Merge pull request #1271 from akohlmey/next-patch-release

Patch release 4 January 2019

.github/CODEOWNERS

@@ -126,3 +126,6 @@ python/*              @rbberger
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger
 doc/README            @rbberger
+
+# for releases
+src/version.h         @sjplimp

.gitignore

@@ -22,6 +22,7 @@ log.cite
 .*.swp
 *.orig
 *.rej
+vgcore.*
 .vagrant
 \#*#
 .#*

cmake/CMakeLists.txt

@@ -171,7 +171,7 @@ set(LAMMPS_DEPS)
 set(LAMMPS_API_DEFINES)
 
 set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
-  KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
+  KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK
   SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
   USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
   USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
@@ -191,11 +191,11 @@ endforeach()
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
-if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
+if(PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
   enable_language(Fortran)
 endif()
 
-if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
+if(PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
   enable_language(C)
 endif()
 
@@ -221,7 +221,7 @@ else()
 endif()
 
 
-set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit")
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
 set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
@@ -354,7 +354,7 @@ if(PKG_KSPACE)
   endif()
 endif()
 
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE OR PKG_USER-PLUMED)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -569,7 +569,7 @@ if(PKG_USER-PLUMED)
     if(PLUMED_MODE STREQUAL "STATIC")
       add_definitions(-D__PLUMED_WRAPPER_CXX=1)
       list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o
-        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS} ${LAPACK_LIBRARIES})
+        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "SHARED")
       list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
@@ -826,7 +826,7 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
   USER-QMMM)
   if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
@@ -856,6 +856,9 @@ if(PKG_USER-AWPMD)
 endif()
 
 if(PKG_USER-ATC)
+  if(LAMMPS_SIZES STREQUAL BIGBIG)
+    message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
+  endif()
   target_link_libraries(atc ${LAPACK_LIBRARIES})
 endif()
 
@@ -1322,7 +1325,7 @@ if(BUILD_LIB)
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
-  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Modules)
 else()
   list(APPEND LMP_SOURCES ${LIB_SOURCES})
 endif()

cmake/README.md

@@ -24,7 +24,7 @@ tasks, act as a reference and provide examples of typical use cases.
       * [Build directory vs. Source Directory](#build-directory-vs-source-directory)
    * [Defining and using presets](#defining-and-using-presets)
    * [Reference](#reference)
-      * [Common CMAKE Configuration Options](#common-cmake-configuration-options)
+      * [Common CMake Configuration Options](#common-cmake-configuration-options)
       * [LAMMPS Configuration Options](#lammps-configuration-options)
       * [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages)
       * [Default Packages](#default-packages)
@@ -179,7 +179,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
 
 # Reference
 
-## Common CMAKE Configuration Options
+## Common CMake Configuration Options
 
 
 <table>
@@ -208,6 +208,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
   </dl>
   </td>
 </tr>
+<tr>
+  <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>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -1729,6 +1739,13 @@ cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`,
   value of `FC` environment variable at first `cmake` run
   </td>
 </tr>
+<tr>
+  <td><code>CXX_COMPILER_LAUNCHER</code></td>
+  <td>CMake will run this tool and pass the compiler and its arguments to the tool. Some example tools are distcc and ccache.</td>
+  <td>
+  (empty)
+  </td>
+</tr>
 </tbody>
 </table>
 

doc/Makefile

@@ -1,7 +1,7 @@
 # Makefile for LAMMPS documentation
 
-SHELL 	      = /bin/bash
-SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
+SHELL         = /bin/bash
+SHA1          = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py)
 BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
 VENV          = $(BUILDDIR)/docenv
@@ -48,6 +48,7 @@ help:
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
 	@echo "  anchor_check  scan for duplicate anchor labels"
+	@echo "  spelling   spell-check the manual"
 
 # ------------------------------------------
 

doc/github-development-workflow.md

@@ -6,7 +6,7 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
 tools, but do not set policies, so it is up to the developers to come to
 an agreement as to how to define and interpret policies. This document
 is likely to change as our experiences and needs change and we try to
-adapt accordingly. Last change 2018-11-15.
+adapt accordingly. Last change 2018-12-19.
 
 ## Table of Contents
 
@@ -129,16 +129,17 @@ Here are some items to check:
     * stdlib.h -> cstdlib
     * string.h -> cstring
     * time.h -> ctime
-  Do not replace (as they are C++-11): `inttypes.h` and `stdint.h`.
+    * Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.
   * Code should follow the C++-98 standard. C++-11 is only accepted
   in individual special purpose packages
-  * indentation is two spaces per level
-  * there should be no tabs and no trailing whitespace
+  * indentation is 2 spaces per level
+  * there should be NO tabs and no trailing whitespace
   * header files, especially of new styles, should not include any
   other headers, except the header with the base class or cstdio.
   Forward declarations should be used instead when possible.
   * iostreams should be avoided. LAMMPS uses stdio from the C-library.
   * use of STL in headers and class definitions should be avoided.
+  * there MUST NOT be any "using namespace XXX;" statements in headers.
   * static class members should be avoided at all cost.
   * anything storing atom IDs should be using `tagint` and not `int`.
   This can be flagged by the compiler only for pointers and only when

doc/src/Build_extras.txt

@@ -36,7 +36,6 @@ This is the list of packages that may require additional steps.
 "OPT"_#opt,
 "POEMS"_#poems,
 "PYTHON"_#python,
-"REAX"_#reax,
 "VORONOI"_#voronoi,
 "USER-ATC"_#user-atc,
 "USER-AWPMD"_#user-awpmd,
@@ -536,45 +535,6 @@ build fails.
 
 :line
 
-REAX package :h4,link(reax)
-
-NOTE: the use of the REAX package and its "pair_style
-reax"_pair_reax.html command is discouraged, as it is no longer
-maintained.  Please use the USER-REAXC package and its "pair_style
-reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
-enabled variant (pair_style reax/c/kk), which has a more robust memory
-management.  See the "pair_style reax/c"_pair_reaxc.html doc page for
-details.
-
-[CMake build]:
-
-No additional settings are needed besides "-D PKG_REAX=yes".
-
-[Traditional make]:
-
-Before building LAMMPS, you must build the REAX library in lib/reax.
-You can do this manually if you prefer; follow the instructions in
-lib/reax/README.  You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/reax/Install.py script with the specified args:
-
-make lib-reax                    # print help message
-make lib-reax args="-m serial"   # build with GNU Fortran compiler (settings as with "make serial")
-make lib-reax args="-m mpi"      # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-reax args="-m ifort"    # build with Intel ifort compiler :pre
-
-The build should produce two files: lib/reax/libreax.a and
-lib/reax/Makefile.lammps.  The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (REAX library).  Typically the two compilers used for LAMMPS
-and the REAX library need to be consistent (e.g. both Intel or both
-GNU compilers).  If necessary, you can edit/create a new
-lib/reax/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-:line
-
 VORONOI package :h4,link(voronoi)
 
 To build with this package, you must download and build the "Voro++
@@ -621,8 +581,8 @@ The USER-ATC package requires the MANYBODY package also be installed.
 
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_REAX=yes" and "-D
-PKG_MANYBODY=yes".
+No additional settings are needed besides "-D PKG_USER-ATC=yes"
+and "-D PKG_MANYBODY=yes".
 
 [Traditional make]:
 
@@ -735,58 +695,69 @@ from LAMMPS using the generic "plumed installation instructions"_plumedinstall.
 :link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)
 
 PLUMED can be linked into MD codes in three different modes: static,
-shared, and runtime.  With the "static" mode, all required PLUMED code
-is linked statically into the MD code. The MD code is then fully
-independent from the PLUMED installation, but also you have to
-rebuild/relink the MD code to update the PLUMED code inside it.  With
-"shared" linkage mode, the MD code is linked to a shared library
-containing the PLUMED code, preferably after it was installed in a
-globally accessible location. This way the same installed PLUMED code
-can be shared across multiple MD packages and can be updated, for as
-long as the shared PLUMED library is ABI-compatible. The third linkage
-mode is "runtime" which allows to switch the PLUMED kernel at runtime
-between different variants through setting the PLUMED_KERNEL environment
-variable, which has to point to the location of the libplumedKernel.so
-dynamical shared object, which is then loaded at runtime. This is
-particularly convenient for doing PLUMED development and comparing
-multiple PLUMED versions without having to recompile the hosting MD
-code. All three linkage modes are supported by LAMMPS on selected
-operating systems (e.g. Linux) and using either CMake or traditional
-make build. The "static" mode should be most portable, the "runtime"
-mode support in LAMMPS makes the most assumptions about operating
-system and compiler environment. If one mode does not work, try a
-different one, or switch to a different build system, or consider
-a global PLUMED installation or downloading it during building LAMMPS.
+shared, and runtime.  With the "static" mode, all the code that PLUMED
+requires is linked statically into LAMMPS. LAMMPS is then fully
+independent from the PLUMED installation, but you have to rebuild/relink
+it in order to update the PLUMED code inside it.  With the "shared"
+linkage mode, LAMMPS is linked to a shared library that contains the
+PLUMED code.  This library should preferably be installed in a globally
+accessible location. When PLUMED is linked in this way the same library
+can be used by multiple MD packages.  Furthermore, the PLUMED library
+LAMMPS uses can be updated without the need for a recompile of LAMMPS
+for as long as the shared PLUMED library is ABI-compatible.
+
+The third linkage mode is "runtime" which allows the user to specify
+which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL
+environment variable. This variable should point to the location of the
+libplumedKernel.so dynamical shared object, which is then loaded at
+runtime. This mode of linking is particularly convenient for doing
+PLUMED development and comparing multiple PLUMED versions as these sorts
+of comparisons can be done without recompiling the hosting MD code. All
+three linkage modes are supported by LAMMPS on selected operating
+systems (e.g. Linux) and using either CMake or traditional make
+build. The "static" mode should be the most portable, while the
+"runtime" mode support in LAMMPS makes the most assumptions about
+operating system and compiler environment. If one mode does not work,
+try a different one, switch to a different build system, consider a
+global PLUMED installation or consider downloading PLUMED during the
+LAMMPS build.
 
 [CMake build]:
 
+When the "-D PKG_USER-PLUMED" flag is included in the cmake command you
+must ensure that GSL is installed in locations that are specified in
+your environment.  There are then two additional commands that control
+the manner in which PLUMED is obtained and linked into LAMMPS.
+
 -D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes
 -D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
 
 If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
-downloaded (the version of that is hard-coded to a vetted version of
-PLUMED, usually a recent stable release version) and built inside the
-CMake build directory.  If DOWNLOAD_PLUMED is set to "no" (the default),
-CMake will try to detect an installed version of PLUMED and link to
-that. For this to work, the PLUMED library has to be installed into a
-location where the pkg-config tool can find it or the PKG_CONFIG_PATH
-environment variable has to be set up accordingly.
+downloaded (the version of PLUMED that will be downloaded is hard-coded
+to a vetted version of PLUMED, usually a recent stable release version)
+and built inside the CMake build directory.  If DOWNLOAD_PLUMED is set
+to "no" (the default), CMake will try to detect and link to an installed
+version of PLUMED.  For this to work, the PLUMED library has to be
+installed into a location where the pkg-config tool can find it or the
+PKG_CONFIG_PATH environment variable has to be set up accordingly.
+PLUMED should be installed in such a location if you compile it using
+the default make; make install commands.
 
-The PLUMED_MODE setting determines the linkage mode of the PLUMED
-library.  Allowed values are "static" (default), "shared", or "runtime".
-For a discussion of PLUMED linkage modes, please see above.  When
-enabling DOWNLOAD_PLUMED, the static linkage mode is recommended.
+The PLUMED_MODE setting determines the linkage mode for the PLUMED
+library.  The allowed values for this flag are "static" (default),
+"shared", or "runtime".  For a discussion of PLUMED linkage modes,
+please see above.  When DOWNLOAD_PLUMED is enabled the static linkage
+mode is recommended.
 
 [Traditional make]:
 
-Before installing the USER-PLUMED package, first the PLUMED library
-needs to be configured so that LAMMPS can find the right settings when
-compiling and linking the LAMMPS executable itself. You can either
-download and build PLUMED inside the LAMMPS plumed library folder or use
-a previously installed PLUMED library and point LAMMPS to its
-location. You also have to choose the linkage mode: "static" (default),
-"shared" or "runtime".  For a discussion of PLUMED linkage modes, please
-see above.
+PLUMED needs to be installed before the USER-PLUMED package is installed
+so that LAMMPS can find the right settings when compiling and linking
+the LAMMPS executable.  You can either download and build PLUMED inside
+the LAMMPS plumed library folder or use a previously installed PLUMED
+library and point LAMMPS to its location. You also have to choose the
+linkage mode: "static" (default), "shared" or "runtime".  For a
+discussion of PLUMED linkage modes, please see above.
 
 Download/compilation/configuration of the plumed library can be done
 from the src folder through the following make args:
@@ -799,11 +770,11 @@ make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installati
 :pre
 
 Note that 2 symbolic (soft) links, "includelink" and "liblink" are
-created in lib/plumed to point into the location of the PLUMED build to
-use and also a new file lib/plumed/Makefile.lammps is created with
-settings suitable for LAMMPS to compile and link PLUMED in the desired
-linkage mode. After this step is completed, you can install the
-USER-PLUMED package and compile LAMMPS in the usual manner:
+created in lib/plumed that point to the location of the PLUMED build to
+use. A new file lib/plumed/Makefile.lammps is also created with settings
+suitable for LAMMPS to compile and link PLUMED using the desired linkage
+mode. After this step is completed, you can install the USER-PLUMED
+package and compile LAMMPS in the usual manner:
 
 make yes-user-plumed
 make machine :pre

doc/src/Build_package.txt

@@ -47,7 +47,6 @@ packages:
 "OPT"_Build_extras.html#opt,
 "POEMS"_Build_extras.html#poems,
 "PYTHON"_Build_extras.html#python,
-"REAX"_Build_extras.html#reax,
 "VORONOI"_Build_extras.html#voronoi,
 "USER-ATC"_Build_extras.html#user-atc,
 "USER-AWPMD"_Build_extras.html#user-awpmd,

doc/src/Commands_fix.txt

@@ -169,8 +169,7 @@ OPT.
 "qmmm"_fix_qmmm.html,
 "qtb"_fix_qtb.html,
 "rattle"_fix_shake.html,
-"reax/bonds"_fix_reax_bonds.html,
-"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/bonds (k)"_fix_reaxc_bonds.html,
 "reax/c/species (k)"_fix_reaxc_species.html,
 "recenter"_fix_recenter.html,
 "restrain"_fix_restrain.html,

doc/src/Commands_pair.txt

@@ -107,6 +107,7 @@ OPT.
 "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
 "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "lcbop"_pair_lcbop.html,
+"lebedeva/z"_pair_lebedeva_z.html,
 "lennard/mdf"_pair_mdf.html,
 "line/lj"_pair_line_lj.html,
 "list"_pair_list.html,
@@ -160,8 +161,7 @@ OPT.
 "lubricateU/poly"_pair_lubricateU.html,
 "mdpd"_pair_meso.html,
 "mdpd/rhosum"_pair_meso.html,
-"meam"_pair_meam.html,
-"meam/c"_pair_meam.html,
+"meam/c"_pair_meamc.html,
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.html,
@@ -194,7 +194,6 @@ OPT.
 "polymorphic"_pair_polymorphic.html,
 "python"_pair_python.html,
 "quip"_pair_quip.html,
-"reax"_pair_reax.html,
 "reax/c (ko)"_pair_reaxc.html,
 "rebo (io)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,

doc/src/Errors_common.txt

@@ -74,7 +74,7 @@ is an integer or floating-point number, respectively, and reject the
 input with an error message (for instance, when an integer is required,
 but a floating-point number 1.0 is provided):
 
-ERROR: Expected integer parameter in input script or data file :pre
+ERROR: Expected integer parameter instead of '1.0' in input script or data file :pre
 
 Some commands allow for using variable references in place of numeric
 constants so that the value can be evaluated and may change over the
@@ -85,6 +85,9 @@ reading the input and before parsing commands,
 
 NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
 the documentation of the corresponding command explicitly says it is.
+Otherwise, you will receive an error message of this kind:
+
+ERROR: Expected floating point parameter instead of 'v_name' in input script or data file :pre
 
 Generally, LAMMPS will print a message to the screen and logfile and
 exit gracefully when it encounters a fatal error.  Sometimes it will

doc/src/Errors_messages.txt

@@ -279,12 +279,6 @@ multibody joint).  The bodies you have defined exceed this limit. :dd
 This is an internal LAMMPS error.  Please report it to the
 developers. :dd
 
-{Atom sorting has bin size = 0.0} :dt
-
-The neighbor cutoff is being used as the bin size, but it is zero.
-Thus you must explicitly list a bin size in the atom_modify sort
-command or turn off sorting. :dd
-
 {Atom style hybrid cannot have hybrid as an argument} :dt
 
 Self-explanatory. :dd

doc/src/Install_linux.txt

@@ -15,7 +15,7 @@ Binaries are available for different versions of Linux:
 "Pre-built Fedora Linux executables"_#fedora
 "Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
 "Pre-built OpenSuse Linux executables"_#opensuse
-"Pre-built Gentoo Linux executable"_#gentoo :all(b)
+"Gentoo Linux executable"_#gentoo :all(b)
 
 :line
 
@@ -87,11 +87,11 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel,
 lammps-openmpi-devel), the header for compiling programs using
 the C library interface (lammps-headers), and the LAMMPS python
 module for Python 3. All packages can be installed at the same
-time and the name of the LAMMPS executable is {lmp} in all 3 cases.
-By default, {lmp} will refer to the serial executable, unless
-one of the MPI environment modules is loaded
+time and the name of the LAMMPS executable is {lmp} and {lmp_openmpi}
+or {lmp_mpich} respectively.  By default, {lmp} will refer to the
+serial executable, unless one of the MPI environment modules is loaded
 ("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
-Then the corresponding parallel LAMMPS executable is used.
+Then the corresponding parallel LAMMPS executable can be used.
 The same mechanism applies when loading the LAMMPS python module.
 
 To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
@@ -150,7 +150,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
 
 :line
 
-Pre-built Gentoo Linux executable :h4,link(gentoo)
+Gentoo Linux executable :h4,link(gentoo)
 
 LAMMPS is part of Gentoo's main package tree and can be installed by
 typing:

doc/src/Install_windows.txt

@@ -23,8 +23,8 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
 needed to run in parallel.
 
 The LAMMPS binaries contain all optional packages included in the
-source distribution except: KIM, REAX, KOKKOS, USER-INTEL,
-and USER-QMMM.  The serial version also does not include the MPIIO and
+source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM.
+The serial version also does not include the MPIIO and
 USER-LB packages.  GPU support is provided for OpenCL.
 
 The installer site also has instructions on how to run LAMMPS under

doc/src/Intro_nonfeatures.txt

@@ -16,7 +16,7 @@ functionality for setting up simulations and analyzing their output.
 Specifically, LAMMPS was not conceived and designed for:
 
 being run thru a GUI
-build molecular systems, or building molecular topologies
+building molecular systems, or building molecular topologies
 assign force-field coefficients automagically
 perform sophisticated analysis of your MD simulation
 visualize your MD simulation interactively
@@ -24,18 +24,18 @@ plot your output data :ul
 
 Although over the years these limitations have been somewhat
 reduced through features added to LAMMPS or external tools
-that either interface with LAMMPS or extend LAMMPS.
+that either closely interface with LAMMPS or extend LAMMPS.
 
 Here are suggestions on how to perform these tasks:
 
-GUI: LAMMPS can be built as a library and a Python wrapper that wraps
+[GUI:] LAMMPS can be built as a library and a Python wrapper that wraps
 the library interface is provided.  Thus, GUI interfaces can be
 written in Python (or C or C++ if desired) that run LAMMPS and
 visualize or plot its output.  Examples of this are provided in the
 python directory and described on the "Python"_Python_head.html doc
-page.  Also, there are several external wrappers or GUI front ends.:ulb,l
+page.  Also, there are several external wrappers or GUI front ends. :ulb,l
 
-Builder: Several pre-processing tools are packaged with LAMMPS.  Some
+[Builder:] Several pre-processing tools are packaged with LAMMPS.  Some
 of them convert input files in formats produced by other MD codes such
 as CHARMM, AMBER, or Insight into LAMMPS input formats.  Some of them
 are simple programs that will build simple molecular systems, such as
@@ -45,15 +45,20 @@ the "Tools"_Tools.html doc page for details on tools packaged with
 LAMMPS.  The "Pre/post processing
 page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
 describes a variety of 3rd party tools for this task.  Furthermore,
-some LAMMPS internal commands to reconstruct topology, as well as
-the option to insert molecule templates instead of atoms.:l
+some LAMMPS internal commands allow to reconstruct, or selectively add
+topology information, as well as provide the option to insert molecule
+templates instead of atoms for building bulk molecular systems. :l
 
-Force-field assignment: The conversion tools described in the previous
+[Force-field assignment:] The conversion tools described in the previous
 bullet for CHARMM, AMBER, and Insight will also assign force field
 coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
-or BIOVIA (formerly Accelrys) force field files. :l
+or BIOVIA (formerly Accelrys) force field files. The tools
+"ParmEd"_https://parmed.github.io/ParmEd/html/index.html and
+"InterMol"_https://github.com/shirtsgroup/InterMol are particularly
+powerful and flexible in converting force field and topology data
+between various MD simulation programs.  :l
 
-Simulation analysis: If you want to perform analysis on-the-fly as
+[Simulation analysis:] If you want to perform analysis on-the-fly as
 your simulation runs, see the "compute"_compute.html and
 "fix"_fix.html doc pages, which list commands that can be used in a
 LAMMPS input script.  Also see the "Modify"_Modify.html doc page for
@@ -71,22 +76,22 @@ tools/python directory can extract and massage data in dump files to
 make it easier to import into other programs.  See the
 "Tools"_Tools.html doc page for details on these various options. :l
 
-Visualization: LAMMPS can produce JPG or PNG snapshot images
+[Visualization:] LAMMPS can produce NETPBM, JPG or PNG snapshot images
 on-the-fly via its "dump image"_dump_image.html command and pass
-them to an external program FFmpeg to generate movies from them.  For
-high-quality, interactive visualization there are many excellent and
-free tools available.  See the "Other Codes
+them to an external program, "FFmpeg"_https://www.ffmpeg.org to generate
+movies from them.  For high-quality, interactive visualization there are
+many excellent and free tools available.  See the "Other Codes
 page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
 visualization packages that can use LAMMPS output data. :l
 
-Plotting: See the next bullet about Pizza.py as well as the
+[Plotting:] See the next bullet about Pizza.py as well as the
 "Python"_Python_head.html doc page for examples of plotting LAMMPS
 output.  Scripts provided with the {python} tool in the tools
 directory will extract and massage data in log and dump files to make
 it easier to analyze and plot.  See the "Tools"_Tools.html doc page
 for more discussion of the various tools. :l
 
-Pizza.py: Our group has also written a separate toolkit called
+[Pizza.py:] Our group has also written a separate toolkit called
 "Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
 setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
 simulations.  It thus provides some functionality for several of the

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="27 Nov 2018 version">
+<META NAME="docnumber" CONTENT="4 Jan 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
-27 Nov 2018 version :c,h2
+4 Jan 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Manual_build.txt

@@ -65,6 +65,8 @@ make epub         # generate LAMMPS.epub in ePUB format using Sphinx
 make mobi         # generate LAMMPS.mobi in MOBI format using ebook-convert
 make clean        # remove intermediate RST files created by HTML build
 make clean-all    # remove entire build folder and any cached data :pre
+make anchor_check # check for duplicate anchor labels
+make spelling     # spell-check the manual
 
 :line
 
@@ -106,7 +108,14 @@ This will install virtualenv from the Python Package Index.
 
 Installing prerequisites for PDF build
 
-[TBA]
+Building the PDF manual requires a working C++ compiler (to
+compile the txt2html tool and a working installation of
+"HTMLDOC"_https://www.msweet.org/htmldoc/
+HTMLDOC has its own list of prerequisites, but in most cases
+you can install a binary package of it either through your
+Linux package manager or MacOS (dmg) and Windows installer
+(msi) packages from its
+"GitHub releases page at"_https://github.com/michaelrsweet/htmldoc/releases
 
 :line
 

doc/src/Modify_contribute.txt

@@ -108,9 +108,13 @@ your contribution(s) to be added to main LAMMPS code or one of its
 standard packages, it needs to be written in a style compatible with
 other LAMMPS source files. This means: 2-character indentation per
 level, [no tabs], no lines over 80 characters. I/O is done via
-the C-style stdio library, class header files should not import any
-system headers outside <stdio.h>, STL containers should be avoided
-in headers, and forward declarations used where possible or needed.
+the C-style stdio library (mixing of stdio and iostreams is generally
+discouraged), class header files should not import any system headers
+outside of <cstdio>, STL containers should be avoided in headers,
+system header from the C library should use the C++-style names
+(<cstdlib>, <cstdio>, or <cstring>) instead of the C-style names
+<stdlib.h>, <stdio.h>, or <string.h>), and forward declarations
+used where possible or needed to avoid including headers.
 All added code should be placed into the LAMMPS_NS namespace or a
 sub-namespace; global or static variables should be avoided, as they
 conflict with the modular nature of LAMMPS and the C++ class structure.

doc/src/Packages_details.txt

@@ -45,7 +45,6 @@ as contained in the file name.
 "LATTE"_#PKG-LATTE,
 "MANYBODY"_#PKG-MANYBODY,
 "MC"_#PKG-MC,
-"MEAM"_#PKG-MEAM,
 "MESSAGE"_#PKG-MESSAGE,
 "MISC"_#PKG-MISC,
 "MOLECULE"_#PKG-MOLECULE,
@@ -56,7 +55,6 @@ as contained in the file name.
 "POEMS"_#PKG-POEMS,
 "PYTHON"_#PKG-PYTHON,
 "QEQ"_#PKG-QEQ,
-"REAX"_#PKG-REAX,
 "REPLICA"_#PKG-REPLICA2,
 "RIGID"_#PKG-RIGID,
 "SHOCK"_#PKG-SHOCK,
@@ -533,37 +531,6 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
 
 :line
 
-MEAM package :link(PKG-MEAM),h4
-
-[Contents:]
-
-A pair style for the modified embedded atom (MEAM) potential.
-
-Please note that the use of the MEAM package is discouraged as
-it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
-which is a direct translation of the MEAM package to C++.
-USER-MEAMC contains additional optimizations making it run faster
-than MEAM on most machines, while providing the identical features
-and user interface.
-
-[Author:] Greg Wagner (Northwestern U) while at Sandia.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/MEAM: filenames -> commands
-src/meam/README
-lib/meam/README
-"pair_style meam"_pair_meam.html
-examples/meam :ul
-
-:line
-
 MESSAGE package :link(PKG-MESSAGE),h4
 
 [Contents:]
@@ -834,38 +801,6 @@ examples/streitz :ul
 
 :line
 
-REAX package :link(PKG-REAX),h4
-
-[Contents:]
-
-NOTE: the use of the REAX package is discouraged, as it is no longer
-maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
-and possibly the KOKKOS enabled variant of that, which has a more robust
-memory management.
-
-A pair style which wraps a Fortran library which implements the ReaxFF
-potential, which is a universal reactive force field.  Also included is
-a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
-as bonds are created and destroyed.
-
-[Author:] Aidan Thompson (Sandia).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/REAX: filenames -> commands
-lib/reax/README
-"pair_style reax"_pair_reax.html
-"fix reax/bonds"_fix_reax_bonds.html
-examples/reax :ul
-
-:line
-
 REPLICA package :link(PKG-REPLICA2),h4
 
 [Contents:]
@@ -1552,10 +1487,9 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
 [Contents:]
 
 A pair style for the modified embedded atom (MEAM) potential
-translated from the Fortran version in the "MEAM"_#PKG-MEAM package
-to plain C++. In contrast to the MEAM package, no library
-needs to be compiled and the pair style can be instantiated
-multiple times.
+translated from the Fortran version in the (obsolete) "MEAM" package
+to plain C++. The USER-MEAMC fully replaces the MEAM package, which
+has been removed from LAMMPS after the 12 December 2018 version.
 
 [Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
 based on the Fortran version of Greg Wagner (Northwestern U) while at
@@ -1565,8 +1499,8 @@ Sandia.
 
 src/USER-MEAMC: filenames -> commands
 src/USER-MEAMC/README
-"pair_style meam/c"_pair_meam.html
-examples/meam :ul
+"pair_style meam/c"_pair_meamc.html
+examples/meamc :ul
 
 :line
 
@@ -1894,9 +1828,8 @@ USER-REAXC package :link(PKG-USER-REAXC),h4
 
 [Contents:]
 
-A pair style which implements the ReaxFF potential in C/C++ (in
-contrast to the "REAX package"_#PKG-REAX and its Fortran library).  ReaxFF
-is universal reactive force field.  See the src/USER-REAXC/README file
+A pair style which implements the ReaxFF potential in C/C++.  ReaxFF
+is a universal reactive force field.  See the src/USER-REAXC/README file
 for more info on differences between the two packages.  Also two fixes
 for monitoring molecules as bonds are created and destroyed.
 
@@ -1907,7 +1840,7 @@ for monitoring molecules as bonds are created and destroyed.
 src/USER-REAXC: filenames -> commands
 src/USER-REAXC/README
 "pair_style reax/c"_pair_reaxc.html
-"fix reax/c/bonds"_fix_reax_bonds.html
+"fix reax/c/bonds"_fix_reaxc_bonds.html
 "fix reax/c/species"_fix_reaxc_species.html
 examples/reax :ul
 

doc/src/Packages_standard.txt

@@ -46,7 +46,6 @@ Package, Description, Doc page, Example, Library
 "LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
 "MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
 "MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
-"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
 "MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
 "MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
 "MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
@@ -57,7 +56,6 @@ Package, Description, Doc page, Example, Library
 "POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
 "PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
 "QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
-"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
 "REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
 "RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
 "SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no

doc/src/Packages_user.txt

@@ -53,7 +53,7 @@ Package, Description, Doc page, Example, Library
 "USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
 "USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
 "USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
-"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
+"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no
 "USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
 "USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
 "USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no

doc/src/Tools.txt

@@ -485,9 +485,9 @@ README for more info on Pizza.py and how to use these scripts.
 
 reax tool :h4,link(reax_tool)
 
-The reax sub-directory contains stand-alond codes that can
-post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
-command from a LAMMPS simulation using "ReaxFF"_pair_reax.html.  See
+The reax sub-directory contains stand-alone codes that can
+post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
+command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html.  See
 the README.txt file for more info.
 
 These tools were written by Aidan Thompson at Sandia.

doc/src/atom_modify.txt

@@ -166,7 +166,8 @@ info), a map is used.  The default map style is array if no atom ID is
 larger than 1 million, otherwise the default is hash.  By default, a
 "first" group is not defined.  By default, sorting is enabled with a
 frequency of 1000 and a binsize of 0.0, which means the neighbor
-cutoff will be used to set the bin size.
+cutoff will be used to set the bin size. If no neighbor cutoff is
+defined, sorting will be turned off.
 
 :line
 

doc/src/compute_pair.txt

@@ -24,7 +24,7 @@ nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a
 compute 1 all pair gauss
 compute 1 all pair lj/cut/coul/cut ecoul
 compute 1 all pair tersoff 2 epair
-compute 1 all pair reax :pre
+compute 1 all pair reax/c :pre
 
 [Description:]
 
@@ -60,8 +60,8 @@ corrections, even if they are enabled via the
 "pair_modify"_pair_modify.html command.
 
 Some pair styles tally additional quantities, e.g. a breakdown of
-potential energy into a dozen or so components is tallied by the
-"pair_style reax"_pair_reax.html command.  These values (1 or more)
+potential energy into 14 components is tallied by the "pair_style
+reax/c"_pair_reaxc.html command.  These values (1 or more)
 are stored as a global vector by this compute.  See the doc page for
 "individual pair styles"_pair_style.html for info on these values.
 

doc/src/dump_modify.txt

@@ -461,10 +461,10 @@ last snapshot.  This can be accomplished with something the following
 commands:
 
 variable        Dhop equal 0.6
-variable        check atom "c_dsp[4] > v_Dhop"
+variable        check atom "c_dsp\[4\] > v_Dhop"
 compute         dsp all displace/atom refresh check
 dump            1 all custom 20 tmp.dump id type x y z
-dump_modify     1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp :pre
+dump_modify     1 append yes thresh c_dsp\[4\] > $\{Dhop\} refresh c_dsp :pre
 
 The "compute displace/atom"_compute_displace_atom.html command
 calculates the displacement of each atom from its reference position.

doc/src/fix.txt

@@ -312,9 +312,8 @@ accelerated styles exist.
 "qmmm"_fix_qmmm.html -
 "qtb"_fix_qtb.html -
 "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
-"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information
-"reax/c/bonds"_fix_reax_bonds.html -
-"reax/c/species"_fix_reaxc_species.html -
+"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
+"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
 "recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
 "restrain"_fix_restrain.html - constrain a bond, angle, dihedral
 "rhok"_fix_rhok.html -

doc/src/fix_bond_react.txt

@@ -69,8 +69,9 @@ Initiate complex covalent bonding (topology) changes. These topology
 changes will be referred to as 'reactions' throughout this
 documentation. Topology changes are defined in pre- and post-reaction
 molecule templates and can include creation and deletion of bonds,
-angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
-atom-types, or atomic charges.
+angles, dihedrals, impropers, bond types, angle types, dihedral types,
+atom types, or atomic charges. In addition, reaction by-products or
+other molecules can be identified and deleted.
 
 Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
 pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
@@ -203,15 +204,16 @@ A discussion of correctly handling this is also provided on the
 The map file is a text document with the following format:
 
 A map file has a header and a body. The header of map file the
-contains one mandatory keyword and two optional keywords. The
+contains one mandatory keyword and three optional keywords. The
 mandatory keyword is 'equivalences' and the optional keywords are
-'edgeIDs' and 'customIDs':
+'edgeIDs' and 'deleteIDs' and 'customIDs':
 
 N {equivalences} = # of atoms N in the reaction molecule templates
 N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
+N {deleteIDs} = # of atoms N that are specified for deletion
 N {customIDs} = # of atoms N that are specified for a custom update :pre
 
-The body of the map file contains two mandatory sections and two
+The body of the map file contains two mandatory sections and three
 optional sections. The first mandatory section begins with the keyword
 'BondingIDs' and lists the atom IDs of the bonding atom pair in the
 pre-reacted molecule template. The second mandatory section begins
@@ -222,10 +224,12 @@ second column is the corresponding atom ID of the post-reacted
 molecule template. The first optional section begins with the keyword
 'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
 molecule template. The second optional section begins with the keyword
-'Custom Edges' and allows for forcing the update of a specific atom's
-atomic charge. The first column is the ID of an atom near the edge of
-the pre-reacted molecule template, and the value of the second column
-is either 'none' or 'charges.' Further details are provided in the
+'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to
+delete. The third optional section begins with the keyword 'Custom
+Edges' and allows for forcing the update of a specific atom's atomic
+charge. The first column is the ID of an atom near the edge of the
+pre-reacted molecule template, and the value of the second column is
+either 'none' or 'charges.' Further details are provided in the
 discussion of the 'update_edges' keyword.
 
 A sample map file is given below:
@@ -309,7 +313,16 @@ edge are unaffected by this setting.
 
 A few other considerations:
 
-It may be beneficial to ensure reacting atoms are at a certain
+Many reactions result in one or more atoms that are considered
+unwanted by-products. Therefore, bond/react provides the option to
+delete a user-specified set of atoms. These pre-reaction atoms are
+identified in the map file. A deleted atom must still be included in
+the post-reaction molecule template, in which it cannot be bonded to
+an atom that is not deleted. In addition to deleting unwanted reaction
+by-products, this feature can be used to remove specific topologies,
+such as small rings, that may be otherwise indistinguishable.
+
+Also, it may be beneficial to ensure reacting atoms are at a certain
 temperature before being released to the overall thermostat. For this,
 you can use the internally-created dynamic group named
 "bond_react_MASTER_group." For example, adding the following command

doc/src/fix_nh.txt

@@ -626,10 +626,10 @@ over time or the atom count becomes very small.
 
 [Default:]
 
-The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
+The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
 ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
-scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
-not coupled to barostat, otherwise no.
+flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd
+dimension and not coupled to barostat, otherwise no.
 
 :line
 

doc/src/fix_plumed.txt

@@ -32,11 +32,10 @@ enhance the sampling of phase space.
 
 The documentation included here only describes the fix plumed command
 itself.  This command is LAMMPS specific, whereas most of the
-functionality implemented in PLUMED, however, will work with a range of
-MD codes, and when PLUMED is used as a stand alone code for analysis.
-The full "documentation for PLUMED"_plumeddocs is available online and
-included in the PLUMED source code.  The PLUMED library development is
-hosted at
+functionality implemented in PLUMED will work with a range of MD codes,
+and when PLUMED is used as a stand alone code for analysis.  The full
+"documentation for PLUMED"_plumeddocs is available online and included
+in the PLUMED source code.  The PLUMED library development is hosted at
 "https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
 A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
 
@@ -54,11 +53,12 @@ have been set.
 
 The {group-ID} entry is ignored. LAMMPS will always pass all the atoms
 to PLUMED and there can only be one instance of the plumed fix at a
-time. The plumed fix communicates the minimum amount of information
-required and the PLUMED supports multiple, completely independent
-collective variables, multiple independent biases and multiple
-independent forms of analysis.  There is thus really no restriction in
-functionality by only allowing only one plumed fix in the LAMMPS input.
+time. The way the plumed fix is implemented ensures that the minimum
+amount of information required is communicated.  Furthermore, PLUMED
+supports multiple, completely independent collective variables, multiple
+independent biases and multiple independent forms of analysis.  There is
+thus really no restriction in functionality by only allowing only one
+plumed fix in the LAMMPS input.
 
 The {plumedfile} keyword allows the user to specify the name of the
 PLUMED input file.  Instructions as to what should be included in a

doc/src/fix_reaxc_bonds.txt

@@ -6,13 +6,12 @@
 
 :line
 
-fix reax/bonds command :h3
 fix reax/c/bonds command :h3
 fix reax/c/bonds/kk command :h3
 
 [Syntax:]
 
-fix ID group-ID reax/bonds Nevery filename :pre
+fix ID group-ID reaxc/bonds Nevery filename :pre
 
 ID, group-ID are documented in "fix"_fix.html command
 reax/bonds = style name of this fix command
@@ -21,16 +20,14 @@ filename = name of output file :ul
 
 [Examples:]
 
-fix 1 all reax/bonds 100 bonds.tatb
 fix 1 all reax/c/bonds 100 bonds.reaxc :pre
 
 [Description:]
 
-Write out the bond information computed by the ReaxFF potential
-specified by "pair_style reax"_pair_reax.html or "pair_style
-reax/c"_pair_reaxc.html in the exact same format as the original
-stand-alone ReaxFF code of Adri van Duin.  The bond information is
-written to {filename} on timesteps that are multiples of {Nevery},
+Write out the bond information computed by the ReaxFF potential specified
+by "pair_style reax/c"_pair_reaxc.html in the exact same format as the
+original stand-alone ReaxFF code of Adri van Duin.  The bond information
+is written to {filename} on timesteps that are multiples of {Nevery},
 including timestep 0.  For time-averaged chemical species analysis,
 please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
 
@@ -94,12 +91,8 @@ more instructions on how to use the accelerated styles effectively.
 
 [Restrictions:]
 
-The fix reax/bonds command requires that the "pair_style
-reax"_pair_reax.html be invoked.  This fix is part of the REAX
-package.  It is only enabled if LAMMPS was built with that package,
-which also requires the REAX library be built and linked with LAMMPS.
 The fix reax/c/bonds command requires that the "pair_style
-reax/c"_pair_reaxc.html be invoked.  This fix is part of the
+reax/c"_pair_reaxc.html is invoked.  This fix is part of the
 USER-REAXC package.  It is only enabled if LAMMPS was built with that
 package.  See the "Build package"_Build_package.html doc page for more
 info.
@@ -109,7 +102,6 @@ To write gzipped bond files, you must compile LAMMPS with the
 
 [Related commands:]
 
-"pair_style reax"_pair_reax.html, "pair_style
-reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
+"pair_style reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
 
 [Default:] none

doc/src/fix_reaxc_species.txt

@@ -161,7 +161,7 @@ more instructions on how to use the accelerated styles effectively.
 
 [Restrictions:]
 
-The fix species currently only works with "pair_style
+The "fix reax/c/species" currently only works with "pair_style
 reax/c"_pair_reaxc.html and it requires that the "pair_style
 reax/c"_pair_reaxc.html be invoked.  This fix is part of the
 USER-REAXC package.  It is only enabled if LAMMPS was built with that
@@ -177,8 +177,7 @@ It should be possible to extend it to other reactive pair_styles (such as
 
 [Related commands:]
 
-"pair_style reax/c"_pair_reaxc.html, "fix
-reax/bonds"_fix_reax_bonds.html
+"pair_style reax/c"_pair_reaxc.html, "fix reax/c/bonds"_fix_reaxc_bonds.html
 
 [Default:]
 

doc/src/fix_rigid_meso.txt

@@ -160,7 +160,7 @@ unaffected by interactions with other particles.  Note that if you
 expect a rigid body not to move or rotate by using these keywords, you
 must insure its initial center-of-mass translational or angular
 velocity is 0.0. Otherwise the initial translational or angular
-momentum the body has will persist.
+momentum, the body has, will persist.
 
 An xflag, yflag, or zflag set to {off} means turn off the component of
 force or torque in that dimension.  A setting of {on} means turn on
@@ -287,9 +287,10 @@ bodies.  The number of columns is 28.  Thus for each rigid body, 28
 values are stored: the xyz coords of the center of mass (COM), the xyz
 components of the COM velocity, the xyz components of the force acting
 on the COM, the components of the 4-vector quaternion representing the
-orientation of the rigid body, the xyz components of the angular momentum
+orientation of the rigid body, the xyz components of the angular velocity
 of the body around its COM, the xyz components of the torque acting on the
-COM, the 3 principal components of the moment of inertia and the xyz image
+COM, the 3 principal components of the moment of inertia, the xyz components
+of the angular momentum of the body around its COM, and the xyz image
 flags of the COM.
 
 The center of mass (COM) for each body is similar to unwrapped

doc/src/fix_tune_kspace.txt

@@ -86,6 +86,9 @@ package"_Build_package.html doc page for more info.
 Do not set "neigh_modify once yes" or else this fix will never be
 called.  Reneighboring is required.
 
+This fix is not compatible with a hybrid pair style, long-range dispersion,
+TIP4P water support, or long-range point dipole support.
+
 [Related commands:]
 
 "kspace_style"_kspace_style.html, "boundary"_boundary.html

doc/src/fixes.txt

@@ -135,7 +135,7 @@ Fixes :h1
    fix_qeq_reax
    fix_qmmm
    fix_qtb
-   fix_reax_bonds
+   fix_reaxc_bonds
    fix_reaxc_species
    fix_recenter
    fix_restrain

doc/src/kspace_style.txt

@@ -58,7 +58,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
     accuracy = desired relative error in forces
     smallq = cutoff for charges to be considered (optional) (charge units)
   {scafacos} values = method accuracy
-    method = fmm or p2nfft or ewald or direct
+    method = fmm or p2nfft or p3m or ewald or direct
     accuracy = desired relative error in forces :pre
 :ule
 
@@ -392,6 +392,8 @@ the same bond/angle/dihedral are weighted by the
 "special_bonds"_special_bonds.html command.  Likewise it does not
 support the "TIP4P water style" where a fictitious charge site is
 introduced in each water molecule.
+Finally, the methods {p3m} and {ewald} do not support computing the
+virial, so this contribution is not included.
 
 [Related commands:]
 

doc/src/lammps.book

@@ -356,7 +356,7 @@ fix_qeq_comb.html
 fix_qeq_reax.html
 fix_qmmm.html
 fix_qtb.html
-fix_reax_bonds.html
+fix_reaxc_bonds.html
 fix_reaxc_species.html
 fix_recenter.html
 fix_restrain.html
@@ -585,6 +585,7 @@ pair_kim.html
 pair_kolmogorov_crespi_full.html
 pair_kolmogorov_crespi_z.html
 pair_lcbop.html
+pair_lebedeva_z.html
 pair_line_lj.html
 pair_list.html
 pair_lj.html
@@ -598,7 +599,7 @@ pair_lj_soft.html
 pair_lubricate.html
 pair_lubricateU.html
 pair_mdf.html
-pair_meam.html
+pair_meamc.html
 pair_meam_spline.html
 pair_meam_sw_spline.html
 pair_meso.html
@@ -617,7 +618,6 @@ pair_peri.html
 pair_polymorphic.html
 pair_python.html
 pair_quip.html
-pair_reax.html
 pair_reaxc.html
 pair_resquared.html
 pair_sdk.html

doc/src/pair_hybrid.txt

@@ -70,15 +70,10 @@ other pairwise potential for several different atom type pairs in your
 model, then you should just list the sub-style once and use the
 pair_coeff command to assign parameters for the different type pairs.
 
-NOTE: There are two exceptions to this option to list an individual
-pair style multiple times.  The first is for pair styles implemented
-as Fortran libraries: "pair_style meam"_pair_meam.html and "pair_style
-reax"_pair_reax.html ("pair_style reax/c"_pair_reaxc.html is OK).
-This is because unlike a C++ class, they can not be instantiated
-multiple times, due to the manner in which they were coded in Fortran.
-The second is for GPU-enabled pair styles in the GPU package.  This is
-b/c the GPU package also currently assumes that only one instance of a
-pair style is being used.
+NOTE: There is one exception to this option to list an individual
+pair style multiple times: GPU-enabled pair styles in the GPU package.
+This is because the GPU package currently assumes that only one
+instance of a pair style is being used.
 
 In the pair_coeff commands, the name of a pair style must be added
 after the I,J type specification, with the remaining coefficients

doc/src/pair_ilp_graphene_hbn.txt

@@ -10,7 +10,7 @@ pair_style ilp/graphene/hbn command :h3
 
 [Syntax:]
 
-pair_style hybrid/overlay ilp/graphene/hbn cutoff tap_flag :pre
+pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre
 
 cutoff = global cutoff (distance units)
 tap_flag = 0/1 to turn off/on the taper function
@@ -110,6 +110,7 @@ units, if your simulation does not use {metal} units.
 "pair_style hybrid/overlay"_pair_hybrid.html,
 "pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html,
 "pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html,
+"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
 "pair_style pair_coul_shield"_pair_coul_shield.html.
 
 [Default:] tap_flag = 1

doc/src/pair_kolmogorov_crespi_full.txt

@@ -100,6 +100,7 @@ units.
 "pair_coeff"_pair_coeff.html,
 "pair_none"_pair_none.html,
 "pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
 "pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
 

doc/src/pair_kolmogorov_crespi_z.txt

@@ -10,7 +10,7 @@ pair_style kolmogorov/crespi/z command :h3
 
 [Syntax:]
 
-pair_style hybrid/overlay kolmogorov/crespi/z cutoff :pre
+pair_style \[hybrid/overlay ...\] kolmogorov/crespi/z cutoff :pre
 
 [Examples:]
 
@@ -56,9 +56,12 @@ package"_Build_package.html doc page for more info.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
-"pair_none"_pair_none.html
-"pair_style hybrid/overlay"_pair_hybrid.html
+"pair_coeff"_pair_coeff.html,
+"pair_none"_pair_none.html,
+"pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
+"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
+"pair_style lebedeva/z"_pair_lebedeva_z.html
 
 [Default:] none
 

doc/src/pair_lebedeva_z.txt

@@ -0,0 +1,66 @@
+"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
+
+pair_style lebedeva/z command :h3
+
+[Syntax:]
+
+pair_style \[hybrid/overlay ...\] lebedeva/z cutoff :pre
+
+[Examples:]
+
+pair_style hybrid/overlay lebedeva/z 20.0
+pair_coeff * * none
+pair_coeff 1 2 lebedeva/z  CC.Lebedeva   C C :pre
+
+pair_style hybrid/overlay rebo lebedeva/z 14.0
+pair_coeff * * rebo                 CH.airebo  C C
+pair_coeff 1 2 lebedeva/z  CC.Lebedeva      C C :pre
+
+[Description:]
+
+The {lebedeva/z} style computes the Lebedeva interaction
+potential as described in "(Lebedeva et al.)"_#Leb01. An important simplification is made,
+which is to take all normals along the z-axis.
+
+:c,image(Eqs/pair_lebedeva.png)
+
+It is important to have a sufficiently large cutoff to ensure smooth forces.
+Energies are shifted so that they go continuously to zero at the cutoff assuming
+that the exponential part of {Vij} (first term) decays sufficiently fast.
+This shift is achieved by the last term in the equation for {Vij} above.
+
+The parameter file (e.g. CC.Lebedeva), is intended for use with metal
+"units"_units.html, with energies in meV. An additional parameter, {S},
+is available to facilitate scaling of energies.
+
+This potential must be used in combination with hybrid/overlay.
+Other interactions can be set to zero using pair_style {none}.
+
+[Restrictions:]
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html,
+"pair_style none"_pair_none.html,
+"pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style ilp/graphene/hbd"_pair_ilp_graphene_hbn.html,
+"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
+"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html.
+
+[Default:] none
+
+:line
+
+:link(Leb01)
+[(Lebedeva et al.)] I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
+

doc/src/pair_meam_spline.txt

@@ -152,7 +152,7 @@ info.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html
+"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html
 
 [Default:] none
 

doc/src/pair_meam_sw_spline.txt

@@ -116,7 +116,7 @@ info.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html,
+"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html,
 "pair_style meam/spline"_pair_meam_spline.html
 
 [Default:] none

doc/src/pair_meamc.txt

@@ -6,18 +6,17 @@
 
 :line
 
-pair_style meam command :h3
 pair_style meam/c command :h3
 
 [Syntax:]
 
 pair_style style :pre
 
-style = {meam} or {meam/c}
+style = {meam/c}
 
 [Examples:]
 
-pair_style meam
+pair_style meam/c
 pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
 pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre
 
@@ -27,14 +26,16 @@ NOTE: The behavior of the MEAM potential for alloy systems has changed
 as of November 2010; see description below of the mixture_ref_t
 parameter
 
-Style {meam} computes pairwise interactions for a variety of materials
+Style {meam/c} computes pairwise interactions for a variety of materials
 using modified embedded-atom method (MEAM) potentials
 "(Baskes)"_#Baskes.  Conceptually, it is an extension to the original
 "EAM potentials"_pair_eam.html which adds angular forces.  It is
 thus suitable for modeling metals and alloys with fcc, bcc, hcp and
 diamond cubic structures, as well as covalently bonded materials like
-silicon and carbon. Style {meam/c} is a translation of the {meam} code
-from (mostly) Fortran to C++. It is functionally equivalent to {meam}.
+silicon and carbon. Style {meam/c} is a translation of the (now obsolete)
+{meam} code from Fortran to C++. It is functionally equivalent to {meam}
+but more efficient, and thus {meam} has been removed from LAMMPS after
+the 12 December 2018 release.
 
 In the MEAM formulation, the total energy E of a system of atoms is
 given by:
@@ -352,13 +353,8 @@ This pair style can only be used via the {pair} keyword of the
 
 [Restrictions:]
 
-The {meam} style is part of the MEAM package.  It is only enabled if
-LAMMPS was built with that package, which also requires the MEAM
-library be built and linked with LAMMPS.  The {meam/c} style is
-provided in the USER-MEAMC package. It is only enabled if LAMMPS was
-built with that package. In contrast to the {meam} style, {meam/c}
-does not require a separate library to be compiled and it can be
-instantiated multiple times in a "hybrid"_pair_hybrid.html pair style.
+The {meam/c} style is provided in the USER-MEAMC package. It is
+only enabled if LAMMPS was built with that package.
 See the "Build package"_Build_package.html doc page for more info.
 
 [Related commands:]

doc/src/pair_reax.txt

@@ -1,216 +0,0 @@
-"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
-
-pair_style reax command :h3
-
-[Syntax:]
-
-pair_style reax hbcut hbnewflag tripflag precision :pre
-
-hbcut = hydrogen-bond cutoff (optional) (distance units)
-hbnewflag = use old or new hbond function style (0 or 1) (optional)
-tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
-precision = precision for charge equilibration (optional) :ul
-
-[Examples:]
-
-pair_style reax
-pair_style reax 10.0 0 1 1.0e-5
-pair_coeff * * ffield.reax 3 1 2 2
-pair_coeff * * ffield.reax 3 NULL NULL 3 :pre
-
-[Description:]
-
-Style {reax} computes the ReaxFF potential of van Duin, Goddard and
-co-workers.  ReaxFF uses distance-dependent bond-order functions to
-represent the contributions of chemical bonding to the potential
-energy. There is more than one version of ReaxFF. The version
-implemented in LAMMPS uses the functional forms documented in the
-supplemental information of the following paper:
-"(Chenoweth)"_#Chenoweth_20081.  The version integrated into LAMMPS matches
-the most up-to-date version of ReaxFF as of summer 2010.
-
-WARNING: pair style reax is now deprecated and will soon be retired. Users
-should switch to "pair_style reax/c"_pair_reaxc.html. The {reax} style
-differs from the {reax/c} style in the lo-level implementation details.
-The {reax} style is a
-Fortran library, linked to LAMMPS.  The {reax/c} style was initially
-implemented as stand-alone C code and is now integrated into LAMMPS as
-a package.
-
-LAMMPS requires that a file called ffield.reax be provided, containing
-the ReaxFF parameters for each atom type, bond type, etc. The format
-is identical to the ffield file used by van Duin and co-workers. The
-filename is required as an argument in the pair_coeff command. Any
-value other than "ffield.reax" will be rejected (see below).
-
-LAMMPS provides several different versions of ffield.reax in its
-potentials dir, each called potentials/ffield.reax.label.  These are
-documented in potentials/README.reax.  The default ffield.reax
-contains parameterizations for the following elements: C, H, O, N.
-
-NOTE: We do not distribute a wide variety of ReaxFF force field files
-with LAMMPS.  Adri van Duin's group at PSU is the central repository
-for this kind of data as they are continuously deriving and updating
-parameterizations for different classes of materials.  You can submit
-a contact request at the Materials Computation Center (MCC) website
-"https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc,
-describing the material(s) you are interested in modeling with ReaxFF.
-They can tell
-you what is currently available or what it would take to create a
-suitable ReaxFF parameterization.
-
-The format of these files is identical to that used originally by van
-Duin.  We have tested the accuracy of {pair_style reax} potential
-against the original ReaxFF code for the systems mentioned above.  You
-can use other ffield files for specific chemical systems that may be
-available elsewhere (but note that their accuracy may not have been
-tested).
-
-The {hbcut}, {hbnewflag}, {tripflag}, and {precision} settings are
-optional arguments.  If none are provided, default settings are used:
-{hbcut} = 6 (which is Angstroms in real units), {hbnewflag} = 1 (use
-new hbond function style), {tripflag} = 1 (apply stabilization to all
-triple bonds), and {precision} = 1.0e-6 (one part in 10^6).  If you
-wish to override any of these defaults, then all of the settings must
-be specified.
-
-Two examples using {pair_style reax} are provided in the examples/reax
-sub-directory, along with corresponding examples for
-"pair_style reax/c"_pair_reaxc.html. Note that while the energy and force
-calculated by both of these pair styles match very closely, the
-contributions due to the valence angles differ slightly due to
-the fact that with {pair_style reax/c} the default value of {thb_cutoff_sq}
-is 0.00001, while for {pair_style reax} it is hard-coded to be 0.001.
-
-Use of this pair style requires that a charge be defined for every
-atom since the {reax} pair style performs a charge equilibration (QEq)
-calculation.  See the "atom_style"_atom_style.html and
-"read_data"_read_data.html commands for details on how to specify
-charges.
-
-The thermo variable {evdwl} stores the sum of all the ReaxFF potential
-energy contributions, with the exception of the Coulombic and charge
-equilibration contributions which are stored in the thermo variable
-{ecoul}.  The output of these quantities is controlled by the
-"thermo"_thermo.html command.
-
-This pair style tallies a breakdown of the total ReaxFF potential
-energy into sub-categories, which can be accessed via the "compute
-pair"_compute_pair.html command as a vector of values of length 14.
-The 14 values correspond to the following sub-categories (the variable
-names in italics match those used in the ReaxFF FORTRAN library):
-
-{eb} = bond energy
-{ea} = atom energy
-{elp} = lone-pair energy
-{emol} = molecule energy (always 0.0)
-{ev} = valence angle energy
-{epen} = double-bond valence angle penalty
-{ecoa} = valence angle conjugation energy
-{ehb} = hydrogen bond energy
-{et} = torsion energy
-{eco} = conjugation energy
-{ew} = van der Waals energy
-{ep} = Coulomb energy
-{efi} = electric field energy (always 0.0)
-{eqeq} = charge equilibration energy :ol
-
-To print these quantities to the log file (with descriptive column
-headings) the following commands could be included in an input script:
-
-compute reax all pair reax
-variable eb  	 equal c_reax\[1\]
-variable ea  	 equal c_reax\[2\]
-...
-variable eqeq 	 equal c_reax\[14\]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
-
-Only a single pair_coeff command is used with the {reax} style which
-specifies a ReaxFF potential file with parameters for all needed
-elements.  These are mapped to LAMMPS atom types by specifying N
-additional arguments after the filename in the pair_coeff command,
-where N is the number of LAMMPS atom types:
-
-filename
-N indices = mapping of ReaxFF elements to atom types :ul
-
-The specification of the filename and the mapping of LAMMPS atom types
-recognized by the ReaxFF is done differently than for other LAMMPS
-potentials, due to the non-portable difficulty of passing character
-strings (e.g. filename, element names) between C++ and Fortran.
-
-The filename has to be "ffield.reax" and it has to exist in the
-directory you are running LAMMPS in.  This means you cannot prepend a
-path to the file in the potentials dir.  Rather, you should copy that
-file into the directory you are running from.  If you wish to use
-another ReaxFF potential file, then name it "ffield.reax" and put it
-in the directory you run from.
-
-In the ReaxFF potential file, near the top, after the general
-parameters, is the atomic parameters section that contains element
-names, each with a couple dozen numeric parameters.  If there are M
-elements specified in the {ffield} file, think of these as numbered 1
-to M. Each of the N indices you specify for the N atom types of LAMMPS
-atoms must be an integer from 1 to M.  Atoms with LAMMPS type 1 will
-be mapped to whatever element you specify as the first index value,
-etc.  If a mapping value is specified as NULL, the mapping is not
-performed.  This can be used when a ReaxFF potential is used as part
-of the {hybrid} pair style.  The NULL values are placeholders for atom
-types that will be used with other potentials.
-
-NOTE: Currently the reax pair style cannot be used as part of the
-{hybrid} pair style.  Some additional changes still need to be made to
-enable this.
-
-As an example, say your LAMMPS simulation has 4 atom types and the
-elements are ordered as C, H, O, N in the {ffield} file.  If you want
-the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
-H, you would use the following pair_coeff command:
-
-pair_coeff * * ffield.reax 1 1 4 2 :pre
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-This pair style does not support the "pair_modify"_pair_modify.html
-mix, shift, table, and tail options.
-
-This pair style does not write its information to "binary restart
-files"_restart.html, since it is stored in potential files.  Thus, you
-need to re-specify the pair_style and pair_coeff commands in an input
-script that reads a restart file.
-
-This pair style can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command.  It does not support the
-{inner}, {middle}, {outer} keywords.
-
-[Restrictions:]
-
-The ReaxFF potential files provided with LAMMPS in the potentials
-directory are parameterized for real "units"_units.html.  You can use
-the ReaxFF potential with any LAMMPS units, but you would need to
-create your own potential file with coefficients listed in the
-appropriate units if your simulation doesn't use "real" units.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reaxc.html,
-"fix_reax_bonds"_fix_reax_bonds.html
-
-[Default:]
-
-The keyword defaults are {hbcut} = 6, {hbnewflag} = 1, {tripflag} = 1,
-{precision} = 1.0e-6.
-
-:line
-
-:link(Chenoweth_20081)
-[(Chenoweth_2008)] Chenoweth, van Duin and Goddard,
-Journal of Physical Chemistry A, 112, 1040-1053 (2008).

doc/src/pair_reaxc.txt

@@ -37,7 +37,7 @@ pair_coeff * * ffield.reax C H O N :pre
 Style {reax/c} computes the ReaxFF potential of van Duin, Goddard and
 co-workers.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
-energy. There is more than one version of ReaxFF.  The version
+energy. There is more than one version of ReaxFF. The version
 implemented in LAMMPS uses the functional forms documented in the
 supplemental information of the following paper: "(Chenoweth et al.,
 2008)"_#Chenoweth_20082.  The version integrated into LAMMPS matches
@@ -56,11 +56,10 @@ consideration when using the {reax/c/kk} style is the choice of either
 half or full neighbor lists. This setting can be changed using the
 Kokkos "package"_package.html command.
 
-The {reax/c} style differs from the "pair_style reax"_pair_reax.html
-command in the lo-level implementation details.  The {reax} style is a
-Fortran library, linked to LAMMPS.  The {reax/c} style was initially
-implemented as stand-alone C code and is now integrated into LAMMPS as
-a package.
+The {reax/c} style differs from the (obsolete) "pair_style reax"
+command in the implementation details.  The {reax} style was a
+Fortran library, linked to LAMMPS.  The {reax} style has been removed
+from LAMMPS after the 12 December 2018 version.
 
 LAMMPS provides several different versions of ffield.reax in its
 potentials dir, each called potentials/ffield.reax.label.  These are
@@ -98,9 +97,8 @@ correspond to those used by Adri van Duin's stand-alone serial
 code. If these are changed by setting control variables in the control
 file, the results from LAMMPS and the serial code will not agree.
 
-Two examples using {pair_style reax/c} are provided in the examples/reax
-sub-directory, along with corresponding examples for
-"pair_style reax"_pair_reax.html.
+Examples using {pair_style reax/c} are provided in the examples/reax
+sub-directory.
 
 Use of this pair style requires that a charge be defined for every
 atom.  See the "atom_style"_atom_style.html and
@@ -193,8 +191,7 @@ where N is the number of LAMMPS atom types:
 filename
 N indices = ReaxFF elements :ul
 
-The filename is the ReaxFF potential file.  Unlike for the {reax}
-pair style, any filename can be used.
+The filename is the ReaxFF potential file.
 
 In the ReaxFF potential file, near the top, after the general
 parameters, is the atomic parameters section that contains element
@@ -337,9 +334,8 @@ appropriate units if your simulation doesn't use "real" units.
 [Related commands:]
 
 "pair_coeff"_pair_coeff.html, "fix qeq/reax"_fix_qeq_reax.html, "fix
-reax/c/bonds"_fix_reax_bonds.html, "fix
-reax/c/species"_fix_reaxc_species.html, "pair_style
-reax"_pair_reax.html
+reax/c/bonds"_fix_reaxc_bonds.html, "fix
+reax/c/species"_fix_reaxc_species.html
 
 [Default:]
 

doc/src/pair_snap.txt

@@ -16,7 +16,7 @@ pair_style snap :pre
 [Examples:]
 
 pair_style snap
-pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
+pair_coeff * * InP.snapcoeff InP.snapparam In In P P :pre
 
 [Description:]
 
@@ -48,14 +48,12 @@ not set in the pair_style or pair_coeff command; they are specified in
 the SNAP potential files themselves.
 
 Only a single pair_coeff command is used with the {snap} style which
-specifies two SNAP files and the list SNAP element(s) to be
-extracted.
-The SNAP elements are mapped to LAMMPS atom types by specifying
-N additional arguments after the 2nd filename in the pair_coeff
-command, where N is the number of LAMMPS atom types:
+specifies a SNAP coefficient file followed by a SNAP parameter file
+and then N additional arguments specifying the mapping of SNAP
+elements to LAMMPS atom types, where N is the number of 
+LAMMPS atom types:
 
-SNAP element file
-Elem1, Elem2, ...
+SNAP coefficient file
 SNAP parameter file
 N element names = mapping of SNAP elements to atom types :ul
 
@@ -63,13 +61,11 @@ As an example, if a LAMMPS indium phosphide simulation has 4 atoms
 types, with the first two being indium and the 3rd and 4th being
 phophorous, the pair_coeff command would look like this:
 
-pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre
+pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P :pre
 
 The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
-The two filenames are for the element and parameter files, respectively.
-The 'In' and 'P' arguments (between the file names) are the two elements
-which will be extracted from the element file. The
-two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
+The two filenames are for the coefficient and parameter files, respectively.
+The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
 SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
 3 and 4 to the SNAP 'P' element.
 
@@ -79,10 +75,11 @@ This can be used when a {snap} potential is used as part of the
 {hybrid} pair style.  The NULL values are placeholders for atom types
 that will be used with other potentials.
 
-The name of the SNAP element file usually ends in the
+The name of the SNAP coefficient file usually ends in the
 ".snapcoeff" extension. It may contain coefficients
-for many SNAP elements.
-Only those elements listed in the pair_coeff command are extracted.
+for many SNAP elements. The only requirement is that it
+contain at least those element names appearing in the
+LAMMPS mapping list. 
 The name of the SNAP parameter file usually ends in the ".snapparam"
 extension. It contains a small number
 of parameters that define the overall form of the SNAP potential.
@@ -103,15 +100,13 @@ by the following commands:
         zbl $\{zblcutinner\} $\{zblcutouter\} snap
         pair_coeff * * zbl 0.0
         pair_coeff 1 1 zbl $\{zblz\}
-        pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
-        ../potentials/Ta06A.snapparam Ta :pre
+        pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta :pre
 
 It is convenient to keep these commands in a separate file that can
 be inserted in any LAMMPS input script using the "include"_include.html
 command.
 
-The top of the SNAP element file can contain any number of blank and comment
-lines (start with #), but follows a strict
+The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict
 format after that. The first non-blank non-comment
 line must contain two integers:
 

doc/src/pair_style.txt

@@ -174,6 +174,7 @@ accelerated styles exist.
 "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications
 "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis
 "lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
+"lebedeva/z"_pair_lebedeva_z.html - Lebedeva inter-layer potential for graphene with normals along z-axis
 "lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
 "line/lj"_pair_line_lj.html - LJ potential between line segments
 "list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file
@@ -226,8 +227,7 @@ accelerated styles exist.
 "lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
 "mdpd"_pair_meso.html - mDPD particle interactions
 "mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density
-"meam"_pair_meam.html - modified embedded atom method (MEAM) in Fortran
-"meam/c"_pair_meam.html - modified embedded atom method (MEAM) in C
+"meam/c"_pair_meamc.html - modified embedded atom method (MEAM) in C
 "meam/spline"_pair_meam_spline.html - splined version of MEAM
 "meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
 "mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
@@ -260,7 +260,6 @@ accelerated styles exist.
 "polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
 "python"_pair_python.html -
 "quip"_pair_quip.html -
-"reax"_pair_reax.html - ReaxFF potential in Fortran
 "reax/c"_pair_reaxc.html - ReaxFF potential in C
 "rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
 "resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential

doc/src/pairs.txt

@@ -50,6 +50,7 @@ Pair Styles :h1
    pair_kolmogorov_crespi_full
    pair_kolmogorov_crespi_z
    pair_lcbop
+   pair_lebedeva_z
    pair_line_lj
    pair_list
    pair_lj
@@ -63,7 +64,7 @@ Pair Styles :h1
    pair_lubricate
    pair_lubricateU
    pair_mdf
-   pair_meam
+   pair_meamc
    pair_meam_spline
    pair_meam_sw_spline
    pair_meso
@@ -82,7 +83,6 @@ Pair Styles :h1
    pair_polymorphic
    pair_python
    pair_quip
-   pair_reax
    pair_reaxc
    pair_resquared
    pair_sdk

doc/src/read_dump.txt

@@ -22,7 +22,8 @@ field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz}
   {ix},{iy},{iz} = image flags in each dimension
   {fx},{fy},{fz} = force components :pre
 zero or more keyword/value pairs may be appended :l
-keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l
+keyword = {nfile} or {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l
+  {nfile} value = Nfiles = how many parallel dump files exist
   {box} value = {yes} or {no} = replace simulation box with dump box
   {replace} value = {yes} or {no} = overwrite atoms with dump atoms
   {purge} value = {yes} or {no} = delete all atoms before adding dump atoms
@@ -85,9 +86,18 @@ command, after the dump snapshot is read.
 
