Merge pull request #1207 from akohlmey/next-patch-release

Patch release 15 November 2018

.github/CODEOWNERS

@@ -29,6 +29,7 @@ src/USER-MEAMC/*      @martok
 src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
+src/USER-PLUMED/*     @gtribello
 src/USER-PHONON/*     @lingtikong
 src/USER-PTM/*        @pmla
 src/USER-OMP/*        @akohlmey

.github/CONTRIBUTING.md

@@ -6,7 +6,7 @@ The following is a set of guidelines as well as explanations of policies and wor
 
 Thus please also have a look at:
 * [The Section on submitting new features for inclusion in LAMMPS of the Manual](http://lammps.sandia.gov/doc/Section_modify.html#mod-15)
-* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/tutorial_github.html)
+* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/Howto_github.html)
 
 ## Table of Contents
 
@@ -62,7 +62,7 @@ To be able to submit an issue on GitHub, you have to register for an account (fo
 
 We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is by submitting a pull request at the LAMMPS project on GitHub. For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others.
 
-How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](http://lammps.sandia.gov/doc/tutorial_github.html)
+How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](http://lammps.sandia.gov/doc/Howto_github.html)
  for instructions on how to submit your changes or new files through a GitHub pull request
 
 Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
@@ -102,11 +102,11 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
 
 ### Pull Requests
 
-For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/tutorial_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here.
+For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.
 Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub.
 Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that.
 You may also receive comments and suggestions on the overall submission or specific details. If permitted, additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
 The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.
-If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will be assigned to the LAMMPS lead developer, Steve Plimpton (@sjplimp), who will then have the final decision on whether the submission will be included, additional changes are required or it will be ultimately rejected. After the pull request is merged, you may delete the pull request branch in your personal LAMMPS fork.
-Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and not set in stone.
+If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request in your personal LAMMPS fork.
+Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and nothing set in stone. So depending on the nature of the contribution, the workflow may be adjusted.
 

cmake/CMakeLists.txt

@@ -171,8 +171,9 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
   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
   USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
-  USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ
-  USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
+  USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
+  USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
+  USER-QUIP USER-QMMM)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 set(OTHER_PACKAGES CORESHELL QEQ)
 foreach(PKG ${DEFAULT_PACKAGES})
@@ -193,6 +194,8 @@ if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
   enable_language(C)
 endif()
 
+include_directories(${LAMMPS_SOURCE_DIR})
+
 # do MPI detection after language activation, if MPI for these language is required
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
@@ -301,7 +304,7 @@ pkg_depends(USER-SCAFACOS MPI)
 
 find_package(OpenMP QUIET)
 option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
-if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
+if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
   find_package(OpenMP REQUIRED)
   set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
@@ -346,7 +349,7 @@ if(PKG_KSPACE)
   endif()
 endif()
 
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE OR PKG_USER-PLUMED)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -526,6 +529,54 @@ if(PKG_USER-SCAFACOS)
   include_directories(${SCAFACOS_INCLUDE_DIRS})
 endif()
 
+if(PKG_USER-PLUMED)
+  find_package(GSL REQUIRED)
+  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+  set(PLUMED_MODE_VALUES static shared runtime)
+  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
+  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
+  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+
+  option(DOWNLOAD_PLUMED "Download Plumed (instead of using the system's one)" OFF)
+  if(DOWNLOAD_PLUMED)
+    include(ExternalProject)
+    ExternalProject_Add(plumed_build
+      URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz 
+      URL_MD5 b1be7c48971627febc11c61b70767fc5
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> 
+                                               $<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic>                                                  )
+    ExternalProject_get_property(plumed_build INSTALL_DIR)
+    set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
+    list(APPEND LAMMPS_DEPS plumed_build)
+    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})
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
+    endif()
+    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(PLUMED plumed REQUIRED)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so)
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+    endif()
+    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
+  endif()
+  include_directories(${PLUMED_INCLUDE_DIRS})
+endif()
+
 if(PKG_USER-MOLFILE)
   add_library(molfile INTERFACE)
   target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
@@ -876,6 +927,20 @@ if(PKG_USER-OMP)
     include_directories(${USER-OMP_SOURCES_DIR})
 endif()
 
+# Fix rigid/meso requires RIGID to be installed
+if(PKG_USER-SDPD)
+  set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
+
+  get_property(hlist GLOBAL PROPERTY FIX)
+  if(NOT PKG_RIGID)
+    list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
+    list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
+  endif()
+  set_property(GLOBAL PROPERTY FIX "${hlist}")
+
+  include_directories(${USER-SDPD_SOURCES_DIR})
+endif()
+
 if(PKG_KOKKOS)
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@@ -1166,7 +1231,6 @@ set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
 
 GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
 
-include_directories(${LAMMPS_SOURCE_DIR})
 include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 
 ######################################

cmake/README.md

@@ -1492,6 +1492,11 @@ target API.
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>BIN2C</code> (CUDA only)</td>
+  <td>Path to bin2c executable, will automatically pick up the first one in your $PATH.</td>
+  <td>(automatic)</td>
+</tr>
 </tbody>
 </table>
 
@@ -1647,9 +1652,8 @@ requires `gzip` to be in your `PATH`
 </tr>
 <tr>
   <td><code>GZIP_EXECUTABLE</code></td>
-  <td></td>
-  <td>
-  </td>
+  <td>Path to gzip executable, will automatically pick up the first one in your $PATH.</td>
+  <td>(automatic)</td>
 </tr>
 </tbody>
 </table>
@@ -1679,9 +1683,8 @@ requires `ffmpeg` to be in your `PATH`
 </tr>
 <tr>
   <td><code>FFMPEG_EXECUTABLE</code></td>
-  <td></td>
-  <td>
-  </td>
+  <td>Path to ffmpeg executable, will automatically pick up the first one in your $PATH.</td>
+  <td>(automatic)</td>
 </tr>
 </tbody>
 </table>

cmake/pkgconfig/liblammps.pc.in

@@ -1,9 +1,29 @@
 # pkg-config file for lammps
 # https://people.freedesktop.org/~dbn/pkg-config-guide.html
-# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c
-# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
+
+# Add the directory where lammps.pc got installed to your PKG_CONFIG_PATH
 # e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
 
+# Use this on commandline with:
+# c++ `pkg-config --cflags --libs lammps` -o myapp myapp.cpp
+
+# Use this in a Makefile:
+# myapp: myapp.cpp
+# 	$(CC) `pkg-config --cflags --libs lammps` -o $@ $<
+
+# Use this in autotools:
+# configure.ac:
+# PKG_CHECK_MODULES([LAMMPS], [lammps])
+# Makefile.am:
+# myapp_CFLAGS = $(LAMMPS_CFLAGS)
+# myapp_LDADD = $(LAMMPS_LIBS)
+
+# Use this in CMake:
+# CMakeLists.txt:
+# find_package(PkgConfig)
+# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps)
+# target_link_libraries(<lib> PkgConfig::LAMMPS)
+
 prefix=@CMAKE_INSTALL_PREFIX@
 libdir=@CMAKE_INSTALL_FULL_LIBDIR@
 includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@

cmake/presets/all_off.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/all_on.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/manual_selection.cmake

@@ -56,11 +56,13 @@ set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
 set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
 set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
 set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
-set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-PHONON OFF CACHE BOOL "" FORCE)
+set(PKG_USER-PLUMED OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
 set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-SDPD OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/std.cmake

@@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI

cmake/presets/std_nolib.cmake

@@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI

cmake/presets/user.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

doc/github-development-workflow.md

@@ -0,0 +1,184 @@
+# Outline of the GitHub Development Workflow
+
+This purpose of this document is to provide a point of reference for the
+core LAMMPS developers and other LAMMPS contibutors to understand the
+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.
+
+## Table of Contents
+
+  * [GitHub Merge Management](#github-merge-management)
+  * [Pull Requests](#pull-requests)
+    * [Pull Request Assignments](#pull-request-assignments)
+    * [Pull Request Reviews](#pull-request-reviews)
+    * [Pull Request Discussions](#pull-request-discussions)
+    * [Checklist for Pull Requests](#checklist-for-pull-requests)
+  * [GitHub Issues](#github-issues)
+  * [Milestones and Release Planning](#milestones-and-release-planning)
+
+## GitHub Merge Management
+
+In the interest of consistency, ONLY ONE of the core LAMMPS developers
+should doing the merging itself.  This is currently
+[@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
+If this assignment needs to be changed, it shall be done right after a
+stable release.
+
+## Pull Requests
+
+ALL changes to the LAMMPS code and documentation, however trivial, MUST
+be submitted as a pull request to GitHub. All changes to the "master"
+branch must be made exclusively through merging pull requests. The
+"unstable" and "stable" branches, respectively are only to be updated
+upon patch or stable releases with fast-forward merges based on the
+associated tags. Pull requests may also be submitted to (long-running)
+feature branches created by LAMMPS developers inside the LAMMPS project,
+if needed. Those are not subject to the merge and review restrictions
+discussed in this document, though, but get manages as needed on a
+case-by-case basis.
+
+### Pull Request Assignments
+
+Pull requests can be "chaperoned" by one of the LAMMPS core developers.
+This is indicated by who the pull request is assigned to. LAMMPS core
+developers can self-assign or they can decide to assign a pull request
+to a different LAMMPS developer. Being assigned to a pull request means,
+that this pull request may need some work and the assignee is tasked to
+determine what this might be needed or not, and may either implement the
+required changes or ask the submitter of the pull request to implement
+them.  Even though, all LAMMPS developers may have write access to pull
+requests (if enabled by the submitter, which is the default), only the
+submitter or the assignee of a pull request may do so.  During this
+period the "work_in_progress" label shall be applied to the pull
+request.  The assignee gets to decide what happens to the pull request
+next, e.g. whether it should be assigned to a different developer for
+additional checks and changes, or is recommended to be merged.  Removing
+the "work_in_progress" label and assigning the pull request to the
+developer tasked with merging signals that a pull request is ready to be
+merged.
+
+### Pull Request Reviews
+
+People can be assigned to review a pull request in two ways:
+
+  * They can be assigned manually to review a pull request
+    by the submitter or a LAMMPS developer
+  * They can be automatically assigned, because a developers matches
+    a file pattern in the `.github/CODEOWNERS` file, which associates
+    developers with the code they contributed and maintain.
+
+Reviewers are requested to state their appraisal of the proposed changes
+and either approve or request changes. People may unassign themselves
+from review, if they feel not competent about the changes proposed. At
+least one review from a LAMMPS developer with write access is required
+before merging in addition to the automated compilation tests.  The
+feature, that reviews from code owners are "hard" reviews (i.e. they
+must all be approved before merging is allowed), is currently disabled
+and it is in the discretion of the merge maintainer to assess when
+a sufficient degree of approval has been reached.  Reviews may be
+(automatically) dismissed, when the reviewed code has been changed,
+and then approval is required a second time.
+
+### Pull Request Discussions
+
+All discussions about a pull request should be kept as much as possible
+on the pull request discussion page on GitHub, so that other developers
+can later review the entire discussion after the fact and understand the
+rationale behind choices made.  Exceptions to this policy are technical
+discussions, that are centered on tools or policies themselves
+(git, github, c++) rather than on the content of the pull request.
+
+### Checklist for Pull Requests
+
+Here are some items to check:
+  * source and text files should not have CR/LF line endings (use dos2unix to remove)
+  * every new command or style should have documentation. The names of
+  source files (c++ and manual) should follow the name of the style.
+  (example: `src/fix_nve.cpp`, `src/fix_nve.h` for `fix nve` command,
+  implementing the class `FixNVE`, documented in `doc/src/fix_nve.txt`)
+  * all new style names should be lower case, the must be no dashes,
+  blanks, or underscores separating words, only forward slashes.
+  * new style docs should be added to the "overview" files in
+  `doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
+  and `doc/src/lammps.book`
+  * new files in packages should be added to `src/.gitignore`
+  * removed or renamed files in packages should be added to `src/Purge.list`
+  * C++ source files should use C++ style include files for accessing
+  C-library APIs, e.g. `#include <cstdlib>` instead of `#include <stdlib.h>`.
+  And they should use angular brackets instead of double quotes. Full list:
+    * assert.h -> cassert
+    * ctype.h -> cctype
+    * errno.h -> cerrno
+    * float.h -> cfloat
+    * limits.h -> climits
+    * math.h -> cmath
+    * omplex.h -> complex
+    * setjmp.h -> csetjmp
+    * signal.h -> csignal
+    * stddef.h -> cstddef
+    * stdint.h -> cstdint
+    * stdio.h -> cstdio
+    * stdlib.h -> cstdlib
+    * string.h -> cstring
+    * time.h -> ctime
+  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
+  * 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.
+  * 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
+  compiling LAMMPS with `-DLAMMPS_BIGBIG`.
+  * when including both `lmptype.h` (and using defines or macros from it)
+  and `mpi.h`, `lmptype.h` must be included first.
+
+## GitHub Issues
+
+The GitHub issue tracker is the location where the LAMMPS developers
+and other contributors or LAMMPS users can report issues or bugs with
+the LAMMPS code or request new features to be added. Feature requests
+are usually indicated by a `[Feature Request]` marker in the subject.
+Issues are assigned to a person, if this person is working on this
+feature or working to resolve an issue. Issues that have nobody working
+on them at the moment, have the label `volunteer needed` attached.
+
+When an issue, say `#125` is resolved by a specific pull request,
+the comment for the pull request shall contain the text `closes #125`
+or `fixes #125`, so that the issue is automatically deleted when
+the pull request is merged.
+
+## Milestones and Release Planning
+
+LAMMPS uses a continuous release development model with incremental
+changes, i.e. significant effort is made - including automated pre-merge
+testing - that the code in the branch "master" does not get broken.
+More extensive testing (including regression testing) is performed after
+code is merged to the "master" branch. There are patch releases of
+LAMMPS every 1-3 weeks at a point, when the LAMMPS developers feel, that
+a sufficient amount of changes have happened, and the post-merge testing
+has been successful. These patch releases are marked with a
+`patch_<version date>` tag and the "unstable" branch follows only these
+versions (and thus is always supposed to be of production quality,
+unlike "master", which may be temporary broken, in the case of larger
+change sets or unexpected incompatibilities or side effects.
+
+About 3-4 times each year, there are going to be "stable" releases
+of LAMMPS.  These have seen additional, manual testing and review of
+results from testing with instrumented code and static code analysis.
+Also, in the last 2-3 patch releases before a stable release are
+"release candidate" versions which only contain bugfixes and
+documentation updates.  For release planning and the information of
+code contributors, issues and pull requests being actively worked on
+are assigned a "milestone", which corresponds to the next stable
+release or the stable release after that, with a tentative release
+date.
+

doc/src/Build_basics.txt

@@ -137,9 +137,9 @@ simply loading the appropriate module before building LAMMPS.
 -D CMAKE_C_COMPILER=name              # name of C compiler
 -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler :pre
 
