue &x_unwrapped) const
 {
-  if ((x.real_value - wrap_center) >= 180.0) {
+  if ((x_unwrapped.real_value - wrap_center) >= 180.0) {
-    x.real_value -= 360.0;
+    x_unwrapped.real_value -= 360.0;
     return;
   }
 
-  if ((x.real_value - wrap_center) < -180.0) {
+  if ((x_unwrapped.real_value - wrap_center) < -180.0) {
-    x.real_value += 360.0;
+    x_unwrapped.real_value += 360.0;
     return;
   }
 

lib/colvars/colvarcomp_coordnums.cpp

@@ -7,8 +7,6 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
-#include <cmath>
-
 #include "colvarmodule.h"
 #include "colvarparse.h"
 #include "colvaratoms.h"
@@ -102,6 +100,12 @@ colvar::coordnum::coordnum(std::string const &conf)
   group1 = parse_group(conf, "group1");
   group2 = parse_group(conf, "group2");
 
+  if (group1 == NULL || group2 == NULL) {
+    cvm::error("Error: failed to initialize atom groups.\n",
+                INPUT_ERROR);
+    return;
+  }
+
   if (int atom_number = cvm::atom_group::overlap(*group1, *group2)) {
     cvm::error("Error: group1 and group2 share a common atom (number: " +
                cvm::to_str(atom_number) + ")\n", INPUT_ERROR);
@@ -408,12 +412,6 @@ colvar::h_bond::h_bond()
 }
 
 
-colvar::h_bond::~h_bond()
-{
-  delete atom_groups[0];
-}
-
-
 void colvar::h_bond::calc_value()
 {
   int const flags = coordnum::ef_null;
@@ -655,8 +653,6 @@ colvar::groupcoordnum::groupcoordnum()
 
 void colvar::groupcoordnum::calc_value()
 {
-  cvm::rvector const r0_vec(0.0); // TODO enable the flag?
-
   // create fake atoms to hold the com coordinates
   cvm::atom group1_com_atom;
   cvm::atom group2_com_atom;
@@ -680,8 +676,6 @@ void colvar::groupcoordnum::calc_value()
 
 void colvar::groupcoordnum::calc_gradients()
 {
-  cvm::rvector const r0_vec(0.0); // TODO enable the flag?
-
   cvm::atom group1_com_atom;
   cvm::atom group2_com_atom;
   group1_com_atom.pos = group1->center_of_mass();

lib/colvars/colvarcomp_distances.cpp

@@ -7,8 +7,6 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
-#include <cmath>
-
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarparse.h"
@@ -102,7 +100,7 @@ colvar::distance_vec::distance_vec(std::string const &conf)
 {
   function_type = "distance_vec";
   enable(f_cvc_com_based);
-  enable(f_cvc_implicit_gradient);
+  disable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_3vector);
 }
 
@@ -112,7 +110,7 @@ colvar::distance_vec::distance_vec()
 {
   function_type = "distance_vec";
   enable(f_cvc_com_based);
-  enable(f_cvc_implicit_gradient);
+  disable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_3vector);
 }
 
@@ -320,7 +318,7 @@ cvm::real colvar::distance_z::dist2(colvarvalue const &x1,
 {
   cvm::real diff = x1.real_value - x2.real_value;
   if (b_periodic) {
-    cvm::real shift = std::floor(diff/period + 0.5);
+    cvm::real shift = cvm::floor(diff/period + 0.5);
     diff -= shift * period;
   }
   return diff * diff;
@@ -332,7 +330,7 @@ colvarvalue colvar::distance_z::dist2_lgrad(colvarvalue const &x1,
 {
   cvm::real diff = x1.real_value - x2.real_value;
   if (b_periodic) {
-    cvm::real shift = std::floor(diff/period + 0.5);
+    cvm::real shift = cvm::floor(diff/period + 0.5);
     diff -= shift * period;
   }
   return 2.0 * diff;
@@ -344,22 +342,23 @@ colvarvalue colvar::distance_z::dist2_rgrad(colvarvalue const &x1,
 {
   cvm::real diff = x1.real_value - x2.real_value;
   if (b_periodic) {
-    cvm::real shift = std::floor(diff/period + 0.5);
+    cvm::real shift = cvm::floor(diff/period + 0.5);
     diff -= shift * period;
   }
   return (-2.0) * diff;
 }
 