 If the dump filename specified as {file} ends with ".gz", the dump
 file is read in gzipped format.  You cannot (yet) read a dump file
-that was written in binary format with a ".bin" suffix, or to multiple
-files via the "%" option in the dump file name.  See the
-"dump"_dump.html command for details.
+that was written in binary format with a ".bin" suffix.
+
+You can read dump files that were written (in parallel) to multiple
+files via the "%" wild-card character in the dump file name.  If any
+specified dump file name contains a "%", they must all contain it.
+See the "dump"_dump.html command for details.
+The "%" wild-card character is only supported by the {native} format
+for dump files, described next.
+
+If reading parallel dump files, you must also use the {nfile} keyword
+to tell LAMMPS how many parallel files exist, via its specified
+{Nfiles} value.
 
 The format of the dump file is selected through the {format} keyword.
 If specified, it must be the last keyword used, since all remaining

doc/src/region.txt

@@ -26,7 +26,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
     dim = {x} or {y} or {z} = axis of cylinder
     c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
     radius = cylinder radius (distance units)
-      radius can be a variable (see below)
+      c1,c2, and radius can be a variable (see below)
     lo,hi = bounds of cylinder in dim (distance units)
   {plane} args = px py pz nx ny nz
     px,py,pz = point on the plane (distance units)
@@ -39,7 +39,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
   {sphere} args = x y z radius
     x,y,z = center of sphere (distance units)
     radius = radius of sphere (distance units)
-      radius can be a variable (see below)
+      x,y,z, and radius can be a variable (see below)
   {union} args = N reg-ID1 reg-ID2 ...
     N = # of regions to follow, must be 2 or greater
     reg-ID1,reg-ID2, ... = IDs of regions to join together
@@ -179,12 +179,17 @@ The {radius} value for style {sphere} and {cylinder} can be specified
 as an equal-style "variable"_variable.html.  If the value is a
 variable, it should be specified as v_name, where name is the variable
 name.  In this case, the variable will be evaluated each timestep, and
-its value used to determine the radius of the region.
+its value used to determine the radius of the region. For style {sphere}
+also the x-, y-, and z- coordinate of the center of the sphere and for
+style {cylinder} the two center positions c1 and c2 for the location of
+the cylinder axes can be a variable with the same kind of effect and
+requirements than for the radius.
 
 Equal-style variables can specify formulas with various mathematical
 functions, and include "thermo_style"_thermo_style.html command
 keywords for the simulation box parameters and timestep and elapsed
-time.  Thus it is easy to specify a time-dependent radius.
+time.  Thus it is easy to specify a time-dependent radius or have
+a time dependent position of the sphere or cylinder region.
 
 See the "Howto tricilinc"_Howto_triclinic.html doc page for a
 geometric description of triclinic boxes, as defined by LAMMPS, and

doc/src/rerun.txt

@@ -89,12 +89,23 @@ this auxiliary information should be defined in the usual way, e.g. in
 a data file read in by a "read_data"_read_data.html command, before
 using the rerun command.
 
+Also note that the frequency of thermodynamic or dump output from the
+rerun simulation will depend on settings made in the rerun script, the
+same as for output from any LAMMPS simulation.  See further info below
+as to what that means if the timesteps for snapshots read from dump
+files do not match the specified output frequency.
+
 :line
 
 If more than one dump file is specified, the dump files are read one
 after the other.  It is assumed that snapshot timesteps will be in
 ascending order.  If a snapshot is encountered that is not in
-ascending order, it will cause the rerun command to complete.
+ascending order, it will skip the snapshot until it reads one that is.
+This allows skipping of a duplicate snapshot (same timestep),
+e.g. that appeared at the end of one file and beginning of the next.
+However if you specify a series of dump files in an incorrect order
+(with respect to the timesteps they contain), you may skip large
+numbers of snapshots
 
 The {first}, {last}, {every}, {skip} keywords determine which
 snapshots are read from the dump file(s).  Snapshots are skipped until
@@ -177,12 +188,12 @@ a timestep it expects to be, LAMMPS will flag an error.
 
 The various forms of LAMMPS output, as defined by the
 "thermo_style"_thermo_style.html, "thermo"_thermo.html,
-"dump"_dump.html, and "restart"_restart.html commands occur on
-specific timesteps.  If successive dump snapshots skip those
-timesteps, then no output will be produced.  E.g. if you request
-thermodynamic output every 100 steps, but the dump file snapshots are
-every 1000 steps, then you will only see thermodynamic output every
-1000 steps.
+"dump"_dump.html, and "restart"_restart.html commands occur with
+specified frequency, e.g. every N steps.  If the timestep for a dump
+snapshot is not a multiple of N, then it will be read and processed,
+but no output will be produced.  If you want output for every dump
+snapshot, you can simply use N=1 for an output frequency, e.g. for
+thermodynamic output or new dump file output.
 
 :line
 

doc/utils/sphinx-config/false_positives.txt

@@ -63,7 +63,6 @@ aliceblue
 allocaters
 allosws
 AlO
-alond
 Alonso
 amap
 Amatrix
@@ -436,6 +435,9 @@ CSiC
 csld
 cslib
 CSlib
+cstdio
+cstdlib
+cstring
 cstyle
 csvr
 Ctypes
@@ -507,6 +509,7 @@ deepskyblue
 defgrad
 deformable
 del
+deleteIDs
 Dellago
 delocalization
 delocalized
@@ -571,6 +574,7 @@ dlopen
 dm
 dmax
 Dmax
+dmg
 dmi
 dnf
 Dobson
@@ -904,6 +908,7 @@ gcc
 gcmc
 gdot
 GeC
+gencode
 georg
 Georg
 Germann
@@ -1133,6 +1138,7 @@ inv
 invariants
 inversed
 ionocovalent
+iostreams
 iparam
 ipi
 ipp
@@ -1270,6 +1276,7 @@ Klapp
 Kloss
 kmax
 Kmax
+Knizhnik
 knl
 Kohlmeyer
 Kohn
@@ -1342,6 +1349,8 @@ lcbop
 ld
 ldfftw
 ldg
+Lebedeva
+lebedeva
 Lebold
 Lechman
 Lehoucq
@@ -1437,6 +1446,7 @@ Lorant
 lorenz
 lossless
 lossy
+Lozovik
 lps
 lpsapi
 lrt
@@ -1521,6 +1531,7 @@ mdf
 mdpd
 mDPD
 meam
+meamc
 MEAMC
 meamf
 meanDist
@@ -2080,12 +2091,14 @@ polydisperse
 polydispersity
 polyhedra
 popen
+Popov
 popstore
 Poresag
 pos
 Poschel
 posix
 Postma
+Potapkin
 potin
 Pourtois
 powderblue
@@ -2498,7 +2511,9 @@ Startstep
 statcoul
 statcoulombs
 statvolt
+stdlib
 stdin
+stdio
 steelblue
 Stegailov
 Steinbach

examples/USER/awpmd/in.h_atom

@@ -1,5 +1,4 @@
 variable	sname index h_atom
-log		${sname}.spe.log
 
 units 		real
 newton		on
@@ -37,4 +36,4 @@ variable        press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
 thermo          1
 thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press 
 
-run 		0
+run 		10

examples/USER/awpmd/in.h_molecule

@@ -1,5 +1,4 @@
 variable	sname index h_molecule
-log		${sname}.spe.log
 
 units 		real
 newton		on
@@ -37,4 +36,4 @@ variable        press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
 thermo          1
 thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press 
 
-run 		0
+run 		10

examples/USER/awpmd/log.27Nov18.h_atom.g++.1

@@ -0,0 +1,100 @@
+LAMMPS (27 Nov 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+  using 1 OpenMP thread(s) per MPI task
+variable	sname index h_atom
+
+units 		real
+newton		on
+boundary        p p p
+processors      1 * *
+
+
+atom_style	wavepacket
+
+read_data  	data.${sname}
+read_data  	data.h_atom
+  orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2 atoms
+
+#neighbor        2.0 nsq
+
+pair_style      awpmd/cut -1. hartree ermscale 0.99 free flex_press
+pair_coeff 	    * *
+
+
+
+timestep        0.001
+
+fix             1 all nve/awpmd
+
+comm_modify	vel yes
+
+compute         energies all pair awpmd/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        estatics equal c_energies[3]
+variable        errestrain equal c_energies[4]
+
+compute         peratom all stress/atom NULL
+compute         p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
+variable        press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
+
+thermo          1
+thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
+
+run 		10
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.52918
+  ghost atom cutoff = 2.52918
+  binsize = 1.26459, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair awpmd/cut, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
+Per MPI rank memory allocation (min/avg/max) = 5.111 | 5.111 | 5.111 Mbytes
+Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press 
+       0    -266.3192    -266.3192            0    266.32732            0   -532.64652            0            0    156.59865           -0 
+       1    -266.3192    -266.3192            0    266.32746            0   -532.64666            0            0    159.30733           -0 
+       2    -266.3192    -266.3192 1.7273458e-17    266.32797            0   -532.64718            0 5.7948873e-15    169.14686 6.6606909e-13 
+       3    -266.3192    -266.3192 4.6899813e-15    266.32927            0   -532.64847            0 1.5733915e-12    194.06892 1.8084691e-10 
+       4    -266.3192    -266.3192 1.4824973e-13    266.33199            0    -532.6512            0 4.9734712e-11    246.65762 5.7165485e-09 
+       5    -266.3192    -266.3192 1.9298888e-12    266.33712            0   -532.65632            0 6.4743771e-10    345.53056 7.441702e-08 
+       6    -266.3192    -266.3192 1.5343223e-11    266.34601            0   -532.66521            0 5.1473332e-09    516.91949 5.9163869e-07 
+       7    -266.3192    -266.3192 8.8661674e-11    266.36051            0    -532.6797            0 2.9744154e-08     796.4357 3.4188175e-06 
+       8   -266.31919   -266.31919 4.0865149e-10    266.38304            0   -532.70223            0 1.3709411e-07    1231.0302 1.5757709e-05 
+       9   -266.31918   -266.31918 1.5889509e-09    266.41674            0   -532.73592            0 5.3306012e-07    1881.1652 6.1270366e-05 
+      10   -266.31916   -266.31916 5.4070747e-09    266.46554            0    -532.7847            0 1.8139615e-06    2823.2238 0.00020849822 
+Loop time of 0.000725031 on 1 procs for 10 steps with 2 atoms
+
+Performance: 1.192 ns/day, 20.140 hours/ns, 13792.516 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    | 0.00030851 | 0.00030851 | 0.00030851 |   0.0 | 42.55
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0001204  | 0.0001204  | 0.0001204  |   0.0 | 16.61
+Output  | 0.00028038 | 0.00028038 | 0.00028038 |   0.0 | 38.67
+Modify  | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 |   0.0 |  0.85
+Other   |            | 9.537e-06  |            |       |  1.32
+
+Nlocal:    2 ave 2 max 2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    248 ave 248 max 248 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    225 ave 225 max 225 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 225
+Ave neighs/atom = 112.5
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/USER/awpmd/log.27Nov18.h_atom.g++.4

@@ -0,0 +1,100 @@
+LAMMPS (27 Nov 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+  using 1 OpenMP thread(s) per MPI task
+variable	sname index h_atom
+
+units 		real
+newton		on
+boundary        p p p
+processors      1 * *
+
+
+atom_style	wavepacket
+
+read_data  	data.${sname}
+read_data  	data.h_atom
+  orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2 atoms
+
+#neighbor        2.0 nsq
+
+pair_style      awpmd/cut -1. hartree ermscale 0.99 free flex_press
+pair_coeff 	    * *
+
+
+
+timestep        0.001
+
+fix             1 all nve/awpmd
+
+comm_modify	vel yes
+
+compute         energies all pair awpmd/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        estatics equal c_energies[3]
+variable        errestrain equal c_energies[4]
+
+compute         peratom all stress/atom NULL
+compute         p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
+variable        press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
+
+thermo          1
+thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
+
+run 		10
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.52918
+  ghost atom cutoff = 2.52918
+  binsize = 1.26459, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair awpmd/cut, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
+Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes
+Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press 
+       0    -266.3192    -266.3192            0    266.32732            0   -532.64652            0            0    156.59865           -0 
+       1    -266.3192    -266.3192            0    266.32789            0   -532.64709            0            0    167.49891           -0 
+       2    -266.3192    -266.3192 1.219316e-15     266.3314            0    -532.6506            0 4.0905525e-13     235.2267 4.7017146e-11 
+       3    -266.3192    -266.3192 8.3179871e-14    266.34548            0   -532.66468            0 2.7905123e-11    506.68594 3.2074377e-09 
+       4    -266.3192    -266.3192 4.4091748e-12    266.39036            0   -532.70955            0 1.4791868e-09    1372.0565 1.7001894e-07 
+       5   -266.31916   -266.31916 9.8904198e-11    266.51357            0   -532.83273            0 3.3180309e-08    3748.6725 3.8137718e-06 
+       6   -266.31893   -266.31893 1.3132578e-09    266.81733            0   -533.13626            0 4.4057077e-07    9611.8807 5.0639565e-05 
+       7   -266.31762   -266.31762 1.2317167e-08    267.50719            0   -533.82481            0 4.1321544e-06     22950.26 0.00047495321 
+       8   -266.31123   -266.31123 9.0048883e-08    268.97689            0   -535.28812            0 3.0209534e-05    51470.197 0.0034723086 
+       9   -266.28324   -266.28324 5.4612621e-07    271.95757            0   -538.24082            0 0.00018321403    109735.25   0.02105877 
+      10   -266.17113   -266.17114 2.8729529e-06    277.79384            0   -543.96498            0 0.00096381615    225424.02   0.11078182 
+Loop time of 0.00176561 on 4 procs for 10 steps with 2 atoms
+
+Performance: 0.489 ns/day, 49.045 hours/ns, 5663.769 timesteps/s
+87.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.3419e-05 | 0.00012642 | 0.00030923 |   0.0 |  7.16
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00073171 | 0.00086534 | 0.001025   |   0.0 | 49.01
+Output  | 0.00063562 | 0.00075388 | 0.00094962 |   0.0 | 42.70
+Modify  | 3.8147e-06 | 4.4703e-06 | 6.1989e-06 |   0.0 |  0.25
+Other   |            | 1.55e-05   |            |       |  0.88
+
+Nlocal:    0.5 ave 2 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost:    249.5 ave 250 max 248 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs:    56.25 ave 225 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 225
+Ave neighs/atom = 112.5
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/USER/awpmd/log.27Nov18.h_molecule.g++.1

@@ -0,0 +1,100 @@
+LAMMPS (27 Nov 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+  using 1 OpenMP thread(s) per MPI task
+variable	sname index h_molecule
+
+units 		real
+newton		on
+boundary        p p p
+processors      1 * *
+
+
+atom_style	wavepacket
+
+read_data  	data.${sname}
+read_data  	data.h_molecule
+  orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  4 atoms
+
+#neighbor        2.0 nsq
+
+pair_style      awpmd/cut -1. hartree ermscale 0.99 free flex_press
+pair_coeff 	    * *
+
+
+
+timestep        0.001
+
+fix             1 all nve/awpmd
+
+comm_modify	vel yes
+
+compute         energies all pair awpmd/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        estatics equal c_energies[3]
+variable        errestrain equal c_energies[4]
+
+compute         peratom all stress/atom NULL
+compute         p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
+variable        press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
+
+thermo          1
+thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
+
+run 		10
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.52918
+  ghost atom cutoff = 2.52918
+  binsize = 1.26459, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair awpmd/cut, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
+Per MPI rank memory allocation (min/avg/max) = 5.142 | 5.142 | 5.142 Mbytes
+Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press 
+       0    30358.159    30358.159            0     39537.73 -1.5916157e-12   -9179.5713            0            0 1.3475994e+09           -0 
+       1     30360.49    30360.489 0.0009272222    39540.081 2.0463631e-12   -9179.5926            0   0.10368794 1.3476061e+09    35.753932 
+       2    67447.779    67447.776   0.00370884     80547.07 -1.1368684e-12   -13099.294            0   0.41474633 2.8529839e+09    143.01385 
+       3    3713046.5    3713046.5 0.0041850026    3803060.3 -1.29603e-10   -90013.788            0   0.46799388 1.4486958e+11     161.3748 
+       4    2445632.1      2445620    12.171486    2452194.4 -9.777068e-11   -6574.4062            0    1361.0937 -6.5572589e+08    469335.68 
+       5    2434860.1    2434845.9    14.215419    2433638.8 -1.0663825e-10    1207.1541            0    1589.6595   -359380.29    548150.31 
+       6    2444984.1    2444969.8    14.215428      2451100 5.1841198e-11   -6130.1373            0    1589.6605 -5.6327282e+08    548150.63 
+       7    2436128.7    2436110.9    17.793789    2434903.7 2.0190782e-10     1207.154            0    1989.8158   -221406.77    686133.18 
+       8    2444786.5    2444768.7    17.793798    2450583.8 -1.1027623e-10   -5815.0651            0    1989.8169 -5.0227031e+08    686133.54 
+       9    2437198.9    2437175.9    22.942086    2435968.8 2.2600943e-10    1207.1538            0    2565.5315   -22903.736    884652.88 
+      10    2444787.1    2444764.2    22.942097    2450333.1 -3.1832315e-11   -5568.9214            0    2565.5327 -4.5741803e+08     884653.3 
+Loop time of 0.00158453 on 1 procs for 10 steps with 4 atoms
+
+Performance: 0.545 ns/day, 44.015 hours/ns, 6311.020 timesteps/s
+85.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00088882 | 0.00088882 | 0.00088882 |   0.0 | 56.09
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00031352 | 0.00031352 | 0.00031352 |   0.0 | 19.79
+Output  | 0.00036216 | 0.00036216 | 0.00036216 |   0.0 | 22.86
+Modify  | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 |   0.0 |  0.38
+Other   |            | 1.407e-05  |            |       |  0.89
+
+Nlocal:    4 ave 4 max 4 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    596 ave 596 max 596 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    966 ave 966 max 966 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 966
+Ave neighs/atom = 241.5
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/USER/awpmd/log.27Nov18.h_molecule.g++.4

@@ -0,0 +1,100 @@
+LAMMPS (27 Nov 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
+  using 1 OpenMP thread(s) per MPI task
+variable	sname index h_molecule
+
+units 		real
+newton		on
+boundary        p p p
+processors      1 * *
+
+
+atom_style	wavepacket
+
+read_data  	data.${sname}
+read_data  	data.h_molecule
+  orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  4 atoms
+
+#neighbor        2.0 nsq
+
+pair_style      awpmd/cut -1. hartree ermscale 0.99 free flex_press
+pair_coeff 	    * *
+
+
+
+timestep        0.001
+
+fix             1 all nve/awpmd
+
+comm_modify	vel yes
+
+compute         energies all pair awpmd/cut
+variable        eke equal c_energies[1]
+variable        epauli equal c_energies[2]
+variable        estatics equal c_energies[3]
+variable        errestrain equal c_energies[4]
+
+compute         peratom all stress/atom NULL
+compute         p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
+variable        press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
+
+thermo          1
+thermo_style    custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
+
+run 		10
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.52918
+  ghost atom cutoff = 2.52918
+  binsize = 1.26459, bins = 1 1 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair awpmd/cut, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933)
+Per MPI rank memory allocation (min/avg/max) = 5.172 | 5.234 | 5.422 Mbytes
+Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press 
+       0    30358.159    30358.159            0     39537.73 -1.5916157e-12   -9179.5713            0            0 1.3475994e+09           -0 
+       1    30360.982    30360.981 0.0009272222    39540.638 -1.1368684e-12   -9179.6571            0   0.10368794 1.3476263e+09    35.753932 
+       2    67459.392    67459.388 0.0037086548     80559.71 6.5938366e-12   -13100.322            0   0.41472561 2.8534514e+09     143.0067 
+       3    3732209.2    3732209.2 0.0041861902    3822452.2 -3.1604941e-11   -90242.984            0   0.46812669 1.4561246e+11    161.42059 
+       4    2482974.7    2482961.9    12.860712    2489531.2 -2.2896529e-10   -6569.2968            0    1438.1675 -6.5458119e+08    495912.44 
+       5    2472238.2    2472223.2    14.933049    2471015.7 -1.6120794e-10    1207.5188            0    1669.9095   -324992.65     575822.3 
+       6    2482233.1    2482218.1    14.933057    2488321.7 -2.0691004e-11   -6103.5677            0    1669.9104 -5.5786438e+08    575822.62 
+       7    2473498.5    2473479.8     18.61401    2472272.3 1.459739e-10    1207.5167            0    2081.5382   -183348.11    717761.12 
+       8    2481621.3    2481602.6    18.614019    2487299.1 7.0258466e-11   -5696.4589            0    2081.5393 -4.7962801e+08    717761.48 
+       9    2474506.2    2474482.2    24.021181    2473274.7 2.1395863e-10     1207.508            0    2686.2029    24318.554    926263.07 
+      10    2480376.3    2480352.2    24.021192      2485505 -8.5719876e-11   -5152.7478            0    2686.2041 -3.8355089e+08    926263.48 
+Loop time of 0.00267726 on 4 procs for 10 steps with 4 atoms
+
+Performance: 0.323 ns/day, 74.368 hours/ns, 3735.160 timesteps/s
+91.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00011826 | 0.00027376 | 0.00073862 |   0.0 | 10.23
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00080514 | 0.0011864  | 0.001574   |   0.9 | 44.31
+Output  | 0.00094914 | 0.0011944  | 0.0017326  |   0.9 | 44.61
+Modify  | 3.3379e-06 | 4.4703e-06 | 6.1989e-06 |   0.0 |  0.17
+Other   |            | 1.824e-05  |            |       |  0.68
+
+Nlocal:    1 ave 4 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost:    599 ave 600 max 596 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs:    241.5 ave 966 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 966
+Ave neighs/atom = 241.5
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/USER/bocs/log.27Nov18.methanol.g++.1

@@ -1,5 +1,4 @@
-LAMMPS (20 Apr 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+LAMMPS (27 Nov 2018)
   using 1 OpenMP thread(s) per MPI task
 units		real
 dimension	3
@@ -21,7 +20,7 @@ pair_style	table spline 15000
 
 pair_coeff	1 1 lammps_nb_MET-MET.table nb_METMET 12.0
 WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:481)
+  Should only be flagged at inflection points (src/pair_table.cpp:481)
 
 neigh_modify	delay 0 every 1 check yes one 10000
 neighbor	12.0 bin
@@ -90,54 +89,54 @@ Neighbor list info ...
 Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
 Step Temp PotEng TotEng Press Volume 
        0          300    1061.5961    1926.3291      107.006    66250.679 
-     500    314.54728    1034.1091    1940.7738    194.42689    65660.282 
-    1000    301.41603    1030.7027    1899.5173   -91.966709    66262.543 
-    1500     298.8308    1014.8276    1876.1905   -80.178606    67053.605 
-    2000    294.78476    1046.8207     1896.521    50.592942    66316.735 
-    2500    301.18564    1033.9214    1902.0719     40.48255    66607.667 
-    3000    301.06632    1022.0381    1889.8447    47.582344    66341.947 
-    3500    297.98361    989.80983    1848.7307   -204.69879    67462.078 
-    4000    299.03493    1034.6571    1896.6083    89.188888    66457.385 
-    4500    306.03351     985.4121    1867.5363   -51.102407    67519.446 
-    5000     305.6903    1013.8613    1894.9963   -141.13704    67240.467 
-    5500    292.23444    1029.5558     1871.905    20.764579    66683.876 
-    6000    287.87735    1017.7325    1847.5226   -35.288049    66630.031 
-    6500    305.26461    960.08118    1839.9891   -352.42596    67612.317 
-    7000    300.34449    1055.0664    1920.7923     22.04027     66187.27 
-    7500    305.48612    1038.6651    1919.2115    17.807254    66324.168 
-    8000    316.03232    1034.6809    1945.6262    27.482857    66502.198 
-    8500    294.28636    1038.8213     1887.085   -72.840559    66851.661 
-    9000    316.69029    1065.7481    1978.5899    245.61677    65678.385 
-    9500    297.46127    1034.5547      1891.97     54.23428    66892.627 
-   10000    301.24799    1036.5432    1904.8735    7.7134029    66150.506 
-Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
+     500    314.70267    1036.3305    1943.4431    205.83301     65603.85 
+    1000    304.99804      1034.15    1913.2896   -79.521176     66268.87 
+    1500     305.2621     996.9303     1876.831    -97.93992    67090.442 
+    2000    311.29317    1083.9171    1981.2021    119.28085    65589.674 
+    2500    305.51905      1051.59    1932.2314   -34.076658    66487.327 
+    3000    291.76224     1053.524    1894.5121    45.522865    65879.535 
+    3500    297.65795    1017.1028     1875.085    -79.41965     67185.19 
+    4000    285.98779    1042.3622    1866.7058    88.549172    66357.051 
+    4500       295.35    1071.4505    1922.7801    -16.75965    65378.949 
+    5000    293.20958    1009.9943    1855.1543   -270.58058     67555.38 
+    5500    292.40422    1085.3901    1928.2287    161.88502    65677.644 
+    6000    318.79663    1012.4832    1931.3964   -65.692451     67458.05 
+    6500    308.03807    1046.1413    1934.0436    249.70237    66052.045 
+    7000    289.33716    1037.9657    1871.9636    47.662734    66782.578 
+    7500     297.3092     1032.356    1889.3329   -24.049617     66129.95 
+    8000    298.27827     1044.118    1903.8882    -26.61809    66720.381 
+    8500    299.52706    1026.7068    1890.0766   -128.14995    67695.559 
+    9000    304.67694    1018.2095    1896.4236   -61.360724      65942.4 
+    9500    293.81117    1019.2221    1866.1162   -47.726496    66843.848 
+   10000     309.9256    1043.5321     1936.875   -103.81403     66222.21 
+Loop time of 42.5056 on 1 procs for 10000 steps with 968 atoms
 
-Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s
+Performance: 20.327 ns/day, 1.181 hours/ns, 235.263 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    | 33.324     | 33.324     | 33.324     |   0.0 | 96.80
-Neigh   | 0.12198    | 0.12198    | 0.12198    |   0.0 |  0.35
-Comm    | 0.42865    | 0.42865    | 0.42865    |   0.0 |  1.25
-Output  | 0.00059938 | 0.00059938 | 0.00059938 |   0.0 |  0.00
-Modify  | 0.42553    | 0.42553    | 0.42553    |   0.0 |  1.24
-Other   |            | 0.1252     |            |       |  0.36
+Pair    | 40.972     | 40.972     | 40.972     |   0.0 | 96.39
+Neigh   | 0.18576    | 0.18576    | 0.18576    |   0.0 |  0.44
+Comm    | 0.71338    | 0.71338    | 0.71338    |   0.0 |  1.68
+Output  | 0.00050306 | 0.00050306 | 0.00050306 |   0.0 |  0.00
+Modify  | 0.52926    | 0.52926    | 0.52926    |   0.0 |  1.25
+Other   |            | 0.1042     |            |       |  0.25
 
 Nlocal:    968 ave 968 max 968 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    9112 ave 9112 max 9112 min
+Nghost:    9215 ave 9215 max 9215 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    404392 ave 404392 max 404392 min
+Neighs:    411837 ave 411837 max 411837 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 404392
-Ave neighs/atom = 417.76
+Total # of neighbors = 411837
+Ave neighs/atom = 425.451
 Neighbor list builds = 13
 Dangerous builds = 0
 
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:34
+Total wall time: 0:00:42

examples/USER/bocs/log.27Nov18.methanol.g++.4

@@ -1,5 +1,4 @@
-LAMMPS (20 Apr 2018)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+LAMMPS (27 Nov 2018)
   using 1 OpenMP thread(s) per MPI task
 units		real
 dimension	3
@@ -21,7 +20,7 @@ pair_style	table spline 15000
 
 pair_coeff	1 1 lammps_nb_MET-MET.table nb_METMET 12.0
 WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:481)
+  Should only be flagged at inflection points (src/pair_table.cpp:481)
 
 neigh_modify	delay 0 every 1 check yes one 10000
 neighbor	12.0 bin
@@ -90,54 +89,54 @@ Neighbor list info ...
 Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
 Step Temp PotEng TotEng Press Volume 
        0          300    1061.5961    1926.3291      107.006    66250.679 
-     500    314.54728    1034.1091    1940.7738    194.42689    65660.282 
-    1000    301.41603    1030.7027    1899.5173   -91.966709    66262.543 
-    1500     298.8308    1014.8276    1876.1905   -80.178606    67053.605 
-    2000    294.78476    1046.8207     1896.521    50.592942    66316.735 
-    2500    301.18564    1033.9214    1902.0719    40.482557    66607.667 
-    3000    301.06631    1022.0381    1889.8447    47.582403    66341.947 
-    3500    297.98353    989.81011    1848.7308   -204.69823    67462.076 
-    4000    299.03465    1034.6603    1896.6108    89.196235    66457.338 
-    4500    306.04532    985.37017    1867.5285   -51.094929    67519.735 
-    5000    304.72903    1014.9543    1893.3184   -127.04402    67238.517 
-    5500    292.52622    1025.6599    1868.8502   -19.753932    66716.551 
-    6000    296.82719    1031.5184    1887.1059   -1.2609328    66368.611 
-    6500    298.63312    1018.4299    1879.2229    -24.75835    66524.898 
-    7000    303.25389    1005.9283    1880.0404   -96.273504    67349.674 
-    7500    292.45089    1068.2863    1911.2595    103.23295     65778.08 
-    8000    301.22765    1040.6294    1908.9011  -0.83635353    66831.038 
-    8500    300.19765    1047.5856    1912.8883   -31.582343    66316.305 
-    9000     295.1108    1023.8234    1874.4635   -88.165532    67192.344 
-    9500     302.1087    1003.6348    1874.4459   -18.707065    66369.361 
-   10000     296.3083     1004.126    1858.2178   -28.293045    66862.576 
-Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
+     500    314.70267    1036.3305    1943.4431    205.83301     65603.85 
+    1000    304.99804      1034.15    1913.2896   -79.521176     66268.87 
+    1500     305.2621     996.9303     1876.831    -97.93992    67090.442 
+    2000    311.29317    1083.9171    1981.2021    119.28085    65589.674 
+    2500    305.51905      1051.59    1932.2314   -34.076657    66487.327 
+    3000    291.76224     1053.524    1894.5121    45.522919    65879.535 
+    3500    297.65792    1017.1041    1875.0862   -79.411904    67185.183 
+    4000    285.99141     1042.379     1866.733    88.735986    66356.756 
+    4500    295.34218    1071.2977    1922.6048   -17.479073    65381.597 
+    5000       292.47    1012.3769     1855.405   -255.07433    67527.215 
+    5500    294.04431    1080.4547    1928.0208     192.6588    65811.742 
+    6000    300.45893    986.16669    1852.2225    -167.3405    67858.175 
+    6500    305.59738    1022.5276    1903.3947   -116.41298    66612.704 
+    7000    312.11968    1032.7392    1932.4065    152.17956    66016.299 
+    7500    306.80585    1032.1157    1916.4662     51.07705    66875.727 
+    8000    292.30957    1048.9003    1891.4661    61.280503    65894.103 
+    8500    297.79592    1013.4061     1871.786   -133.01136    66842.574 
+    9000    290.36753    1043.7732    1880.7412    65.208248     66010.86 
+    9500    288.92211    1077.8835    1910.6851    46.291982    65674.639 
+   10000    311.51608    1015.3567    1913.2842   -146.49492    66882.692 
+Loop time of 13.9823 on 4 procs for 10000 steps with 968 atoms
 
-Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
-95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 61.792 ns/day, 0.388 hours/ns, 715.190 timesteps/s
+98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 19.929     | 21.765     | 23.391     |  27.8 | 75.56
-Neigh   | 0.067397   | 0.071231   | 0.077313   |   1.5 |  0.25
-Comm    | 3.9226     | 5.5183     | 7.3214     |  53.7 | 19.16
-Output  | 0.00069928 | 0.0016099  | 0.0043275  |   3.9 |  0.01
-Modify  | 1.0874     | 1.1376     | 1.1888     |   4.2 |  3.95
-Other   |            | 0.3112     |            |       |  1.08
+Pair    | 10.131     | 11.235     | 12.333     |  23.2 | 80.35
+Neigh   | 0.044854   | 0.046303   | 0.047541   |   0.5 |  0.33
+Comm    | 1.1939     | 2.2964     | 3.4087     |  51.7 | 16.42
+Output  | 0.0004735  | 0.0032033  | 0.01137    |   8.3 |  0.02
+Modify  | 0.30542    | 0.31846    | 0.32508    |   1.4 |  2.28
+Other   |            | 0.08323    |            |       |  0.60
 