--D CMAKE_CXX_FlAGS=string             # flags to use with C++ compiler
--D CMAKE_C_FlAGS=string               # flags to use with C compiler
--D CMAKE_Fortran_FlAGS=string         # flags to use with Fortran compiler :pre
+-D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
+-D CMAKE_C_FLAGS=string               # flags to use with C compiler
+-D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler :pre
 
 By default CMake will use a compiler it finds and it will add
 optimization flags appropriate to that compiler and any "accelerator

doc/src/Build_extras.txt

@@ -45,6 +45,7 @@ This is the list of packages that may require additional steps.
 "USER-INTEL"_#user-intel,
 "USER-MOLFILE"_#user-molfile,
 "USER-NETCDF"_#user-netcdf,
+"USER-PLUMED"_#user-plumed,
 "USER-OMP"_#user-omp,
 "USER-QMMM"_#user-qmmm,
 "USER-QUIP"_#user-quip,
@@ -712,6 +713,103 @@ a corresponding Makefile.lammps.machine file.
 
 :line
 
+USER-PLUMED package :h4,link(user-plumed)
+
+Before building LAMMPS with this package, you must first build PLUMED.
+PLUMED can be built as part of the LAMMPS build or installed separately
+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
+varible, 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.
+
+[CMake build]:
+
+-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 hardcoded 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.
+
+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.
+
+[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.
+
+Download/compilation/configuration of the plumed library can be done
+from the src folder through the following make args:
+
+make lib-plumed                         # print help message
+make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
+make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
+make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
+                                                # /usr/local and use shared linkage mode
+: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 compleded, you can install the
+USER-PLUMED package and compile LAMMPS in the usual manner:
+
+make yes-user-plumed 
+make machine :pre
+
+Once this compilation completes you should be able to run LAMMPS in the
+usual way.  For shared linkage mode, libplumed.so must be found by the
+LAMMPS executable, which on many operating systems means, you have to
+set the LD_LIBRARY_PATH environment variable accordingly.
+
+Support for the different linkage modes in LAMMPS varies for different
+operating systems, using the static linkage is expected to be the most
+portable, and thus set to be the default.
+
+If you want to change the linkage mode, you have to re-run "make
+lib-plumed" with the desired settings [and] do a reinstall if the
+USER-PLUMED package with "make yes-user-plumed" to update the required
+makefile settings with the changes in the lib/plumed folder.
+
+:line
+
 USER-H5MD package :h4,link(user-h5md)
 
 To build with this package you must have the HDF5 software package

doc/src/Build_package.txt

@@ -56,6 +56,7 @@ packages:
 "USER-INTEL"_Build_extras.html#user-intel,
 "USER-MOLFILE"_Build_extras.html#user-molfile,
 "USER-NETCDF"_Build_extras.html#user-netcdf,
+"USER-PLUMED"_Build_extras.html#user-plumed,
 "USER-OMP"_Build_extras.html#user-omp,
 "USER-QMMM"_Build_extras.html#user-qmmm,
 "USER-QUIP"_Build_extras.html#user-quip,

doc/src/Commands_all.txt

@@ -59,6 +59,7 @@ An alphabetic list of all LAMMPS commands.
 "fix_modify"_fix_modify.html,
 "group"_group.html,
 "group2ndx"_group2ndx.html,
+"hyper"_hyper.html,
 "if"_if.html,
 "info"_info.html,
 "improper_coeff"_improper_coeff.html,

doc/src/Commands_fix.txt

@@ -78,6 +78,8 @@ OPT.
 "grem"_fix_grem.html,
 "halt"_fix_halt.html,
 "heat"_fix_heat.html,
+"hyper/global"_fix_hyper_global.html,
+"hyper/local"_fix_hyper_local.html,
 "imd"_fix_imd.html,
 "indent"_fix_indent.html,
 "ipi"_fix_ipi.html,
@@ -94,6 +96,7 @@ OPT.
 "lineforce"_fix_lineforce.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso"_fix_meso.html,
+"meso/move"_fix_meso_move.html,
 "meso/stationary"_fix_meso_stationary.html,
 "momentum (k)"_fix_momentum.html,
 "move"_fix_move.html,
@@ -107,7 +110,7 @@ OPT.
 "nph/asphere (o)"_fix_nph_asphere.html,
 "nph/body"_fix_nph_body.html,
 "nph/eff"_fix_nh_eff.html,
-"nph/sphere (ko)"_fix_nph_sphere.html,
+"nph/sphere (o)"_fix_nph_sphere.html,
 "nphug (o)"_fix_nphug.html,
 "npt (iko)"_fix_nh.html,
 "npt/asphere (o)"_fix_npt_asphere.html,
@@ -127,7 +130,7 @@ OPT.
 "nve/line"_fix_nve_line.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
 "nve/noforce"_fix_nve_noforce.html,
-"nve/sphere (o)"_fix_nve_sphere.html,
+"nve/sphere (ko)"_fix_nve_sphere.html,
 "nve/spin"_fix_nve_spin.html,
 "nve/tri"_fix_nve_tri.html,
 "nvk"_fix_nvk.html,
@@ -146,6 +149,7 @@ OPT.
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "planeforce"_fix_planeforce.html,
+"plumed"_fix_plumed.html,
 "poems"_fix_poems.html,
 "pour"_fix_pour.html,
 "precession/spin"_fix_precession_spin.html,
@@ -172,6 +176,7 @@ OPT.
 "restrain"_fix_restrain.html,
 "rhok"_fix_rhok.html,
 "rigid (o)"_fix_rigid.html,
+"rigid/meso"_fix_rigid_meso.html,
 "rigid/nph (o)"_fix_rigid.html,
 "rigid/nph/small"_fix_rigid.html,
 "rigid/npt (o)"_fix_rigid.html,

doc/src/Commands_pair.txt

@@ -198,6 +198,7 @@ OPT.
 "reax/c (ko)"_pair_reaxc.html,
 "rebo (io)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
+"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
 "smd/hertz"_pair_smd_hertz.html,
 "smd/tlsph"_pair_smd_tlsph.html,
 "smd/tri_surface"_pair_smd_triangulated_surface.html,

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="24 Oct 2018 version">
+<META NAME="docnumber" CONTENT="15 Nov 2018 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
-24 Oct 2018 version :c,h2
+15 Nov 2018 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -89,12 +89,14 @@ as contained in the file name.
 "USER-NETCDF"_#PKG-USER-NETCDF,
 "USER-OMP"_#PKG-USER-OMP,
 "USER-PHONON"_#PKG-USER-PHONON,
+"USER-PLUMED"_#PKG-USER-PLUMED,
 "USER-PTM"_#PKG-USER-PTM,
 "USER-QMMM"_#PKG-USER-QMMM,
 "USER-QTB"_#PKG-USER-QTB,
 "USER-QUIP"_#PKG-USER-QUIP,
 "USER-REAXC"_#PKG-USER-REAXC,
 "USER-SCAFACOS"_#PKG-USER-SCAFACOS,
+"USER-SDPD"_#PKG-USER-SDPD,
 "USER-SMD"_#PKG-USER-SMD,
 "USER-SMTBQ"_#PKG-USER-SMTBQ,
 "USER-SPH"_#PKG-USER-SPH,
@@ -1186,7 +1188,7 @@ the NAMD MD code, but with portability in mind.  Axel Kohlmeyer
 [Install:] 
 
 This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
+instructions"_Build_extras.html#user-colvars on the "Build
 extras"_Build_extras.html doc page.
 
 [Supporting info:]
@@ -1200,6 +1202,36 @@ examples/USER/colvars :ul
 
 :line
 
+USER-PLUMED package :link(PKG-USER-PLUMED),h4
+
+[Contents:]
+
+The fix plumed command allows you to use the PLUMED free energy plugin
+for molecular dynamics to analyse and bias your LAMMPS trajectory on
+the fly.  The PLUMED library is called from within the LAMMPS input
+script by using the "fix plumed _fix_plumed.html command.
+
+[Authors:] The "PLUMED library"_#PLUMED is written and maintained by
+Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth
+Tribello.
+
+:link(PLUMED,http://www.plumed.org)
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-PLUMED/README
+lib/plumed/README
+"fix plumed"_fix_plumed.html
+examples/USER/plumed :ul
+
+:line
+
 USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
 
 [Contents:]
@@ -1916,6 +1948,31 @@ examples/USER/scafacos :ul
 
 :line
 
+USER-SDPD package :link(PKG-USER-SDPD),h4
+
+[Contents:]
+
+A pair style for smoothed dissipative particle dynamics (SDPD), which
+is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
+where thermal fluctuations are important (see the
+"USER-SPH package"_#PKG-USER-SPH).
+Also two fixes for moving and rigid body integration of SPH/SDPD particles
+(particles of atom_style meso).
+
+[Author:] Morteza Jalalvand (Institute for Advanced Studies in Basic
+Sciences, Iran).
+
+[Supporting info:]
+
+src/USER-SDPD: filenames -> commands
+src/USER-SDPD/README
+"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html
+"fix meso/move"_fix_meso_move.html
+"fix rigid/meso"_fix_rigid_meso.html
+examples/USER/sdpd :ul
+
+:line
+
 USER-SMD package :link(PKG-USER-SMD),h4
 
 [Contents:]

doc/src/Packages_user.txt

@@ -62,16 +62,20 @@ Package, Description, Doc page, Example, Library
 "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
 "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
 "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
+"USER-PLUMED"_Packages_details.html#PKG-USER-PLUMED, "PLUMED"_#PLUMED free energy library,"fix plumed"_fix_plumed.html, USER/plumed, ext
 "USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no
 "USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
 "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
 "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
 "USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
 "USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext
+"USER-SDPD"_Packages_details.html#PKG-USER-SDPD, smoothed dissipative particle dynamics,"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html, USER/sdpd, no
 "USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
 "USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
 "USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
 "USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
 "USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
 "USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
+
 :link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
+:link(PLUMED,http://www.plumed.org)

doc/src/commands_list.txt

@@ -44,6 +44,7 @@ Commands :h1
    fix_modify
    group
    group2ndx
+   hyper
    if
    improper_coeff
    improper_style

doc/src/compute.txt

@@ -176,6 +176,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 (g,i,k,o,t) to indicate which accelerated styles exist.
 