 
-void colvar::distance_z::wrap(colvarvalue &x) const
+void colvar::distance_z::wrap(colvarvalue &x_unwrapped) 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);
+  cvm::real shift =
-  x.real_value -= shift * period;
+    cvm::floor((x_unwrapped.real_value - wrap_center) / period + 0.5);
+  x_unwrapped.real_value -= shift * period;
   return;
 }
 
@@ -481,7 +480,7 @@ colvar::distance_dir::distance_dir(std::string const &conf)
 {
   function_type = "distance_dir";
   enable(f_cvc_com_based);
-  enable(f_cvc_implicit_gradient);
+  disable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_unit3vector);
 }
 
@@ -491,7 +490,7 @@ colvar::distance_dir::distance_dir()
 {
   function_type = "distance_dir";
   enable(f_cvc_com_based);
-  enable(f_cvc_implicit_gradient);
+  disable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_unit3vector);
 }
 
@@ -629,7 +628,7 @@ void colvar::distance_inv::calc_value()
   }
 
   x.real_value *= 1.0 / cvm::real(group1->size() * group2->size());
-  x.real_value = std::pow(x.real_value, -1.0/cvm::real(exponent));
+  x.real_value = cvm::pow(x.real_value, -1.0/cvm::real(exponent));
 
   cvm::real const dxdsum = (-1.0/(cvm::real(exponent))) *
     cvm::integer_power(x.real_value, exponent+1) /
@@ -671,7 +670,7 @@ colvar::distance_pairs::distance_pairs(std::string const &conf)
   group2 = parse_group(conf, "group2");
 
   x.type(colvarvalue::type_vector);
-  enable(f_cvc_implicit_gradient);
+  disable(f_cvc_explicit_gradient);
   x.vector1d_value.resize(group1->size() * group2->size());
 }
 
@@ -679,7 +678,7 @@ colvar::distance_pairs::distance_pairs(std::string const &conf)
 colvar::distance_pairs::distance_pairs()
 {
   function_type = "distance_pairs";
-  enable(f_cvc_implicit_gradient);
+  disable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_vector);
 }
 
@@ -747,6 +746,63 @@ void colvar::distance_pairs::apply_force(colvarvalue const &force)
 
 
 
+colvar::dipole_magnitude::dipole_magnitude(std::string const &conf)
+  : cvc(conf)
+{
+  function_type = "dipole_magnitude";
+  atoms = parse_group(conf, "atoms");
+  init_total_force_params(conf);
+  x.type(colvarvalue::type_scalar);
+}
+
+
+colvar::dipole_magnitude::dipole_magnitude(cvm::atom const &a1)
+{
+  atoms = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
+  register_atom_group(atoms);
+  x.type(colvarvalue::type_scalar);
+}
+
+
+colvar::dipole_magnitude::dipole_magnitude()
+{
+  function_type = "dipole_magnitude";
+  x.type(colvarvalue::type_scalar);
+}
+
+
+void colvar::dipole_magnitude::calc_value()
+{
+  cvm::atom_pos const atomsCom = atoms->center_of_mass();
+  atoms->calc_dipole(atomsCom);
+  dipoleV = atoms->dipole();
+  x.real_value = dipoleV.norm();
+}
+
+
+void colvar::dipole_magnitude::calc_gradients()
+{
+  cvm::real const aux1 = atoms->total_charge/atoms->total_mass;
+  cvm::atom_pos const dipVunit = dipoleV.unit();
+
+  for (cvm::atom_iter ai = atoms->begin(); ai != atoms->end(); ai++) {
+    ai->grad = (ai->charge - aux1*ai->mass) * dipVunit;
+  }
+}
+
+
+void colvar::dipole_magnitude::apply_force(colvarvalue const &force)
+{
+  if (!atoms->noforce) {
+    atoms->apply_colvar_force(force.real_value);
+  }
+}
+
+
+simple_scalar_dist_functions(dipole_magnitude)
+
+
+
 colvar::gyration::gyration(std::string const &conf)
   : cvc(conf)
 {
@@ -782,7 +838,7 @@ void colvar::gyration::calc_value()
   for (cvm::atom_iter ai = atoms->begin(); ai != atoms->end(); ai++) {
     x.real_value += (ai->pos).norm2();
   }
-  x.real_value = std::sqrt(x.real_value / cvm::real(atoms->size()));
+  x.real_value = cvm::sqrt(x.real_value / cvm::real(atoms->size()));
 }
 