-Nlocal:    242 ave 244 max 239 min
+Nlocal:    242 ave 248 max 232 min
 Histogram: 1 0 0 0 0 0 1 0 1 1
-Nghost:    5718.5 ave 5736 max 5702 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Neighs:    100703 ave 108064 max 93454 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:    5845.75 ave 5877 max 5808 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+Neighs:    104313 ave 113860 max 95507 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
 
-Total # of neighbors = 402813
-Ave neighs/atom = 416.129
-Neighbor list builds = 14
+Total # of neighbors = 417252
+Ave neighs/atom = 431.045
+Neighbor list builds = 13
 Dangerous builds = 0
 
 
 Please see the log.cite file for references relevant to this simulation
 
-Total wall time: 0:00:28
+Total wall time: 0:00:14

examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1

@@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${e
 #dump_modify out sort id
 #dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
 
-run 1000000
+run 10000
 
 #write_restart config.${number}.*

examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.1

@@ -0,0 +1,172 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+variable number	equal 1
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  10 atoms
+  reading velocities ...
+  10 velocities
+  10 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  8 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+
+set atom * mass 3.1575
+  10 settings made for mass
+
+group all type 1 4
+10 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+fix 1 all nve/dot
+#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.92828
+  ghost atom cutoff = 1.92828
+  binsize = 0.964142, bins = 42 42 42
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair oxdna/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.4711818 0.0069384985   -1.4642433 -6.2745089e-05 
+1000  ekin = 0.00113448721737003 |  erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
+2000  ekin = 0.00449927223902336 |  erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
+3000  ekin = 0.00997964450841065 |  erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
+4000  ekin = 0.0173888111295073 |  erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436
+5000  ekin = 0.0264744514136619 |  erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104
+6000  ekin = 0.0369277948556079 |  erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875
+7000  ekin = 0.04839505571915 |  erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172
+8000  ekin = 0.0604909336920643 |  erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611
+9000  ekin = 0.0728137406440561 |  erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514
+10000  ekin = 0.0849615563085879 |  erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398
+   10000 0.0062934486   -1.5138305 0.0067255788   -1.4986088 -9.9021593e-05 
+Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms
+
+Performance: 60875.649 tau/day, 70457.927 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.11467    | 0.11467    | 0.11467    |   0.0 | 80.79
+Bond    | 0.0050094  | 0.0050094  | 0.0050094  |   0.0 |  3.53
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0013616  | 0.0013616  | 0.0013616  |   0.0 |  0.96
+Output  | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 |   0.0 |  0.00
+Modify  | 0.017901   | 0.017901   | 0.017901   |   0.0 | 12.61
+Other   |            | 0.002982   |            |       |  2.10
+
+Nlocal:    10 ave 10 max 10 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    43 ave 43 max 43 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 43
+Ave neighs/atom = 4.3
+Ave special neighs/atom = 3.6
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:00

examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.4

@@ -0,0 +1,172 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+variable number	equal 1
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  10 atoms
+  reading velocities ...
+  10 velocities
+  10 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  8 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+
+set atom * mass 3.1575
+  10 settings made for mass
+
+group all type 1 4
+10 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+fix 1 all nve/dot
+#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.92828
+  ghost atom cutoff = 1.92828
+  binsize = 0.964142, bins = 42 42 42
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair oxdna/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.4711818 0.0069384985   -1.4642433 -6.2745089e-05 
+1000  ekin = 0.00113448721737009 |  erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
+2000  ekin = 0.00449927223902292 |  erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
+3000  ekin = 0.00997964450840756 |  erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892
+4000  ekin = 0.017388811129498 |  erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436
+5000  ekin = 0.0264744514136422 |  erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104
+6000  ekin = 0.0369277948555727 |  erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875
+7000  ekin = 0.0483950557190949 |  erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172
+8000  ekin = 0.0604909336919856 |  erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611
+9000  ekin = 0.0728137406439517 |  erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514
+10000  ekin = 0.0849615563084573 |  erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398
+   10000 0.0062934486   -1.5138305 0.0067255788   -1.4986088 -0.00010196899 
+Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms
+
+Performance: 64220.659 tau/day, 74329.466 timesteps/s
+97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0030077  | 0.052212   | 0.093066   |  17.4 | 38.81
+Bond    | 0.00061846 | 0.00234    | 0.0039451  |   2.8 |  1.74
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.013431   | 0.014091   | 0.014596   |   0.4 | 10.47
+Output  | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 |   0.0 |  0.04
+Modify  | 0.0011578  | 0.0059478  | 0.010331   |   4.8 |  4.42
+Other   |            | 0.05989    |            |       | 44.52
+
+Nlocal:    2.5 ave 5 max 0 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost:    7.5 ave 10 max 5 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Neighs:    17.5 ave 33 max 0 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+
+Total # of neighbors = 70
+Ave neighs/atom = 7
+Ave special neighs/atom = 3.6
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:00

examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2

@@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${e
 #dump_modify out sort id
 #dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
 
-run 1000000
+run 10000
 
 #write_restart config.${number}.*

examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.1

@@ -0,0 +1,172 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+variable number	equal 2
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  16 atoms
+  reading velocities ...
+  16 velocities
+  16 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  13 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+
+set atom * mass 3.1575
+  16 settings made for mass
+
+group all type 1 4
+16 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+#fix 1 all nve/dot
+fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.92828
+  ghost atom cutoff = 1.92828
+  binsize = 0.964142, bins = 42 42 42
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair oxdna/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.5402493 0.0070469125   -1.5332024 -8.5641987e-05 
+1000  ekin = 1.54234964773389 |  erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
+2000  ekin = 1.85988866919215 |  erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
+3000  ekin = 2.68354339452998 |  erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
+4000  ekin = 2.04461800191989 |  erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832
+5000  ekin = 1.76794859210155 |  erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266
+6000  ekin = 3.1106424806079 |  erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964
+7000  ekin = 3.21360097519306 |  erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
+8000  ekin = 2.82489935901743 |  erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989
+9000  ekin = 2.69381302856378 |  erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
+10000  ekin = 2.65765007662471 |  erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
+   10000   0.11811778   -1.4992295  0.011864944   -1.3212615 -0.00013416809 
+Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms
+
+Performance: 29234.801 tau/day, 33836.575 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    | 0.20959    | 0.20959    | 0.20959    |   0.0 | 70.92
+Bond    | 0.0073669  | 0.0073669  | 0.0073669  |   0.0 |  2.49
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0016472  | 0.0016472  | 0.0016472  |   0.0 |  0.56
+Output  | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 |   0.0 |  0.00
+Modify  | 0.073117   | 0.073117   | 0.073117   |   0.0 | 24.74
+Other   |            | 0.003813   |            |       |  1.29
+
+Nlocal:    16 ave 16 max 16 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    88 ave 88 max 88 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 88
+Ave neighs/atom = 5.5
+Ave special neighs/atom = 3.75
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:00

examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.4

@@ -0,0 +1,172 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+variable number	equal 2
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  16 atoms
+  reading velocities ...
+  16 velocities
+  16 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  13 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+
+set atom * mass 3.1575
+  16 settings made for mass
+
+group all type 1 4
+16 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna/fene
+bond_coeff * 2.0 0.25 0.7525
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
+pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
+
+# NVE ensemble
+#fix 1 all nve/dot
+fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.92828
+  ghost atom cutoff = 1.92828
+  binsize = 0.964142, bins = 42 42 42
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair oxdna/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.5402493 0.0070469125   -1.5332024 -8.5641987e-05 
+1000  ekin = 1.34565986428024 |  erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
+2000  ekin = 2.15911766687235 |  erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504
+3000  ekin = 3.26561948796015 |  erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198
+4000  ekin = 1.92438809241066 |  erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506
+5000  ekin = 1.35986357015476 |  erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
+6000  ekin = 2.19432475124593 |  erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
+7000  ekin = 2.65619274477635 |  erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
+8000  ekin = 2.51333548501168 |  erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614
+9000  ekin = 2.24506493169711 |  erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
+10000  ekin = 2.36632635249862 |  erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463
+   10000   0.10517006   -1.5057137  0.011947302    -1.345871 -9.5924016e-05 
+Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms
+
+Performance: 34303.820 tau/day, 39703.495 timesteps/s
+97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0035377  | 0.092047   | 0.17435    |  26.0 | 36.55
+Bond    | 0.00065637 | 0.0031857  | 0.0053554  |   3.8 |  1.26
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.013929   | 0.01497    | 0.015733   |   0.6 |  5.94
+Output  | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 |   0.0 |  0.02
+Modify  | 0.0013576  | 0.020825   | 0.040231   |  11.8 |  8.27
+Other   |            | 0.1208     |            |       | 47.96
+
+Nlocal:    4 ave 8 max 0 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    9 ave 10 max 8 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    34.5 ave 67 max 0 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 138
+Ave neighs/atom = 8.625
+Ave special neighs/atom = 3.75
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:00

examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1

@@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${e
 #dump_modify out sort id
 #dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
 
-run 1000000
+run 10000
 
 #write_restart config.${number}.*

examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.1

@@ -0,0 +1,178 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+variable number	equal 1
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  10 atoms
+  reading velocities ...
+  10 velocities
+  10 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  8 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+
+set atom * mass 3.1575
+  10 settings made for mass
+
+group all type 1 4
+10 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      0.1 1.0 0.815
+
+# NVE ensemble
+fix 1 all nve/dot
+#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.6274
+  ghost atom cutoff = 2.6274
+  binsize = 1.3137, bins = 31 31 31
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.4712768  0.009525411   -1.4617514 -5.8922361e-05 
+1000  ekin = 0.00113086229080528 |  erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
+2000  ekin = 0.0044853322434243 |  erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675
+3000  ekin = 0.00995035259649284 |  erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093
+4000  ekin = 0.0173418024862054 |  erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659
+5000  ekin = 0.0264109356286075 |  erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355
+6000  ekin = 0.0368533113591442 |  erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157
+7000  ekin = 0.0483200640564843 |  erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036
+8000  ekin = 0.0604312317605998 |  erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962
+9000  ekin = 0.0727907119671751 |  erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899
+10000  ekin = 0.0850022498875221 |  erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815
+   10000  0.006296463   -1.5144685 0.0085391004   -1.4974292 -0.00010794792 
+Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms
+
+Performance: 57828.835 tau/day, 66931.522 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.11971    | 0.11971    | 0.11971    |   0.0 | 80.12
+Bond    | 0.0051196  | 0.0051196  | 0.0051196  |   0.0 |  3.43
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0013614  | 0.0013614  | 0.0013614  |   0.0 |  0.91
+Output  | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 |   0.0 |  0.00
+Modify  | 0.018941   | 0.018941   | 0.018941   |   0.0 | 12.68
+Other   |            | 0.004268   |            |       |  2.86
+
+Nlocal:    10 ave 10 max 10 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    45 ave 45 max 45 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 45
+Ave neighs/atom = 4.5
+Ave special neighs/atom = 3.6
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:00

examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.4

@@ -0,0 +1,178 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+variable number	equal 1
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex1
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  10 atoms
+  reading velocities ...
+  10 velocities
+  10 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  8 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+
+set atom * mass 3.1575
+  10 settings made for mass
+
+group all type 1 4
+10 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      0.1 1.0 0.815
+
+# NVE ensemble
+fix 1 all nve/dot
+#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.6274
+  ghost atom cutoff = 2.6274
+  binsize = 1.3137, bins = 31 31 31
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.4712768  0.009525411   -1.4617514 -5.8922361e-05 
+1000  ekin = 0.00113086229080478 |  erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
+2000  ekin = 0.00448533224342286 |  erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675
+3000  ekin = 0.0099503525964896 |  erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093
+4000  ekin = 0.0173418024861991 |  erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659
+5000  ekin = 0.0264109356285965 |  erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355
+6000  ekin = 0.0368533113591268 |  erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156
+7000  ekin = 0.0483200640564584 |  erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036
+8000  ekin = 0.0604312317605635 |  erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962
+9000  ekin = 0.072790711967127 |  erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899
+10000  ekin = 0.0850022498874609 |  erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815
+   10000  0.006296463   -1.5144685 0.0085391004   -1.4974292 -0.00010794792 
+Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms
+
+Performance: 59247.054 tau/day, 68572.979 timesteps/s
+97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0034175  | 0.055587   | 0.10059    |  17.9 | 38.12
+Bond    | 0.00064635 | 0.002131   | 0.0035357  |   2.5 |  1.46
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.014538   | 0.014932   | 0.015271   |   0.2 | 10.24
+Output  | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 |   0.0 |  0.04
+Modify  | 0.0012829  | 0.0063873  | 0.011321   |   5.2 |  4.38
+Other   |            | 0.06674    |            |       | 45.76
+
+Nlocal:    2.5 ave 5 max 0 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Nghost:    7.5 ave 10 max 5 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+Neighs:    18.5 ave 35 max 0 min
+Histogram: 1 0 1 0 0 0 0 0 1 1
+
+Total # of neighbors = 74
+Ave neighs/atom = 7.4
+Ave special neighs/atom = 3.6
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:00

examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2

@@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${e
 #dump_modify out sort id
 #dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
 
-run 1000000
+run 10000
 
 #write_restart config.${number}.*

examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.1

@@ -0,0 +1,178 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+variable number	equal 2
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  16 atoms
+  reading velocities ...
+  16 velocities
+  16 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  13 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+
+set atom * mass 3.1575
+  16 settings made for mass
+
+group all type 1 4
+16 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      0.1 1.0 0.815
+
+# NVE ensemble
+#fix 1 all nve/dot
+fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.6274
+  ghost atom cutoff = 2.6274
+  binsize = 1.3137, bins = 31 31 31
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.5358787 0.0096742456   -1.5262045 -7.9568629e-05 
+1000  ekin = 1.54282272464468 |  erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
+2000  ekin = 1.86109566690716 |  erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591
+3000  ekin = 2.68769182431188 |  erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324
+4000  ekin = 2.04710303757243 |  erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247
+5000  ekin = 1.77654023802719 |  erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361
+6000  ekin = 3.12253137872527 |  erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178
+7000  ekin = 3.22418765752177 |  erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928
+8000  ekin = 2.83204202112963 |  erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092
+9000  ekin = 2.69585642754481 |  erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833
+10000  ekin = 2.66058119525512 |  erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566
+   10000   0.11824805   -1.4953627  0.013284973   -1.3157914 -0.00012999454 
+Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms
+
+Performance: 26356.746 tau/day, 30505.493 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.24211    | 0.24211    | 0.24211    |   0.0 | 73.86
+Bond    | 0.0075173  | 0.0075173  | 0.0075173  |   0.0 |  2.29
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0014515  | 0.0014515  | 0.0014515  |   0.0 |  0.44
+Output  | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 |   0.0 |  0.00
+Modify  | 0.073331   | 0.073331   | 0.073331   |   0.0 | 22.37
+Other   |            | 0.003398   |            |       |  1.04
+
+Nlocal:    16 ave 16 max 16 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    116 ave 116 max 116 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 116
+Ave neighs/atom = 7.25
+Ave special neighs/atom = 3.75
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:00

examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.4

@@ -0,0 +1,178 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+variable number	equal 2
+variable ofreq	equal 1000
+variable efreq	equal 1000
+
+units lj
+
+dimension 3
+
+newton off
+
+boundary  p p p
+
+atom_style hybrid bond ellipsoid
+atom_modify sort 0 1.0
+
+# Pair interactions require lists of neighbours to be calculated
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+read_data data.duplex2
+  orthogonal box = (-20 -20 -20) to (20 20 20)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  16 atoms
+  reading velocities ...
+  16 velocities
+  16 ellipsoids
+  scanning bonds ...
+  2 = max bonds/atom
+  reading bonds ...
+  13 bonds
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+
+set atom * mass 3.1575
+  16 settings made for mass
+
+group all type 1 4
+16 atoms in group all
+
+# oxDNA bond interactions - FENE backbone
+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
+pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      0.1 1.0 0.815
+
+# NVE ensemble
+#fix 1 all nve/dot
+fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+timestep 1e-5
+
+#comm_style tiled
+#fix 3 all balance 10000 1.1 rcb
+
+#compute mol all chunk/atom molecule
+#compute mychunk all vcm/chunk mol
+#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
+
+#dump pos all xyz ${ofreq} traj.${number}.xyz
+
+#compute quat all property/atom quatw quati quatj quatk
+#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
+#dump_modify quat sort id
+#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
+
+compute erot all erotate/asphere
+compute ekin all ke
+compute epot all pe
+variable erot equal c_erot
+variable ekin equal c_ekin
+variable epot equal c_epot
+variable etot equal c_erot+c_ekin+c_epot
+fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+fix 5 all print 1000 "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
+
+#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
+#dump_modify out sort id
+#dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
+
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.6274
+  ghost atom cutoff = 2.6274
+  binsize = 1.3137, bins = 31 31 31
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair oxdna2/excv, perpetual
+      attributes: half, newton off
+      pair build: half/bin/newtoff
+      stencil: half/bin/3d/newtoff
+      bin: standard
+  (2) pair oxdna2/stk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) pair oxdna2/hbond, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (4) pair oxdna2/xstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) pair oxdna2/coaxstk, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) pair oxdna2/dh, perpetual, copy from (1)
+      attributes: half, newton off
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -1.5358787 0.0096742456   -1.5262045 -7.9568629e-05 
+1000  ekin = 1.34554291364716 |  erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
+2000  ekin = 2.15972469811184 |  erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481
+3000  ekin = 3.26433550542939 |  erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125
+4000  ekin = 1.9203212531997 |  erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703
+5000  ekin = 1.35481075814721 |  erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963
+6000  ekin = 2.18974627635306 |  erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531
+7000  ekin = 2.65472853187395 |  erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691
+8000  ekin = 2.51192327964357 |  erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058
+9000  ekin = 2.24554900802464 |  erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658
+10000  ekin = 2.36227360512089 |  erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535
+   10000   0.10498994   -1.5020657  0.015857071   -1.3385665 -8.8930899e-05 
+Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms
+
+Performance: 29625.313 tau/day, 34288.557 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    | 0.0035026  | 0.1107     | 0.20674    |  28.3 | 37.96
+Bond    | 0.00062203 | 0.0029532  | 0.0049176  |   3.6 |  1.01
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.016712   | 0.018041   | 0.01914    |   0.7 |  6.19
+Output  | 5.0306e-05 | 5.424e-05  | 5.579e-05  |   0.0 |  0.02
+Modify  | 0.0013862  | 0.020914   | 0.039594   |  11.7 |  7.17
+Other   |            | 0.139      |            |       | 47.65
+
+Nlocal:    4 ave 8 max 0 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    11 ave 14 max 8 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:    46 ave 89 max 0 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 184
+Ave neighs/atom = 11.5
+Ave special neighs/atom = 3.75
+Neighbor list builds = 0
+Dangerous builds = 0
+
+#write_restart config.${number}.*
+Total wall time: 0:00:00

examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1

@@ -1,5 +1,4 @@
-LAMMPS (20 Mar 2014-ICMS)
-WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
+LAMMPS (27 Nov 2018)
   using 1 OpenMP thread(s) per MPI task
 # Solvated 5-mer peptide
 
@@ -19,7 +18,7 @@ special_bonds	lj/coul 0.0 0.0 1.0
 
 read_data	data.pegc12e8.gz
   orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
-  2 by 1 by 1 MPI processor grid
+  1 by 1 by 1 MPI processor grid
   reading atoms ...
   40140 atoms
   reading velocities ...
@@ -52,59 +51,71 @@ fix		1 all nvt temp 303.0 303.0 100.0
 thermo_style	multi
 thermo		200
 run		1000
-Memory usage per processor = 12.4188 Mbytes
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 15 15 45
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/sdk, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes
 ---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
 TotEng   =   -217835.8659 KinEng   =     36252.9606 Temp     =       303.0000 
 PotEng   =   -254088.8265 E_bond   =      4468.5931 E_angle  =      3565.0955 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262122.5151 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =       114.4952 
----------------- Step      200 ----- CPU =      8.7547 (sec) ----------------
+---------------- Step      200 ----- CPU =     11.2079 (sec) ----------------
 TotEng   =   -217870.2208 KinEng   =     36451.9852 Temp     =       304.6634 
 PotEng   =   -254322.2060 E_bond   =      4534.3652 E_angle  =      3349.2174 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262205.7887 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =        39.4030 
----------------- Step      400 ----- CPU =     17.7479 (sec) ----------------
+---------------- Step      400 ----- CPU =     22.6137 (sec) ----------------
 TotEng   =   -218169.7022 KinEng   =     36263.1022 Temp     =       303.0848 
 PotEng   =   -254432.8045 E_bond   =      4598.1819 E_angle  =      3416.3763 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262447.3627 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =         9.8923 
----------------- Step      600 ----- CPU =     26.7299 (sec) ----------------
+---------------- Step      600 ----- CPU =     33.9441 (sec) ----------------
 TotEng   =   -217912.9317 KinEng   =     36465.5757 Temp     =       304.7770 
 PotEng   =   -254378.5074 E_bond   =      4648.1881 E_angle  =      3412.8346 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262439.5301 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =        25.6392 
----------------- Step      800 ----- CPU =     35.8941 (sec) ----------------
+---------------- Step      800 ----- CPU =     45.4291 (sec) ----------------
 TotEng   =   -218439.8078 KinEng   =     36035.8518 Temp     =       301.1854 
 PotEng   =   -254475.6596 E_bond   =      4557.5842 E_angle  =      3438.5605 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262471.8043 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =        -1.6281 
----------------- Step     1000 ----- CPU =     45.1542 (sec) ----------------
+---------------- Step     1000 ----- CPU =     56.9328 (sec) ----------------
 TotEng   =   -217925.0543 KinEng   =     36271.3928 Temp     =       303.1541 
 PotEng   =   -254196.4471 E_bond   =      4624.7673 E_angle  =      3487.7805 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262308.9949 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =        -7.3081 
+Loop time of 56.9329 on 1 procs for 1000 steps with 40140 atoms
 
-Loop time of 45.1542 on 2 procs for 1000 steps with 40140 atoms
-99.5% CPU use with 2 MPI tasks x 1 OpenMP threads
-Performance: 9.567 ns/day  2.509 hours/ns  22.146 timesteps/s
+Performance: 7.588 ns/day, 3.163 hours/ns, 17.565 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
-MPI task timings breakdown:
+MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 38.906     | 38.953     | 39.001     |   0.8 | 86.27
-Bond    | 0.90927    | 0.96844    | 1.0276     |   6.0 |  2.14
-Neigh   | 3.7623     | 3.7641     | 3.766      |   0.1 |  8.34
-Comm    | 0.56974    | 0.67309    | 0.77643    |  12.6 |  1.49
-Output  | 0.00067949 | 0.00072169 | 0.00076389 |   0.2 |  0.00
-Modify  | 0.52627    | 0.53756    | 0.54885    |   1.5 |  1.19
-Other   |            | 0.2571     |            |       |  0.57
+Pair    | 50.734     | 50.734     | 50.734     |   0.0 | 89.11
+Bond    | 0.94032    | 0.94032    | 0.94032    |   0.0 |  1.65
+Neigh   | 4.5195     | 4.5195     | 4.5195     |   0.0 |  7.94
+Comm    | 0.15045    | 0.15045    | 0.15045    |   0.0 |  0.26
+Output  | 0.00056767 | 0.00056767 | 0.00056767 |   0.0 |  0.00
+Modify  | 0.47228    | 0.47228    | 0.47228    |   0.0 |  0.83
+Other   |            | 0.1154     |            |       |  0.20
 
-Nlocal:    20070 ave 20100 max 20040 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    20230.5 ave 20241 max 20220 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    2.84338e+06 ave 2.85198e+06 max 2.83477e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
+Nlocal:    40140 ave 40140 max 40140 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    25966 ave 25966 max 25966 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5.68676e+06 ave 5.68676e+06 max 5.68676e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 5686756
 Ave neighs/atom = 141.673
@@ -113,3 +124,4 @@ Neighbor list builds = 38
 Dangerous builds = 0
 #write_restart	pegc12e8-1.restart
 
+Total wall time: 0:00:57

examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4

@@ -0,0 +1,127 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+
+units		real
+dimension	3
+atom_style	angle
+
+# enforce that in z-direction there is only one
+# processor (could be two) for optimal performance
+processors * * 1
+
+# read topology and force field
+pair_style	lj/sdk 15.0
+bond_style	harmonic
+angle_style	sdk
+special_bonds	lj/coul 0.0 0.0 1.0
+
+read_data	data.pegc12e8.gz
+  orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  40140 atoms
+  reading velocities ...
+  40140 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  13284 bonds
+  reading angles ...
+  12177 angles
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of special neighbors
+
+neighbor	3.0 bin
+neigh_modify	delay 5
+
+timestep	5.0
+#dump            1 all xtc 200 pegc12e8-1.xtc
+#dump_modify  1 unwrap yes
+#dump            2 all dcd 200 pegc12e8-1.dcd unwrap
+#dump_modify  2 unwrap yes
+
+velocity all create 303.0 46659 mom yes rot yes dist gaussian
+
+fix		1 all nvt temp 303.0 303.0 100.0
+
+thermo_style	multi
+thermo		200
+run		1000
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 15 15 45
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/sdk, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =   -217835.8659 KinEng   =     36252.9606 Temp     =       303.0000 
+PotEng   =   -254088.8265 E_bond   =      4468.5931 E_angle  =      3565.0955 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262122.5151 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =       114.4952 
+---------------- Step      200 ----- CPU =      3.0597 (sec) ----------------
+TotEng   =   -217870.2208 KinEng   =     36451.9852 Temp     =       304.6634 
+PotEng   =   -254322.2060 E_bond   =      4534.3652 E_angle  =      3349.2174 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262205.7887 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =        39.4030 
+---------------- Step      400 ----- CPU =      6.2514 (sec) ----------------
+TotEng   =   -218169.7022 KinEng   =     36263.1022 Temp     =       303.0848 
+PotEng   =   -254432.8045 E_bond   =      4598.1819 E_angle  =      3416.3763 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262447.3627 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =         9.8923 
+---------------- Step      600 ----- CPU =      9.4073 (sec) ----------------
+TotEng   =   -217912.9317 KinEng   =     36465.5757 Temp     =       304.7770 
+PotEng   =   -254378.5074 E_bond   =      4648.1881 E_angle  =      3412.8346 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262439.5301 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =        25.6392 
+---------------- Step      800 ----- CPU =     12.6096 (sec) ----------------
+TotEng   =   -218439.8078 KinEng   =     36035.8518 Temp     =       301.1854 
+PotEng   =   -254475.6596 E_bond   =      4557.5842 E_angle  =      3438.5605 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262471.8043 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =        -1.6281 
+---------------- Step     1000 ----- CPU =     15.9134 (sec) ----------------
+TotEng   =   -217925.0543 KinEng   =     36271.3928 Temp     =       303.1541 
+PotEng   =   -254196.4471 E_bond   =      4624.7673 E_angle  =      3487.7805 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262308.9949 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =        -7.3081 
+Loop time of 15.9135 on 4 procs for 1000 steps with 40140 atoms
+
+Performance: 27.147 ns/day, 0.884 hours/ns, 62.840 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    | 13.325     | 13.6       | 13.755     |   4.7 | 85.46
+Bond    | 0.2432     | 0.25007    | 0.25671    |   1.0 |  1.57
+Neigh   | 1.2394     | 1.2399     | 1.2402     |   0.0 |  7.79
+Comm    | 0.41026    | 0.5737     | 0.85471    |  23.4 |  3.61
+Output  | 0.00025368 | 0.0004195  | 0.00091338 |   0.0 |  0.00
+Modify  | 0.17159    | 0.17316    | 0.17459    |   0.3 |  1.09
+Other   |            | 0.0768     |            |       |  0.48
+
+Nlocal:    10035 ave 10084 max 9971 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Nghost:    14548.8 ave 14610 max 14509 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs:    1.42169e+06 ave 1.42961e+06 max 1.40922e+06 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+
+Total # of neighbors = 5686756
+Ave neighs/atom = 141.673
+Ave special neighs/atom = 1.26861
+Neighbor list builds = 38
+Dangerous builds = 0
+#write_restart	pegc12e8-1.restart
+
+Total wall time: 0:00:16

examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1

@@ -1,5 +1,4 @@
-LAMMPS (20 Mar 2014-ICMS)
-WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
+LAMMPS (27 Nov 2018)
   using 1 OpenMP thread(s) per MPI task
 # Solvated 5-mer peptide
 
@@ -19,7 +18,7 @@ special_bonds	lj/coul 0.0 0.0 1.0
 
 read_data	data.pegc12e8.gz
   orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
-  2 by 1 by 1 MPI processor grid
+  1 by 1 by 1 MPI processor grid
   reading atoms ...
   40140 atoms
   reading velocities ...
@@ -52,59 +51,71 @@ fix		1 all nvt temp 303.0 303.0 100.0
 thermo_style	multi
 thermo		200
 run		1000
-Memory usage per processor = 12.4188 Mbytes
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 15 15 45
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/sdk, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes
 ---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
 TotEng   =   -217990.7972 KinEng   =     36252.9606 Temp     =       303.0000 
 PotEng   =   -254243.7577 E_bond   =      4468.5931 E_angle  =      3410.1642 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262122.5151 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =       105.8245 
----------------- Step      200 ----- CPU =      8.6552 (sec) ----------------
+---------------- Step      200 ----- CPU =     11.2074 (sec) ----------------
 TotEng   =   -218203.1886 KinEng   =     36162.5201 Temp     =       302.2441 
 PotEng   =   -254365.7087 E_bond   =      4568.6683 E_angle  =      3409.8838 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262344.2608 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =        29.3660 
----------------- Step      400 ----- CPU =     17.5807 (sec) ----------------
+---------------- Step      400 ----- CPU =     22.6113 (sec) ----------------
 TotEng   =   -217955.7366 KinEng   =     36340.4946 Temp     =       303.7316 
 PotEng   =   -254296.2312 E_bond   =      4621.0208 E_angle  =      3512.1547 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262429.4067 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =        16.4419 
----------------- Step      600 ----- CPU =     28.1043 (sec) ----------------
+---------------- Step      600 ----- CPU =     34.0551 (sec) ----------------
 TotEng   =   -218291.9151 KinEng   =     36079.2122 Temp     =       301.5478 
 PotEng   =   -254371.1273 E_bond   =      4626.3494 E_angle  =      3476.1668 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262473.6435 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =        14.0304 
----------------- Step      800 ----- CPU =     40.5132 (sec) ----------------
+---------------- Step      800 ----- CPU =     45.5316 (sec) ----------------
 TotEng   =   -218539.5667 KinEng   =     36042.0419 Temp     =       301.2372 
 PotEng   =   -254581.6086 E_bond   =      4563.0010 E_angle  =      3616.1814 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262760.7910 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =        -6.8312 
----------------- Step     1000 ----- CPU =     52.8166 (sec) ----------------
+---------------- Step     1000 ----- CPU =     56.9111 (sec) ----------------
 TotEng   =   -217783.9370 KinEng   =     36453.9620 Temp     =       304.6800 
 PotEng   =   -254237.8990 E_bond   =      4693.8725 E_angle  =      3528.1925 
 E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262459.9639 
 E_coul   =         0.0000 E_long   =         0.0000 Press    =         0.0980 
+Loop time of 56.9112 on 1 procs for 1000 steps with 40140 atoms
 
-Loop time of 52.8166 on 2 procs for 1000 steps with 40140 atoms
-99.6% CPU use with 2 MPI tasks x 1 OpenMP threads
-Performance: 8.179 ns/day  2.934 hours/ns  18.933 timesteps/s
+Performance: 7.591 ns/day, 3.162 hours/ns, 17.571 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
-MPI task timings breakdown:
+MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 45.657     | 45.84      | 46.022     |   2.7 | 86.79
-Bond    | 0.98427    | 0.99283    | 1.0014     |   0.9 |  1.88
-Neigh   | 4.4454     | 4.4458     | 4.4462     |   0.0 |  8.42
-Comm    | 0.49872    | 0.6719     | 0.84508    |  21.1 |  1.27
-Output  | 0.00076818 | 0.00083113 | 0.00089407 |   0.2 |  0.00
-Modify  | 0.59218    | 0.59264    | 0.5931     |   0.1 |  1.12
-Other   |            | 0.2731     |            |       |  0.52
+Pair    | 50.775     | 50.775     | 50.775     |   0.0 | 89.22
+Bond    | 0.88358    | 0.88358    | 0.88358    |   0.0 |  1.55
+Neigh   | 4.5176     | 4.5176     | 4.5176     |   0.0 |  7.94
+Comm    | 0.14942    | 0.14942    | 0.14942    |   0.0 |  0.26
+Output  | 0.00057101 | 0.00057101 | 0.00057101 |   0.0 |  0.00
+Modify  | 0.4728     | 0.4728     | 0.4728     |   0.0 |  0.83
+Other   |            | 0.1127     |            |       |  0.20
 
-Nlocal:    20070 ave 20109 max 20031 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    20234 ave 20281 max 20187 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    2.84584e+06 ave 2.85375e+06 max 2.83793e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
+Nlocal:    40140 ave 40140 max 40140 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    25968 ave 25968 max 25968 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    5.69168e+06 ave 5.69168e+06 max 5.69168e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 5691680
 Ave neighs/atom = 141.796
@@ -113,3 +124,4 @@ Neighbor list builds = 38
 Dangerous builds = 0
 #write_restart	pegc12e8-1.restart
 