 "ackland/atom"_compute_ackland_atom.html - 
+"adf"_compute_adf.html - angular distribution function
 "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
 "angle"_compute_angle.html - 
 "angle/local"_compute_angle_local.html - 

doc/src/compute_ptm_atom.txt

@@ -117,5 +117,5 @@ package"_Build_package.html doc page for more info.
 :line
 
 :link(Larsen)
-[(Larsen)] Larsen, Schmidt, Schiøtz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
+[(Larsen)] Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
 

doc/src/fix.txt

@@ -221,6 +221,8 @@ accelerated styles exist.
 "grem"_fix_grem.html - 
 "halt"_fix_halt.html - terminate a dynamics run or minimization
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
+"hyper/global"_fix_hyper_global.html - global hyperdynamics
+"hyper/local"_fix_hyper_local.html - local hyperdynamics
 "imd"_fix_imd.html - 
 "indent"_fix_indent.html - impose force due to an indenter
 "ipi"_fix_ipi.html - 
@@ -237,6 +239,8 @@ accelerated styles exist.
 "lineforce"_fix_lineforce.html - constrain atoms to move in a line
 "manifoldforce"_fix_manifoldforce.html - 
 "meso"_fix_meso.html - 
+"meso"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
+"meso/move"_fix_meso_move.html - 
 "meso/stationary"_fix_meso_stationary.html - 
 "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
 "move"_fix_move.html - move atoms in a prescribed fashion
@@ -292,6 +296,7 @@ accelerated styles exist.
 "phonon"_fix_phonon.html - 
 "pimd"_fix_pimd.html - 
 "planeforce"_fix_planeforce.html - constrain atoms to move in a plane
+"plumed"_fix_plumed.html - wrapper on PLUMED free energy library
 "poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies
 "pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain
 "precession/spin"_fix_precession_spin.html - 
@@ -331,6 +336,7 @@ accelerated styles exist.
 "rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
 "rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
 "rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
+"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
 "rx"_fix_rx.html - 
 "saed/vtk"_fix_saed_vtk.html - 
 "setforce"_fix_setforce.html - set the force on each atom

doc/src/fix_bond_break.txt

@@ -137,8 +137,8 @@ doc page for more info.
 [Related commands:]
 
 "fix bond/create"_fix_bond_create.html, "fix
-bond/swap"_fix_bond_swap.html, "dump local"_dump.html,
-"special_bonds"_special_bonds.html
+bond/react"_fix_bond_react.html, "fix bond/swap"_fix_bond_swap.html,
+"dump local"_dump.html, "special_bonds"_special_bonds.html
 
 [Default:]
 

doc/src/fix_bond_create.txt

@@ -232,8 +232,8 @@ doc page for more info.
 [Related commands:]
 
 "fix bond/break"_fix_bond_break.html, "fix
-bond/swap"_fix_bond_swap.html, "dump local"_dump.html,
-"special_bonds"_special_bonds.html
+bond/react"_fix_bond_react.html, "fix bond/swap"_fix_bond_swap.html,
+"dump local"_dump.html, "special_bonds"_special_bonds.html
 
 [Default:]
 

doc/src/fix_bond_react.txt

@@ -24,11 +24,11 @@ common_keyword = {stabilization} :l
   {stabilization} values = {no} or {yes} {group-ID} {xmax}
     {no} = no reaction site stabilization
     {yes} = perform reaction site stabilization
-      {group-ID} = user-assigned ID for all non-reacting atoms (group created internally)
+      {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms
       {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre
 react = mandatory argument indicating new reaction specification :l
   react-ID = user-assigned name for the reaction :l
-  react-group-ID = only atoms in this group are available for the reaction :l
+  react-group-ID = only atoms in this group are considered for the reaction :l
   Nevery = attempt reaction every this many steps :l
   Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
   Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
@@ -41,14 +41,18 @@ react = mandatory argument indicating new reaction specification :l
       fraction = initiate reaction with this probability if otherwise eligible
       seed = random number seed (positive integer)
     {stabilize_steps} value = timesteps
-      timesteps = number of timesteps to apply internally created nve/limit.html :pre
+      timesteps = number of timesteps to apply internally created nve/limit fix :pre
+    {update_edges} value = {none} or {charges} :l
+      none = do not update topology near the edges of reaction templates
+      charges = update atomic charges of all atoms in reaction templates
+      custom = force the update of user-specified atomic charges :pre
 :ule
 
 [Examples:]
 
 molecule mol1 pre_reacted_topology.txt
 molecule mol2 post_reacted_topology.txt
-fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
+fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
 
 molecule mol1 pre_reacted_rxn1.txt
 molecule mol2 post_reacted_rxn1.txt
@@ -57,7 +61,7 @@ molecule mol4 post_reacted_rxn2.txt
 fix 5 all bond/react stabilization yes nvt_grp .03 &
   react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
   react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
-fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre
+fix 6 nvt_grp_REACT nvt temp 300 300 100 # set thermostat after bond/react :pre
 
 [Description:]
 
@@ -99,19 +103,29 @@ involved in any new reactions. The {xmax} value keyword should
 typically be set to the maximum distance that non-reacting atoms move
 during the simulation.
 
-The group-ID set using the {stabilization} keyword should be a
-previously unused group-ID. It cannot be specified as 'all'. The fix
-bond/react command creates a "dynamic group"_group.html of this name
-that includes all non-reacting atoms. This dynamic group-ID should
-then be used by a subsequent system-wide time integrator such as nvt,
-npt, or nve, as shown in the second example above. It is currently
-necessary to place the time integration command after the fix
-bond/react command due to the internal dynamic grouping performed by
-fix bond/react.
+The group-ID set using the {stabilization} keyword can be an existing
+static group or a previously-unused group-ID. It cannot be specified
+as 'all'. If the group-ID is previously unused, the fix bond/react
+command creates a "dynamic group"_group.html that is initialized to
+include all atoms. If the group-ID is that of an existing static
+group, the group is used as the parent group of new,
+internally-created dynamic group. In both cases, this new dynamic
+group is named by appending '_REACT' to the group-ID, e.g.
+nvt_grp_REACT. By specifying an existing group, you may thermostat
+constant-topology parts of your system separately. The dynamic group
+contains only non-reacting atoms at a given timestep, and therefore
+should be used by a subsequent system-wide time integrator such as
+nvt, npt, or nve, as shown in the second example above. The time
+integration command should be placed after the fix bond/react command
+due to the internal dynamic grouping performed by fix bond/react.
 
-NOTE: The internally created group currently applies to all atoms in
-the system, i.e. you should generally not have a separate thermostat
-which acts on the 'all' group.
+NOTE: If the group-ID is an existing static group, react-group-IDs
+should also be specified as this static group, or a subset.
+
+NOTE: If the group-ID is previously unused, the internally created
+group applies to all atoms in the system, i.e. you should generally
+not have a separate thermostat which acts on the 'all' group, or any
+other group.
 
 The following comments pertain to each {react} argument:
 
@@ -155,7 +169,17 @@ Some atoms in the pre-reacted template that are not reacting may have
 missing topology with respect to the simulation. For example, the
 pre-reacted template may contain an atom that would connect to the
 rest of a long polymer chain. These are referred to as edge atoms, and
-are also specified in the map file.
+are also specified in the map file. When the pre-reaction template
+contains edge atoms, not all atoms, bonds, charges, etc. specified in
+the reaction templates will be updated. Specifically, topology that
+involves only atoms that are 'too near' to template edges will not be
+updated. The definition of 'too near the edge' depends on which
+interactions are defined in the simulation. If the simulation has
+defined dihedrals, atoms within two bonds of edge atoms are considered
+'too near the edge.' If the simulation defines angles, but not
+dihedrals, atoms within one bond of edge atoms are considered 'too
+near the edge.' If just bonds are defined, only edge atoms are
+considered 'too near the edge.'
 
 Note that some care must be taken when a building a molecule template
 for a given simulation. All atom types in the pre-reacted template
@@ -178,23 +202,30 @@ 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 one optional keyword. The mandatory
-keyword is 'equivalences' and the optional keyword is 'edgeIDs':
+contains one mandatory keyword and two optional keywords. The mandatory
+keyword is 'equivalences' and the optional keywords are 'edgeIDs' and
+'customIDs':
 
 N {equivalences} = # of atoms N in the reaction molecule templates
-N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template :pre
+N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
+N {customIDs} = # of atoms N that are specified for a custom update :pre
 
-The body of the map file contains two mandatory sections and one
-optional section. The first mandatory section begins with the keyword
+The body of the map file contains two mandatory sections and two
+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
 with the keyword 'Equivalences' and lists a one-to-one correspondence
 between atom IDs of the pre- and post-reacted templates. The first
 column is an atom ID of the pre-reacted molecule template, and the
 second column is the corresponding atom ID of the post-reacted
-molecule template. The optional section begins with the keyword
+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.
+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
+discussion of the 'update_edges' keyword.
 
 A sample map file is given below:
 
@@ -255,6 +286,18 @@ The {stabilize_steps} keyword allows for the specification of how many
 timesteps a reaction site is stabilized before being returned to the
 overall system thermostat.
 
+The {update_edges} keyword can increase the number of atoms whose
+atomic charges are updated, when the pre-reaction template contains
+edge atoms. When the value is set to 'charges,' all atoms' atomic
+charges are updated to those specified by the post-reaction template,
+including atoms near the edge of reaction templates. When the value is
+set to 'custom,' an additional section must be included in the map
+file that specifies whether to update charges, on a per-atom basis.
+The format of this section is detailed above. Listing a pre-reaction
+atom ID with a value of 'charges' will force the update of the atom's
+charge, even if it is near a template edge. Atoms not near a template
+edge are unaffected by this setting.
+
 In order to produce the most physical behavior, this 'reaction site
 equilibration time' should be tuned to be as small as possible while
 retaining stability for a given system or reaction step. After a
@@ -323,7 +366,7 @@ bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
 
 [Default:]
 
-The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60
+The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none
 
 :line
 

doc/src/fix_colvars.txt

@@ -116,7 +116,8 @@ not a limitation of functionality.
 
 [Related commands:]
 
-"fix smd"_fix_smd.html
+"fix smd"_fix_smd.html, "fix spring"_fix_spring.html,
+"fix plumed"_fix_plumed.html
 
 [Default:]
 
@@ -126,4 +127,4 @@ and tstat = NULL.
 :line
 
 :link(Fiorin)
-[(Fiorin)] Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
+[(Fiorin)] Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594