 
@@ -1029,7 +1085,7 @@ void colvar::rmsd::calc_value()
     x.real_value += ((*atoms)[ia].pos - ref_pos[ia]).norm2();
   }
   x.real_value /= cvm::real(atoms->size()); // MSD
-  x.real_value = std::sqrt(x.real_value);
+  x.real_value = cvm::sqrt(x.real_value);
 }
 
 
@@ -1405,7 +1461,7 @@ void colvar::eigenvector::calc_Jacobian_derivative()
     }
   }
 
-  jd.real_value = sum * std::sqrt(eigenvec_invnorm2);
+  jd.real_value = sum * cvm::sqrt(eigenvec_invnorm2);
 }
 
 
@@ -1436,7 +1492,7 @@ colvar::cartesian::cartesian(std::string const &conf)
   }
 
   x.type(colvarvalue::type_vector);
-  enable(f_cvc_implicit_gradient);
+  disable(f_cvc_explicit_gradient);
   x.vector1d_value.resize(atoms->size() * axes.size());
 }
 

lib/colvars/colvarcomp_protein.cpp

@@ -7,8 +7,6 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
-#include <cmath>
-
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarparse.h"
@@ -27,7 +25,7 @@ colvar::alpha_angles::alpha_angles(std::string const &conf)
     cvm::log("Initializing alpha_angles object.\n");
 
   function_type = "alpha_angles";
-  enable(f_cvc_implicit_gradient);
+  enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
 
   std::string segment_id;
@@ -118,7 +116,7 @@ colvar::alpha_angles::alpha_angles()
   : cvc()
 {
   function_type = "alpha_angles";
-  enable(f_cvc_implicit_gradient);
+  enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
 }
 
@@ -133,6 +131,8 @@ colvar::alpha_angles::~alpha_angles()
     delete hb.back();
     hb.pop_back();
   }
+  // Our references to atom groups have become invalid now that children cvcs are deleted
+  atom_groups.clear();
 }
 
 
@@ -191,6 +191,58 @@ void colvar::alpha_angles::calc_gradients()
 }
 
 
+void colvar::alpha_angles::collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients)
+{
+  cvm::real cvc_coeff = sup_coeff * cvm::real(sup_np) * cvm::integer_power(value().real_value, sup_np-1);
+
+  if (theta.size()) {
+    cvm::real const theta_norm = (1.0-hb_coeff) / cvm::real(theta.size());
+
+    for (size_t i = 0; i < theta.size(); i++) {
+      cvm::real const t = ((theta[i])->value().real_value-theta_ref)/theta_tol;
+      cvm::real const f = ( (1.0 - (t*t)) /
+                            (1.0 - (t*t*t*t)) );
+      cvm::real const dfdt =
+        1.0/(1.0 - (t*t*t*t)) *
+        ( (-2.0 * t) + (-1.0*f)*(-4.0 * (t*t*t)) );
+
+      // Coeficient of this CVC's gradient in the colvar gradient, times coefficient of this
+      // angle's gradient in the CVC's gradient
+      cvm::real const coeff = cvc_coeff * theta_norm * dfdt * (1.0/theta_tol);
+
+      for (size_t j = 0; j < theta[i]->atom_groups.size(); j++) {
+        cvm::atom_group &ag = *(theta[i]->atom_groups[j]);
+        for (size_t k = 0; k < ag.size(); k++) {
+          size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
+                                      ag[k].id) - atom_ids.begin();
+          atomic_gradients[a] += coeff * ag[k].grad;
+        }
+      }
+    }
+  }
+
+  if (hb.size()) {
+
+    cvm::real const hb_norm = hb_coeff / cvm::real(hb.size());
+
+    for (size_t i = 0; i < hb.size(); i++) {
+      // Coeficient of this CVC's gradient in the colvar gradient, times coefficient of this
+      // hbond's gradient in the CVC's gradient
+      cvm::real const coeff = cvc_coeff * 0.5 * hb_norm;
+
+      for (size_t j = 0; j < hb[i]->atom_groups.size(); j++) {
+        cvm::atom_group &ag = *(hb[i]->atom_groups[j]);
+        for (size_t k = 0; k < ag.size(); k++) {
+          size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
+                                      ag[k].id) - atom_ids.begin();
+          atomic_gradients[a] += coeff * ag[k].grad;
+        }
+      }
+    }
+  }
+}
+
+
 void colvar::alpha_angles::apply_force(colvarvalue const &force)
 {
 