+Total wall time: 0:00:57

examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4

@@ -0,0 +1,127 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+
+units		real
+dimension	3
+atom_style	angle
+
+# enforce that in z-direction there is only one
+# processor (could be two) for optimal performance
+processors * * 1
+
+# read topology and force field
+pair_style	lj/sdk 15.0
+bond_style	harmonic
+angle_style	harmonic
+special_bonds	lj/coul 0.0 0.0 1.0
+
+read_data	data.pegc12e8.gz
+  orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  40140 atoms
+  reading velocities ...
+  40140 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  13284 bonds
+  reading angles ...
+  12177 angles
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of special neighbors
+
+neighbor	3.0 bin
+neigh_modify	delay 5
+
+timestep	5.0
+#dump            1 all xtc 200 pegc12e8-1.xtc
+#dump_modify  1 unwrap yes
+#dump            2 all dcd 200 pegc12e8-1.dcd unwrap
+#dump_modify  2 unwrap yes
+
+velocity all create 303.0 46659 mom yes rot yes dist gaussian
+
+fix		1 all nvt temp 303.0 303.0 100.0
+
+thermo_style	multi
+thermo		200
+run		1000
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 15 15 45
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/sdk, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =   -217990.7972 KinEng   =     36252.9606 Temp     =       303.0000 
+PotEng   =   -254243.7577 E_bond   =      4468.5931 E_angle  =      3410.1642 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262122.5151 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =       105.8245 
+---------------- Step      200 ----- CPU =      3.0107 (sec) ----------------
+TotEng   =   -218203.1886 KinEng   =     36162.5201 Temp     =       302.2441 
+PotEng   =   -254365.7087 E_bond   =      4568.6683 E_angle  =      3409.8838 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262344.2608 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =        29.3660 
+---------------- Step      400 ----- CPU =      6.1324 (sec) ----------------
+TotEng   =   -217955.7366 KinEng   =     36340.4946 Temp     =       303.7316 
+PotEng   =   -254296.2312 E_bond   =      4621.0208 E_angle  =      3512.1547 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262429.4067 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =        16.4419 
+---------------- Step      600 ----- CPU =      9.3443 (sec) ----------------
+TotEng   =   -218291.9151 KinEng   =     36079.2122 Temp     =       301.5478 
+PotEng   =   -254371.1273 E_bond   =      4626.3494 E_angle  =      3476.1668 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262473.6435 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =        14.0304 
+---------------- Step      800 ----- CPU =     12.5388 (sec) ----------------
+TotEng   =   -218539.5667 KinEng   =     36042.0419 Temp     =       301.2372 
+PotEng   =   -254581.6086 E_bond   =      4563.0010 E_angle  =      3616.1814 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262760.7910 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =        -6.8312 
+---------------- Step     1000 ----- CPU =     15.7416 (sec) ----------------
+TotEng   =   -217783.9370 KinEng   =     36453.9620 Temp     =       304.6800 
+PotEng   =   -254237.8990 E_bond   =      4693.8725 E_angle  =      3528.1925 
+E_dihed  =         0.0000 E_impro  =         0.0000 E_vdwl   =   -262459.9639 
+E_coul   =         0.0000 E_long   =         0.0000 Press    =         0.0980 
+Loop time of 15.7417 on 4 procs for 1000 steps with 40140 atoms
+
+Performance: 27.443 ns/day, 0.875 hours/ns, 63.525 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    | 13.591     | 13.612     | 13.626     |   0.4 | 86.47
+Bond    | 0.22508    | 0.23213    | 0.23791    |   1.0 |  1.47
+Neigh   | 1.2257     | 1.2261     | 1.2266     |   0.0 |  7.79
+Comm    | 0.39628    | 0.41769    | 0.44666    |   2.9 |  2.65
+Output  | 0.000247   | 0.00041109 | 0.00090098 |   0.0 |  0.00
+Modify  | 0.17674    | 0.17803    | 0.17952    |   0.2 |  1.13
+Other   |            | 0.07576    |            |       |  0.48
+
+Nlocal:    10035 ave 10098 max 10004 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+Nghost:    14546.5 ave 14564 max 14503 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs:    1.42292e+06 ave 1.43408e+06 max 1.41615e+06 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 5691680
+Ave neighs/atom = 141.796
+Ave special neighs/atom = 1.26861
+Neighbor list builds = 38
+Dangerous builds = 0
+#write_restart	pegc12e8-1.restart
+
+Total wall time: 0:00:15

examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1

@@ -0,0 +1,145 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# coarse grained SDS surfactant monolayer
+
+units           real
+dimension       3
+atom_style      full
+processors  * * 1
+
+pair_style hybrid/overlay  lj/sdk 15.0  coul/long 26.5
+bond_style      harmonic
+angle_style     sdk
+special_bonds   lj/coul 0.0 0.0 1.0
+
+read_data       data.sds.gz
+  orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  31280 atoms
+  reading velocities ...
+  31280 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  4096 bonds
+  reading angles ...
+  3072 angles
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of special neighbors
+
+pair_coeff  1     4    coul/long # SO4  SOD
+pair_coeff  4     4    coul/long # SOD  SOD
+pair_coeff  1     1    lj/sdk  lj9_6  0.7000 4.3210 # SO4  SO4
+pair_coeff  1     2    lj/sdk  lj9_6  0.3830 4.4135 # SO4  CM
+pair_coeff  1     3    lj/sdk  lj9_6  0.4050 4.4530 # SO4  CT
+pair_coeff  1     4    lj/sdk  lj12_4 1.1000 4.1000 # SO4  SOD
+pair_coeff  1     5    lj/sdk  lj12_4 1.1000 4.1000 # SO4  W
+pair_coeff  2     2    lj/sdk  lj9_6  0.4200 4.5060 # CM   CM
+pair_coeff  2     3    lj/sdk  lj9_6  0.4440 4.5455 # CT   CM
+pair_coeff  2     4    lj/sdk  lj12_4 0.3400 4.4385 # SOD  CM
+pair_coeff  2     5    lj/sdk  lj12_4 0.3400 4.4385 # W    CM
+pair_coeff  3     3    lj/sdk  lj9_6  0.4690 4.5850 # CT   CT
+pair_coeff  3     4    lj/sdk  lj12_4 0.3600 4.4780 # SOD  CT
+pair_coeff  3     5    lj/sdk  lj12_4 0.3600 4.4780 # W    CT
+pair_coeff  4     4    lj/sdk  lj12_4 0.3500 4.3710 # SOD  SOD
+pair_coeff  4     5    lj/sdk  lj12_4 0.8950 4.3710 # SOD  W
+pair_coeff  5     5    lj/sdk  lj12_4 0.8950 4.3710 # W    W
+
+
+group charged   type 1 4
+2048 atoms in group charged
+atom_modify     first charged
+
+kspace_style    pppm/cg 0.00001
+kspace_modify   order 3
+
+comm_modify     mode multi
+neighbor        2.0 multi
+neigh_modify    delay 4 every 2 check yes
+
+timestep        10.0
+
+fix             1 all nvt temp 310.0 310.0 100.0
+
+thermo          10
+
+run              100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+  G vector (1/distance) = 0.0416781
+  grid = 8 4 12
+  stencil order = 3
+  estimated absolute RMS force accuracy = 0.00248777
+  estimated relative force accuracy = 7.49185e-06
+  using double precision FFTs
+  3d grid and FFT values/proc = 1155 384
+Neighbor list info ...
+  update every 2 steps, delay 4 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 28.5
+  ghost atom cutoff = 28.5
+  binsize = 8.5, bins = 27 14 48
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair lj/sdk, perpetual
+      attributes: half, newton on
+      pair build: half/multi/newton
+      stencil: half/multi/3d/newton
+      bin: standard
+  (2) pair coul/long, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  PPPM/cg optimization cutoff: 1e-05
+  Total charged atoms: 6.5%
+  Min/max charged atoms/proc: 6.5% 6.5%
+Per MPI rank memory allocation (min/avg/max) = 35.49 | 35.49 | 35.49 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0     310.0934   -249339.72    2566.2036   -217861.41   -25.664516 
+      10    310.88051    -249369.1    2549.1166   -217834.49   -29.095262 
+      20    310.33025   -249325.09    2543.0138   -217847.89   -30.069751 
+      30    308.24273   -249331.54    2604.3227   -217987.66   -28.033129 
+      40    309.41339    -249363.5    2560.6727   -217954.13   -25.802838 
+      50    309.16857   -249071.94    2571.9117   -217674.15   -17.946457 
+      60    312.67237   -249288.77    2621.0185   -217515.19   -25.723545 
+      70    310.13623   -249262.32     2595.874   -217750.35   -26.276067 
+      80    310.60448   -249415.99    2596.6752   -217859.56   -27.942924 
+      90    309.63209   -249403.14    2606.3186   -217927.73   -24.456575 
+     100    309.40793   -249341.62    2599.6402   -217893.79   -22.554823 
+Loop time of 9.61984 on 1 procs for 100 steps with 31280 atoms
+
+Performance: 8.981 ns/day, 2.672 hours/ns, 10.395 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.2928     | 7.2928     | 7.2928     |   0.0 | 75.81
+Bond    | 0.036198   | 0.036198   | 0.036198   |   0.0 |  0.38
+Kspace  | 0.053125   | 0.053125   | 0.053125   |   0.0 |  0.55
+Neigh   | 2.117      | 2.117      | 2.117      |   0.0 | 22.01
+Comm    | 0.029731   | 0.029731   | 0.029731   |   0.0 |  0.31
+Output  | 0.0014369  | 0.0014369  | 0.0014369  |   0.0 |  0.01
+Modify  | 0.079014   | 0.079014   | 0.079014   |   0.0 |  0.82
+Other   |            | 0.01051    |            |       |  0.11
+
+Nlocal:    31280 ave 31280 max 31280 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    16629 ave 16629 max 16629 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3.40168e+06 ave 3.40168e+06 max 3.40168e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3401676
+Ave neighs/atom = 108.749
+Ave special neighs/atom = 0.458312
+Neighbor list builds = 10
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:10

examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4

@@ -1,5 +1,4 @@
-LAMMPS (20 Mar 2014-ICMS)
-WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
+LAMMPS (27 Nov 2018)
   using 1 OpenMP thread(s) per MPI task
 # coarse grained SDS surfactant monolayer
 
@@ -58,7 +57,7 @@ atom_modify     first charged
 kspace_style    pppm/cg 0.00001
 kspace_modify   order 3
 
-communicate     multi
+comm_modify     mode multi
 neighbor        2.0 multi
 neigh_modify    delay 4 every 2 check yes
 
@@ -70,6 +69,7 @@ thermo          10
 
 run              100
 PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
   G vector (1/distance) = 0.0416781
   grid = 8 4 12
   stencil order = 3
@@ -77,10 +77,27 @@ PPPM initialization ...
   estimated relative force accuracy = 7.49185e-06
   using double precision FFTs
   3d grid and FFT values/proc = 525 96
+Neighbor list info ...
+  update every 2 steps, delay 4 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 28.5
+  ghost atom cutoff = 28.5
+  binsize = 8.5, bins = 27 14 48
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair lj/sdk, perpetual
+      attributes: half, newton on
+      pair build: half/multi/newton
+      stencil: half/multi/3d/newton
+      bin: standard
+  (2) pair coul/long, perpetual, skip from (1)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
   PPPM/cg optimization cutoff: 1e-05
   Total charged atoms: 6.5%
   Min/max charged atoms/proc: 6.4% 6.7%
-Memory usage per processor = 7.66668 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 17.48 | 17.48 | 17.48 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0     310.0934   -249339.72    2566.2036   -217861.41   -25.664516 
       10    310.88051    -249369.1    2549.1166   -217834.49   -29.095262 
@@ -93,22 +110,22 @@ Step Temp E_pair E_mol TotEng Press
       80    310.60448   -249415.99    2596.6752   -217859.56   -27.942924 
       90    309.63209   -249403.14    2606.3186   -217927.73   -24.456575 
      100    309.40793   -249341.62    2599.6402   -217893.79   -22.554823 
+Loop time of 2.54454 on 4 procs for 100 steps with 31280 atoms
 
-Loop time of 4.07239 on 4 procs for 100 steps with 31280 atoms
-98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-Performance: 21.216 ns/day  1.131 hours/ns  24.556 timesteps/s
+Performance: 33.955 ns/day, 0.707 hours/ns, 39.300 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
 
-MPI task timings breakdown:
+MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 3.082      | 3.0928     | 3.1091     |   0.6 | 75.95
-Bond    | 0.021077   | 0.021421   | 0.021823   |   0.2 |  0.53
-Kspace  | 0.042646   | 0.058859   | 0.069797   |   4.1 |  1.45
-Neigh   | 0.79689    | 0.79696    | 0.79711    |   0.0 | 19.57
-Comm    | 0.048668   | 0.049552   | 0.050446   |   0.3 |  1.22
-Output  | 0.00072145 | 0.00095147 | 0.0016341  |   1.3 |  0.02
-Modify  | 0.034767   | 0.035175   | 0.035714   |   0.2 |  0.86
-Other   |            | 0.01665    |            |       |  0.41
+Pair    | 1.8639     | 1.8913     | 1.9283     |   1.8 | 74.33
+Bond    | 0.0092797  | 0.0094567  | 0.0095828  |   0.1 |  0.37
+Kspace  | 0.018389   | 0.056616   | 0.084424   |  10.7 |  2.23
+Neigh   | 0.53553    | 0.53569    | 0.53605    |   0.0 | 21.05
+Comm    | 0.023819   | 0.02433    | 0.02506    |   0.3 |  0.96
+Output  | 0.00058866 | 0.00084978 | 0.0016243  |   0.0 |  0.03
+Modify  | 0.021841   | 0.022059   | 0.022308   |   0.1 |  0.87
+Other   |            | 0.004233   |            |       |  0.17
 
 Nlocal:    7820 ave 7866 max 7774 min
 Histogram: 1 1 0 0 0 0 0 0 1 1
@@ -125,3 +142,4 @@ Dangerous builds = 0
 
 Please see the log.cite file for references relevant to this simulation
 
+Total wall time: 0:00:02

examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1

@@ -0,0 +1,129 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# coarse grained SDS surfactant monolayer
+
+units           real
+dimension       3
+atom_style      full
+processors  * * 1
+
+pair_style lj/sdk/coul/long 15.0
+bond_style      harmonic
+angle_style     sdk
+special_bonds   lj/coul 0.0 0.0 1.0
+
+read_data       data.sds.gz
+  orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  31280 atoms
+  reading velocities ...
+  31280 velocities
+  scanning bonds ...
+  1 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  4096 bonds
+  reading angles ...
+  3072 angles
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of special neighbors
+
+pair_coeff  1     1      lj9_6  0.7000 4.3210 # SO4  SO4
+pair_coeff  1     2      lj9_6  0.3830 4.4135 # SO4  CM
+pair_coeff  1     3      lj9_6  0.4050 4.4530 # SO4  CT
+pair_coeff  1     4      lj12_4 1.1000 4.1000 # SO4  SOD
+pair_coeff  1     5      lj12_4 1.1000 4.1000 # SO4  W
+pair_coeff  2     2      lj9_6  0.4200 4.5060 # CM   CM
+pair_coeff  2     3      lj9_6  0.4440 4.5455 # CT   CM
+pair_coeff  2     4      lj12_4 0.3400 4.4385 # SOD  CM
+pair_coeff  2     5      lj12_4 0.3400 4.4385 # W    CM
+pair_coeff  3     3      lj9_6  0.4690 4.5850 # CT   CT
+pair_coeff  3     4      lj12_4 0.3600 4.4780 # SOD  CT
+pair_coeff  3     5      lj12_4 0.3600 4.4780 # W    CT
+pair_coeff  4     4      lj12_4 0.3500 4.3710 # SOD  SOD
+pair_coeff  4     5      lj12_4 0.8950 4.3710 # SOD  W
+pair_coeff  5     5      lj12_4 0.8950 4.3710 # W    W
+
+kspace_style    pppm/cg 0.00001
+kspace_modify   order 3
+
+neighbor        2.0 bin
+neigh_modify    delay 4 every 2 check yes
+
+timestep        10.0
+
+fix             1 all nvt temp 310.0 310.0 100.0
+
+thermo          10
+
+run              100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+  G vector (1/distance) = 0.0789325
+  grid = 15 8 25
+  stencil order = 3
+  estimated absolute RMS force accuracy = 0.00275556
+  estimated relative force accuracy = 8.29828e-06
+  using double precision FFTs
+  3d grid and FFT values/proc = 5544 3000
+Neighbor list info ...
+  update every 2 steps, delay 4 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 17
+  ghost atom cutoff = 17
+  binsize = 8.5, bins = 27 14 48
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/sdk/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  PPPM/cg optimization cutoff: 1e-05
+  Total charged atoms: 6.5%
+  Min/max charged atoms/proc: 6.5% 6.5%
+Per MPI rank memory allocation (min/avg/max) = 35.36 | 35.36 | 35.36 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0     310.0934   -247030.21    2566.2036    -215551.9   -14.547393 
+      10    310.89138   -247061.61    2549.4854   -215525.62   -18.043512 
+      20    310.29287    -247017.8    2542.4491   -215544.65   -19.148631 
+      30    308.13371   -247024.82    2602.1061   -215693.32   -17.390902 
+      40    309.40426   -247058.41    2558.7402   -215651.82   -15.445066 
+      50    309.11317   -246753.92    2570.8603   -215362.36   -7.4232007 
+      60    312.52974   -246964.73    2618.8108   -215206.66    -15.23965 
+      70    310.11675   -246941.68    2591.8668   -215435.53   -16.153691 
+      80    310.48262   -247090.02    2595.0493   -215546.58   -18.080368 
+      90    309.60017    -247067.1    2604.6545   -215596.33   -14.583764 
+     100     309.7356   -247004.05    2604.8729   -215520.43    -12.78624 
+Loop time of 9.23618 on 1 procs for 100 steps with 31280 atoms
+
+Performance: 9.355 ns/day, 2.566 hours/ns, 10.827 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    | 7.7363     | 7.7363     | 7.7363     |   0.0 | 83.76
+Bond    | 0.032901   | 0.032901   | 0.032901   |   0.0 |  0.36
+Kspace  | 0.078907   | 0.078907   | 0.078907   |   0.0 |  0.85
+Neigh   | 1.2706     | 1.2706     | 1.2706     |   0.0 | 13.76
+Comm    | 0.026005   | 0.026005   | 0.026005   |   0.0 |  0.28
+Output  | 0.0014131  | 0.0014131  | 0.0014131  |   0.0 |  0.02
+Modify  | 0.079446   | 0.079446   | 0.079446   |   0.0 |  0.86
+Other   |            | 0.01055    |            |       |  0.11
+
+Nlocal:    31280 ave 31280 max 31280 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    15812 ave 15812 max 15812 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3.3521e+06 ave 3.3521e+06 max 3.3521e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3352103
+Ave neighs/atom = 107.164
+Ave special neighs/atom = 0.458312
+Neighbor list builds = 10
+Dangerous builds = 0
+Total wall time: 0:00:09

examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4

@@ -1,5 +1,4 @@
-LAMMPS (20 Mar 2014-ICMS)
-WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
+LAMMPS (27 Nov 2018)
   using 1 OpenMP thread(s) per MPI task
 # coarse grained SDS surfactant monolayer
 
@@ -62,6 +61,7 @@ thermo          10
 
 run              100
 PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
   G vector (1/distance) = 0.0789325
   grid = 15 8 25
   stencil order = 3
@@ -69,10 +69,22 @@ PPPM initialization ...
   estimated relative force accuracy = 8.29828e-06
   using double precision FFTs
   3d grid and FFT values/proc = 2156 840
+Neighbor list info ...
+  update every 2 steps, delay 4 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 17
+  ghost atom cutoff = 17
+  binsize = 8.5, bins = 27 14 48
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/sdk/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
   PPPM/cg optimization cutoff: 1e-05
   Total charged atoms: 6.5%
   Min/max charged atoms/proc: 6.4% 6.7%
-Memory usage per processor = 8.05923 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 17.32 | 17.32 | 17.32 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0     310.0934   -247030.21    2566.2036    -215551.9   -14.547393 
       10    310.89138   -247061.61    2549.4854   -215525.62   -18.043512 
@@ -85,22 +97,22 @@ Step Temp E_pair E_mol TotEng Press
       80    310.48262   -247090.02    2595.0493   -215546.58   -18.080368 
       90    309.60017    -247067.1    2604.6545   -215596.33   -14.583764 
      100     309.7356   -247004.05    2604.8729   -215520.43    -12.78624 
+Loop time of 2.45408 on 4 procs for 100 steps with 31280 atoms
 
-Loop time of 3.44972 on 4 procs for 100 steps with 31280 atoms
-98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
-Performance: 25.046 ns/day  0.958 hours/ns  28.988 timesteps/s
+Performance: 35.207 ns/day, 0.682 hours/ns, 40.748 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
 
-MPI task timings breakdown:
+MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.7883     | 2.817      | 2.8415     |   1.1 | 81.66
-Bond    | 0.017868   | 0.018973   | 0.020636   |   0.7 |  0.55
-Kspace  | 0.063881   | 0.088012   | 0.11571    |   6.2 |  2.55
-Neigh   | 0.42765    | 0.42828    | 0.42882    |   0.1 | 12.41
-Comm    | 0.043887   | 0.044575   | 0.045079   |   0.2 |  1.29
-Output  | 0.00072694 | 0.00096422 | 0.0016718  |   1.3 |  0.03
-Modify  | 0.035513   | 0.035955   | 0.036887   |   0.3 |  1.04
-Other   |            | 0.01597    |            |       |  0.46
+Pair    | 2.0065     | 2.0143     | 2.0326     |   0.8 | 82.08
+Bond    | 0.0084255  | 0.0086145  | 0.0088007  |   0.1 |  0.35
+Kspace  | 0.033373   | 0.052041   | 0.060933   |   4.8 |  2.12
+Neigh   | 0.32741    | 0.32748    | 0.32754    |   0.0 | 13.34
+Comm    | 0.022403   | 0.023025   | 0.023735   |   0.4 |  0.94
+Output  | 0.00060058 | 0.00086623 | 0.0016549  |   0.0 |  0.04
+Modify  | 0.022533   | 0.022723   | 0.022876   |   0.1 |  0.93
+Other   |            | 0.005038   |            |       |  0.21
 
 Nlocal:    7820 ave 7866 max 7775 min
 Histogram: 1 1 0 0 0 0 0 1 0 1
@@ -114,3 +126,4 @@ Ave neighs/atom = 107.164
 Ave special neighs/atom = 0.458312
 Neighbor list builds = 10
 Dangerous builds = 0
+Total wall time: 0:00:02

examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1

@@ -1,5 +1,4 @@
-LAMMPS (20 Mar 2014-ICMS)
-WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
+LAMMPS (27 Nov 2018)
   using 1 OpenMP thread(s) per MPI task
 # Solvated 5-mer peptide
 
@@ -15,7 +14,7 @@ kspace_style	pppm 0.0001
 
 read_data	data.peptide
   orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
-  1 by 1 by 2 MPI processor grid
+  1 by 1 by 1 MPI processor grid
   reading atoms ...
   2004 atoms
   reading velocities ...
@@ -78,134 +77,179 @@ thermo		10
 
 run		100
 PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
   G vector (1/distance) = 0.268725
   grid = 15 15 15
   stencil order = 5
   estimated absolute RMS force accuracy = 0.0228209
   estimated relative force accuracy = 6.87243e-05
   using double precision FFTs
-  3d grid and FFT values/proc = 6776 1800
+  3d grid and FFT values/proc = 10648 3375
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
 colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
-colvars: Initializing the collective variables module, version 2013-10-22.
-colvars: # indexFile = "" [default]
-colvars: # analysis = off [default]
+colvars: Initializing the collective variables module, version 2018-11-16.
+colvars: Please cite Fiorin et al, Mol Phys 2013:
+colvars:  http://dx.doi.org/10.1080/00268976.2013.813594
+colvars: in any publication based on this calculation.
+colvars: SMP parallelism is available.
+colvars: Using LAMMPS interface, version 2018-08-29.
+colvars: ----------------------------------------------------------------------
+colvars: Reading new configuration from file "peptide.colvars":
+colvars: # smp = on [default]
 colvars: # colvarsTrajFrequency = 1
 colvars: # colvarsRestartFrequency = 1000
-colvars: # colvarsTrajAppend = off [default]
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "out.colvars.state".
-colvars: Writing to colvar trajectory file "out.colvars.traj".
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
 colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new collective variable.
-colvars:   # name = one
+colvars:   # name = "one"
 colvars:   Initializing a new "distance" component.
+colvars:     # name = "" [default]
 colvars:     # componentCoeff = 1 [default]
 colvars:     # componentExp = 1 [default]
 colvars:     # period = 0 [default]
 colvars:     # wrapAround = 0 [default]
 colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
+colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "" [default]
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
 colvars:       # enableForces = on [default]
-colvars:       # disableForces = off [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
 colvars:       # enableFitGradients = on [default]
-colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 0.
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
 colvars:       Initializing atom group "group2".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "" [default]
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
 colvars:       # enableForces = on [default]
-colvars:       # disableForces = off [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
 colvars:       # enableFitGradients = on [default]
-colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 0.
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
+colvars:     # oneSiteSystemForce = off [default]
+colvars:     # oneSiteTotalForce = off [default]
 colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
 colvars:   # width = 1 [default]
 colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
 colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
 colvars:   # expandBoundaries = off [default]
 colvars:   # extendedLagrangian = off [default]
 colvars:   # outputValue = on [default]
 colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
+colvars:   # outputTotalForce = off [default]
 colvars:   # outputAppliedForce = off [default]
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
 colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new collective variable.
-colvars:   # name = two
+colvars:   # name = "two"
 colvars:   Initializing a new "distance" component.
+colvars:     # name = "" [default]
 colvars:     # componentCoeff = 1 [default]
 colvars:     # componentExp = 1 [default]
 colvars:     # period = 0 [default]
 colvars:     # wrapAround = 0 [default]
 colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
+colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "" [default]
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
 colvars:       # enableForces = on [default]
-colvars:       # disableForces = off [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
 colvars:       # enableFitGradients = on [default]
-colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 0.
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
 colvars:       Initializing atom group "group2".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "" [default]
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
 colvars:       # enableForces = on [default]
-colvars:       # disableForces = off [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
 colvars:       # enableFitGradients = on [default]
-colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 0.
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
+colvars:     # oneSiteSystemForce = off [default]
+colvars:     # oneSiteTotalForce = off [default]
 colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
 colvars:   # width = 1 [default]
 colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
 colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
 colvars:   # expandBoundaries = off [default]
 colvars:   # extendedLagrangian = off [default]
 colvars:   # outputValue = on [default]
 colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
+colvars:   # outputTotalForce = off [default]
 colvars:   # outputAppliedForce = off [default]
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables initialized, 2 in total.
 colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "harmonic" instance.
-colvars:   # name = h_pot
+colvars:   # name = "h_pot"
 colvars:   # colvars = { one, two }
 colvars:   # outputEnergy = off [default]
-colvars:   # forceConstant = 100
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # writeTISamples = off [default]
+colvars:   # writeTIPMF = off [default]
 colvars:   # centers = { 10, 10 }
 colvars:   # targetCenters = { 10, 10 } [default]
-colvars:   # targetForceConstant = 0 [default]
 colvars:   # outputCenters = off [default]
-colvars:   # outputAccumulatedWork = off [default]
+colvars:   # forceConstant = 100
+colvars:   # targetForceConstant = -1 [default]
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
-colvars: Collective variables module initialized.
+colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
+colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
+colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
+colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
+colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
+colvars: The restart output state file will be "rest.colvars.state".
+colvars: The final output state file will be "out.colvars.state".
+colvars: Writing to colvar trajectory file "out.colvars.traj".
 colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
 colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
 colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
 colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
+colvars: Performing analysis.
 SHAKE stats (type/ave/delta) on step 0
   4 1.111 1.44264e-05
   6 0.996998 7.26967e-06
@@ -215,51 +259,52 @@ SHAKE stats (type/ave/delta) on step 0
   14 0.96 0
   18 0.957206 4.37979e-05
   31 104.519 0.00396029
-Memory usage per processor = 10.4104 Mbytes
-Step Temp TotEng PotEng KinEng E_pair E_bond 2 
+Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
        0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    292.14604 
-      10    305.06198     -5058.89   -6286.1848    1227.2948   -6413.0968    58.849896    103.38344 
-      20    311.00591   -4999.0544   -6250.2623    1251.2079   -6417.0983    47.695275    36.699706 
-      30    314.22398   -4993.6951   -6257.8496    1264.1545   -6421.9641    35.344161    10.563914 
-      40    297.87525   -5020.8339   -6219.2158    1198.3819   -6389.8501      27.7232    3.8354396 
-      50    304.02085   -5056.2539   -6279.3602    1223.1063    -6456.818    55.459511   0.20679816 
-      60    285.92595   -5104.0436   -6254.3523    1150.3087   -6435.5793    32.767289   0.69356527 
-      70    277.83498   -5163.9751    -6281.733    1117.7579   -6447.7013     39.62715    11.433633 
-      80    267.51476   -5206.4041   -6282.6428    1076.2386   -6456.6352    31.611841    6.3553235 
-      90    278.15512    -5245.383   -6364.4288    1119.0458   -6499.8036    28.849902   0.36938817 
+      10    305.06149   -5058.8972   -6286.1901    1227.2929   -6413.1021      58.8499    103.38345 
+      20    311.00516   -4999.0612    -6250.266    1251.2048   -6417.1021    47.695297    36.699695 
+      30    314.22337   -4993.7012   -6257.8532     1264.152   -6421.9679    35.344144    10.563933 
+      40    297.87491   -5020.8378   -6219.2184    1198.3805   -6389.8528    27.723133    3.8354517 
+      50    304.02071   -5056.2576   -6279.3633    1223.1057   -6456.8214    55.459505   0.20678217 
+      60    285.92576   -5104.0461    -6254.354    1150.3079   -6435.5814    32.767229   0.69352945 
+      70    277.83519   -5163.9758   -6281.7345    1117.7587   -6447.7033    39.627168    11.433603 
+      80    267.51495   -5206.4046    -6282.644    1076.2394   -6456.6369    31.611883    6.3554178 
+      90    278.15579   -5245.3824    -6364.431    1119.0485   -6499.8063    28.849773   0.36941576 
 SHAKE stats (type/ave/delta) on step 100
-  4 1.11098 8.97185e-05
-  6 0.996996 1.00569e-05
-  8 1.08 6.02346e-06
-  10 1.111 1.84257e-05
-  12 1.08 7.27136e-06
+  4 1.11098 8.97155e-05
+  6 0.996996 1.00568e-05
+  8 1.08 6.02345e-06
+  10 1.111 1.84253e-05
+  12 1.08 7.2713e-06
   14 0.959996 0
-  18 0.957198 3.36078e-05
-  31 104.52 0.00306008
-     100    260.10505    -5292.689   -6339.1177    1046.4286   -6471.6693    25.361881   0.21986866 
+  18 0.957198 3.36079e-05
+  31 104.52 0.0030599
+     100    260.10613   -5292.6885   -6339.1215     1046.433   -6471.6734    25.362042   0.21987323 
+colvars: Saving collective variables state to "out.colvars.state".
+Loop time of 2.17304 on 1 procs for 100 steps with 2004 atoms
 
-Loop time of 1.04673 on 2 procs for 100 steps with 2004 atoms
-99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
-Performance: 16.509 ns/day  1.454 hours/ns  95.536 timesteps/s
+Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
 
-MPI task timings breakdown:
+MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.76537    | 0.76832    | 0.77127    |   0.3 | 73.40
-Bond    | 0.0024452  | 0.0025067  | 0.0025682  |   0.1 |  0.24
-Kspace  | 0.088877   | 0.092861   | 0.096845   |   1.3 |  8.87
-Neigh   | 0.13657    | 0.13657    | 0.13658    |   0.0 | 13.05
-Comm    | 0.0172     | 0.018169   | 0.019137   |   0.7 |  1.74
-Output  | 0.0002296  | 0.00031686 | 0.00040412 |   0.5 |  0.03
-Modify  | 0.025518   | 0.025554   | 0.025591   |   0.0 |  2.44
-Other   |            | 0.002431   |            |       |  0.23
+Pair    | 1.5817     | 1.5817     | 1.5817     |   0.0 | 72.79
+Bond    | 0.0031469  | 0.0031469  | 0.0031469  |   0.0 |  0.14
+Kspace  | 0.17366    | 0.17366    | 0.17366    |   0.0 |  7.99
+Neigh   | 0.37354    | 0.37354    | 0.37354    |   0.0 | 17.19
+Comm    | 0.013652   | 0.013652   | 0.013652   |   0.0 |  0.63
+Output  | 0.00026059 | 0.00026059 | 0.00026059 |   0.0 |  0.01
+Modify  | 0.025484   | 0.025484   | 0.025484   |   0.0 |  1.17
+Other   |            | 0.001615   |            |       |  0.07
 
-Nlocal:    1002 ave 1013 max 991 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    8629.5 ave 8641 max 8618 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    354118 ave 356534 max 351703 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
+Nlocal:    2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11124 ave 11124 max 11124 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    708237 ave 708237 max 708237 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
 