doc/src/fix_hyper_global.txt

@@ -0,0 +1,260 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix hyper/global command :h3
+
+[Syntax:]
+
+fix ID group-ID hyper/global cutbond qfactor Vmax Tequil :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+hyper/global = style name of this fix command
+cutbond = max distance at which a pair of atoms is considered bonded (distance units)
+qfactor = max strain at which bias potential goes to 0.0 (unitless)
+Vmax = height of bias potential (energy units)
+Tequil = equilibration temperature (temperature units) :ul
+
+[Examples:]
+
+fix 1 all hyper/global 1.0 0.3 0.8 300.0 :pre
+
+[Description:]
+
+This fix is meant to be used with the "hyper"_hyper.html command to
+perform a bond-boost global hyperdynamics (GHD) simulation.  The role
+of this fix is to a select a single pair of atoms in the system at
+each timestep to add a global bias potential to, which will alter the
+dynamics of the system in a manner that effectively accelerates time.
+This is in contrast to the "fix hyper/local"_fix_hyper_local.html
+command, which can be user to perform a local hyperdynamics (LHD)
+simulation, by adding a local bias potential to multiple pairs of
+atoms at each timestep.  GHD can time accelerate a small simulation
+with up to a few 100 atoms.  For larger systems, LHD is needed to
+achieve good time acceleration.
+
+For a system that undergoes rare transition events, where one or more
+atoms move over an energy barrier to a new potential energy basin, the
+effect of the bias potential is to induce more rapid transitions.
+This can lead to a dramatic speed-up in the rate at which events
+occurs, without altering their relative frequencies, thus leading to
+an overall increase in the elapsed real time of the simulation as
+compared to running for the same number of timesteps with normal MD.
+See the "hyper"_hyper.html doc page for a more general discussion of
+hyperdynamics and citations that explain both GHD and LHD.
+
+The equations and logic used by this fix and described here to perform
+GHD follow the description given in "(Voter2013)"_#Voter2013ghd.  The
+bond-boost form of a bias potential for HD is due to Miron and
+Fichthorn as described in "(Miron)"_#Mironghd.  In LAMMPS we use a
+simplified version of bond-boost GHD where a single bond in the system
+is biased at any one timestep.
+
+Bonds are defined between each pair of I,J atoms whose R0ij distance
+is less than {cutbond}, when the system is in a quenched state
+(minimum) energy.  Note that these are not "bonds" in a covalent
+sense.  A bond is simply any pair of atoms that meet the distance
+criterion.  {Cutbond} is an argument to this fix; it is discussed
+below.  A bond is only formed if one or both of the I.J atoms are in
+the specified group.
+
+The current strain of bond IJ (when running dynamics) is defined as
+
+Eij = (Rij - R0ij) / R0ij :pre
+
+where Rij is the current distance between atoms I,J, and R0ij is the
+equilibrium distance in the quenched state.
+
+The bias energy Vij of any bond IJ is defined as
+
+Vij = Vmax * (1 - (Eij/q)^2) for abs(Eij) < qfactor
+    = 0 otherwise :pre
+
+where the prefactor {Vmax} and the cutoff {qfactor} are arguments to
+this fix; they are discussed below.  This functional form is an
+inverse parabola centered at 0.0 with height Vmax and which goes to
+0.0 at +/- qfactor.
+
+Let Emax = the maximum of abs(Eij) for all IJ bonds in the system on a
+given timestep.  On that step, Vij is added as a bias potential to
+only the single bond with strain Emax, call it Vij(max).  Note that
+Vij(max) will be 0.0 if Emax >= qfactor on that timestep.  Also note
+that Vij(max) is added to the normal interatomic potential that is
+computed between all atoms in the system at every step.
+
+The derivative of Vij(max) with respect to the position of each atom
+in the Emax bond gives a bias force Fij(max) acting on the bond as
+
+Fij(max) = - dVij(max)/dEij = 2 Vmax Eij / qfactor^2   for abs(Eij) < qfactor
+         = 0 otherwise :pre
+
+which can be decomposed into an equal and opposite force acting on
+only the two I,J atoms in the Emax bond.
+
+The time boost factor for the system is given each timestep I by
+
+Bi = exp(beta * Vij(max)) :pre
+
+where beta = 1/kTequil, and {Tequil} is the temperature of the system
+and an argument to this fix.  Note that Bi >= 1 at every step.
+
+NOTE: To run GHD, the input script must also use the "fix
+langevin"_fix_langevin.html command to thermostat the atoms at the
+same {Tequil} as specified by this fix, so that the system is running
+constant-temperature (NVT) dynamics.  LAMMPS does not check that this
+is done.
+
+The elapsed time t_hyper for a GHD simulation running for {N}
+timesteps is simply
+
+t_hyper = Sum (i = 1 to N) Bi * dt :pre
+
+where dt is the timestep size defined by the "timestep"_timestep.html
+command.  The effective time acceleration due to GHD is thus t_hyper /
+N*dt, where N*dt is elapsed time for a normal MD run of N timesteps.
+
+Note that in GHD, the boost factor varies from timestep to timestep.
+Likewise, which bond has Emax strain and thus which pair of atoms the
+bias potential is added to, will also vary from timestep to timestep.
+This is in contrast to local hyperdynamics (LHD) where the boost
+factor is an input parameter; see the "fix
+hyper/local"_fix_hyper_local.html doc page for details.
+
+:line
+
+Here is additional information on the input parameters for GHD.
+
+The {cutbond} argument is the cutoff distance for defining bonds
+between pairs of nearby atoms.  A pair of I,J atoms in their
+equilibrium, minimum-energy configuration, which are separated by a
+distance Rij < {cutbond}, are flagged as a bonded pair.  Setting
+{cubond} to be ~25% larger than the nearest-neighbor distance in a
+crystalline lattice is a typical choice for solids, so that bonds
+exist only between nearest neighbor pairs.
+
+The {qfactor} argument is the limiting strain at which the bias
+potential goes to 0.0.  It is dimensionless, so a value of 0.3 means a
+bond distance can be up to 30% larger or 30% smaller than the
+equilibrium (quenched) R0ij distance and the two atoms in the bond
+could still experience a non-zero bias force.
+
+If {qfactor} is set too large, then transitions from one energy basin
+to another are affected because the bias potential is non-zero at the
+transition state (e.g. saddle point).  If {qfactor} is set too small
+than little boost is achieved because the Eij strain of some bond in
+the system will (nearly) always exceed {qfactor}.  A value of 0.3 for
+{qfactor} is typically reasonable.
+
+The {Vmax} argument is the prefactor on the bias potential.  Ideally,
+tt should be set to a value slightly less than the smallest barrier
+height for an event to occur.  Otherwise the applied bias potential
+may be large enough (when added to the interatomic potential) to
+produce a local energy basin with a maxima in the center.  This can
+produce artificial energy minima in the same basin that trap an atom.
+Or if {Vmax} is even larger, it may induce an atom(s) to rapidly
+transition to another energy basin.  Both cases are "bad dynamics"
+which violate the assumptions of GHD that guarantee an accelerated
+time-accurate trajectory of the system.
+
+Note that if {Vmax} is set too small, the GHD simulation will run
+correctly.  There will just be fewer events because the hyper time
+(t_hyper equation above) will be shorter.
+
+NOTE: If you have no physical intuition as to the smallest barrier
+height in your system, a reasonable strategy to determine the largest
+{Vmax} you can use for an LHD model, is to run a sequence of
+simulations with smaller and smaller {Vmax} values, until the event
+rate does not change.
+
+The {Tequil} argument is the temperature at which the system is
+simulated; see the comment above about the "fix
+langevin"_fix_langevin.html thermostatting.  It is also part of the
+beta term in the exponential factor that determines how much boost is
+achieved as a function of the bias potential.
+
+In general, the lower the value of {Tequil} and the higher the value
+of {Vmax}, the more boost will be achievable by the GHD algorithm.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy of the bias potential to the the system's
+potential energy as part of "thermodynamic output"_thermo_style.html.
+
+This fix computes a global scalar and global vector of length 11, which
+can be accessed by various "output commands"_Howto_output.html.  The
+scalar is the magnitude of the bias potential (energy units) applied on
+the current timestep.  The vector stores the following quantities:
+
+1 = boost factor on this step (unitless)
+2 = max strain Eij of any bond on this step (unitless)
+3 = ID of first atom in the max-strain bond
+4 = ID of second atom in the max-strain bond
+5 = average # of bonds/atom on this step :ul
+
+6 = fraction of timesteps with bias = 0.0 during this run
+7 = max drift distance of any atom during this run (distance units)
+8 = max bond length during this run (distance units) :ul
+
+9 = cummulative hyper time since fix was defined (time units)
+10 = cummulative count of event timesteps since fix was defined
+11 = cummulative count of atoms in events since fix was defined :ul
+
+The first 5 quantities are for the current timestep.  Quantities 6-8
+are for the current hyper run.  Quantities 9-11 are cummulative across
+multiple runs (since the fix was defined in the input script).
+
+For value 7, drift is the distance an atom moves between timesteps
+when the bond list is reset, i.e. between events.  Atoms involved in
+an event will typically move the greatest distance since others are
+typically oscillating around their lattice site.
+
+For value 10, events are checked for by the "hyper"_hyper.html command
+once every {Nevent} timesteps.  This value is the count of those
+timesteps on which one (or more) events was detected.  It is NOT the
+number of distinct events, since more than one event may occur in the
+same {Nevent} time window.
+
+For value 11, each time the "hyper"_hyper.html command checks for an
+event, it invokes a compute to flag zero or more atoms as
+participating in one or more events.  E.g. atoms that have displaced
+more than some distance from the previous quench state.  Value 11 is
+the cummulative count of the number of atoms participating in any of
+the events that were found.
+
+The scalar and vector values calculated by this fix are all
+"intensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the "Build package"_Build_package.html doc page for more
+info.
+
+[Related commands:]
+
+"hyper"_hyper.html, "fix hyper/local"_fix_hyper_local.html
+
+[Default:] None
+
+:line
+
+:link(Voter2013ghd)
+[(Voter2013)] S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139,
+144110 (2013).
+
+:link(Mironghd)
+[(Miron)] R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003).