@@ -242,7 +294,8 @@ colvar::dihedPC::dihedPC(std::string const &conf)
     cvm::log("Initializing dihedral PC object.\n");
 
   function_type = "dihedPC";
-  enable(f_cvc_implicit_gradient);
+  // Supported through references to atom groups of children cvcs
+  enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
 
   std::string segment_id;
@@ -372,7 +425,8 @@ colvar::dihedPC::dihedPC()
   : cvc()
 {
   function_type = "dihedPC";
-  enable(f_cvc_implicit_gradient);
+  // Supported through references to atom groups of children cvcs
+  enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
 }
 
@@ -383,6 +437,8 @@ colvar::dihedPC::~dihedPC()
     delete theta.back();
     theta.pop_back();
   }
+  // Our references to atom groups have become invalid now that children cvcs are deleted
+  atom_groups.clear();
 }
 
 
@@ -392,8 +448,8 @@ void colvar::dihedPC::calc_value()
   for (size_t i = 0; i < theta.size(); i++) {
     theta[i]->calc_value();
     cvm::real const t = (PI / 180.) * theta[i]->value().real_value;
-    x.real_value += coeffs[2*i  ] * std::cos(t)
+    x.real_value += coeffs[2*i  ] * cvm::cos(t)
-                  + coeffs[2*i+1] * std::sin(t);
+                  + coeffs[2*i+1] * cvm::sin(t);
   }
 }
 
@@ -406,12 +462,35 @@ void colvar::dihedPC::calc_gradients()
 }
 
 
+void colvar::dihedPC::collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients)
+{
+  cvm::real cvc_coeff = sup_coeff * cvm::real(sup_np) * cvm::integer_power(value().real_value, sup_np-1);
+  for (size_t i = 0; i < theta.size(); i++) {
+    cvm::real const t = (PI / 180.) * theta[i]->value().real_value;
+    cvm::real const dcosdt = - (PI / 180.) * cvm::sin(t);
+    cvm::real const dsindt =   (PI / 180.) * cvm::cos(t);
+    // Coeficient of this dihedPC's gradient in the colvar gradient, times coefficient of this
+    // dihedral's gradient in the dihedPC's gradient
+    cvm::real const coeff = cvc_coeff * (coeffs[2*i] * dcosdt + coeffs[2*i+1] * dsindt);
+
+    for (size_t j = 0; j < theta[i]->atom_groups.size(); j++) {
+      cvm::atom_group &ag = *(theta[i]->atom_groups[j]);
+      for (size_t k = 0; k < ag.size(); k++) {
+        size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
+                                    ag[k].id) - atom_ids.begin();
+        atomic_gradients[a] += coeff * ag[k].grad;
+      }
+    }
+  }
+}
+
+
 void colvar::dihedPC::apply_force(colvarvalue const &force)
 {
   for (size_t i = 0; i < theta.size(); i++) {
     cvm::real const t = (PI / 180.) * theta[i]->value().real_value;
-    cvm::real const dcosdt = - (PI / 180.) * std::sin(t);
+    cvm::real const dcosdt = - (PI / 180.) * cvm::sin(t);
-    cvm::real const dsindt =   (PI / 180.) * std::cos(t);
+    cvm::real const dsindt =   (PI / 180.) * cvm::cos(t);
 