 Total # of neighbors = 708237
 Ave neighs/atom = 353.412
@@ -269,279 +314,316 @@ Dangerous builds = 2
 
 run     100
 PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
   G vector (1/distance) = 0.268725
   grid = 15 15 15
   stencil order = 5
   estimated absolute RMS force accuracy = 0.0228209
   estimated relative force accuracy = 6.87243e-05
   using double precision FFTs
-  3d grid and FFT values/proc = 6776 1800
+  3d grid and FFT values/proc = 10648 3375
 colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
 colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
 colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
 colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
 SHAKE stats (type/ave/delta) on step 100
-  4 1.11098 8.97185e-05
-  6 0.996996 1.00569e-05
-  8 1.08 6.02346e-06
-  10 1.111 1.84257e-05
-  12 1.08 7.27136e-06
+  4 1.11098 8.97155e-05
+  6 0.996996 1.00568e-05
+  8 1.08 6.02345e-06
+  10 1.111 1.84253e-05
+  12 1.08 7.2713e-06
   14 0.959996 0
-  18 0.957198 3.36078e-05
-  31 104.52 0.00306008
-Memory usage per processor = 10.4104 Mbytes
-Step Temp TotEng PotEng KinEng E_pair E_bond 2 
-     100    260.10505    -5292.689   -6339.1177    1046.4286   -6471.6693    25.361881   0.21986866 
-     110    266.26279   -5341.2085   -6412.4103    1071.2018   -6552.7566    33.572973    1.9229795 
-     120    262.66439   -5386.2495   -6442.9746    1056.7251   -6587.5499    29.859549     2.712489 
-     130    252.83437   -5422.5446   -6439.7226    1017.1779   -6580.4751    25.979056    1.2031649 
-     140    253.85101   -5452.1904   -6473.4584     1021.268   -6609.4883    26.071526   0.30586448 
-     150    261.31821   -5490.4808   -6541.7901    1051.3093    -6646.615    16.258546     6.904992 
-     160    255.73714   -5521.6048   -6550.4609    1028.8561   -6658.1531    19.717543    12.339834 
-     170    253.42881   -5540.0985    -6559.668    1019.5695   -6656.6862    23.293616    10.289885 
-     180    248.51049   -5550.3254   -6550.1079    999.78252   -6661.4178    26.200082    3.4339077 
-     190    250.80375   -5555.2616   -6564.2702    1009.0086   -6666.1496    25.536628    3.3495235 
+  18 0.957198 3.36079e-05
+  31 104.52 0.0030599
+Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
+     100    260.10613   -5292.6885   -6339.1215     1046.433   -6471.6734    25.362042   0.21987323 
+     110    266.26438   -5341.1991   -6412.4073    1071.2082   -6552.7551    33.573173    1.9229657 
+     120    262.66604   -5386.2387   -6442.9704    1056.7317   -6587.5483    29.859587    2.7124812 
+     130    252.83379   -5422.5401   -6439.7157    1017.1756   -6580.4703    25.979343    1.2031592 
+     140    253.85111   -5452.1838   -6473.4522    1021.2684   -6609.4826    26.071651   0.30585517 
+     150    261.31816   -5490.4727   -6541.7817    1051.3091   -6646.6076    16.258823    6.9051008 
+     160     255.7352   -5521.5941   -6550.4424    1028.8483   -6658.1373    19.717399    12.339679 
+     170    253.42527   -5540.0942   -6559.6494    1019.5552   -6656.6678    23.293812    10.290217 
+     180    248.51161   -5550.3253   -6550.1124    999.78705   -6661.4235    26.200127    3.4336038 
+     190    250.80862   -5555.2554   -6564.2836    1009.0282    -6666.164     25.53634    3.3494288 
 SHAKE stats (type/ave/delta) on step 200
-  4 1.111 1.81287e-06
-  6 0.997 7.79626e-07
-  8 1.08 1.08933e-06
-  10 1.111 2.96498e-07
-  12 1.08 4.69169e-07
+  4 1.111 1.81266e-06
+  6 0.997 7.79424e-07
+  8 1.08 1.08903e-06
+  10 1.111 2.96503e-07
+  12 1.08 4.69038e-07
   14 0.960001 0
-  18 0.957201 3.76617e-06
-  31 104.52 0.000411076
-     200    251.50646   -5557.4204    -6569.256    1011.8356   -6674.0889    24.805155      7.13891 
+  18 0.957201 3.76471e-06
+  31 104.52 0.000411055
+     200    251.50475   -5557.4251   -6569.2538    1011.8287   -6674.0845    24.804906    7.1387574 
+colvars: Saving collective variables state to "out.colvars.state".
+Loop time of 2.03298 on 1 procs for 100 steps with 2004 atoms
 
-Loop time of 1.00434 on 2 procs for 100 steps with 2004 atoms
-99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
-Performance: 17.205 ns/day  1.395 hours/ns  99.568 timesteps/s
+Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
 
-MPI task timings breakdown:
+MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.78001    | 0.78091    | 0.78181    |   0.1 | 77.75
-Bond    | 0.0025158  | 0.0025688  | 0.0026219  |   0.1 |  0.26
-Kspace  | 0.093375   | 0.094821   | 0.096266   |   0.5 |  9.44
-Neigh   | 0.080238   | 0.08025    | 0.080261   |   0.0 |  7.99
-Comm    | 0.01671    | 0.017204   | 0.017699   |   0.4 |  1.71
-Output  | 0.0002296  | 0.00031531 | 0.00040102 |   0.5 |  0.03
-Modify  | 0.025788   | 0.025804   | 0.02582    |   0.0 |  2.57
-Other   |            | 0.002469   |            |       |  0.25
+Pair    | 1.5975     | 1.5975     | 1.5975     |   0.0 | 78.58
+Bond    | 0.0033164  | 0.0033164  | 0.0033164  |   0.0 |  0.16
+Kspace  | 0.17349    | 0.17349    | 0.17349    |   0.0 |  8.53
+Neigh   | 0.21971    | 0.21971    | 0.21971    |   0.0 | 10.81
+Comm    | 0.012045   | 0.012045   | 0.012045   |   0.0 |  0.59
+Output  | 0.00026226 | 0.00026226 | 0.00026226 |   0.0 |  0.01
+Modify  | 0.025034   | 0.025034   | 0.025034   |   0.0 |  1.23
+Other   |            | 0.001596   |            |       |  0.08
 
-Nlocal:    1002 ave 1014 max 990 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    8654 ave 8667 max 8641 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    354044 ave 355332 max 352756 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
+Nlocal:    2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11159 ave 11159 max 11159 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    708083 ave 708083 max 708083 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 708088
-Ave neighs/atom = 353.337
+Total # of neighbors = 708083
+Ave neighs/atom = 353.335
 Ave special neighs/atom = 2.34032
 Neighbor list builds = 7
 Dangerous builds = 0
 
 fix 2 all colvars peptide.colvars input out.colvars.state output out2
-colvars: Saving collective variables state to "out.colvars.state".
+colvars: Resetting the Collective Variables module.
 
 run     100
 PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
   G vector (1/distance) = 0.268725
   grid = 15 15 15
   stencil order = 5
   estimated absolute RMS force accuracy = 0.0228209
   estimated relative force accuracy = 6.87243e-05
   using double precision FFTs
-  3d grid and FFT values/proc = 6776 1800
+  3d grid and FFT values/proc = 10648 3375
 colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
-colvars: Initializing the collective variables module, version 2013-10-22.
-colvars: # indexFile = "" [default]
-colvars: # analysis = off [default]
+colvars: Initializing the collective variables module, version 2018-11-16.
+colvars: Please cite Fiorin et al, Mol Phys 2013:
+colvars:  http://dx.doi.org/10.1080/00268976.2013.813594
+colvars: in any publication based on this calculation.
+colvars: SMP parallelism is available.
+colvars: Using LAMMPS interface, version 2018-08-29.
+colvars: ----------------------------------------------------------------------
+colvars: Reading new configuration from file "peptide.colvars":
+colvars: # smp = on [default]
 colvars: # colvarsTrajFrequency = 1
 colvars: # colvarsRestartFrequency = 1000
-colvars: # colvarsTrajAppend = off [default]
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "out2.colvars.state".
-colvars: Writing to colvar trajectory file "out2.colvars.traj".
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
 colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new collective variable.
-colvars:   # name = one
+colvars:   # name = "one"
 colvars:   Initializing a new "distance" component.
+colvars:     # name = "" [default]
 colvars:     # componentCoeff = 1 [default]
 colvars:     # componentExp = 1 [default]
 colvars:     # period = 0 [default]
 colvars:     # wrapAround = 0 [default]
 colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
+colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "" [default]
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
 colvars:       # enableForces = on [default]
-colvars:       # disableForces = off [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
 colvars:       # enableFitGradients = on [default]
-colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 0.
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
 colvars:       Initializing atom group "group2".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "" [default]
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
 colvars:       # enableForces = on [default]
-colvars:       # disableForces = off [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
 colvars:       # enableFitGradients = on [default]
-colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 0.
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
+colvars:     # oneSiteSystemForce = off [default]
+colvars:     # oneSiteTotalForce = off [default]
 colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
 colvars:   # width = 1 [default]
 colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
 colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
 colvars:   # expandBoundaries = off [default]
 colvars:   # extendedLagrangian = off [default]
 colvars:   # outputValue = on [default]
 colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
+colvars:   # outputTotalForce = off [default]
 colvars:   # outputAppliedForce = off [default]
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
 colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new collective variable.
-colvars:   # name = two
+colvars:   # name = "two"
 colvars:   Initializing a new "distance" component.
+colvars:     # name = "" [default]
 colvars:     # componentCoeff = 1 [default]
 colvars:     # componentExp = 1 [default]
 colvars:     # period = 0 [default]
 colvars:     # wrapAround = 0 [default]
 colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
+colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "" [default]
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
 colvars:       # enableForces = on [default]
-colvars:       # disableForces = off [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
 colvars:       # enableFitGradients = on [default]
-colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 0.
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
 colvars:       Initializing atom group "group2".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "" [default]
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
 colvars:       # enableForces = on [default]
-colvars:       # disableForces = off [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
 colvars:       # enableFitGradients = on [default]
-colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 0.
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
+colvars:     # oneSiteSystemForce = off [default]
+colvars:     # oneSiteTotalForce = off [default]
 colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
 colvars:   # width = 1 [default]
 colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
 colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
 colvars:   # expandBoundaries = off [default]
 colvars:   # extendedLagrangian = off [default]
 colvars:   # outputValue = on [default]
 colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
+colvars:   # outputTotalForce = off [default]
 colvars:   # outputAppliedForce = off [default]
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables initialized, 2 in total.
 colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "harmonic" instance.
-colvars:   # name = h_pot
+colvars:   # name = "h_pot"
 colvars:   # colvars = { one, two }
 colvars:   # outputEnergy = off [default]
-colvars:   # forceConstant = 100
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # writeTISamples = off [default]
+colvars:   # writeTIPMF = off [default]
 colvars:   # centers = { 10, 10 }
 colvars:   # targetCenters = { 10, 10 } [default]
-colvars:   # targetForceConstant = 0 [default]
 colvars:   # outputCenters = off [default]
-colvars:   # outputAccumulatedWork = off [default]
+colvars:   # forceConstant = 100
+colvars:   # targetForceConstant = -1 [default]
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
+colvars: Collective variables module (re)initialized.
+colvars: ----------------------------------------------------------------------
+colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
+colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
+colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
+colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
+colvars: ----------------------------------------------------------------------
 colvars: Restarting from file "out.colvars.state".
 colvars:   Restarting collective variable "one" from value: 10.0128
 colvars:   Restarting collective variable "two" from value: 9.62236
-colvars:   Restarting harmonic bias "h_pot".
 colvars: ----------------------------------------------------------------------
-colvars: Collective variables module initialized.
-colvars: ----------------------------------------------------------------------
-colvars: Initializing step number as firstTimestep.
+colvars: The restart output state file will be "rest.colvars.state".
+colvars: The final output state file will be "out2.colvars.state".
+colvars: Writing to colvar trajectory file "out2.colvars.traj".
+colvars: Setting initial step number from LAMMPS: 200
 colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
 colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
 colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
 colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
+colvars: Performing analysis.
 SHAKE stats (type/ave/delta) on step 200
-  4 1.111 1.81287e-06
-  6 0.997 7.79626e-07
-  8 1.08 1.08933e-06
-  10 1.111 2.96498e-07
-  12 1.08 4.69169e-07
+  4 1.111 1.81266e-06
+  6 0.997 7.79424e-07
+  8 1.08 1.08903e-06
+  10 1.111 2.96503e-07
+  12 1.08 4.69038e-07
   14 0.960001 0
-  18 0.957201 3.76617e-06
-  31 104.52 0.000411076
-Memory usage per processor = 10.4104 Mbytes
-Step Temp TotEng PotEng KinEng E_pair E_bond 2 
-     200    251.50646   -5557.4204    -6569.256    1011.8356   -6674.0889    24.805155      7.13891 
-     210    253.15173   -5538.5647   -6557.0194    1018.4547    -6672.044    37.671405   0.61299805 
-     220    245.19832   -5522.5253   -6508.9826    986.45735   -6628.2043    36.656213   0.04862311 
-     230    258.65093   -5495.7204   -6536.2989    1040.5785   -6658.0891    34.855426   0.22044707 
-     240    260.80348   -5469.8527   -6519.0912    1049.2385   -6624.1806    31.576284    3.7570152 
-     250    269.06517   -5438.3941   -6520.8701    1082.4761   -6616.3835    25.443998    8.6642401 
-     260    266.10873   -5397.3229    -6467.905     1070.582   -6580.6583    26.873845    8.3331291 
-     270    272.81399   -5350.8435   -6448.4015    1097.5579   -6563.7941     23.11303    10.972811 
-     280    279.52614   -5307.9857   -6432.5473    1124.5616   -6557.7474    33.640052    8.5474491 
-     290     286.8015     -5260.87   -6414.7011    1153.8311   -6515.4961    28.571844    5.9093384 
+  18 0.957201 3.76471e-06
+  31 104.52 0.000411055
+Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
+     200    251.50475   -5557.4251   -6569.2538    1011.8287   -6674.0845    24.804906    7.1387574 
+     210    253.15303   -5538.5615   -6557.0215      1018.46   -6672.0498     37.67662   0.61219496 
+     220    245.19621    -5522.519   -6508.9679    986.44888   -6628.1899    36.657688   0.04864338 
+     230    258.69884   -5495.7275   -6536.4988    1040.7713   -6658.2885    34.857911   0.22092547 
+     240    260.79635   -5469.8678   -6519.0776    1049.2098   -6624.1801    31.576951    3.7574816 
+     250    269.07527   -5438.3946   -6520.9114    1082.5167   -6616.4383    25.447674    8.6600014 
+     260    266.01049   -5397.3485   -6467.5353    1070.1868   -6580.2897    26.871917    8.3323097 
+     270    272.81313    -5350.882   -6448.4365    1097.5545   -6563.8231    23.114195    10.973131 
+     280    279.42263   -5307.9798    -6432.125    1124.1452   -6557.3367    33.644027    8.5490492 
+     290    286.85172    -5260.841   -6414.8741    1154.0331   -6515.6798    28.574838    5.9100133 
 SHAKE stats (type/ave/delta) on step 300
-  4 1.111 1.79747e-05
-  6 0.997005 1.02624e-05
-  8 1.08 1.84986e-05
-  10 1.111 9.9852e-06
-  12 1.08 8.8315e-06
+  4 1.111 1.79792e-05
+  6 0.997005 1.02512e-05
+  8 1.08 1.85102e-05
+  10 1.111 9.98839e-06
+  12 1.08 8.84111e-06
   14 0.960008 0
-  18 0.957203 1.84856e-05
-  31 104.52 0.00169095
-     300    291.51723   -5216.3366   -6389.1396     1172.803   -6503.1168    27.877108    2.2481775 
+  18 0.957203 1.8445e-05
+  31 104.52 0.00168383
+     300    291.52798    -5216.288   -6389.1341    1172.8462   -6503.1276    27.889154    2.2482459 
+colvars: Saving collective variables state to "out2.colvars.state".
+Loop time of 2.07171 on 1 procs for 100 steps with 2004 atoms
 
-Loop time of 1.0092 on 2 procs for 100 steps with 2004 atoms
-99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
-Performance: 17.123 ns/day  1.402 hours/ns  99.089 timesteps/s
+Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s
+98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
 
-MPI task timings breakdown:
+MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.77015    | 0.77511    | 0.78007    |   0.6 | 76.80
-Bond    | 0.0022984  | 0.0024998  | 0.0027013  |   0.4 |  0.25
-Kspace  | 0.088884   | 0.093076   | 0.097267   |   1.4 |  9.22
-Neigh   | 0.092871   | 0.092888   | 0.092905   |   0.0 |  9.20
-Comm    | 0.016476   | 0.017      | 0.017524   |   0.4 |  1.68
-Output  | 0.00022602 | 0.00031459 | 0.00040317 |   0.5 |  0.03
-Modify  | 0.025814   | 0.025818   | 0.025823   |   0.0 |  2.56
-Other   |            | 0.002488   |            |       |  0.25
+Pair    | 1.6047     | 1.6047     | 1.6047     |   0.0 | 77.46
+Bond    | 0.0031033  | 0.0031033  | 0.0031033  |   0.0 |  0.15
+Kspace  | 0.17325    | 0.17325    | 0.17325    |   0.0 |  8.36
+Neigh   | 0.25117    | 0.25117    | 0.25117    |   0.0 | 12.12
+Comm    | 0.012173   | 0.012173   | 0.012173   |   0.0 |  0.59
+Output  | 0.00026488 | 0.00026488 | 0.00026488 |   0.0 |  0.01
+Modify  | 0.025317   | 0.025317   | 0.025317   |   0.0 |  1.22
+Other   |            | 0.001731   |            |       |  0.08
 
-Nlocal:    1002 ave 1024 max 980 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    8717.5 ave 8755 max 8680 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    354073 ave 358151 max 349995 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
+Nlocal:    2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11296 ave 11296 max 11296 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    708152 ave 708152 max 708152 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 708146
-Ave neighs/atom = 353.366
+Total # of neighbors = 708152
+Ave neighs/atom = 353.369
 Ave special neighs/atom = 2.34032
 Neighbor list builds = 8
 Dangerous builds = 0
 
-colvars: Saving collective variables state to "out2.colvars.state".
+colvars: Resetting the Collective Variables module.
 
 Please see the log.cite file for references relevant to this simulation
 
+Total wall time: 0:00:06

examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4

@@ -0,0 +1,629 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+
+units		real
+atom_style	full
+
+pair_style	lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style	pppm 0.0001
+
+read_data	data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor	2.0 bin
+neigh_modify	delay 5
+
+timestep	2.0
+
+group		peptide type <= 12
+84 atoms in group peptide
+group		one id 2 4 5 6
+4 atoms in group one
+group		two id 80 82 83 84
+4 atoms in group two
+group		ref id 37
+1 atoms in group ref
+group		colvar union one two ref
+9 atoms in group colvar
+
+fix		1 all nvt temp  275.0 275.0 100.0 tchain 1
+
+shell "rm -f out*.colvars.*"
+fix		2 all colvars peptide.colvars
+fix		2a ref setforce 0.0 0.0 0.0
+
+fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+
+#dump		1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
+#dump_modify 1 sort id
+
+thermo_style	custom step temp etotal pe ke epair ebond f_2
+thermo		10
+
+
+run		100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 4312 960
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+colvars: Creating proxy instance
+colvars: ----------------------------------------------------------------------
+colvars: Initializing the collective variables module, version 2018-11-16.
+colvars: Please cite Fiorin et al, Mol Phys 2013:
+colvars:  http://dx.doi.org/10.1080/00268976.2013.813594
+colvars: in any publication based on this calculation.
+colvars: SMP parallelism is available.
+colvars: Using LAMMPS interface, version 2018-08-29.
+colvars: ----------------------------------------------------------------------
+colvars: Reading new configuration from file "peptide.colvars":
+colvars: # smp = on [default]
+colvars: # colvarsTrajFrequency = 1
+colvars: # colvarsRestartFrequency = 1000
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new collective variable.
+colvars:   # name = "one"
+colvars:   Initializing a new "distance" component.
+colvars:     # name = "" [default]
+colvars:     # componentCoeff = 1 [default]
+colvars:     # componentExp = 1 [default]
+colvars:     # period = 0 [default]
+colvars:     # wrapAround = 0 [default]
+colvars:     # forceNoPBC = off [default]
+colvars:     # scalable = on [default]
+colvars:       Initializing atom group "group1".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "" [default]
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [default]
+colvars:       # enableFitGradients = on [default]
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
+colvars:       Initializing atom group "group2".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "" [default]
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [default]
+colvars:       # enableFitGradients = on [default]
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
+colvars:     # oneSiteSystemForce = off [default]
+colvars:     # oneSiteTotalForce = off [default]
+colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 1 [default]
+colvars:   # lowerBoundary = 0 [default]
+colvars:   # upperBoundary = 0 [default]
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = off [default]
+colvars:   # outputValue = on [default]
+colvars:   # outputVelocity = off [default]
+colvars:   # outputTotalForce = off [default]
+colvars:   # outputAppliedForce = off [default]
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new collective variable.
+colvars:   # name = "two"
+colvars:   Initializing a new "distance" component.
+colvars:     # name = "" [default]
+colvars:     # componentCoeff = 1 [default]
+colvars:     # componentExp = 1 [default]
+colvars:     # period = 0 [default]
+colvars:     # wrapAround = 0 [default]
+colvars:     # forceNoPBC = off [default]
+colvars:     # scalable = on [default]
+colvars:       Initializing atom group "group1".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "" [default]
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [default]
+colvars:       # enableFitGradients = on [default]
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
+colvars:       Initializing atom group "group2".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "" [default]
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [default]
+colvars:       # enableFitGradients = on [default]
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
+colvars:     # oneSiteSystemForce = off [default]
+colvars:     # oneSiteTotalForce = off [default]
+colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 1 [default]
+colvars:   # lowerBoundary = 0 [default]
+colvars:   # upperBoundary = 0 [default]
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = off [default]
+colvars:   # outputValue = on [default]
+colvars:   # outputVelocity = off [default]
+colvars:   # outputTotalForce = off [default]
+colvars:   # outputAppliedForce = off [default]
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables initialized, 2 in total.
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new "harmonic" instance.
+colvars:   # name = "h_pot"
+colvars:   # colvars = { one, two }
+colvars:   # outputEnergy = off [default]
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # writeTISamples = off [default]
+colvars:   # writeTIPMF = off [default]
+colvars:   # centers = { 10, 10 }
+colvars:   # targetCenters = { 10, 10 } [default]
+colvars:   # outputCenters = off [default]
+colvars:   # forceConstant = 100
+colvars:   # targetForceConstant = -1 [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables biases initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables module (re)initialized.
+colvars: ----------------------------------------------------------------------
+colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
+colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
+colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
+colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
+colvars: The restart output state file will be "rest.colvars.state".
+colvars: The final output state file will be "out.colvars.state".
+colvars: Writing to colvar trajectory file "out.colvars.traj".
+colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
+colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
+colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
+colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
+colvars: Performing analysis.
+SHAKE stats (type/ave/delta) on step 0
+  4 1.111 1.44264e-05
+  6 0.996998 7.26967e-06
+  8 1.08 1.32536e-05
+  10 1.111 1.22749e-05
+  12 1.08 1.11767e-05
+  14 0.96 0
+  18 0.957206 4.37979e-05
+  31 104.519 0.00396029
+Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
+       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    292.14604 
+      10    305.06149   -5058.8972   -6286.1901    1227.2929   -6413.1021      58.8499    103.38345 
+      20    311.00516   -4999.0612    -6250.266    1251.2048   -6417.1021    47.695297    36.699695 
+      30    314.22337   -4993.7012   -6257.8532     1264.152   -6421.9679    35.344144    10.563933 
+      40    297.87491   -5020.8378   -6219.2184    1198.3805   -6389.8528    27.723133    3.8354517 
+      50    304.02071   -5056.2576   -6279.3633    1223.1057   -6456.8214    55.459505   0.20678217 
+      60    285.92576   -5104.0461    -6254.354    1150.3079   -6435.5814    32.767229   0.69352945 
+      70    277.83519   -5163.9758   -6281.7345    1117.7587   -6447.7033    39.627168    11.433603 
+      80    267.51495   -5206.4046    -6282.644    1076.2394   -6456.6369    31.611883    6.3554178 
+      90    278.15579   -5245.3824    -6364.431    1119.0485   -6499.8063    28.849773   0.36941576 
+SHAKE stats (type/ave/delta) on step 100
+  4 1.11098 8.97155e-05
+  6 0.996996 1.00568e-05
+  8 1.08 6.02345e-06
+  10 1.111 1.84253e-05
+  12 1.08 7.2713e-06
+  14 0.959996 0
+  18 0.957198 3.36079e-05
+  31 104.52 0.0030599
+     100    260.10613   -5292.6885   -6339.1215     1046.433   -6471.6734    25.362042   0.21987323 
+colvars: Saving collective variables state to "out.colvars.state".
+Loop time of 0.614168 on 4 procs for 100 steps with 2004 atoms
+
+Performance: 28.136 ns/day, 0.853 hours/ns, 162.822 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.40413    | 0.41468    | 0.42573    |   1.4 | 67.52
+Bond    | 0.00056815 | 0.0011595  | 0.0017791  |   1.6 |  0.19
+Kspace  | 0.056367   | 0.066512   | 0.076213   |   3.3 | 10.83
+Neigh   | 0.095025   | 0.09507    | 0.095124   |   0.0 | 15.48
+Comm    | 0.015385   | 0.015831   | 0.01623    |   0.2 |  2.58
+Output  | 0.00026512 | 0.00034493 | 0.00057554 |   0.0 |  0.06
+Modify  | 0.01938    | 0.019431   | 0.019474   |   0.0 |  3.16
+Other   |            | 0.001141   |            |       |  0.19
+
+Nlocal:    501 ave 513 max 489 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost:    6563.25 ave 6596 max 6519 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs:    177059 ave 181742 max 172942 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 708237
+Ave neighs/atom = 353.412
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 12
+Dangerous builds = 2
+
+run     100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 4312 960
+colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
+colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
+colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
+colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
+SHAKE stats (type/ave/delta) on step 100
+  4 1.11098 8.97155e-05
+  6 0.996996 1.00568e-05
+  8 1.08 6.02345e-06
+  10 1.111 1.84253e-05
+  12 1.08 7.2713e-06
+  14 0.959996 0
+  18 0.957198 3.36079e-05
+  31 104.52 0.0030599
+Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
+     100    260.10613   -5292.6885   -6339.1215     1046.433   -6471.6734    25.362042   0.21987323 
+     110    266.26438   -5341.1991   -6412.4073    1071.2082   -6552.7551    33.573173    1.9229657 
+     120    262.66604   -5386.2387   -6442.9704    1056.7317   -6587.5483    29.859587    2.7124812 
+     130    252.83379   -5422.5401   -6439.7157    1017.1756   -6580.4703    25.979343    1.2031592 
+     140    253.85111   -5452.1838   -6473.4521    1021.2684   -6609.4826    26.071651   0.30585517 
+     150    261.31816   -5490.4726   -6541.7817    1051.3091   -6646.6075    16.258823    6.9051008 
+     160     255.7352   -5521.5941   -6550.4423    1028.8483   -6658.1373    19.717399    12.339679 
+     170    253.42527   -5540.0941   -6559.6493    1019.5552   -6656.6677    23.293812    10.290217 
+     180    248.51161   -5550.3253   -6550.1124    999.78704   -6661.4235    26.200127    3.4336037 
+     190    250.80862   -5555.2553   -6564.2834    1009.0282   -6666.1638     25.53634    3.3494287 
+SHAKE stats (type/ave/delta) on step 200
+  4 1.111 1.81266e-06
+  6 0.997 7.79424e-07
+  8 1.08 1.08903e-06
+  10 1.111 2.96503e-07
+  12 1.08 4.69038e-07
+  14 0.960001 0
+  18 0.957201 3.76471e-06
+  31 104.52 0.000411055
+     200    251.50475   -5557.4251   -6569.2539    1011.8288   -6674.0845    24.804905    7.1387572 
+colvars: Saving collective variables state to "out.colvars.state".
+Loop time of 0.569733 on 4 procs for 100 steps with 2004 atoms
+
+Performance: 30.330 ns/day, 0.791 hours/ns, 175.521 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.40512    | 0.41306    | 0.42363    |   1.3 | 72.50
+Bond    | 0.00061107 | 0.001151   | 0.0017512  |   1.4 |  0.20
+Kspace  | 0.054393   | 0.063988   | 0.07198    |   3.0 | 11.23
+Neigh   | 0.056063   | 0.056079   | 0.05609    |   0.0 |  9.84
+Comm    | 0.013584   | 0.014145   | 0.014649   |   0.3 |  2.48
+Output  | 0.00026965 | 0.00042897 | 0.00090265 |   0.0 |  0.08
+Modify  | 0.019253   | 0.019257   | 0.01926    |   0.0 |  3.38
+Other   |            | 0.001623   |            |       |  0.28
+
+Nlocal:    501 ave 513 max 481 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost:    6556.5 ave 6608 max 6514 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs:    177021 ave 182259 max 172089 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 708083
+Ave neighs/atom = 353.335
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 7
+Dangerous builds = 0
+
+fix 2 all colvars peptide.colvars input out.colvars.state output out2
+colvars: Resetting the Collective Variables module.
+
+run     100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 4312 960
+colvars: Creating proxy instance
+colvars: ----------------------------------------------------------------------
+colvars: Initializing the collective variables module, version 2018-11-16.
+colvars: Please cite Fiorin et al, Mol Phys 2013:
+colvars:  http://dx.doi.org/10.1080/00268976.2013.813594
+colvars: in any publication based on this calculation.
+colvars: SMP parallelism is available.
+colvars: Using LAMMPS interface, version 2018-08-29.
+colvars: ----------------------------------------------------------------------
+colvars: Reading new configuration from file "peptide.colvars":
+colvars: # smp = on [default]
+colvars: # colvarsTrajFrequency = 1
+colvars: # colvarsRestartFrequency = 1000
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new collective variable.
+colvars:   # name = "one"
+colvars:   Initializing a new "distance" component.
+colvars:     # name = "" [default]
+colvars:     # componentCoeff = 1 [default]
+colvars:     # componentExp = 1 [default]
+colvars:     # period = 0 [default]
+colvars:     # wrapAround = 0 [default]
+colvars:     # forceNoPBC = off [default]
+colvars:     # scalable = on [default]
+colvars:       Initializing atom group "group1".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "" [default]
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [default]
+colvars:       # enableFitGradients = on [default]
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
+colvars:       Initializing atom group "group2".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "" [default]
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [default]
+colvars:       # enableFitGradients = on [default]
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
+colvars:     # oneSiteSystemForce = off [default]
+colvars:     # oneSiteTotalForce = off [default]
+colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 1 [default]
+colvars:   # lowerBoundary = 0 [default]
+colvars:   # upperBoundary = 0 [default]
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = off [default]
+colvars:   # outputValue = on [default]
+colvars:   # outputVelocity = off [default]
+colvars:   # outputTotalForce = off [default]
+colvars:   # outputAppliedForce = off [default]
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new collective variable.
+colvars:   # name = "two"
+colvars:   Initializing a new "distance" component.
+colvars:     # name = "" [default]
+colvars:     # componentCoeff = 1 [default]
+colvars:     # componentExp = 1 [default]
+colvars:     # period = 0 [default]
+colvars:     # wrapAround = 0 [default]
+colvars:     # forceNoPBC = off [default]
+colvars:     # scalable = on [default]
+colvars:       Initializing atom group "group1".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "" [default]
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [default]
+colvars:       # enableFitGradients = on [default]
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
+colvars:       Initializing atom group "group2".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "" [default]
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [default]
+colvars:       # enableFitGradients = on [default]
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
+colvars:     # oneSiteSystemForce = off [default]
+colvars:     # oneSiteTotalForce = off [default]
+colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 1 [default]
+colvars:   # lowerBoundary = 0 [default]
+colvars:   # upperBoundary = 0 [default]
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = off [default]
+colvars:   # outputValue = on [default]
+colvars:   # outputVelocity = off [default]
+colvars:   # outputTotalForce = off [default]
+colvars:   # outputAppliedForce = off [default]
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables initialized, 2 in total.
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new "harmonic" instance.
+colvars:   # name = "h_pot"
+colvars:   # colvars = { one, two }
+colvars:   # outputEnergy = off [default]
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # writeTISamples = off [default]
+colvars:   # writeTIPMF = off [default]
+colvars:   # centers = { 10, 10 }
+colvars:   # targetCenters = { 10, 10 } [default]
+colvars:   # outputCenters = off [default]
+colvars:   # forceConstant = 100
+colvars:   # targetForceConstant = -1 [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables biases initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables module (re)initialized.
+colvars: ----------------------------------------------------------------------
+colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
+colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
+colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
+colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
+colvars: ----------------------------------------------------------------------
+colvars: Restarting from file "out.colvars.state".
+colvars:   Restarting collective variable "one" from value: 10.0128
+colvars:   Restarting collective variable "two" from value: 9.62236
+colvars: ----------------------------------------------------------------------
+colvars: The restart output state file will be "rest.colvars.state".
+colvars: The final output state file will be "out2.colvars.state".
+colvars: Writing to colvar trajectory file "out2.colvars.traj".
+colvars: Setting initial step number from LAMMPS: 200
+colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
+colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
+colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
+colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
+colvars: Performing analysis.
+SHAKE stats (type/ave/delta) on step 200
+  4 1.111 1.81266e-06
+  6 0.997 7.79424e-07
+  8 1.08 1.08903e-06
+  10 1.111 2.96503e-07
+  12 1.08 4.69038e-07
+  14 0.960001 0
+  18 0.957201 3.76471e-06
+  31 104.52 0.000411055
+Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
+     200    251.50475   -5557.4251   -6569.2539    1011.8288   -6674.0845    24.804905    7.1387572 
+     210    253.15304   -5538.5615   -6557.0215      1018.46   -6672.0498    37.676621   0.61219486 
+     220    245.19621   -5522.5189   -6508.9678    986.44888   -6628.1898    36.657688  0.048643368 
+     230    258.69885   -5495.7276   -6536.4989    1040.7713   -6658.2887    34.857911   0.22092541 
+     240    260.79635   -5469.8677   -6519.0775    1049.2098     -6624.18    31.576952    3.7574818 
+     250    269.07527   -5438.3947   -6520.9115    1082.5167   -6616.4384    25.447674    8.6600013 
+     260     266.0105   -5397.3486   -6467.5354    1070.1868   -6580.2898    26.871917    8.3323096 
+     270    272.81314   -5350.8819   -6448.4364    1097.5545    -6563.823    23.114195    10.973131 
+     280    279.42263   -5307.9799    -6432.125    1124.1452   -6557.3367    33.644027    8.5490488 
+     290     286.8517   -5260.8409    -6414.874    1154.0331   -6515.6797    28.574839    5.9100135 
+SHAKE stats (type/ave/delta) on step 300
+  4 1.111 1.79792e-05
+  6 0.997005 1.02512e-05
+  8 1.08 1.85102e-05
+  10 1.111 9.98838e-06
+  12 1.08 8.84113e-06
+  14 0.960008 0
+  18 0.957203 1.8445e-05
+  31 104.52 0.00168382
+     300    291.52794   -5216.2881   -6389.1342     1172.846   -6503.1276    27.889153     2.248246 
+colvars: Saving collective variables state to "out2.colvars.state".
+Loop time of 0.584942 on 4 procs for 100 steps with 2004 atoms
+
+Performance: 29.541 ns/day, 0.812 hours/ns, 170.957 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    | 0.41044    | 0.41882    | 0.42773    |   1.1 | 71.60
+Bond    | 0.00056911 | 0.0011486  | 0.0018017  |   1.4 |  0.20
+Kspace  | 0.056211   | 0.064277   | 0.072168   |   2.7 | 10.99
+Neigh   | 0.064606   | 0.064613   | 0.064617   |   0.0 | 11.05
+Comm    | 0.013311   | 0.013966   | 0.015175   |   0.6 |  2.39
+Output  | 0.00027871 | 0.00051689 | 0.0012221  |   0.0 |  0.09
+Modify  | 0.019776   | 0.0199     | 0.020015   |   0.1 |  3.40
+Other   |            | 0.001705   |            |       |  0.29
+
+Nlocal:    501 ave 513 max 472 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Nghost:    6612.75 ave 6681 max 6561 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Neighs:    177038 ave 180136 max 170218 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+
+Total # of neighbors = 708152
+Ave neighs/atom = 353.369
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 8
+Dangerous builds = 0
+
+colvars: Resetting the Collective Variables module.
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01

examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1

@@ -1,5 +1,4 @@
-LAMMPS (20 Mar 2014-ICMS)
-WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
+LAMMPS (27 Nov 2018)
   using 1 OpenMP thread(s) per MPI task
 # Solvated 5-mer peptide
 