doc/src/fix_hyper_local.txt

@@ -0,0 +1,404 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix hyper/local command :h3
+
+[Syntax:]
+
+fix ID group-ID hyper/local cutbond qfactor Vmax Tequil Dcut alpha Btarget :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+hyper/local = style name of this fix command :l
+cutbond = max distance at which a pair of atoms is considered bonded (distance units) :l
+qfactor = max strain at which bias potential goes to 0.0 (unitless) :l
+Vmax = estimated height of bias potential (energy units) :l
+Tequil = equilibration temperature (temperature units) :l
+Dcut = minimum distance between boosted bonds (distance units) :l
+alpha = boostostat relaxation time (time units) :l
+Btarget = desired time boost factor (unitless) :l
+zero or more keyword/value pairs may be appended :l
+keyword = {lost} or {check/bias} or {check/coeff}
+  {lostbond} value = error/warn/ignore
+  {check/bias} values = Nevery error/warn/ignore
+  {check/coeff} values = Nevery error/warn/ignore :pre
+:ule
+
+[Examples:]
+
+fix 1 all hyper/local 1.0 0.3 0.8 300.0 :pre
+
+[Description:]
+
+This fix is meant to be used with the "hyper"_hyper.html command to
+perform a bond-boost local hyperdynamics (LHD) simulation.  The role
+of this fix is to a select multiple pairs of atoms in the system at
+each timestep to add a local bias potential to, which will alter the
+dynamics of the system in a manner that effectively accelerates time.
+This is in contrast to the "fix hyper/global"_fix_hyper_global.html
+command, which can be user to perform a global hyperdynamics (GHD)
+simulation, by adding a global bias potential to a single pair of
+atoms at each timestep.  GHD can time accelerate a small simulation
+with up to a few 100 atoms.  For larger systems, LHD is needed to
+achieve good time acceleration.
+
+For a system that undergoes rare transition events, where one or more
+atoms move over an energy barrier to a new potential energy basin, the
+effect of the bias potential is to induce more rapid transitions.
+This can lead to a dramatic speed-up in the rate at which events
+occurs, without altering their relative frequencies, thus leading to
+an overall increase in the elapsed real time of the simulation as
+compared to running for the same number of timesteps with normal MD.
+See the "hyper"_hyper.html doc page for a more general discussion of
+hyperdynamics and citations that explain both GHD and LHD.
+
+The equations and logic used by this fix and described here to perform
+LHD follow the description given in "(Voter2013)"_#Voter2013lhd.  The
+bond-boost form of a bias potential for HD is due to Miron and
+Fichthorn as described in "(Miron)"_#Mironlhd.
+
+To understand this description, you should first read the description
+of the GHD algorithm on the "fix hyper/global"_fix_hyper_global.html
+doc page.  This description of LHD builds on the GHD description.
+
+The definition of bonds, Eij, and Emax are the same for GHD and LHD.
+The formulas for Vij(max) and Fij(max) are also the same except for a
+pre-factor Cij, explained below.
+
+The bias energy Vij applied to a bond IJ with maximum strain is
+
+Vij(max) = Cij * Vmax * (1 - (Eij/q)^2) for abs(Eij) < qfactor
+         = 0 otherwise :pre
+
+The derivative of Vij(max) with respect to the position of each atom
+in the IJ bond gives a bias force Fij(max) acting on the bond as
+
+Fij(max) = - dVij(max)/dEij = 2 Cij Vmax Eij / qfactor^2   for abs(Eij) < qfactor
+         = 0 otherwise :pre
+
+which can be decomposed into an equal and opposite force acting on
+only the two I,J atoms in the IJ bond.
+
+The key difference is that in GHD a bias energy and force is added (on
+a particular timestep) to only one bond (pair of atoms) in the system,
+which is the bond with maximum strain Emax.
+
+In LHD, a bias energy and force can be added to multiple bonds
+separated by the specified {Dcut} distance or more.  A bond IJ is
+biased if it is the maximum strain bond within its local
+"neighborhood", which is defined as the bond IJ plus any neighbor
+bonds within a distance {Dcut} from IJ.  The "distance" between bond
+IJ and bond KL is the minimum distance between any of the IK, IL, JK,
+JL pairs of atoms.
+
+For a large system, multiple bonds will typically meet this
+requirement, and thus a bias potential Vij(max) will be applied to
+many bonds on the same timestep.
+
+In LHD, all bonds store a Cij prefactor which appears in the Vij(max)
+and Fij(max) equations above.  Note that the Cij factor scales the
+strength of the bias energy and forces whenever bond IJ is the maximum
+strain bond in its neighborhood.
+
+Cij is initialized to 1.0 when a bond between the I,J atoms is first
+defined.  The specified {Btarget} factor is then used to adjust the
+Cij prefactors for each bond every timestep in the following manner.
+
+An instantaneous boost factor Bij is computed each timestep
+for each bond, as
+
+Bij = exp(beta * Vkl(max)) :pre
+
+where Vkl(max) is the bias energy of the maxstrain bond KL within bond
+IJ's neighborhood, beta = 1/kTequil, and {Tequil} is the temperature
+of the system and an argument to this fix.
+
+NOTE: To run LHD, the input script must also use the "fix
+langevin"_fix_langevin.html command to thermostat the atoms at the
+same {Tequil} as specified by this fix, so that the system is running
+constant-temperature (NVT) dynamics.  LAMMPS does not check that this
+is done.
+
+Note that if IJ = KL, then bond IJ is a biased bond on that timestep,
+otherwise it is not.  But regardless, the boost factor Bij can be
+thought of an estimate of time boost currently being applied within a
+local region centered on bond IJ.  For LHD, we want this to be the
+specified {Btarget} value everywhere in the simulation domain.
+
+To accomplish this, if Bij < Btarget, the Cij prefactor for bond IJ is
+incremented on the current timestep by an amount proportional to the
+inverse of the specified {alpha} and the difference (Bij - Btarget).
+Conversely if Bij > Btarget, Cij is decremented by the same amount.
+This procedure is termed "boostostatting" in
+"(Voter2013)"_#Voter2013lhd.  It drives all of the individual Cij to
+values such that when Vij{max} is applied as a bias to bond IJ, the
+resulting boost factor Bij will be close to {Btarget} on average.
+Thus the LHD time acceleration factor for the overall system is
+effectively {Btarget}.
+
+Note that in LHD, the boost factor {Btarget} is specified by the user.
+This is in contrast to global hyperdynamics (GHD) where the boost
+factor varies each timestep and is computed as a function of {Vmax},
+Emax, and {Tequil}; see the "fix hyper/global"_fix_hyper_global.html
+doc page for details.
+
+:line
+
+Here is additional information on the input parameters for LHD.
+
+Note that the {cutbond}, {qfactor}, and {Tequil} arguments have the
+same meaning as for GHD.  The {Vmax} argument is slightly different.
+The {Dcut}, {alpha}, and {Btarget} parameters are unique to LHD.
+
+The {cutbond} argument is the cutoff distance for defining bonds
+between pairs of nearby atoms.  A pair of I,J atoms in their
+equilibrium, minimum-energy configuration, which are separated by a
+distance Rij < {cutbond}, are flagged as a bonded pair.  Setting
+{cubond} to be ~25% larger than the nearest-neighbor distance in a
+crystalline lattice is a typical choice for solids, so that bonds
+exist only between nearest neighbor pairs.
+
+The {qfactor} argument is the limiting strain at which the bias
+potential goes to 0.0.  It is dimensionless, so a value of 0.3 means a
+bond distance can be up to 30% larger or 30% smaller than the
+equilibrium (quenched) R0ij distance and the two atoms in the bond
+could still experience a non-zero bias force.
+
+If {qfactor} is set too large, then transitions from one energy basin
+to another are affected because the bias potential is non-zero at the
+transition state (e.g. saddle point).  If {qfactor} is set too small
+than little boost can be achieved because the Eij strain of some bond in
+the system will (nearly) always exceed {qfactor}.  A value of 0.3 for
+{qfactor} is typically a reasonable value.
+
+The {Vmax} argument is a fixed prefactor on the bias potential.  There
+is a also a dynamic prefactor Cij, driven by the choice of {Btarget}
+as discussed above.  The product of these should be a value less than
+the smallest barrier height for an event to occur.  Otherwise the
+applied bias potential may be large enough (when added to the
+interatomic potential) to produce a local energy basin with a maxima
+in the center.  This can produce artificial energy minima in the same
+basin that trap an atom.  Or if Cij*{Vmax} is even larger, it may
+induce an atom(s) to rapidly transition to another energy basin.  Both
+cases are "bad dynamics" which violate the assumptions of LHD that
+guarantee an accelerated time-accurate trajectory of the system.
+
+NOTE: It may seem that {Vmax} can be set to any value, and Cij will
+compensate to reduce the overall prefactor if necessary.  However the
+Cij are initialized to 1.0 and the boostostatting procedure typically
+operates slowly enough that there can be a time period of bad dynamics
+if {Vmax} is set too large.  A better strategy is to set {Vmax} to the
+smallest barrier height for an event (the same as for GHD), so that
+the Cij remain near unity.
+
+The {Tequil} argument is the temperature at which the system is
+simulated; see the comment above about the "fix
+langevin"_fix_langevin.html thermostatting.  It is also part of the
+beta term in the exponential factor that determines how much boost is
+achieved as a function of the bias potential.  See the discussion of
+the {Btarget} argument below.
+
+As discussed above, the {Dcut} argument is the distance required
+between two locally maxstrain bonds for them to both be selected as
+biased bonds on the same timestep.  Computationally, the larger {Dcut}
+is, the more work (computation and communication) must be done each
+timestep within the LHD algorithm.  And the fewer bonds can be
+simultaneously biased, which may mean the specified {Btarget} time
+acceleration cannot be achieved.
+
+Physically {Dcut} should be a long enough distance that biasing two
+pairs of atoms that close together will not influence the dynamics of
+each pair.  E.g. something like 2x the cutoff of the interatomic
+potential.  In practice a {Dcut} value of ~10 Angstroms seems to work
+well for many solid-state systems.
+
+NOTE: You must also insure that ghost atom communication is performed
+for a distance of at least {Dcut} + {cutevent} where {cutevent} = the
+distance one or more atoms move (between quenched states) to be
+considered an "event".  It is an argument to the "compute
+event/displace" command used to detect events.  By default the ghost
+communication distance is set by the pair_style cutoff, which will
+typically be < {Dcut}.  The "comm_modify cutoff"_comm_modify.html
+command can be used to set the ghost cutoff explicitly, e.g.
+
+comm_modify cutoff 12.0 :pre
+
+This fix does not know the {cutevent} parameter, but uses half the
+bond length as an estimate to warn if the ghost cutoff is not long
+enough.
+
+As described above the {alpha} argument is a pre-factor in the
+boostostat update equation for each bond's Cij prefactor.  {Alpha} is
+specified in time units, similar to other thermostat or barostat
+damping parameters.  It is roughly the physical time it will take the
+boostostat to adjust a Cij value from a too high (or too low) value to
+a correct one.  An {alpha} setting of a few ps is typically good for
+solid-state systems.  Note that the {alpha} argument here is the
+inverse of the alpha parameter discussed in
+"(Voter2013)"_#Voter2013lhd.
+
+The {Btarget} argument is the desired time boost factor (a value > 1)
+that all the atoms in the system will experience.  The elapsed time
+t_hyper for an LHD simulation running for {N} timesteps is simply
+
+t_hyper = Btarget * N*dt :pre
+
+where dt is the timestep size defined by the "timestep"_timestep.html
+command.  The effective time acceleration due to LHD is thus t_hyper /
+N*dt = Btarget, where N*dt is elapsed time for a normal MD run
+of N timesteps.
+
+You cannot choose an arbitrarily large setting for {Btarget}.  The
+maximum value you should choose is
+
+Btarget = exp(beta * Vsmall) :pre
+
+where Vsmall is the smallest event barrier height in your system, beta
+= 1/kTequil, and {Tequil} is the specified temperature of the system
+(both by this fix and the Langevin thermostat).
+
+Note that if {Btarget} is set smaller than this, the LHD simulation
+will run correctly.  There will just be fewer events because the hyper
+time (t_hyper equation above) will be shorter.
+
+NOTE: If you have no physical intuition as to the smallest barrier
+height in your system, a reasonable strategy to determine the largest
+{Btarget} you can use for an LHD model, is to run a sequence of
+simulations with smaller and smaller {Btarget} values, until the event
+rate does not change.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy of the bias potential to the the system's
+potential energy as part of "thermodynamic output"_thermo_style.html.
+
+This fix computes a global scalar and global vector of length 23,
+which can be accessed by various "output
+commands"_Howto_output.html.  The scalar is the magnitude of
+the bias potential (energy units) applied on the current timestep,
+summed over all biased bonds.  The vector stores the following
+quantities:
+
+1 = # of biased bonds on this step
+2 = max strain Eij of any bond on this step (unitless)
+3 = average bias potential for all biased bonds on this step (energy units)
+4 = average # of bonds/atom on this step
+5 = average neighbor bonds/bond on this step within {Dcut} :ul
+
+6 = fraction of steps and bonds with no bias during this run
+7 = max drift distance of any atom during this run (distance units)
+8 = max bond length during this run (distance units)
+9 = average # of biased bonds/step during this run
+10 = average bias potential for all biased bonds during this run (energy units)
+11 = max bias potential for any biased bond during this run (energy units)
+12 = min bias potential for any biased bond during this run (energy units)
+13 = max distance from my sub-box of any ghost atom with maxstrain < qfactor during this run (distance units)
+14 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
+15 = count of ghost neighbor atoms not found on reneighbor steps during this run
+16 = count of lost bond partners during this run
+17 = average bias coeff for lost bond partners during this run
+18 = count of bias overlaps found during this run
+19 = count of non-matching bias coefficients found during this run :ul
+
+20 = cummulative hyper time since fix created (time units)
+21 = cummulative count of event timesteps since fix created
+22 = cummulative count of atoms in events since fix created
+23 = cummulative # of new bonds since fix created :ul
+
+The first quantities (1-5) are for the current timestep.  Quantities
+6-19 are for the current hyper run.  They are reset each time a new
+hyper run is performed.  Quantities 20-23 are cummulative across
+multiple runs (since the fix was defined in the input script).
+
+For value 6, the numerator is a count of all biased bonds on every
+timestep whose bias energy = 0.0 due to Eij >= {qfactor}.  The
+denominator is the count of all biased bonds on all timesteps.
+
+For value 7, drift is the distance an atom moves between timesteps
+when the bond list is reset, i.e. between events.  Atoms involved in
+an event will typically move the greatest distance since others are
+typically oscillating around their lattice site.
+
+For values 13 and 14, the maxstrain of a ghost atom is the maxstrain
+of any bond it is part of, and it is checked for ghost atoms within
+the bond neighbor cutoff.
+
+Values 15-19 are mostly useful for debugging and diagnositc purposes.
+
+For values 15-17, it is possible that a ghost atom owned by another
+processor will move far enough (e.g. as part of an event-in-progress)
+that it will no longer be within the communication cutoff distance for
+acquiring ghost atoms.  Likewise it may be a ghost atom bond partner
+that cannot be found because it has moved too far.  These values count
+those occurrences.  Because they typically involve atoms that are part
+of events, they do not usually indicate bad dynamics.  Value 16 is the
+average bias coefficient for bonds where a partner atom was lost.
+
+For value 18, no two bonds should be biased if they are within a
+{Dcut} distance of each other.  This value should be zero, indicating
+that no pair of bonds "overlap", meaning they are closer than {Dcut}
+from each other.
+
+For value 19, the same bias coefficient is stored by both atoms in an
+IJ bond.  This value should be zero, indicating that for all bonds,
+each atom in the bond stores the a bias coefficient with the same
+value.
+
+Value 20 is simply the specified {boost} factor times the number of
+timestep times the timestep size.
+
+For value 21, events are checked for by the "hyper"_hyper.html command
+once every {Nevent} timesteps.  This value is the count of those
+timesteps on which one (or more) events was detected.  It is NOT the
+number of distinct events, since more than one event may occur in the
+same {Nevent} time window.
+
+For value 22, each time the "hyper"_hyper.html command checks for an
+event, it invokes a compute to flag zero or more atoms as
+participating in one or more events.  E.g. atoms that have displaced
+more than some distance from the previous quench state.  Value 22 is
+the cummulative count of the number of atoms participating in any of
+the events that were found.
+
+Value 23 tallies the number of new bonds created by the bond reset
+operation.  Bonds between a specific I,J pair of atoms may persist for
+the entire hyperdynamics simulation if neither I or J are involved in
+an event.
+
+The scalar and vector values calculated by this fix are all
+"intensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the REPLICA 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:]
+
+"hyper"_hyper.html, "fix hyper/global"_fix_hyper_global.html
+
+[Default:] None
+
+:line
+
+:link(Voter2013lhd)
+[(Voter2013)] S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139,
+144110 (2013).
+
+:link(Mironlhd)
+[(Miron)] R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003).