     theta[i]->apply_force((coeffs[2*i  ] * dcosdt +
                            coeffs[2*i+1] * dsindt) * force);

lib/colvars/colvarcomp_rotations.cpp

@@ -7,8 +7,6 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
-#include <cmath>
-
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarparse.h"
@@ -18,21 +16,27 @@
 
 
 colvar::orientation::orientation(std::string const &conf)
-  : cvc(conf)
+  : cvc()
 {
   function_type = "orientation";
-  atoms = parse_group(conf, "atoms");
+  disable(f_cvc_explicit_gradient);
-  enable(f_cvc_implicit_gradient);
   x.type(colvarvalue::type_quaternion);
+  init(conf);
+}
 
+
+int colvar::orientation::init(std::string const &conf)
+{
+  int error_code = cvc::init(conf);
+
+  atoms = parse_group(conf, "atoms");
   ref_pos.reserve(atoms->size());
 
   if (get_keyval(conf, "refPositions", ref_pos, ref_pos)) {
     cvm::log("Using reference positions from input file.\n");
     if (ref_pos.size() != atoms->size()) {
-      cvm::error("Error: reference positions do not "
+      return cvm::error("Error: reference positions do not "
-                        "match the number of requested atoms.\n");
+                        "match the number of requested atoms.\n", INPUT_ERROR);
-      return;
     }
   }
 
@@ -46,9 +50,8 @@ colvar::orientation::orientation(std::string const &conf)
         // use PDB flags if column is provided
         bool found = get_keyval(conf, "refPositionsColValue", file_col_value, 0.0);
         if (found && file_col_value==0.0) {
-          cvm::error("Error: refPositionsColValue, "
+          return cvm::error("Error: refPositionsColValue, "
-                            "if provided, must be non-zero.\n");
+                            "if provided, must be non-zero.\n", INPUT_ERROR);
-          return;
         }
       }
 
@@ -59,9 +62,8 @@ colvar::orientation::orientation(std::string const &conf)
   }
 
   if (!ref_pos.size()) {
-    cvm::error("Error: must define a set of "
+    return cvm::error("Error: must define a set of "
-                      "reference coordinates.\n");
+                      "reference coordinates.\n", INPUT_ERROR);
-    return;
   }
 
 
@@ -85,6 +87,7 @@ colvar::orientation::orientation(std::string const &conf)
     rot.request_group2_gradients(atoms->size());
   }
 
+  return error_code;
 }
 
 
@@ -92,7 +95,7 @@ colvar::orientation::orientation()
   : cvc()
 {
   function_type = "orientation";
-  enable(f_cvc_implicit_gradient);
+  disable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_quaternion);
 }
 
@@ -158,10 +161,18 @@ colvarvalue colvar::orientation::dist2_rgrad(colvarvalue const &x1,
 
 
 colvar::orientation_angle::orientation_angle(std::string const &conf)
-  : orientation(conf)
+  : orientation()
 {
   function_type = "orientation_angle";
+  enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
+  init(conf);
+}
+
+
+int colvar::orientation_angle::init(std::string const &conf)
+{
+  return orientation::init(conf);
 }
 
 
@@ -169,6 +180,7 @@ colvar::orientation_angle::orientation_angle()
   : orientation()
 {
   function_type = "orientation_angle";
+  enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
 }
 
@@ -180,9 +192,9 @@ void colvar::orientation_angle::calc_value()
   rot.calc_optimal_rotation(ref_pos, atoms->positions_shifted(-1.0 * atoms_cog));
 
   if ((rot.q).q0 >= 0.0) {
-    x.real_value = (180.0/PI) * 2.0 * std::acos((rot.q).q0);
+    x.real_value = (180.0/PI) * 2.0 * cvm::acos((rot.q).q0);
   } else {
-    x.real_value = (180.0/PI) * 2.0 * std::acos(-1.0 * (rot.q).q0);
+    x.real_value = (180.0/PI) * 2.0 * cvm::acos(-1.0 * (rot.q).q0);
   }
 }
 