@@ -15,7 +14,7 @@ kspace_style	pppm 0.0001
 
 read_data	data.peptide
   orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
-  1 by 1 by 2 MPI processor grid
+  1 by 1 by 1 MPI processor grid
   reading atoms ...
   2004 atoms
   reading velocities ...
@@ -77,88 +76,122 @@ thermo		10
 
 run		100
 PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
   G vector (1/distance) = 0.268725
   grid = 15 15 15
   stencil order = 5
   estimated absolute RMS force accuracy = 0.0228209
   estimated relative force accuracy = 6.87243e-05
   using double precision FFTs
-  3d grid and FFT values/proc = 6776 1800
+  3d grid and FFT values/proc = 10648 3375
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
 colvars: Creating proxy instance
 colvars: ----------------------------------------------------------------------
-colvars: Initializing the collective variables module, version 2013-10-22.
-colvars: # indexFile = "" [default]
-colvars: # analysis = off [default]
+colvars: Initializing the collective variables module, version 2018-11-16.
+colvars: Please cite Fiorin et al, Mol Phys 2013:
+colvars:  http://dx.doi.org/10.1080/00268976.2013.813594
+colvars: in any publication based on this calculation.
+colvars: SMP parallelism is available.
+colvars: Using LAMMPS interface, version 2018-08-29.
+colvars: ----------------------------------------------------------------------
+colvars: Reading new configuration from file "peptide.colvars2":
+colvars: # smp = on [default]
 colvars: # colvarsTrajFrequency = 1
 colvars: # colvarsRestartFrequency = 1000
-colvars: # colvarsTrajAppend = off [default]
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "peptide2.colvars.state".
-colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
 colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new collective variable.
-colvars:   # name = one
+colvars:   # name = "one"
 colvars:   Initializing a new "distance" component.
+colvars:     # name = "" [default]
 colvars:     # componentCoeff = 1 [default]
 colvars:     # componentExp = 1 [default]
 colvars:     # period = 0 [default]
 colvars:     # wrapAround = 0 [default]
 colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
+colvars:     # scalable = on [default]
 colvars:       Initializing atom group "group1".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "" [default]
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
 colvars:       # enableForces = on [default]
-colvars:       # disableForces = off [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
 colvars:       # enableFitGradients = on [default]
-colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 0.
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
 colvars:       Initializing atom group "group2".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
 colvars:       # indexGroup = "" [default]
 colvars:       # psfSegID =  [default]
 colvars:       # atomsFile = "" [default]
 colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
 colvars:       # enableForces = on [default]
-colvars:       # disableForces = off [default]
-colvars:       # centerReference = off [default]
-colvars:       # rotateReference = off [default]
 colvars:       # enableFitGradients = on [default]
-colvars:       Atom group "group2" defined, 4 atoms initialized: total mass = 0.
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
+colvars:     # oneSiteSystemForce = off [default]
+colvars:     # oneSiteTotalForce = off [default]
 colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
 colvars:   # width = 1 [default]
 colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
 colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
 colvars:   # expandBoundaries = off [default]
 colvars:   # extendedLagrangian = off [default]
 colvars:   # outputValue = on [default]
 colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
+colvars:   # outputTotalForce = off [default]
 colvars:   # outputAppliedForce = off [default]
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
 colvars:   Initializing a new "harmonic" instance.
-colvars:   # name = h_pot
+colvars:   # name = "h_pot"
 colvars:   # colvars = { one }
 colvars:   # outputEnergy = off [default]
-colvars:   # forceConstant = 100
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # writeTISamples = off [default]
+colvars:   # writeTIPMF = off [default]
 colvars:   # centers = { 10 }
 colvars:   # targetCenters = { 10 } [default]
-colvars:   # targetForceConstant = 0 [default]
 colvars:   # outputCenters = off [default]
-colvars:   # outputAccumulatedWork = off [default]
+colvars:   # forceConstant = 100
+colvars:   # targetForceConstant = -1 [default]
 colvars: ----------------------------------------------------------------------
 colvars: Collective variables biases initialized, 1 in total.
 colvars: ----------------------------------------------------------------------
-colvars: Collective variables module initialized.
+colvars: Collective variables module (re)initialized.
 colvars: ----------------------------------------------------------------------
+colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
+colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
+colvars: The restart output state file will be "rest.colvars.state".
+colvars: The final output state file will be "peptide2.colvars.state".
+colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
 colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
 colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
+colvars: Performing analysis.
 SHAKE stats (type/ave/delta) on step 0
   4 1.111 1.44264e-05
   6 0.996998 7.26967e-06
@@ -168,58 +201,60 @@ SHAKE stats (type/ave/delta) on step 0
   14 0.96 0
   18 0.957206 4.37979e-05
   31 104.519 0.00396029
-Memory usage per processor = 10.4103 Mbytes
-Step Temp TotEng PotEng KinEng E_pair E_bond 2 
+Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
        0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    273.74323 
-      10    333.47973   -4982.3893   -6324.0116    1341.6223    -6400.417    21.367753    12.393269 
-      20    309.56974   -4999.4934   -6244.9234      1245.43   -6401.6969    43.595447    13.004393 
-      30    316.97689   -5025.5598   -6300.7895    1275.2297   -6422.5335    27.323113    6.7588862 
-      40    297.55811   -5088.2155   -6285.3215     1197.106   -6395.3714    13.676871    25.625154 
-      50    296.80002   -5117.2927   -6311.3488    1194.0561   -6451.8274    30.631277    5.3320302 
-      60    281.72798    -5188.494   -6321.9138    1133.4198   -6427.8833     26.28765    20.573958 
-      70    277.26045   -5224.8416   -6340.2881    1115.4465   -6447.8495    27.742889   0.69414895 
-      80    268.01458   -5281.8501   -6360.0996    1078.2495   -6496.6062    20.300729     5.260642 
-      90    270.43384   -5334.0847   -6422.0671    1087.9824   -6563.2486    39.845992     1.183249 
+      10    333.47919   -4982.3968   -6324.0169    1341.6201   -6400.4223    21.367762    12.393263 
+      20    309.56902   -4999.4978   -6244.9249    1245.4271   -6401.6981     43.59542    13.004314 
+      30     316.9763   -5025.5662   -6300.7935    1275.2273   -6422.5375    27.323196    6.7589585 
+      40    297.55779   -5088.2204   -6285.3252    1197.1047    -6395.375      13.6769    25.625024 
+      50    296.79994   -5117.2966   -6311.3525    1194.0558   -6451.8309    30.631241    5.3320863 
+      60    281.72778   -5188.4969   -6321.9159     1133.419   -6427.8856    26.287723    20.574037 
+      70    277.26053   -5224.8434   -6340.2902    1115.4468   -6447.8521    27.742893   0.69420283 
+      80    268.01484   -5281.8509   -6360.1014    1078.2505   -6496.6086    20.300754    5.2607186 
+      90    270.43472   -5334.0835   -6422.0694    1087.9859   -6563.2511    39.846095    1.1832272 
 SHAKE stats (type/ave/delta) on step 100
-  4 1.11096 0.000191466
-  6 0.996989 3.5552e-05
-  8 1.08 9.10001e-06
-  10 1.111 1.58547e-05
-  12 1.08 5.80613e-06
+  4 1.11096 0.000191462
+  6 0.996989 3.55508e-05
+  8 1.08 9.0997e-06
+  10 1.111 1.58544e-05
+  12 1.08 5.80604e-06
   14 0.959997 0
-  18 0.957198 2.92454e-05
-  31 104.52 0.00239929
-     100    260.35617   -5387.2298   -6434.6687    1047.4389   -6534.1957    20.246734  0.075048991 
+  18 0.957198 2.92445e-05
+  31 104.52 0.00239923
+     100    260.35636   -5387.2284   -6434.6681    1047.4397   -6534.1956    20.246866  0.075048487 
+colvars: Saving collective variables state to "peptide2.colvars.state".
+Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms
 
-Loop time of 1.07439 on 2 procs for 100 steps with 2004 atoms
-98.2% CPU use with 2 MPI tasks x 1 OpenMP threads
-Performance: 16.084 ns/day  1.492 hours/ns  93.076 timesteps/s
+Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
-MPI task timings breakdown:
+MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.77154    | 0.77308    | 0.77462    |   0.2 | 71.96
-Bond    | 0.0023637  | 0.0025266  | 0.0026896  |   0.3 |  0.24
-Kspace  | 0.095779   | 0.097411   | 0.099043   |   0.5 |  9.07
-Neigh   | 0.15521    | 0.15521    | 0.15522    |   0.0 | 14.45
-Comm    | 0.018134   | 0.018364   | 0.018594   |   0.2 |  1.71
-Output  | 0.00024295 | 0.00032854 | 0.00041413 |   0.5 |  0.03
-Modify  | 0.024936   | 0.024973   | 0.02501    |   0.0 |  2.32
-Other   |            | 0.002498   |            |       |  0.23
+Pair    | 1.6373     | 1.6373     | 1.6373     |   0.0 | 72.46
+Bond    | 0.0031531  | 0.0031531  | 0.0031531  |   0.0 |  0.14
+Kspace  | 0.17439    | 0.17439    | 0.17439    |   0.0 |  7.72
+Neigh   | 0.40442    | 0.40442    | 0.40442    |   0.0 | 17.90
+Comm    | 0.014091   | 0.014091   | 0.014091   |   0.0 |  0.62
+Output  | 0.00027752 | 0.00027752 | 0.00027752 |   0.0 |  0.01
+Modify  | 0.024481   | 0.024481   | 0.024481   |   0.0 |  1.08
+Other   |            | 0.001465   |            |       |  0.06
 
-Nlocal:    1002 ave 1010 max 994 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Nghost:    8645 ave 8652 max 8638 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
-Neighs:    354116 ave 356373 max 351860 min
-Histogram: 1 0 0 0 0 0 0 0 0 1
+Nlocal:    2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11143 ave 11143 max 11143 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    708234 ave 708234 max 708234 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 708233
+Total # of neighbors = 708234
 Ave neighs/atom = 353.41
 Ave special neighs/atom = 2.34032
 Neighbor list builds = 13
 Dangerous builds = 1
-colvars: Saving collective variables state to "peptide2.colvars.state".
+colvars: Resetting the Collective Variables module.
 
 Please see the log.cite file for references relevant to this simulation
 
+Total wall time: 0:00:02

examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4

@@ -0,0 +1,260 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+
+units		real
+atom_style	full
+
+pair_style	lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style	pppm 0.0001
+
+read_data	data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor	2.0 bin
+neigh_modify	delay 5
+
+timestep	2.0
+
+group		peptide type <= 12
+84 atoms in group peptide
+group		one id 2 4 5 6
+4 atoms in group one
+group		two id 80 82 83 84
+4 atoms in group two
+group		ref id 37
+1 atoms in group ref
+group		colvar union one two ref
+9 atoms in group colvar
+
+fix		1 all nvt temp 275.0 275.0 100.0 tchain 1
+
+shell "rm -f peptide2.colvars.*"
+fix		2 all colvars peptide.colvars2 output peptide2
+
+fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+
+#dump		1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
+#dump_modify 1 sort id
+
+thermo_style	custom step temp etotal pe ke epair ebond f_2
+thermo		10
+
+
+run		100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 4312 960
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+colvars: Creating proxy instance
+colvars: ----------------------------------------------------------------------
+colvars: Initializing the collective variables module, version 2018-11-16.
+colvars: Please cite Fiorin et al, Mol Phys 2013:
+colvars:  http://dx.doi.org/10.1080/00268976.2013.813594
+colvars: in any publication based on this calculation.
+colvars: SMP parallelism is available.
+colvars: Using LAMMPS interface, version 2018-08-29.
+colvars: ----------------------------------------------------------------------
+colvars: Reading new configuration from file "peptide.colvars2":
+colvars: # smp = on [default]
+colvars: # colvarsTrajFrequency = 1
+colvars: # colvarsRestartFrequency = 1000
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new collective variable.
+colvars:   # name = "one"
+colvars:   Initializing a new "distance" component.
+colvars:     # name = "" [default]
+colvars:     # componentCoeff = 1 [default]
+colvars:     # componentExp = 1 [default]
+colvars:     # period = 0 [default]
+colvars:     # wrapAround = 0 [default]
+colvars:     # forceNoPBC = off [default]
+colvars:     # scalable = on [default]
+colvars:       Initializing atom group "group1".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "" [default]
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [default]
+colvars:       # enableFitGradients = on [default]
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
+colvars:       Initializing atom group "group2".
+colvars:       # name = "" [default]
+colvars:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "" [default]
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [default]
+colvars:       # enableFitGradients = on [default]
+colvars:       # printAtomIDs = off [default]
+colvars:       Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
+colvars:     # oneSiteSystemForce = off [default]
+colvars:     # oneSiteTotalForce = off [default]
+colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 1 [default]
+colvars:   # lowerBoundary = 0 [default]
+colvars:   # upperBoundary = 0 [default]
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = off [default]
+colvars:   # outputValue = on [default]
+colvars:   # outputVelocity = off [default]
+colvars:   # outputTotalForce = off [default]
+colvars:   # outputAppliedForce = off [default]
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new "harmonic" instance.
+colvars:   # name = "h_pot"
+colvars:   # colvars = { one }
+colvars:   # outputEnergy = off [default]
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # writeTISamples = off [default]
+colvars:   # writeTIPMF = off [default]
+colvars:   # centers = { 10 }
+colvars:   # targetCenters = { 10 } [default]
+colvars:   # outputCenters = off [default]
+colvars:   # forceConstant = 100
+colvars:   # targetForceConstant = -1 [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables biases initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables module (re)initialized.
+colvars: ----------------------------------------------------------------------
+colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
+colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
+colvars: The restart output state file will be "rest.colvars.state".
+colvars: The final output state file will be "peptide2.colvars.state".
+colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
+colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
+colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
+colvars: Performing analysis.
+SHAKE stats (type/ave/delta) on step 0
+  4 1.111 1.44264e-05
+  6 0.996998 7.26967e-06
+  8 1.08 1.32536e-05
+  10 1.111 1.22749e-05
+  12 1.08 1.11767e-05
+  14 0.96 0
+  18 0.957206 4.37979e-05
+  31 104.519 0.00396029
+Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond f_2 
+       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    273.74323 
+      10    333.47919   -4982.3968   -6324.0169    1341.6201   -6400.4223    21.367762    12.393263 
+      20    309.56902   -4999.4978   -6244.9249    1245.4271   -6401.6981     43.59542    13.004314 
+      30     316.9763   -5025.5662   -6300.7935    1275.2273   -6422.5375    27.323196    6.7589585 
+      40    297.55779   -5088.2204   -6285.3252    1197.1047    -6395.375      13.6769    25.625024 
+      50    296.79994   -5117.2966   -6311.3525    1194.0558   -6451.8309    30.631241    5.3320863 
+      60    281.72778   -5188.4969   -6321.9159     1133.419   -6427.8856    26.287723    20.574037 
+      70    277.26053   -5224.8434   -6340.2902    1115.4468   -6447.8521    27.742893   0.69420283 
+      80    268.01484   -5281.8509   -6360.1014    1078.2505   -6496.6086    20.300754    5.2607186 
+      90    270.43472   -5334.0835   -6422.0694    1087.9859   -6563.2511    39.846095    1.1832272 
+SHAKE stats (type/ave/delta) on step 100
+  4 1.11096 0.000191462
+  6 0.996989 3.55508e-05
+  8 1.08 9.0997e-06
+  10 1.111 1.58544e-05
+  12 1.08 5.80604e-06
+  14 0.959997 0
+  18 0.957198 2.92445e-05
+  31 104.52 0.00239923
+     100    260.35636   -5387.2284   -6434.6681    1047.4397   -6534.1956    20.246866  0.075048487 
+colvars: Saving collective variables state to "peptide2.colvars.state".
+Loop time of 0.629325 on 4 procs for 100 steps with 2004 atoms
+
+Performance: 27.458 ns/day, 0.874 hours/ns, 158.900 timesteps/s
+99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.4012     | 0.41532    | 0.42829    |   1.9 | 65.99
+Bond    | 0.0005219  | 0.0011545  | 0.0018291  |   1.8 |  0.18
+Kspace  | 0.059271   | 0.071301   | 0.084393   |   4.4 | 11.33
+Neigh   | 0.10416    | 0.10419    | 0.10424    |   0.0 | 16.56
+Comm    | 0.015643   | 0.016628   | 0.017256   |   0.5 |  2.64
+Output  | 0.00025177 | 0.00033599 | 0.00058722 |   0.0 |  0.05
+Modify  | 0.01912    | 0.019129   | 0.019141   |   0.0 |  3.04
+Other   |            | 0.001264   |            |       |  0.20
+
+Nlocal:    501 ave 513 max 494 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+Nghost:    6572.5 ave 6593 max 6548 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs:    177058 ave 181778 max 174301 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 708234
+Ave neighs/atom = 353.41
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 13
+Dangerous builds = 1
+colvars: Resetting the Collective Variables module.
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/USER/colvars/log.27Nov18.peptide-spring.g++.1

@@ -0,0 +1,163 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+
+units		real
+atom_style	full
+
+pair_style	lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style	pppm 0.0001
+
+read_data	data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor	2.0 bin
+neigh_modify	delay 5
+
+timestep	2.0
+
+group		peptide type <= 12
+84 atoms in group peptide
+group		one id 2 4 5 6
+4 atoms in group one
+group		two id 80 82 83 84
+4 atoms in group two
+group		ref id 37
+1 atoms in group ref
+group		colvar union one two ref
+9 atoms in group colvar
+
+fix		1 all nvt temp 275.0 275.0 100.0 tchain 1
+
+fix		3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
+fix		3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
+
+fix		2a ref setforce 0.0 0.0 0.0
+
+fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+
+#dump		1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
+#dump_modify 1  sort id
+
+variable sp equal f_3a+f_3b
+
+thermo_style	custom step temp etotal pe ke epair ebond v_sp
+thermo		10
+
+
+run		100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 10648 3375
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+SHAKE stats (type/ave/delta) on step 0
+  4 1.111 1.44264e-05
+  6 0.996998 7.26967e-06
+  8 1.08 1.32536e-05
+  10 1.111 1.22749e-05
+  12 1.08 1.11767e-05
+  14 0.96 0
+  18 0.957206 4.37979e-05
+  31 104.519 0.00396029
+Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond v_sp 
+       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    292.14604 
+      10    305.06149   -5058.8972   -6286.1901    1227.2929   -6413.1021      58.8499    103.38345 
+      20    311.00516   -4999.0612    -6250.266    1251.2048   -6417.1021    47.695297    36.699695 
+      30    314.22337   -4993.7012   -6257.8532     1264.152   -6421.9679    35.344144    10.563933 
+      40    297.87491   -5020.8378   -6219.2184    1198.3805   -6389.8528    27.723133    3.8354517 
+      50    304.02071   -5056.2576   -6279.3633    1223.1057   -6456.8214    55.459505   0.20678217 
+      60    285.92576   -5104.0461    -6254.354    1150.3079   -6435.5814    32.767229   0.69352945 
+      70    277.83519   -5163.9758   -6281.7345    1117.7587   -6447.7033    39.627168    11.433603 
+      80    267.51495   -5206.4046    -6282.644    1076.2394   -6456.6369    31.611883    6.3554178 
+      90    278.15579   -5245.3824    -6364.431    1119.0485   -6499.8063    28.849773   0.36941576 
+SHAKE stats (type/ave/delta) on step 100
+  4 1.11098 8.97155e-05
+  6 0.996996 1.00568e-05
+  8 1.08 6.02345e-06
+  10 1.111 1.84253e-05
+  12 1.08 7.2713e-06
+  14 0.959996 0
+  18 0.957198 3.36079e-05
+  31 104.52 0.0030599
+     100    260.10613   -5292.6885   -6339.1215     1046.433   -6471.6734    25.362042   0.21987323 
+Loop time of 2.21146 on 1 procs for 100 steps with 2004 atoms
+
+Performance: 7.814 ns/day, 3.071 hours/ns, 45.219 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.6195     | 1.6195     | 1.6195     |   0.0 | 73.23
+Bond    | 0.0033534  | 0.0033534  | 0.0033534  |   0.0 |  0.15
+Kspace  | 0.17464    | 0.17464    | 0.17464    |   0.0 |  7.90
+Neigh   | 0.37337    | 0.37337    | 0.37337    |   0.0 | 16.88
+Comm    | 0.013891   | 0.013891   | 0.013891   |   0.0 |  0.63
+Output  | 0.00037336 | 0.00037336 | 0.00037336 |   0.0 |  0.02
+Modify  | 0.024753   | 0.024753   | 0.024753   |   0.0 |  1.12
+Other   |            | 0.001613   |            |       |  0.07
+
+Nlocal:    2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11124 ave 11124 max 11124 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    708237 ave 708237 max 708237 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 708237
+Ave neighs/atom = 353.412
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 12
+Dangerous builds = 2
+Total wall time: 0:00:02

examples/USER/colvars/log.27Nov18.peptide-spring.g++.4

@@ -0,0 +1,163 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+
+units		real
+atom_style	full
+
+pair_style	lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style	pppm 0.0001
+
+read_data	data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor	2.0 bin
+neigh_modify	delay 5
+
+timestep	2.0
+
+group		peptide type <= 12
+84 atoms in group peptide
+group		one id 2 4 5 6
+4 atoms in group one
+group		two id 80 82 83 84
+4 atoms in group two
+group		ref id 37
+1 atoms in group ref
+group		colvar union one two ref
+9 atoms in group colvar
+
+fix		1 all nvt temp 275.0 275.0 100.0 tchain 1
+
+fix		3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
+fix		3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
+
+fix		2a ref setforce 0.0 0.0 0.0
+
+fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+
+#dump		1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
+#dump_modify 1  sort id
+
+variable sp equal f_3a+f_3b
+
+thermo_style	custom step temp etotal pe ke epair ebond v_sp
+thermo		10
+
+
+run		100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 4312 960
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+SHAKE stats (type/ave/delta) on step 0
+  4 1.111 1.44264e-05
+  6 0.996998 7.26967e-06
+  8 1.08 1.32536e-05
+  10 1.111 1.22749e-05
+  12 1.08 1.11767e-05
+  14 0.96 0
+  18 0.957206 4.37979e-05
+  31 104.519 0.00396029
+Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond v_sp 
+       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    292.14604 
+      10    305.06149   -5058.8972   -6286.1901    1227.2929   -6413.1021      58.8499    103.38345 
+      20    311.00516   -4999.0612    -6250.266    1251.2048   -6417.1021    47.695297    36.699695 
+      30    314.22337   -4993.7012   -6257.8532     1264.152   -6421.9679    35.344144    10.563933 
+      40    297.87491   -5020.8378   -6219.2184    1198.3805   -6389.8528    27.723133    3.8354517 
+      50    304.02071   -5056.2576   -6279.3633    1223.1057   -6456.8214    55.459505   0.20678217 
+      60    285.92576   -5104.0461    -6254.354    1150.3079   -6435.5814    32.767229   0.69352945 
+      70    277.83519   -5163.9758   -6281.7345    1117.7587   -6447.7033    39.627168    11.433603 
+      80    267.51495   -5206.4046    -6282.644    1076.2394   -6456.6369    31.611883    6.3554178 
+      90    278.15579   -5245.3824    -6364.431    1119.0485   -6499.8063    28.849773   0.36941576 
+SHAKE stats (type/ave/delta) on step 100
+  4 1.11098 8.97155e-05
+  6 0.996996 1.00568e-05
+  8 1.08 6.02345e-06
+  10 1.111 1.84253e-05
+  12 1.08 7.2713e-06
+  14 0.959996 0
+  18 0.957198 3.36079e-05
+  31 104.52 0.0030599
+     100    260.10613   -5292.6885   -6339.1215     1046.433   -6471.6734    25.362042   0.21987323 
+Loop time of 0.620672 on 4 procs for 100 steps with 2004 atoms
+
+Performance: 27.841 ns/day, 0.862 hours/ns, 161.116 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.4029     | 0.41752    | 0.4307     |   1.7 | 67.27
+Bond    | 0.00054789 | 0.0011698  | 0.0018225  |   1.8 |  0.19
+Kspace  | 0.055853   | 0.069798   | 0.083975   |   4.3 | 11.25
+Neigh   | 0.096553   | 0.096622   | 0.096707   |   0.0 | 15.57
+Comm    | 0.015383   | 0.016022   | 0.01632    |   0.3 |  2.58
+Output  | 0.00033116 | 0.00057495 | 0.0012989  |   0.0 |  0.09
+Modify  | 0.017549   | 0.017693   | 0.017826   |   0.1 |  2.85
+Other   |            | 0.001274   |            |       |  0.21
+
+Nlocal:    501 ave 513 max 489 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost:    6563.25 ave 6596 max 6519 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs:    177059 ave 181742 max 172942 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 708237
+Ave neighs/atom = 353.412
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 12
+Dangerous builds = 2
+Total wall time: 0:00:00

examples/USER/colvars/log.27Nov18.peptide-spring2.g++.1

@@ -0,0 +1,158 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+
+units		real
+atom_style	full
+
+pair_style	lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style	pppm 0.0001
+
+read_data	data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor	2.0 bin
+neigh_modify	delay 5
+
+timestep	2.0
+
+group		peptide type <= 12
+84 atoms in group peptide
+group		one id 2 4 5 6
+4 atoms in group one
+group		two id 80 82 83 84
+4 atoms in group two
+group		ref id 37
+1 atoms in group ref
+group		colvar union one two ref
+9 atoms in group colvar
+
+fix		1 all nvt temp  275.0 275.0 100.0 tchain 1
+
+fix		3  one spring couple two 100.0 0.0 0.0 0.0 10.0
+
+fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+
+#dump		1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
+#dump_modify 1  sort id
+
+thermo_style	custom step temp etotal pe ke epair ebond f_3
+thermo		10
+
+
+run		100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 10648 3375
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+SHAKE stats (type/ave/delta) on step 0
+  4 1.111 1.44264e-05
+  6 0.996998 7.26967e-06
+  8 1.08 1.32536e-05
+  10 1.111 1.22749e-05
+  12 1.08 1.11767e-05
+  14 0.96 0
+  18 0.957206 4.37979e-05
+  31 104.519 0.00396029
+Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond f_3 
+       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    273.74323 
+      10    333.47919   -4982.3968   -6324.0169    1341.6201   -6400.4223    21.367762    12.393263 
+      20    309.56902   -4999.4978   -6244.9249    1245.4271   -6401.6981     43.59542    13.004314 
+      30     316.9763   -5025.5662   -6300.7935    1275.2273   -6422.5375    27.323196    6.7589585 
+      40    297.55779   -5088.2204   -6285.3252    1197.1047    -6395.375      13.6769    25.625024 
+      50    296.79994   -5117.2966   -6311.3525    1194.0558   -6451.8309    30.631241    5.3320863 
+      60    281.72778   -5188.4969   -6321.9159     1133.419   -6427.8856    26.287723    20.574037 
+      70    277.26053   -5224.8434   -6340.2902    1115.4468   -6447.8521    27.742893   0.69420283 
+      80    268.01484   -5281.8509   -6360.1014    1078.2505   -6496.6086    20.300754    5.2607186 
+      90    270.43472   -5334.0835   -6422.0694    1087.9859   -6563.2511    39.846095    1.1832272 
+SHAKE stats (type/ave/delta) on step 100
+  4 1.11096 0.000191462
+  6 0.996989 3.55508e-05
+  8 1.08 9.0997e-06
+  10 1.111 1.58544e-05
+  12 1.08 5.80604e-06
+  14 0.959997 0
+  18 0.957198 2.92445e-05
+  31 104.52 0.00239923
+     100    260.35636   -5387.2284   -6434.6681    1047.4397   -6534.1956    20.246866  0.075048487 
+Loop time of 2.2037 on 1 procs for 100 steps with 2004 atoms
+
+Performance: 7.841 ns/day, 3.061 hours/ns, 45.378 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.5852     | 1.5852     | 1.5852     |   0.0 | 71.93
+Bond    | 0.0032725  | 0.0032725  | 0.0032725  |   0.0 |  0.15
+Kspace  | 0.17308    | 0.17308    | 0.17308    |   0.0 |  7.85
+Neigh   | 0.4027     | 0.4027     | 0.4027     |   0.0 | 18.27
+Comm    | 0.014041   | 0.014041   | 0.014041   |   0.0 |  0.64
+Output  | 0.00032306 | 0.00032306 | 0.00032306 |   0.0 |  0.01
+Modify  | 0.023546   | 0.023546   | 0.023546   |   0.0 |  1.07
+Other   |            | 0.001546   |            |       |  0.07
+
+Nlocal:    2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11143 ave 11143 max 11143 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    708234 ave 708234 max 708234 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 708234
+Ave neighs/atom = 353.41
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 13
+Dangerous builds = 1
+Total wall time: 0:00:02

examples/USER/colvars/log.27Nov18.peptide-spring2.g++.4

@@ -0,0 +1,158 @@
+LAMMPS (27 Nov 2018)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+
+units		real
+atom_style	full
+
+pair_style	lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style	pppm 0.0001
+
+read_data	data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor	2.0 bin
+neigh_modify	delay 5
+
+timestep	2.0
+
+group		peptide type <= 12
+84 atoms in group peptide
+group		one id 2 4 5 6
+4 atoms in group one
+group		two id 80 82 83 84
+4 atoms in group two
+group		ref id 37
+1 atoms in group ref
+group		colvar union one two ref
+9 atoms in group colvar
+
+fix		1 all nvt temp  275.0 275.0 100.0 tchain 1
+
+fix		3  one spring couple two 100.0 0.0 0.0 0.0 10.0
+
+fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+
+#dump		1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
+#dump_modify 1  sort id
+
+thermo_style	custom step temp etotal pe ke epair ebond f_3
+thermo		10
+
+
+run		100
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 4312 960
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+SHAKE stats (type/ave/delta) on step 0
+  4 1.111 1.44264e-05
+  6 0.996998 7.26967e-06
+  8 1.08 1.32536e-05
+  10 1.111 1.22749e-05
+  12 1.08 1.11767e-05
+  14 0.96 0
+  18 0.957206 4.37979e-05
+  31 104.519 0.00396029
+Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
+Step Temp TotEng PotEng KinEng E_pair E_bond f_3 
+       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152    273.74323 
+      10    333.47919   -4982.3968   -6324.0169    1341.6201   -6400.4223    21.367762    12.393263 
+      20    309.56902   -4999.4978   -6244.9249    1245.4271   -6401.6981     43.59542    13.004314 
+      30     316.9763   -5025.5662   -6300.7935    1275.2273   -6422.5375    27.323196    6.7589585 
+      40    297.55779   -5088.2204   -6285.3252    1197.1047    -6395.375      13.6769    25.625024 
+      50    296.79994   -5117.2966   -6311.3525    1194.0558   -6451.8309    30.631241    5.3320863 
+      60    281.72778   -5188.4969   -6321.9159     1133.419   -6427.8856    26.287723    20.574037 
+      70    277.26053   -5224.8434   -6340.2902    1115.4468   -6447.8521    27.742893   0.69420283 
+      80    268.01484   -5281.8509   -6360.1014    1078.2505   -6496.6086    20.300754    5.2607186 
+      90    270.43472   -5334.0835   -6422.0694    1087.9859   -6563.2511    39.846095    1.1832272 
+SHAKE stats (type/ave/delta) on step 100
+  4 1.11096 0.000191462
+  6 0.996989 3.55508e-05
+  8 1.08 9.0997e-06
+  10 1.111 1.58544e-05
+  12 1.08 5.80604e-06
+  14 0.959997 0
+  18 0.957198 2.92445e-05
+  31 104.52 0.00239923
+     100    260.35636   -5387.2284   -6434.6681    1047.4397   -6534.1956    20.246866  0.075048487 
+Loop time of 0.616036 on 4 procs for 100 steps with 2004 atoms
+
+Performance: 28.050 ns/day, 0.856 hours/ns, 162.328 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.40372    | 0.41244    | 0.41714    |   0.8 | 66.95
+Bond    | 0.00053573 | 0.0011384  | 0.0017946  |   1.8 |  0.18
+Kspace  | 0.060087   | 0.063993   | 0.07306    |   2.1 | 10.39
+Neigh   | 0.1033     | 0.10349    | 0.1036     |   0.0 | 16.80
+Comm    | 0.01568    | 0.016453   | 0.017178   |   0.5 |  2.67
+Output  | 0.00028253 | 0.00032026 | 0.00043178 |   0.0 |  0.05
+Modify  | 0.016238   | 0.016955   | 0.017704   |   0.5 |  2.75
+Other   |            | 0.001239   |            |       |  0.20
+
+Nlocal:    501 ave 513 max 494 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+Nghost:    6572.5 ave 6593 max 6548 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs:    177058 ave 181778 max 174301 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 708234
+Ave neighs/atom = 353.41
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 13
+Dangerous builds = 1
+Total wall time: 0:00:00