doc/src/fix_meso_move.txt

@@ -0,0 +1,233 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix meso/move command :h3
+
+[Syntax:]
+
+fix ID group-ID meso/move style args keyword values ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+meso/move = style name of this fix command :l
+style = {linear} or {wiggle} or {rotate} or {variable} :l
+  {linear} args = Vx Vy Vz
+    Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+  {wiggle} args = Ax Ay Az period
+    Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
+    period = period of oscillation (time units)
+  {rotate} args = Px Py Pz Rx Ry Rz period
+    Px,Py,Pz = origin point of axis of rotation (distance units)
+    Rx,Ry,Rz = axis of rotation vector
+    period = period of rotation (time units)
+  {variable} args = v_dx v_dy v_dz v_vx v_vy v_vz
+    v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
+    v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL :pre
+
+zero or more keyword/value pairs may be appended :l
+keyword = {units} :l
+  {units} value = {box} or {lattice} :pre
+:ule
+
+[Examples:]
+
+fix 1 boundary meso/move wiggle 3.0 0.0 0.0 1.0 units box
+fix 2 boundary meso/move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
+fix 2 boundary meso/move variable v_myx v_myy NULL v_VX v_VY NULL :pre
+
+[Description:]
+
+Perform updates of position, velocity, internal energy and local
+density for mesoscopic particles in the group each timestep using the
+specified settings or formulas, without regard to forces on the
+particles. This can be useful for boundary, solid bodies or other
+particles, whose movement can influence nearby particles.
+
+The operation of this fix is exactly like that described by the
+"fix move"_fix_move.html command, except that particles' density,
+internal energy and extrapolated velocity are also updated.
+
+NOTE: The particles affected by this fix should not be time integrated
+by other fixes (e.g. "fix meso"_fix_meso.html, "fix
+meso/stationary"_fix_meso_stationary.html), since that will change their
+positions and velocities twice.
+
+NOTE: As particles move due to this fix, they will pass thru periodic
+boundaries and be remapped to the other side of the simulation box,
+just as they would during normal time integration (e.g. via the "fix
+meso"_fix_meso.html command).  It is up to you to decide whether periodic
+boundaries are appropriate with the kind of particle motion you are
+prescribing with this fix.
+
+NOTE: As dicsussed below, particles are moved relative to their initial
+position at the time the fix is specified.  These initial coordinates
+are stored by the fix in "unwrapped" form, by using the image flags
+associated with each particle.  See the "dump custom"_dump.html command
+for a discussion of "unwrapped" coordinates.  See the Atoms section of
+the "read_data"_read_data.html command for a discussion of image flags
+and how they are set for each particle.  You can reset the image flags
+(e.g. to 0) before invoking this fix by using the "set image"_set.html
+command.
+
+:line
+
+The {linear} style moves particles at a constant velocity, so that their
+position {X} = (x,y,z) as a function of time is given in vector
+notation as
+
+X(t) = X0 + V * delta :pre
+
+where {X0} = (x0,y0,z0) is their position at the time the fix is
+specified, {V} is the specified velocity vector with components
+(Vx,Vy,Vz), and {delta} is the time elapsed since the fix was
+specified.  This style also sets the velocity of each particle to V =
+(Vx,Vy,Vz).  If any of the velocity components is specified as NULL,
+then the position and velocity of that component is time integrated
+the same as the "fix meso"_fix_meso.html command would perform, using
+the corresponding force component on the particle.
+
+Note that the {linear} style is identical to using the {variable}
+style with an "equal-style variable"_variable.html that uses the
+vdisplace() function.  E.g.
+
+variable V equal 10.0
+variable x equal vdisplace(0.0,$V)
+fix 1 boundary move variable v_x NULL NULL v_V NULL NULL :pre
+
+The {wiggle} style moves particles in an oscillatory fashion, so that
+their position {X} = (x,y,z) as a function of time is given in vector
+notation as
+
+X(t) = X0 + A sin(omega*delta) :pre
+
+where {X0} = (x0,y0,z0) is their position at the time the fix is
+specified, {A} is the specified amplitude vector with components
+(Ax,Ay,Az), {omega} is 2 PI / {period}, and {delta} is the time
+elapsed since the fix was specified.  This style also sets the
+velocity of each particle to the time derivative of this expression.
+If any of the amplitude components is specified as NULL, then the
+position and velocity of that component is time integrated the same as
+the "fix meso"_fix_meso.html command would perform, using the
+corresponding force component on the particle.
+
+Note that the {wiggle} style is identical to using the {variable}
+style with "equal-style variables"_variable.html that use the
+swiggle() and cwiggle() functions.  E.g.
+
+variable A equal 10.0
+variable T equal 5.0
+variable omega equal 2.0*PI/$T
+variable x equal swiggle(0.0,$A,$T)
+variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
+fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
+
+The {rotate} style rotates particles around a rotation axis {R} =
+(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The {period} of
+the rotation is also specified.  The direction of rotation for the
+particles around the rotation axis is consistent with the right-hand
+rule: if your right-hand thumb points along {R}, then your fingers wrap
+around the axis in the direction of rotation.
+
+This style also sets the velocity of each particle to (omega cross
+Rperp) where omega is its angular velocity around the rotation axis and
+Rperp is a perpendicular vector from the rotation axis to the particle.
+
+The {variable} style allows the position and velocity components of
+each particle to be set by formulas specified via the
+"variable"_variable.html command.  Each of the 6 variables is
+specified as an argument to the fix as v_name, where name is the
+variable name that is defined elsewhere in the input script.
+
+Each variable must be of either the {equal} or {atom} style.
+{Equal}-style variables compute a single numeric quantity, that can be
+a function of the timestep as well as of other simulation values.
+{Atom}-style variables compute a numeric quantity for each particle, that
+can be a function per-atom quantities, such as the particle's position, as
+well as of the timestep and other simulation values.  Note that this
+fix stores the original coordinates of each particle (see note below) so
+that per-atom quantity can be used in an atom-style variable formula.
+See the "variable"_variable.html command for details.
+
+The first 3 variables (v_dx,v_dy,v_dz) specified for the {variable}
+style are used to calculate a displacement from the particle's original
+position at the time the fix was specified.  The second 3 variables
+(v_vx,v_vy,v_vz) specified are used to compute a velocity for each
+particle.
+
+Any of the 6 variables can be specified as NULL.  If both the
+displacement and velocity variables for a particular x,y,z component
+are specified as NULL, then the position and velocity of that
+component is time integrated the same as the "fix meso"_fix_meso.html
+command would perform, using the corresponding force component on the
+particle.  If only the velocity variable for a component is specified as
+NULL, then the displacement variable will be used to set the position
+of the particle, and its velocity component will not be changed. If only
+the displacement variable for a component is specified as NULL, then
+the velocity variable will be used to set the velocity of the particle,
+and the position of the particle will be time integrated using that
+velocity.
+
+The {units} keyword determines the meaning of the distance units used
+to define the {linear} velocity and {wiggle} amplitude and {rotate}
+origin.  This setting is ignored for the {variable} style.  A {box}
+value selects standard units as defined by the "units"_units.html
+command, e.g. velocity in Angstroms/fmsec and amplitude and position
+in Angstroms for units = real.  A {lattice} value means the velocity
+units are in lattice spacings per time and the amplitude and position
+are in lattice spacings.  The "lattice"_lattice.html command must have
+been previously used to define the lattice spacing.  Each of these 3
+quantities may be dependent on the x,y,z dimension, since the lattice
+spacings can be different in x,y,z.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+This fix writes the original coordinates of moving particles to "binary
+restart files"_restart.html, as well as the initial timestep, so that
+the motion can be continuous in a restarted simulation.  See the
+"read_restart"_read_restart.html command for info on how to re-specify
+a fix in an input script that reads a restart file, so that the
+operation of the fix continues in an uninterrupted fashion.
+
+NOTE: Because the move positions are a function of the current
+timestep and the initial timestep, you cannot reset the timestep to a
+different value after reading a restart file, if you expect a fix move
+command to work in an uninterrupted fashion.
+
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix.
+
+This fix produces a per-atom array which can be accessed by various
+"output commands"_Howto_output.html.  The number of columns for each
+atom is 3, and the columns store the original unwrapped x,y,z coords
+of each particle.  The per-atom values can be accessed on any timestep.
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-SDPD package.  It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+This fix requires that atoms store density and internal energy as
+defined by the "atom_style meso"_atom_style.html command.
+
+All particles in the group must be mesoscopic SPH/SDPD particles.
+
+[Related commands:]
+
+"fix move"_fix_move.html, "fix meso"_fix_meso.html,
+"displace_atoms"_displace_atoms.html
+
+[Default:]
+
+The option default is units = lattice.

doc/src/fix_nve_dot.txt

@@ -36,8 +36,8 @@ The command is equivalent to the "fix nve"_fix_nve.html.
 The particles are always considered to have a finite size.
 
 An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
-A technical report with more information on this integrator can be found
-"here"_PDF/USER-CGDNA-overview.pdf.
+Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3. 
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
 
 :line
 
@@ -59,3 +59,5 @@ See the "Build package"_Build_package.html doc page for more info.
 [(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
 :link(Miller1)
 [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
+:link(Henrich3)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).

doc/src/fix_nve_dotc_langevin.txt

@@ -114,8 +114,8 @@ The scale factor after the {angmom} keyword gives the ratio of the rotational to
 the translational friction coefficient.
 
 An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
-A technical report with more information on this integrator can be found
-"here"_PDF/USER-CGDNA-overview.pdf.
+Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4.              
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
 
 :line
 
@@ -139,3 +139,5 @@ See the "Build package"_Build_package.html doc page for more info.
 [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
 :link(Dunweg3)
 [(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
+:link(Henrich4)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).

doc/src/fix_plumed.txt

@@ -0,0 +1,117 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix plumed command :h3
+
+[Syntax:]
+
+fix ID group-ID plumed keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+plumed = style name of this fix command :l
+keyword = {plumedfile} or {outfile} :l
+  {plumedfile} arg = name of PLUMED input file to use (default: NULL)
+  {outfile} arg = name of file on which to write the PLUMED log (default: NULL) :pre
+:ule
+
+[Examples:]
+
+fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
+
+[Description:]
+
+This fix instructs LAMMPS to call the "PLUMED"_plumedhome library, which
+allows one to perform various forms of trajectory analysis on the fly
+and to also use methods such as umbrella sampling and metadynamics to
+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
+"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
+A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
+
+There is an example input for using this package with LAMMPS in the
+examples/USER/plumed directory.
+
+:line
+
+The command to make LAMMPS call PLUMED during a run requires two keyword
+value pairs pointing to the PLUMED input file and an output file for the
+PLUMED log. The user must specify these arguments every time PLUMED is
+to be used.  Furthermore, the fix plumed command should appear in the
+LAMMPS input file [after] relevant input paramters (e.g. the timestep)
+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.
+
+The {plumedfile} keyword allows the user to specify the name of the
+PLUMED input file.  Instructions as to what should be included in a
+plumed input file can be found in the "documentation for
+PLUMED"_plumeddocs
+
+The {outfile} keyword allows the user to specify the name of a file on
+which to output the PLUMED log.  This log file normally just parrots the
+information that is contained in the input file.  The names of the files
+on which the results from the various analyses that have been performed
+using PLUMED will be specified by the user in the PLUMED input file.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+When performing a restart of a calculation that involves PLUMED you must
+include a RESTART command in the PLUMED input file as detailed in the
+"PLUMED documentation"_plumeddocs.  When the restart command is found in
+the PLUMED input PLUMED will append to the files that were generated in
+the run that was performed previously.  No part of the PLUMED restart
+data is included in the LAMMPS restart files.  Furthermore, any history
+dependent bias potentials that were accumulated in previous calculations
+will be read in when the RESTART command is included in the PLUMED
+input.
+
+The "fix_modify"_fix_modify.html {energy} option is not supported by
+this fix.
+
+Nothing is computed by this fix that can be accessed by any of the
+"output commands"_Howto_output.html within LAMMPS.  All the quantities
+of interest can be output by commands that are native to PLUMED,
+however.
+
+[Restrictions:]
+
+This fix is part of the USER-PLUMED package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+There can only be one plumed fix active at a time.
+
+[Related commands:]
+
+"fix smd"_fix_smd.html
+"fix colvars"_fix_colvars.html
+
+[Default:]
+
+The default options are plumedfile = NULL and outfile = NULL
+
+:line
+
+:link(PLUMED)
+[(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
+
+:link(plumeddocs,http://www.plumed.org/documentation)
+:link(plumedhome,http://www.plumed.org/)