@@ -191,7 +203,7 @@ void colvar::orientation_angle::calc_gradients()
 {
   cvm::real const dxdq0 =
     ( ((rot.q).q0 * (rot.q).q0 < 1.0) ?
-      ((180.0 / PI) * (-2.0) / std::sqrt(1.0 - ((rot.q).q0 * (rot.q).q0))) :
+      ((180.0 / PI) * (-2.0) / cvm::sqrt(1.0 - ((rot.q).q0 * (rot.q).q0))) :
       0.0 );
 
   for (size_t ia = 0; ia < atoms->size(); ia++) {
@@ -214,10 +226,18 @@ simple_scalar_dist_functions(orientation_angle)
 
 
 colvar::orientation_proj::orientation_proj(std::string const &conf)
-  : orientation(conf)
+  : orientation()
 {
   function_type = "orientation_proj";
+  enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
+  init(conf);
+}
+
+
+int colvar::orientation_proj::init(std::string const &conf)
+{
+  return orientation::init(conf);
 }
 
 
@@ -225,6 +245,7 @@ colvar::orientation_proj::orientation_proj()
   : orientation()
 {
   function_type = "orientation_proj";
+  enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
 }
 
@@ -261,18 +282,28 @@ simple_scalar_dist_functions(orientation_proj)
 
 
 colvar::tilt::tilt(std::string const &conf)
-  : orientation(conf)
+  : orientation()
 {
   function_type = "tilt";
+  enable(f_cvc_explicit_gradient);
+  x.type(colvarvalue::type_scalar);
+  init(conf);
+}
+
+
+int colvar::tilt::init(std::string const &conf)
+{
+  int error_code = COLVARS_OK;
+
+  error_code |= orientation::init(conf);
 
   get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0));
-
   if (axis.norm2() != 1.0) {
     axis /= axis.norm();
     cvm::log("Normalizing rotation axis to "+cvm::to_str(axis)+".\n");
   }
 
-  x.type(colvarvalue::type_scalar);
+  return error_code;
 }
 
 
@@ -280,6 +311,7 @@ colvar::tilt::tilt()
   : orientation()
 {
   function_type = "tilt";
+  enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
 }
 
@@ -322,20 +354,30 @@ simple_scalar_dist_functions(tilt)
 
 
 colvar::spin_angle::spin_angle(std::string const &conf)
-  : orientation(conf)
+  : orientation()
 {
   function_type = "spin_angle";
+  period = 360.0;
+  b_periodic = true;
+  enable(f_cvc_explicit_gradient);
+  x.type(colvarvalue::type_scalar);
+  init(conf);
+}
+
+
+int colvar::spin_angle::init(std::string const &conf)
+{
+  int error_code = COLVARS_OK;
+
+  error_code |= orientation::init(conf);
 
   get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0));
-
   if (axis.norm2() != 1.0) {
     axis /= axis.norm();
     cvm::log("Normalizing rotation axis to "+cvm::to_str(axis)+".\n");
   }
 
-  period = 360.0;
+  return error_code;
-  b_periodic = true;
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -345,6 +387,7 @@ colvar::spin_angle::spin_angle()
   function_type = "spin_angle";
   period = 360.0;
   b_periodic = true;
+  enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
 }
 
@@ -410,15 +453,15 @@ colvarvalue colvar::spin_angle::dist2_rgrad(colvarvalue const &x1,
 }
 
 
-void colvar::spin_angle::wrap(colvarvalue &x) const
+void colvar::spin_angle::wrap(colvarvalue &x_unwrapped) const
 {
-  if ((x.real_value - wrap_center) >= 180.0) {
+  if ((x_unwrapped.real_value - wrap_center) >= 180.0) {
-    x.real_value -= 360.0;
+    x_unwrapped.real_value -= 360.0;
     return;
   }
 
-  if ((x.real_value - wrap_center) < -180.0) {
+  if ((x_unwrapped.real_value - wrap_center) < -180.0) {
-    x.real_value += 360.0;
+    x_unwrapped.real_value += 360.0;
     return;
   }