examples/USER/colvars/log.peptide-colvars-1

@@ -1,516 +0,0 @@
-LAMMPS (21 May 2012-ICMS)
-# Solvated 5-mer peptide
-
-units		real
-atom_style	full
-
-pair_style	lj/charmm/coul/long 8.0 10.0 10.0
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-kspace_style	pppm 0.0001
-
-read_data	data.peptide
-  3 = max bonds/atom
-  6 = max angles/atom
-  14 = max dihedrals/atom
-  1 = max impropers/atom
-  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
-  1 by 1 by 1 MPI processor grid
-  2004 atoms
-  2004 velocities
-  1365 bonds
-  786 angles
-  207 dihedrals
-  12 impropers
-  4 = max # of 1-2 neighbors
-  7 = max # of 1-3 neighbors
-  14 = max # of 1-4 neighbors
-  18 = max # of special neighbors
-
-neighbor	2.0 bin
-neigh_modify	delay 5
-
-timestep	2.0
-
-group		peptide type <= 12
-84 atoms in group peptide
-group		one id 2 4 5 6
-4 atoms in group one
-group		two id 80 82 83 84
-4 atoms in group two
-group		ref id 37
-1 atoms in group ref
-group		colvar union one two ref
-9 atoms in group colvar
-
-fix		1 all nvt temp  275.0 275.0 100.0 tchain 1
-
-shell "rm -f out*.colvars.*"
-fix		2 all colvars peptide.colvars
-fix		2a ref setforce 0.0 0.0 0.0
-
-fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
-  19 = # of size 2 clusters
-  6 = # of size 3 clusters
-  3 = # of size 4 clusters
-  640 = # of frozen angles
-
-#dump		1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
-#dump_modify 1 sort id
-
-thermo_style	custom step temp etotal pe ke epair ebond f_2
-thermo		10
-
-
-run		100
-PPPM initialization ...
-  G vector (1/distance) = 0.268721
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.01614
-  estimated relative force accuracy = 4.86052e-05
-  using single precision FFTs
-  brick FFT buffer size/proc = 10648 3375 5808
-colvars: ----------------------------------------------------------------------
-colvars: Initializing the collective variables module, version 2012-03-23.
-colvars: # analysis = off [default]
-colvars: # colvarsTrajFrequency = 1
-colvars: # colvarsRestartFrequency = 1000
-colvars: # colvarsTrajAppend = off [default]
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "out.colvars.state".
-colvars: The trajectory file will be "out.colvars.traj".
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = one
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = two
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables initialized, 2 in total.
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new "harmonic" instance.
-colvars:   # name = h_pot
-colvars:   # colvars = { one, two }
-colvars:   # forceConstant = 100
-colvars:   # centers = { 10, 10 }
-colvars:   # targetCenters = { 10, 10 } [default]
-colvars:   # targetForceConstant = 0 [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables biases initialized, 1 in total.
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables module initialized.
-colvars: ----------------------------------------------------------------------
-SHAKE stats (type/ave/delta) on step 0
-  4 1.111 1.44264e-05
-  6 0.996998 7.26967e-06
-  8 1.08 1.32536e-05
-  10 1.111 1.22749e-05
-  12 1.08 1.11767e-05
-  14 0.96 0
-  18 0.957206 4.37979e-05
-  31 104.519 0.00396029
-Memory usage per processor = 22.5866 Mbytes
-Step Temp TotEng PotEng KinEng E_pair E_bond 2 
-       0    282.10052    -5237.458   -6372.3765    1134.9186   -6442.7679    16.557152    292.14604 
-      10    305.06198   -5058.8899   -6286.1847    1227.2948   -6413.0967    58.849896    103.38344 
-      20    311.00592   -4999.0544   -6250.2623    1251.2079   -6417.0984    47.695274    36.699706 
-      30    314.22398   -4993.6953   -6257.8498    1264.1545   -6421.9643    35.344163    10.563914 
-      40    297.87524   -5020.8339   -6219.2158    1198.3819   -6389.8501    27.723201    3.8354392 
-      50    304.02086   -5056.2539   -6279.3602    1223.1063   -6456.8181    55.459508   0.20679801 
-      60    285.92594   -5104.0436   -6254.3523    1150.3086   -6435.5793     32.76729   0.69356508 
-      70      277.835   -5163.9752   -6281.7332     1117.758   -6447.7015    39.627148    11.433632 
-      80    267.51473   -5206.4042   -6282.6427    1076.2385   -6456.6352    31.611843    6.3553235 
-      90    278.15513    -5245.383   -6364.4289    1119.0459   -6499.8037    28.849899   0.36938867 
-SHAKE stats (type/ave/delta) on step 100
-  4 1.11098 8.97184e-05
-  6 0.996996 1.00568e-05
-  8 1.08 6.02345e-06
-  10 1.111 1.84257e-05
-  12 1.08 7.27136e-06
-  14 0.959996 0
-  18 0.957198 3.36077e-05
-  31 104.52 0.00306008
-     100    260.10505   -5292.6892   -6339.1178    1046.4286   -6471.6694    25.361885    0.2198687 
-colvars: Saving collective variables state to "out.colvars.state".
-Loop time of 2.39102 on 1 procs for 100 steps with 2004 atoms
-
- Pair time (%) = 1.86583 (78.0347)
- Bond time (%) = 0.00628591 (0.262896)
-Kspace time (%) = 0.165128 (6.90614)
-Neigh time (%) = 0.314792 (13.1656)
- Comm time (%) = 0.0111108 (0.464687)
-Output time (%) = 0.000252724 (0.0105697)
-Modify time (%) = 0.0253747 (1.06125)
-Other time (%) = 0.0022521 (0.0941899)
-
-FFT time (% of Kspce) = 0.0274372 (16.6158)
-FFT Gflps 3d (1d only) = 1.99867 2.86506
-
-Nlocal:    2004 ave 2004 max 2004 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    11124 ave 11124 max 11124 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    708237 ave 708237 max 708237 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 708237
-Ave neighs/atom = 353.412
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 12
-Dangerous builds = 2
-
-run     100
-PPPM initialization ...
-  G vector (1/distance) = 0.268721
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.01614
-  estimated relative force accuracy = 4.86052e-05
-  using single precision FFTs
-  brick FFT buffer size/proc = 10648 3375 5808
-colvars: ----------------------------------------------------------------------
-colvars: Initializing the collective variables module, version 2012-03-23.
-colvars: # analysis = off [default]
-colvars: # colvarsTrajFrequency = 1
-colvars: # colvarsRestartFrequency = 1000
-colvars: # colvarsTrajAppend = off [default]
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "out.colvars.state".
-colvars: The trajectory file will be "out.colvars.traj".
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = one
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = two
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables initialized, 2 in total.
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new "harmonic" instance.
-colvars:   # name = h_pot
-colvars:   # colvars = { one, two }
-colvars:   # forceConstant = 100
-colvars:   # centers = { 10, 10 }
-colvars:   # targetCenters = { 10, 10 } [default]
-colvars:   # targetForceConstant = 0 [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables biases initialized, 1 in total.
-colvars: ----------------------------------------------------------------------
-colvars: Restarting from file "out.colvars.state".
-colvars:   Restarting collective variable "one" from value: 10.0137
-colvars:   Restarting collective variable "two" from value: 10.0649
-colvars:   Restarting harmonic bias "h_pot".
-colvars:   Reading current stage from the restart.
-colvars:   # stage = 3900175693153042431
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables module initialized.
-colvars: ----------------------------------------------------------------------
-colvars: Initializing step number as firstTimestep.
-SHAKE stats (type/ave/delta) on step 100
-  4 1.11098 8.97184e-05
-  6 0.996996 1.00568e-05
-  8 1.08 6.02345e-06
-  10 1.111 1.84257e-05
-  12 1.08 7.27136e-06
-  14 0.959996 0
-  18 0.957198 3.36077e-05
-  31 104.52 0.00306008
-Memory usage per processor = 22.5866 Mbytes
-Step Temp TotEng PotEng KinEng E_pair E_bond 2 
-     100    260.10505   -5292.6892   -6339.1178    1046.4286   -6471.6694    25.361885    0.2198687 
-     110    266.26278   -5341.2103    -6412.412    1071.2018   -6552.7583    33.572968    1.9229782 
-     120    262.66442   -5386.2494   -6442.9746    1056.7252   -6587.5499    29.859553    2.7124877 
-     130     252.8344   -5422.5446   -6439.7226    1017.1781   -6580.4752    25.979049    1.2031628 
-     140    253.85115   -5452.1905   -6473.4591    1021.2686    -6609.489    26.071514   0.30586247 
-     150    261.31825     -5490.48   -6541.7895    1051.3095   -6646.6144    16.258548    6.9049974 
-     160     255.7368   -5521.6048   -6550.4596    1028.8547   -6658.1517    19.717533    12.339821 
-     170    253.42877   -5540.1003   -6559.6695    1019.5693   -6656.6878    23.293662    10.289878 
-     180    248.51086   -5550.3244   -6550.1084    999.78404   -6661.4182    26.200056    3.4339065 
-     190     250.8039   -5555.2614   -6564.2706    1009.0092     -6666.15    25.536594    3.3495152 
-SHAKE stats (type/ave/delta) on step 200
-  4 1.111 1.8129e-06
-  6 0.997 7.7964e-07
-  8 1.08 1.08934e-06
-  10 1.111 2.96501e-07
-  12 1.08 4.69174e-07
-  14 0.960001 0
-  18 0.957201 3.76571e-06
-  31 104.52 0.000411068
-     200    251.50581   -5557.4209   -6569.2539     1011.833   -6674.0867    24.805164    7.1388858 
-colvars: Saving collective variables state to "out.colvars.state".
-Loop time of 2.23495 on 1 procs for 100 steps with 2004 atoms
-
- Pair time (%) = 1.84544 (82.572)
- Bond time (%) = 0.00609159 (0.27256)
-Kspace time (%) = 0.163201 (7.30223)
-Neigh time (%) = 0.183405 (8.20622)
- Comm time (%) = 0.00959301 (0.429227)
-Output time (%) = 0.000245094 (0.0109664)
-Modify time (%) = 0.0247326 (1.10663)
-Other time (%) = 0.00223875 (0.10017)
-
-FFT time (% of Kspce) = 0.0272989 (16.7271)
-FFT Gflps 3d (1d only) = 2.0088 2.93901
-
-Nlocal:    2004 ave 2004 max 2004 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    11159 ave 11159 max 11159 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    708088 ave 708088 max 708088 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 708088
-Ave neighs/atom = 353.337
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 7
-Dangerous builds = 0
-
-fix 2 all colvars peptide.colvars input out.colvars.state output out2
-
-run     100
-PPPM initialization ...
-  G vector (1/distance) = 0.268721
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.01614
-  estimated relative force accuracy = 4.86052e-05
-  using single precision FFTs
-  brick FFT buffer size/proc = 10648 3375 5808
-colvars: ----------------------------------------------------------------------
-colvars: Initializing the collective variables module, version 2012-03-23.
-colvars: # analysis = off [default]
-colvars: # colvarsTrajFrequency = 1
-colvars: # colvarsRestartFrequency = 1000
-colvars: # colvarsTrajAppend = off [default]
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "out2.colvars.state".
-colvars: The trajectory file will be "out2.colvars.traj".
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = one
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = two
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables initialized, 2 in total.
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new "harmonic" instance.
-colvars:   # name = h_pot
-colvars:   # colvars = { one, two }
-colvars:   # forceConstant = 100
-colvars:   # centers = { 10, 10 }
-colvars:   # targetCenters = { 10, 10 } [default]
-colvars:   # targetForceConstant = 0 [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables biases initialized, 1 in total.
-colvars: ----------------------------------------------------------------------
-colvars: Restarting from file "out.colvars.state".
-colvars:   Restarting collective variable "one" from value: 10.0128
-colvars:   Restarting collective variable "two" from value: 9.62236
-colvars:   Restarting harmonic bias "h_pot".
-colvars:   Reading current stage from the restart.
-colvars:   # stage = 3900175693153042431
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables module initialized.
-colvars: ----------------------------------------------------------------------
-colvars: Initializing step number as firstTimestep.
-SHAKE stats (type/ave/delta) on step 200
-  4 1.111 1.8129e-06
-  6 0.997 7.7964e-07
-  8 1.08 1.08934e-06
-  10 1.111 2.96501e-07
-  12 1.08 4.69174e-07
-  14 0.960001 0
-  18 0.957201 3.76571e-06
-  31 104.52 0.000411068
-Memory usage per processor = 22.5866 Mbytes
-Step Temp TotEng PotEng KinEng E_pair E_bond 2 
-     200    251.50581   -5557.4209   -6569.2539     1011.833   -6674.0867    24.805164    7.1388858 
-     210    253.15043   -5538.5668   -6557.0163    1018.4495    -6672.041     37.67158   0.61296982 
-     220    245.19746   -5522.5242   -6508.9781     986.4539   -6628.1999    36.656356  0.048624555 
-     230    258.65299   -5495.7177   -6536.3046    1040.5868   -6658.0952    34.855726   0.22046598 
-     240    260.80143   -5469.8517   -6519.0819    1049.2302   -6624.1723    31.576409    3.7570726 
-     250    269.06507   -5438.3971   -6520.8727    1082.4757   -6616.3871    25.444125    8.6640978 
-     260    266.10282   -5397.3162   -6467.8744    1070.5583    -6580.628    26.873936    8.3330854 
-     270    272.81993   -5350.8393   -6448.4211    1097.5819   -6563.8139    23.113421    10.972906 
-     280    279.52079   -5307.9855   -6432.5256    1124.5401   -6557.7274    33.641095    8.5474821 
-     290    286.81184   -5260.8728   -6414.7455    1153.8727   -6515.5418    28.572468    5.9092648 
-SHAKE stats (type/ave/delta) on step 300
-  4 1.111 1.79733e-05
-  6 0.997005 1.02622e-05
-  8 1.08 1.84996e-05
-  10 1.111 9.98595e-06
-  12 1.08 8.83195e-06
-  14 0.960008 0
-  18 0.957203 1.84801e-05
-  31 104.52 0.00169221
-     300    291.51842   -5216.3285   -6389.1362    1172.8077   -6503.1141    27.877464    2.2482411 
-colvars: Saving collective variables state to "out2.colvars.state".
-Loop time of 2.25031 on 1 procs for 100 steps with 2004 atoms
-
- Pair time (%) = 1.83745 (81.6533)
- Bond time (%) = 0.00609803 (0.270987)
-Kspace time (%) = 0.162178 (7.20694)
-Neigh time (%) = 0.207886 (9.23812)
- Comm time (%) = 0.00977254 (0.434276)
-Output time (%) = 0.000240803 (0.0107009)
-Modify time (%) = 0.024461 (1.08701)
-Other time (%) = 0.00221944 (0.0986283)
-
-FFT time (% of Kspce) = 0.0273609 (16.8709)
-FFT Gflps 3d (1d only) = 2.00425 2.94806
-
-Nlocal:    2004 ave 2004 max 2004 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    11292 ave 11292 max 11292 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    708145 ave 708145 max 708145 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 708145
-Ave neighs/atom = 353.366
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 8
-Dangerous builds = 0
-

examples/USER/colvars/log.peptide-colvars-4

@@ -1,516 +0,0 @@
-LAMMPS (21 May 2012-ICMS)
-# Solvated 5-mer peptide
-
-units		real
-atom_style	full
-
-pair_style	lj/charmm/coul/long 8.0 10.0 10.0
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-kspace_style	pppm 0.0001
-
-read_data	data.peptide
-  3 = max bonds/atom
-  6 = max angles/atom
-  14 = max dihedrals/atom
-  1 = max impropers/atom
-  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
-  1 by 2 by 2 MPI processor grid
-  2004 atoms
-  2004 velocities
-  1365 bonds
-  786 angles
-  207 dihedrals
-  12 impropers
-  4 = max # of 1-2 neighbors
-  7 = max # of 1-3 neighbors
-  14 = max # of 1-4 neighbors
-  18 = max # of special neighbors
-
-neighbor	2.0 bin
-neigh_modify	delay 5
-
-timestep	2.0
-
-group		peptide type <= 12
-84 atoms in group peptide
-group		one id 2 4 5 6
-4 atoms in group one
-group		two id 80 82 83 84
-4 atoms in group two
-group		ref id 37
-1 atoms in group ref
-group		colvar union one two ref
-9 atoms in group colvar
-
-fix		1 all nvt temp  275.0 275.0 100.0 tchain 1
-
-shell "rm -f out*.colvars.*"
-fix		2 all colvars peptide.colvars
-fix		2a ref setforce 0.0 0.0 0.0
-
-fix		4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
-  19 = # of size 2 clusters
-  6 = # of size 3 clusters
-  3 = # of size 4 clusters
-  640 = # of frozen angles
-
-#dump		1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
-#dump_modify 1 sort id
-
-thermo_style	custom step temp etotal pe ke epair ebond f_2
-thermo		10
-
-
-run		100
-PPPM initialization ...
-  G vector (1/distance) = 0.268721
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.01614
-  estimated relative force accuracy = 4.86052e-05
-  using single precision FFTs
-  brick FFT buffer size/proc = 4312 960 3696
-colvars: ----------------------------------------------------------------------
-colvars: Initializing the collective variables module, version 2012-03-23.
-colvars: # analysis = off [default]
-colvars: # colvarsTrajFrequency = 1
-colvars: # colvarsRestartFrequency = 1000
-colvars: # colvarsTrajAppend = off [default]
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "out.colvars.state".
-colvars: The trajectory file will be "out.colvars.traj".
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = one
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = two
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables initialized, 2 in total.
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new "harmonic" instance.
-colvars:   # name = h_pot
-colvars:   # colvars = { one, two }
-colvars:   # forceConstant = 100
-colvars:   # centers = { 10, 10 }
-colvars:   # targetCenters = { 10, 10 } [default]
-colvars:   # targetForceConstant = 0 [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables biases initialized, 1 in total.
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables module initialized.
-colvars: ----------------------------------------------------------------------
-SHAKE stats (type/ave/delta) on step 0
-  4 1.111 1.44264e-05
-  6 0.996998 7.26967e-06
-  8 1.08 1.32536e-05
-  10 1.111 1.22749e-05
-  12 1.08 1.11767e-05
-  14 0.96 0
-  18 0.957206 4.37979e-05
-  31 104.519 0.00396029
-Memory usage per processor = 10.1924 Mbytes
-Step Temp TotEng PotEng KinEng E_pair E_bond 2 
-       0    282.10052    -5237.458   -6372.3765    1134.9186   -6442.7679    16.557152    292.14604 
-      10    305.06198   -5058.8898   -6286.1847    1227.2948   -6413.0967    58.849896    103.38344 
-      20    311.00592   -4999.0545   -6250.2624    1251.2079   -6417.0984    47.695274    36.699706 
-      30    314.22398   -4993.6953   -6257.8498    1264.1545   -6421.9643    35.344162    10.563914 
-      40    297.87524   -5020.8339   -6219.2157    1198.3819     -6389.85    27.723201    3.8354392 
-      50    304.02086    -5056.254   -6279.3603    1223.1063   -6456.8182    55.459508     0.206798 
-      60    285.92594   -5104.0436   -6254.3523    1150.3086   -6435.5793    32.767289   0.69356507 
-      70      277.835   -5163.9751   -6281.7331     1117.758   -6447.7014    39.627147    11.433632 
-      80    267.51474   -5206.4042   -6282.6428    1076.2385   -6456.6352    31.611843    6.3553237 
-      90    278.15513    -5245.383   -6364.4289    1119.0459   -6499.8036    28.849898   0.36938879 
-SHAKE stats (type/ave/delta) on step 100
-  4 1.11098 8.97184e-05
-  6 0.996996 1.00568e-05
-  8 1.08 6.02345e-06
-  10 1.111 1.84257e-05
-  12 1.08 7.27136e-06
-  14 0.959996 0
-  18 0.957198 3.36077e-05
-  31 104.52 0.00306008
-     100    260.10504   -5292.6891   -6339.1176    1046.4286   -6471.6693    25.361886   0.21986866 
-colvars: Saving collective variables state to "out.colvars.state".
-Loop time of 0.686681 on 4 procs for 100 steps with 2004 atoms
-
- Pair time (%) = 0.47104 (68.5966)
- Bond time (%) = 0.00184608 (0.26884)
-Kspace time (%) = 0.0808357 (11.7719)
-Neigh time (%) = 0.0772016 (11.2427)
- Comm time (%) = 0.0293136 (4.26888)
-Output time (%) = 0.000323951 (0.0471764)
-Modify time (%) = 0.0247293 (3.60128)
-Other time (%) = 0.00139064 (0.202516)
-
-FFT time (% of Kspce) = 0.0117171 (14.4949)
-FFT Gflps 3d (1d only) = 4.68018 10.009
-
-Nlocal:    501 ave 513 max 489 min
-Histogram: 1 0 0 0 1 1 0 0 0 1
-Nghost:    6563.25 ave 6596 max 6519 min
-Histogram: 1 0 1 0 0 0 0 0 0 2
-Neighs:    177059 ave 181741 max 172943 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-
-Total # of neighbors = 708237
-Ave neighs/atom = 353.412
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 12
-Dangerous builds = 2
-
-run     100
-PPPM initialization ...
-  G vector (1/distance) = 0.268721
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.01614
-  estimated relative force accuracy = 4.86052e-05
-  using single precision FFTs
-  brick FFT buffer size/proc = 4312 960 3696
-colvars: ----------------------------------------------------------------------
-colvars: Initializing the collective variables module, version 2012-03-23.
-colvars: # analysis = off [default]
-colvars: # colvarsTrajFrequency = 1
-colvars: # colvarsRestartFrequency = 1000
-colvars: # colvarsTrajAppend = off [default]
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "out.colvars.state".
-colvars: The trajectory file will be "out.colvars.traj".
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = one
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = two
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables initialized, 2 in total.
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new "harmonic" instance.
-colvars:   # name = h_pot
-colvars:   # colvars = { one, two }
-colvars:   # forceConstant = 100
-colvars:   # centers = { 10, 10 }
-colvars:   # targetCenters = { 10, 10 } [default]
-colvars:   # targetForceConstant = 0 [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables biases initialized, 1 in total.
-colvars: ----------------------------------------------------------------------
-colvars: Restarting from file "out.colvars.state".
-colvars:   Restarting collective variable "one" from value: 10.0137
-colvars:   Restarting collective variable "two" from value: 10.0649
-colvars:   Restarting harmonic bias "h_pot".
-colvars:   Reading current stage from the restart.
-colvars:   # stage = 8103505641670189088
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables module initialized.
-colvars: ----------------------------------------------------------------------
-colvars: Initializing step number as firstTimestep.
-SHAKE stats (type/ave/delta) on step 100
-  4 1.11098 8.97184e-05
-  6 0.996996 1.00568e-05
-  8 1.08 6.02345e-06
-  10 1.111 1.84257e-05
-  12 1.08 7.27136e-06
-  14 0.959996 0
-  18 0.957198 3.36077e-05
-  31 104.52 0.00306008
-Memory usage per processor = 10.1967 Mbytes
-Step Temp TotEng PotEng KinEng E_pair E_bond 2 
-     100    260.10504   -5292.6891   -6339.1176    1046.4286   -6471.6693    25.361886   0.21986866 
-     110    266.26278   -5341.2101   -6412.4119    1071.2018   -6552.7582    33.572969    1.9229778 
-     120    262.66442   -5386.2494   -6442.9746    1056.7252   -6587.5499    29.859555    2.7124877 
-     130    252.83442   -5422.5444   -6439.7226    1017.1781   -6580.4752    25.979048    1.2031628 
-     140    253.85116   -5452.1905   -6473.4591    1021.2686    -6609.489    26.071518   0.30586252 
-     150    261.31828     -5490.48   -6541.7895    1051.3096   -6646.6145     16.25855    6.9049978 
-     160    255.73681   -5521.6048   -6550.4596    1028.8548   -6658.1518    19.717536    12.339819 
-     170    253.42879   -5540.1004   -6559.6697    1019.5694    -6656.688    23.293657    10.289879 
-     180    248.51083   -5550.3244   -6550.1084    999.78393   -6661.4181    26.200057     3.433906 
-     190    250.80387   -5555.2613   -6564.2703     1009.009   -6666.1497    25.536596    3.3495164 
-SHAKE stats (type/ave/delta) on step 200
-  4 1.111 1.8129e-06
-  6 0.997 7.79639e-07
-  8 1.08 1.08934e-06
-  10 1.111 2.96501e-07
-  12 1.08 4.69175e-07
-  14 0.960001 0
-  18 0.957201 3.76571e-06
-  31 104.52 0.000411069
-     200    251.50575   -5557.4209   -6569.2537    1011.8328   -6674.0864    24.805164    7.1388874 
-colvars: Saving collective variables state to "out.colvars.state".
-Loop time of 0.653275 on 4 procs for 100 steps with 2004 atoms
-
- Pair time (%) = 0.47279 (72.3723)
- Bond time (%) = 0.00182116 (0.278774)
-Kspace time (%) = 0.079544 (12.1762)
-Neigh time (%) = 0.0451868 (6.91696)
- Comm time (%) = 0.027427 (4.19838)
-Output time (%) = 0.000316501 (0.0484483)
-Modify time (%) = 0.0247022 (3.78129)
-Other time (%) = 0.00148731 (0.227671)
-
-FFT time (% of Kspce) = 0.0109947 (13.8221)
-FFT Gflps 3d (1d only) = 4.98769 10.1728
-
-Nlocal:    501 ave 513 max 481 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-Nghost:    6556.5 ave 6608 max 6514 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Neighs:    177022 ave 182261 max 172093 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 708086
-Ave neighs/atom = 353.336
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 7
-Dangerous builds = 0
-
-fix 2 all colvars peptide.colvars input out.colvars.state output out2
-
-run     100
-PPPM initialization ...
-  G vector (1/distance) = 0.268721
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.01614
-  estimated relative force accuracy = 4.86052e-05
-  using single precision FFTs
-  brick FFT buffer size/proc = 4312 960 3696
-colvars: ----------------------------------------------------------------------
-colvars: Initializing the collective variables module, version 2012-03-23.
-colvars: # analysis = off [default]
-colvars: # colvarsTrajFrequency = 1
-colvars: # colvarsRestartFrequency = 1000
-colvars: # colvarsTrajAppend = off [default]
-colvars: The restart output state file will be "rest.colvars.state".
-colvars: The final output state file will be "out2.colvars.state".
-colvars: The trajectory file will be "out2.colvars.traj".
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = one
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new collective variable.
-colvars:   # name = two
-colvars:   Initializing a new "distance" component.
-colvars:     # componentCoeff = 1 [default]
-colvars:     # componentExp = 1 [default]
-colvars:     # period = 0 [default]
-colvars:     # wrapAround = 0 [default]
-colvars:     # forceNoPBC = off [default]
-colvars:     # oneSiteSystemForce = off [default]
-colvars:       Initializing atom group "group1".
-colvars:       Atom group "group1" defined, 4 initialized: total mass = 15.035.
-colvars:       Initializing atom group "group2".
-colvars:       Atom group "group2" defined, 1 initialized: total mass = 12.011.
-colvars:   All components initialized.
-colvars:   # width = 1 [default]
-colvars:   # lowerBoundary = 0 [default]
-colvars:   # lowerWallConstant = 0 [default]
-colvars:   # upperBoundary = 0 [default]
-colvars:   # upperWallConstant = 0 [default]
-colvars:   # expandBoundaries = off [default]
-colvars:   # extendedLagrangian = off [default]
-colvars:   # outputValue = on [default]
-colvars:   # outputVelocity = off [default]
-colvars:   # outputSystemForce = off [default]
-colvars:   # outputAppliedForce = off [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables initialized, 2 in total.
-colvars: ----------------------------------------------------------------------
-colvars:   Initializing a new "harmonic" instance.
-colvars:   # name = h_pot
-colvars:   # colvars = { one, two }
-colvars:   # forceConstant = 100
-colvars:   # centers = { 10, 10 }
-colvars:   # targetCenters = { 10, 10 } [default]
-colvars:   # targetForceConstant = 0 [default]
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables biases initialized, 1 in total.
-colvars: ----------------------------------------------------------------------
-colvars: Restarting from file "out.colvars.state".
-colvars:   Restarting collective variable "one" from value: 10.0128
-colvars:   Restarting collective variable "two" from value: 9.62236
-colvars:   Restarting harmonic bias "h_pot".
-colvars:   Reading current stage from the restart.
-colvars:   # stage = 8103505641670189088
-colvars: ----------------------------------------------------------------------
-colvars: Collective variables module initialized.
-colvars: ----------------------------------------------------------------------
-colvars: Initializing step number as firstTimestep.
-SHAKE stats (type/ave/delta) on step 200
-  4 1.111 1.8129e-06
-  6 0.997 7.79639e-07
-  8 1.08 1.08934e-06
-  10 1.111 2.96501e-07
-  12 1.08 4.69175e-07
-  14 0.960001 0
-  18 0.957201 3.76571e-06
-  31 104.52 0.000411069
-Memory usage per processor = 10.201 Mbytes
-Step Temp TotEng PotEng KinEng E_pair E_bond 2 
-     200    251.50575   -5557.4209   -6569.2537    1011.8328   -6674.0864    24.805164    7.1388874 
-     210    253.15047   -5538.5669   -6557.0165    1018.4497   -6672.0412    37.671574   0.61297094 
-     220    245.19752   -5522.5242   -6508.9784    986.45412   -6628.2001    36.656348  0.048624447 
-     230    258.65297   -5495.7177   -6536.3044    1040.5868   -6658.0951    34.855726   0.22046446 
-     240     260.8016   -5469.8518   -6519.0827    1049.2309    -6624.173    31.576408     3.757081 
-     250    269.06524   -5438.3971   -6520.8735    1082.4764   -6616.3878    25.444134    8.6641098 
-     260    266.10241    -5397.317   -6467.8736    1070.5566   -6580.6272     26.87393     8.333095 
-     270    272.82004   -5350.8402   -6448.4225    1097.5823   -6563.8152    23.113398    10.972914 
-     280    279.52006   -5307.9867   -6432.5238    1124.5371   -6557.7256    33.641067    8.5474809 
-     290    286.81221   -5260.8707   -6414.7449    1153.8742   -6515.5413    28.572449    5.9092582 
-SHAKE stats (type/ave/delta) on step 300
-  4 1.111 1.79733e-05
-  6 0.997005 1.02621e-05
-  8 1.08 1.84996e-05
-  10 1.111 9.98591e-06
-  12 1.08 8.83192e-06
-  14 0.960008 0
-  18 0.957203 1.84805e-05
-  31 104.52 0.00169223
-     300    291.51901   -5216.3298   -6389.1399    1172.8101   -6503.1178    27.877408    2.2482392 
-colvars: Saving collective variables state to "out2.colvars.state".
-Loop time of 0.662081 on 4 procs for 100 steps with 2004 atoms
-
- Pair time (%) = 0.47307 (71.452)
- Bond time (%) = 0.00178617 (0.269781)
-Kspace time (%) = 0.0802494 (12.1208)
-Neigh time (%) = 0.0528576 (7.98355)
- Comm time (%) = 0.0277618 (4.19311)
-Output time (%) = 0.000293612 (0.0443469)
-Modify time (%) = 0.0245907 (3.71416)
-Other time (%) = 0.00147164 (0.222275)
-
-FFT time (% of Kspce) = 0.011487 (14.3141)
-FFT Gflps 3d (1d only) = 4.77392 9.91625
-
-Nlocal:    501 ave 514 max 471 min
-Histogram: 1 0 0 0 0 0 0 0 1 2
-Nghost:    6609.75 ave 6681 max 6555 min
-Histogram: 1 1 0 0 0 1 0 0 0 1
-Neighs:    177036 ave 180240 max 169752 min
-Histogram: 1 0 0 0 0 0 0 0 1 2
-
-Total # of neighbors = 708146
-Ave neighs/atom = 353.366
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 8
-Dangerous builds = 0
-