doc/src/fix_rigid_meso.txt

@@ -0,0 +1,349 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix rigid/meso command :h3
+
+[Syntax:]
+
+fix ID group-ID rigid/meso bodystyle args keyword values ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+rigid/meso = style name of this fix command :l
+bodystyle = {single} or {molecule} or {group} :l
+  {single} args = none
+  {molecule} args = none
+  {custom} args = {i_propname} or {v_varname}
+    i_propname = an integer property defined via fix property/atom
+    v_varname  = an atom-style or atomfile-style variable
+  {group} args = N groupID1 groupID2 ...
+    N = # of groups
+    groupID1, groupID2, ... = list of N group IDs :pre
+
+zero or more keyword/value pairs may be appended :l
+keyword = {reinit} or {force} or {torque} or {infile} :l
+  {reinit} = {yes} or {no}
+  {force} values = M xflag yflag zflag
+    M = which rigid body from 1-Nbody (see asterisk form below)
+    xflag,yflag,zflag = off/on if component of center-of-mass force is active
+  {torque} values = M xflag yflag zflag
+    M = which rigid body from 1-Nbody (see asterisk form below)
+    xflag,yflag,zflag = off/on if component of center-of-mass torque is active
+  {infile} filename
+    filename = file with per-body values of mass, center-of-mass, moments of inertia :pre
+:ule
+
+[Examples:]
+
+fix 1 ellipsoid rigid/meso single
+fix 1 rods      rigid/meso molecule
+fix 1 spheres   rigid/meso single force 1 off off on
+fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on
+fix 2 spheres   rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off  :pre
+	
+[Description:]
+
+Treat one or more sets of mesoscopic SPH/SDPD particles as independent
+rigid bodies.  This means that each timestep the total force and torque
+on each rigid body is computed as the sum of the forces and torques on
+its constituent particles.  The coordinates and velocities of the
+particles in each body are then updated so that the body moves and
+rotates as a single entity using the methods described in the paper by
+"(Miller)"_#Miller. Density and internal energy of the particles will
+also be updated. This is implemented by creating internal data structures
+for each rigid body and performing time integration on these data
+structures.  Positions and velocities of the constituent particles are
+regenerated from the rigid body data structures in every time step. This
+restricts which operations and fixes can be applied to rigid bodies. See
+below for a detailed discussion.
+
+The operation of this fix is exactly like that described by the
+"fix rigid/nve"_fix_rigid.html command, except that particles' density,
+internal energy and extrapolated velocity are also updated.
+
+NOTE: You should not update the particles in rigid bodies via other
+time-integration fixes (e.g. "fix meso"_fix_meso.html,
+"fix meso/stationary"_fix_meso_stationary.html), or you will have conflicting
+updates to positions and velocities resulting in unphysical behavior in most
+cases. When performing a hybrid simulation with some atoms in rigid bodies,
+and some not, a separate time integration fix like "fix meso"_fix_meso.html
+should be used for the non-rigid particles.
+
+NOTE: These fixes are overkill if you simply want to hold a collection
+of particles stationary or have them move with a constant velocity. To
+hold particles stationary use "fix
+meso/stationary"_fix_meso_stationary.html instead. If you would like to
+move particles with a constant velocity use "fix
+meso/move"_fix_meso_move.html.
+
+IMPORTANT NOTE: The aggregate properties of each rigid body are
+calculated at the start of a simulation run and are maintained in
+internal data structures. The properties include the position and
+velocity of the center-of-mass of the body, its moments of inertia, and
+its angular momentum.  This is done using the properties of the
+constituent particles of the body at that point in time (or see the {infile}
+keyword option).  Thereafter, changing these properties of individual
+particles in the body will have no effect on a rigid body's dynamics, unless
+they effect any computation of per-particle forces or torques. If the
+keyword {reinit} is set to {yes} (the default), the rigid body data
+structures will be recreated at the beginning of each {run} command;
+if the keyword {reinit} is set to {no}, the rigid body data structures
+will be built only at the very first {run} command and maintained for
+as long as the rigid fix is defined. For example, you might think you
+could displace the particles in a body or add a large velocity to each particle
+in a body to make it move in a desired direction before a 2nd run is
+performed, using the "set"_set.html or
+"displace_atoms"_displace_atoms.html or "velocity"_velocity.html
+commands.  But these commands will not affect the internal attributes
+of the body unless {reinit} is set to {yes}. With {reinit} set to {no}
+(or using the {infile} option, which implies {reinit} {no}) the position
+and velocity of individual particles in the body will be reset when time
+integration starts again.
+
+:line
+
+Each rigid body must have two or more particles.  A particle can belong
+to at most one rigid body.  Which particles are in which bodies can be
+defined via several options.
+
+For bodystyle {single} the entire fix group of particles is treated as
+one rigid body.
+
+For bodystyle {molecule}, particles are grouped into rigid bodies by their
+respective molecule IDs: each set of particles in the fix group with the
+same molecule ID is treated as a different rigid body.  Note that particles
+with a molecule ID = 0 will be treated as a single rigid body. For a
+system with solvent (typically this is particles with molecule ID = 0)
+surrounding rigid bodies, this may not be what you want.  Thus you
+should be careful to use a fix group that only includes particles you
+want to be part of rigid bodies.
+
+Bodystyle {custom} is similar to bodystyle {molecule} except that it
+is more flexible in using other per-atom properties to define the sets
+of particles that form rigid bodies.  An integer vector defined by the
+"fix property/atom"_fix_property_atom.html command can be used.  Or an
+"atom-style or atomfile-style variable"_variable.html can be used; the
+floating-point value produced by the variable is rounded to an
+integer.  As with bondstyle {molecule}, each set of particles in the fix
+groups with the same integer value is treated as a different rigid
+body.  Since fix property/atom vectors and atom-style variables
+produce values for all particles, you should be careful to use a fix group
+that only includes particles you want to be part of rigid bodies.
+
+For bodystyle {group}, each of the listed groups is treated as a
+separate rigid body.  Only particles that are also in the fix group are
+included in each rigid body.
+
+NOTE: To compute the initial center-of-mass position and other
+properties of each rigid body, the image flags for each particle in the
+body are used to "unwrap" the particle coordinates.  Thus you must
+insure that these image flags are consistent so that the unwrapping
+creates a valid rigid body (one where the particles are close together)
+, particularly if the particles in a single rigid body straddle a
+periodic boundary.  This means the input data file or restart file must
+define the image flags for each particle consistently or that you have
+used the "set"_set.html command to specify them correctly.  If a
+dimension is non-periodic then the image flag of each particle must be
+0 in that dimension, else an error is generated.
+
+By default, each rigid body is acted on by other particles which induce
+an external force and torque on its center of mass, causing it to
+translate and rotate.  Components of the external center-of-mass force
+and torque can be turned off by the {force} and {torque} keywords.
+This may be useful if you wish a body to rotate but not translate, or
+vice versa, or if you wish it to rotate or translate continuously
+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.
+
+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
+the component, which is the default.  Which rigid body(s) the settings
+apply to is determined by the first argument of the {force} and
+{torque} keywords.  It can be an integer M from 1 to Nbody, where
+Nbody is the number of rigid bodies defined.  A wild-card asterisk can
+be used in place of, or in conjunction with, the M argument to set the
+flags for multiple rigid bodies.  This takes the form "*" or "*n" or
+"n*" or "m*n".  If N = the number of rigid bodies, then an asterisk
+with no numeric values means all bodies from 1 to N.  A leading
+asterisk means all bodies from 1 to n (inclusive).  A trailing
+asterisk means all bodies from n to N (inclusive).  A middle asterisk
+means all bodies from m to n (inclusive).  Note that you can use the
+{force} or {torque} keywords as many times as you like.  If a
+particular rigid body has its component flags set multiple times, the
+settings from the final keyword are used.
+
+For computational efficiency, you should typically define one fix
+rigid/meso command which includes all the desired rigid bodies. LAMMPS
+will allow multiple rigid/meso fixes to be defined, but it is more
+expensive.
+
+:line
+
+The keyword/value option pairs are used in the following ways.
+
+The {reinit} keyword determines, whether the rigid body properties
+are re-initialized between run commands. With the option {yes} (the
+default) this is done, with the option {no} this is not done. Turning
+off the re-initialization can be helpful to protect rigid bodies against
+unphysical manipulations between runs or when properties cannot be
+easily re-computed (e.g. when read from a file). When using the {infile}
+keyword, the {reinit} option is automatically set to {no}.
+
+:line
+
+The {infile} keyword allows a file of rigid body attributes to be read
+in from a file, rather then having LAMMPS compute them.  There are 5
+such attributes: the total mass of the rigid body, its center-of-mass
+position, its 6 moments of inertia, its center-of-mass velocity, and
+the 3 image flags of the center-of-mass position.  For rigid bodies
+consisting of point particles or non-overlapping finite-size
+particles, LAMMPS can compute these values accurately.  However, for
+rigid bodies consisting of finite-size particles which overlap each
+other, LAMMPS will ignore the overlaps when computing these 4
+attributes.  The amount of error this induces depends on the amount of
+overlap.  To avoid this issue, the values can be pre-computed
+(e.g. using Monte Carlo integration).
+
+The format of the file is as follows.  Note that the file does not
+have to list attributes for every rigid body integrated by fix rigid.
+Only bodies which the file specifies will have their computed
+attributes overridden.  The file can contain initial blank lines or
+comment lines starting with "#" which are ignored.  The first
+non-blank, non-comment line should list N = the number of lines to
+follow.  The N successive lines contain the following information:
+
+ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
+...
+IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm :pre
+
+The rigid body IDs are all positive integers.  For the {single}
+bodystyle, only an ID of 1 can be used.  For the {group} bodystyle,
+IDs from 1 to Ng can be used where Ng is the number of specified
+groups.  For the {molecule} bodystyle, use the molecule ID for the
+atoms in a specific rigid body as the rigid body ID.
+
+The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are
+self-explanatory.  The center-of-mass should be consistent with what
+is calculated for the position of the rigid body with all its atoms
+unwrapped by their respective image flags.  If this produces a
+center-of-mass that is outside the simulation box, LAMMPS wraps it
+back into the box.
+
+The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
+values consistent with the current orientation of the rigid body
+around its center of mass.  The values are with respect to the
+simulation box XYZ axes, not with respect to the principal axes of the
+rigid body itself.  LAMMPS performs the latter calculation internally.
+
+The (vxcm,vycm,vzcm) values are the velocity of the center of mass.
+The (lx,ly,lz) values are the angular momentum of the body.  The
+(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you
+wish the body to have no initial motion.
+
+The (ixcm,iycm,izcm) values are the image flags of the center of mass
+of the body.  For periodic dimensions, they specify which image of the
+simulation box the body is considered to be in.  An image of 0 means
+it is inside the box as defined.  A value of 2 means add 2 box lengths
+to get the true value.  A value of -1 means subtract 1 box length to
+get the true value.  LAMMPS updates these flags as the rigid bodies
+cross periodic boundaries during the simulation.
+
+NOTE: If you use the {infile} keyword and write restart
+files during a simulation, then each time a restart file is written,
+the fix also write an auxiliary restart file with the name
+rfile.rigid, where "rfile" is the name of the restart file,
+e.g. tmp.restart.10000 and tmp.restart.10000.rigid.  This auxiliary
+file is in the same format described above.  Thus it can be used in a
+new input script that restarts the run and re-specifies a rigid fix
+using an {infile} keyword and the appropriate filename.  Note that the
+auxiliary file will contain one line for every rigid body, even if the
+original file only listed a subset of the rigid bodies.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information is written to "binary restart files"_restart.html.
+If the {infile} keyword is used, an auxiliary file is written out
+with rigid body information each time a restart file is written, as
+explained above for the {infile} keyword.
+
+None of the "fix_modify"_fix_modify.html options are relevant to this
+fix.
+
+This fix computes a global array of values which can be accessed by
+various "output commands"_Howto_output.html.
+
+The number of rows in the array is equal to the number of rigid
+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
+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
+flags of the COM.
+
+The center of mass (COM) for each body is similar to unwrapped
+coordinates written to a dump file.  It will always be inside (or
+slightly outside) the simulation box.  The image flags have the same
+meaning as image flags for particle positions (see the "dump" command).
+This means you can calculate the unwrapped COM by applying the image
+flags to the COM, the same as when unwrapped coordinates are written
+to a dump file.
+
+The force and torque values in the array are not affected by the
+{force} and {torque} keywords in the fix rigid command; they reflect
+values before any changes are made by those keywords.
+
+The ordering of the rigid bodies (by row in the array) is as follows.
+For the {single} keyword there is just one rigid body.  For the
+{molecule} keyword, the bodies are ordered by ascending molecule ID.
+For the {group} keyword, the list of group IDs determines the ordering
+of bodies.
+
+The array values calculated by this fix are "intensive", meaning they
+are independent of the number of particles in the simulation.
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+This fix is not invoked during "energy minimization"_minimize.html.
+
+:line
+
+[Restrictions:]
+
+This fix is part of the USER-SDPD package and also depends on the RIGID
+package.  It is only enabled if LAMMPS was built with both packages. See
+the "Build package"_Build_package.html doc page for more info.
+
+This fix requires that atoms store density and internal energy as
+defined by the "atom_style meso"_atom_style.html command.
+
+All particles in the group must be mesoscopic SPH/SDPD particles.
+
+[Related commands:]
+
+"fix meso/move"_fix_meso_move.html, "fix rigid"_fix_rigid.html,
+"neigh_modify exclude"_neigh_modify.html
+
+[Default:]
+
+The option defaults are force * on on on and torque * on on on,
+meaning all rigid bodies are acted on by center-of-mass force and
+torque. Also reinit = yes.
+
+:line
+
+:link(Miller)
+[(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, 
+J Chem Phys, 116, 8649 (2002).

doc/src/fix_smd.txt

@@ -137,7 +137,8 @@ package"_Build_package.html doc page for more info.
 
 "fix drag"_fix_drag.html, "fix spring"_fix_spring.html,
 "fix spring/self"_fix_spring_self.html,
-"fix spring/rg"_fix_spring_rg.html
+"fix spring/rg"_fix_spring_rg.html,
+"fix colvars"_fix_colvars.html, "fix plumed"_fix_plumed.html
 
 [Default:] none
 

doc/src/fixes.txt

@@ -57,6 +57,8 @@ Fixes :h1
    fix_grem
    fix_halt
    fix_heat
+   fix_hyper_global
+   fix_hyper_local
    fix_imd
    fix_indent
    fix_ipi
@@ -73,6 +75,7 @@ Fixes :h1
    fix_lineforce
    fix_manifoldforce
    fix_meso
+   fix_meso_move
    fix_meso_stationary
    fix_momentum
    fix_move
@@ -117,6 +120,7 @@ Fixes :h1
    fix_phonon
    fix_pimd
    fix_planeforce
+   fix_plumed
    fix_poems
    fix_pour
    fix_precession_spin
@@ -137,6 +141,7 @@ Fixes :h1
    fix_restrain
    fix_rhok
    fix_rigid
+   fix_rigid_meso
    fix_rx
    fix_saed_vtk
    fix_setforce

doc/src/group.txt

@@ -225,8 +225,7 @@ atomfile-style variable.  The variable is evaluated and atoms whose
 per-atom values are 0.0, are removed from the dynamic group. If the {property}
 keyword is used, the per-atom property name must be a previously defined
 per-atom property.  The per-atom property is evaluated and atoms whose
-values are 0.0 are removed from the dynamic group, otherwise they
-are added to the group.
+values are 0.0 are removed from the dynamic group.
 
 The assignment of atoms to a dynamic group is done at the beginning of
 each run and on every timestep that is a multiple of {N}, which is the

doc/src/hyper.txt

@@ -0,0 +1,192 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+hyper command :h3
+
+[Syntax:]
+
+hyper N Nevent fix-ID compute-ID keyword values ... :pre
+
+N = # of timesteps to run :ulb,l
+Nevent = check for events every this many steps :l
+fix-ID = ID of a fix that applies a global or local bias potential, can be NULL :l
+compute-ID = ID of a compute that identifies when an event has occurred :l
+zero or more keyword/value pairs may be appended :l
+keyword = {min} or {dump} or {rebond} :l
+  {min} values = etol ftol maxiter maxeval
+    etol = stopping tolerance for energy, used in quenching
+    ftol = stopping tolerance for force, used in quenching
+    maxiter = max iterations of minimize, used in quenching
+    maxeval = max number of force/energy evaluations, used in quenching
+  {dump} value = dump-ID
+    dump-ID = ID of dump to trigger whenever an event takes place
+  {rebond} value = Nrebond
+    Nrebond = frequency at which to reset bonds, even if no event has occurred
+ :pre
+:ule
+
+[Examples:]
+
+compute event all event/displace 1.0
+fix HG mobile hyper/global 3.0 0.3 0.4 800.0
+hyper 5000 100 HG event min 1.0e-6 1.0e-6 100 100 dump 1 dump 5 :pre
+
+[Description:]
+
+Run a bond-boost hyperdynamics (HD) simulation where time is
+accelerated by application of a bias potential to one or more pairs of
+nearby atoms in the system.  This command can be used to run both
+global and local hyperdyamics.  In global HD a single bond within the
+system is biased on each timestep.  In local HD multiple bonds
+(separated by a sufficient distance) can be biased simultaneously at
+each timestep.  In the bond-boost hyperdynamics context, a "bond" is
+not a covalent bond between a pair of atoms in a molecule.  Rather it
+is simply a pair of nearby atoms as discussed below.
+
+Both global and local HD are described in "(Voter2013)"_#Voter2013 by
+Art Voter and collaborators.  Similar to parallel replica dynamics
+(PRD), global and local HD are methods for performing accelerated
+dynamics that are suitable for infrequent-event systems that obey
+first-order kinetics.  A good overview of accelerated dynamics methods
+for such systems in given in "(Voter2002)"_#Voter2002hd from the same
+group.  To quote from the review paper: "The dynamical evolution is
+characterized by vibrational excursions within a potential basin,
+punctuated by occasional transitions between basins."  The transition
+probability is characterized by p(t) = k*exp(-kt) where k is the rate
+constant.  Running multiple replicas gives an effective enhancement in
+the timescale spanned by the multiple simulations, while waiting for
+an event to occur.
+
+Both HD and PRD produce a time-accurate trajectory that effectively
+extends the timescale over which a system can be simulated, but they
+do it differently.  HD uses a single replica of the system and
+accelerates time by biasing the interaction potential in a manner such
+that each timestep is effectively longer.  PRD creates Nr replicas of
+the system and runs dynamics on each independently with a normal
+unbiased potential until an event occurs in one of the replicas.  The
+time between events is reduced by a factor of Nr replicas.  For both
+methods, per CPU second, more physical time elapses and more events
+occur.  See the "prd"_prd.html doc page for more info about PRD.
+
+An HD run has several stages, which are repeated each time an event
+occurs, as explained below.  The logic for an HD run is as follows:
+
+quench
+create initial list of bonds :pre
+
+while (time remains):
+  run dynamics for Nevent steps
+  quench
+  check for an event
+  if event occurred: reset list of bonds
+  restore pre-quench state :pre
+
+The list of bonds is the list of atom pairs of atoms that are within a
+short cutoff distance of each other after the system energy is
+minimized (quenched).  This list is created and reset by a "fix
+hyper/global"_fix_hyper_global.html or "fix
+hyper/local"_fix_hyper_local.html command specified as {fix-ID}.  At
+every dynamics timestep, the same fix selects one of more bonds to
+apply a bias potential to.
+
+IMPORTANT NOTE: The style of fix associated with the specified
+{fix-ID} determines whether you are running the global versus local
+hyperdynamics algorithm.
+
+Dynamics (with the bias potential) is run continuously, stopping every
+{Nevent} steps to check if a transition event has occurred.  The
+specified {N} for total steps must be a multiple of {Nevent}.  check
+is performed by quenching the system and comparing the resulting atom
+coordinates to the coordinates from the previous basin.
+
+A quench is an energy minimization and is performed by whichever
+algorithm has been defined by the "min_style"_min_style.html command.
+Minimization parameters may be set via the
+"min_modify"_min_modify.html command and by the {min} keyword of the
+hyper command.  The latter are the settings that would be used with
+the "minimize"_minimize.html command.  Note that typically, you do not
+need to perform a highly-converged minimization to detect a transition
+event, though you may need to in order to prevent a set of atoms in
+the system from relaxing to a saddle point.
+
+The event check is performed by a compute with the specified
+{compute-ID}.  Currently there is only one compute that works with the
+hyper command, which is the "compute
+event/displace"_compute_event_displace.html command.  Other
+event-checking computes may be added.  "Compute
+event/displace"_compute_event_displace.html checks whether any atom in
+the compute group has moved further than a specified threshold
+distance.  If so, an event has occurred.
+
+If this happens, the list of bonds is reset, since some bond pairs
+are likely now too far apart, and new pairs are likely close enough
+to be considered a bond.  The pre-quenched state of the
+system (coordinates and velocities) is restored, and dynamics continue.
+
+At the end of the hyper run, a variety of statistics are output to the
+screen and logfile.  These include info relevant to both global and
+local hyperdynamics, such as the number of events and the elapsed
+hyper time (acclerated time), And it includes info specific to one or
+the other, depending on which style of fix was specified by {fix-ID}.
+
+:line
+
+The optional keywords operate as follows.
+
+As explained above, the {min} keyword can be used to specify
+parameters for the quench.  Their meaning is the same
+as for the "minimize"_minimize.html command
+
+The {dump} keyword can be used to trigger a specific dump command with
+the specified {dump-ID} to output a snapshot each time an event is
+detected.  It can be specified multiple times with different {dump-ID}
+values, as in the example above.  These snapshots will be for the
+quenched state of the system on a timestep that is a multiple of
+{Nevent}, i.e. a timestep after the event has occurred.  Note that any
+dump command in the input script will also output snapshots at
+whatever timestep interval it defines via its {N} argument; see the
+"dump"_dump.html command for details.  This means if you only want a
+particular dump to output snapshots when events are detected, you
+should specify its {N} as a value larger than the length of the
+hyperdynamics run.
+
+As in the code logic above, the bond list is normally only reset when
+an event occurs.  The {rebond} keyword will force a reset of the bond
+list every {Nrebond} steps, even if an event has not occurred.
+{Nrebond} must be a multiple of {Nevent}.  This can be useful to check
+if more frequent resets alter event statistics, perhaps because the
+parameters chosen for defining what is a bond and what is an event are
+producing bad dynamics in the presence of the bias potential.
+
+:line
+
+[Restrictions:]
+
+This command can only be used if LAMMPS was built with the REPLICA
+package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"fix hyper/global"_fix_hyper_global.html, "fix
+hyper/local"_fix_hyper_local.html, "compute
+event/displace"_compute_event_displace.html, "prd"_prd.html
+
+[Default:]
+
+The option defaults are min = 0.1 0.1 40 50 and time = steps.
+
+:line
+
+:link(Voter2013)
+[(Voter2013)] S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139,
+144110 (2013).
+
+:link(Voter2002hd)
+[(Voter2002)] Voter, Montalenti, Germann, Annual Review of Materials
+Research 32, 321 (2002).

doc/src/lammps.book

@@ -160,6 +160,7 @@ dump_cfg_uef.html
 echo.html
 group.html
 group2ndx.html
+hyper.html
 if.html
 include.html
 info.html
@@ -277,6 +278,8 @@ fix_gravity.html
 fix_grem.html
 fix_halt.html
 fix_heat.html
+fix_hyper_global.html
+fix_hyper_local.html
 fix_imd.html
 fix_indent.html
 fix_ipi.html
@@ -293,6 +296,7 @@ fix_lb_viscous.html
 fix_lineforce.html
 fix_manifoldforce.html
 fix_meso.html
+fix_meso_move.html
 fix_meso_stationary.html
 fix_momentum.html
 fix_move.html
@@ -337,6 +341,7 @@ fix_orient.html
 fix_phonon.html
 fix_pimd.html
 fix_planeforce.html
+fix_plumed.html
 fix_poems.html
 fix_pour.html
 fix_precession_spin.html
@@ -356,6 +361,7 @@ fix_reaxc_species.html
 fix_recenter.html
 fix_restrain.html
 fix_rigid.html
+fix_rigid_meso.html
 fix_rhok.html
 fix_rx.html
 fix_saed_vtk.html
@@ -615,6 +621,7 @@ pair_reax.html
 pair_reaxc.html
 pair_resquared.html
 pair_sdk.html
+pair_sdpd_taitwater_isothermal.html
 pair_smd_hertz.html
 pair_smd_tlsph.html
 pair_smd_triangulated_surface.html

doc/src/pair_sdpd_taitwater_isothermal.txt

@@ -0,0 +1,108 @@
+"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 sdpd/taitwater/isothermal command :h3
+
+[Syntax:]
+
+pair_style sdpd/taitwater/isothermal temperature viscosity seed
+:pre
+
+temperature = temperature of the fluid (temperature units)
+viscosity = dynamic viscosity of the fluid (mass*distance/time units)
+seed = random number generator seed (positive integer, optional) :ul
+
+[Examples:]
+
+pair_style sdpd/taitwater/isothermal 300. 1. 28681
+pair_coeff * * 1000.0 1430.0 2.4 :pre
+
+[Description:]
+
+The sdpd/taitwater/isothermal style computes forces between mesoscopic
+particles according to the Smoothed Dissipative Particle Dynamics model
+described in this paper by "(Espanol and Revenga)"_#Espanol_Revenga under
+the following assumptions:
+
+:olb
+The temperature is constant and uniform. :l
+The shear viscosity is constant and uniform. :l
+The volume viscosity is negligible before the shear viscosity. :l
+The Boltzmann constant is negligible before the heat capacity of a
+single mesoscopic particle of fluid. :ole,l
+
+The third assumption is true for water in nearly incompressible flows.
+The fourth holds true for water for any reasonable size one can
+imagine for a mesoscopic particle.
+
+The pressure forces between particles will be computed according to
+Tait's equation of state:
+
+:c,image(Eqs/pair_sph_tait.jpg)
+
+where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
+reference density and c_0 the reference speed of sound.
+
+The laminar viscosity and the random forces will be computed according
+to formulas described in "(Espanol and Revenga)"_#Espanol_Revenga.
+
+IMPORTANT NOTE: Similar to "brownian"_pair_brownian.html and
+"dpd"_pair_dpd.html styles, the "newton"_newton.html setting for
+pairwise interactions needs to be on when running LAMMPS in parallel
+if you want to ensure linear momentum conservation. Otherwise random
+forces generated for pairs straddling processor boundary will not be
+equal and opposite.
+
+NOTE: The actual random seed used will be a mix of what you specify
+and other parameters like the MPI ranks. This is to ensure that
+different MPI tasks have distinct seeds.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above.
+
+rho0 reference density (mass/volume units)
+c0 reference soundspeed (distance/time units)
+h kernel function cutoff (distance units) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This style does not write information to "binary restart
+files"_restart.html.  Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+
+This 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:]
+
+This pair style is part of the USER-SDPD 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 sph/rhosum"_pair_sph_rhosum.html
+
+[Default:]
+
+The default seed is 0 (before mixing).
+
+:line
+
+:link(Espanol_Revenga)
+[(Espanol and Revenga)] Espanol, Revenga, Physical Review E, 67, 026705 (2003).

doc/src/pair_style.txt

@@ -268,6 +268,7 @@ pair"_Commands_pair.html doc page are followed by one or more of
 "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
+"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html - smoothed dissipative particle dynamics for water at isothermal conditions
 "smd/hertz"_pair_smd_hertz.html - 
 "smd/tlsph"_pair_smd_tlsph.html - 
 "smd/tri_surface"_pair_smd_triangulated_surface.html - 

doc/src/pairs.txt

@@ -86,6 +86,7 @@ Pair Styles :h1
    pair_reaxc
    pair_resquared
    pair_sdk
+   pair_sdpd_taitwater_isothermal
    pair_smd_hertz
    pair_smd_tlsph
    pair_smd_triangulated_surface

doc/src/prd.txt

@@ -48,11 +48,12 @@ replicas of a system.  One or more replicas can be used.  The total
 number of steps {N} to run can be interpreted in one of two ways; see
 discussion of the {time} keyword below.
 
-PRD is described in "this paper"_#Voter1998 by Art Voter.  It is a method
-for performing accelerated dynamics that is suitable for
-infrequent-event systems that obey first-order kinetics.  A good
-overview of accelerated dynamics methods for such systems in given in
-"this review paper"_#Voter2002prd from the same group.  To quote from the
+PRD is described in "(Voter1998)"_#Voter1998 by Art Voter.  Similar to
+global or local hyperdynamics (HD), PRD is a method for performing
+accelerated dynamics that is suitable for infrequent-event systems
+that obey first-order kinetics.  A good overview of accelerated
+dynamics methods for such systems in given in this review paper
+"(Voter2002)"_#Voter2002prd from Art's group.  To quote from the
 paper: "The dynamical evolution is characterized by vibrational
 excursions within a potential basin, punctuated by occasional
 transitions between basins."  The transition probability is
@@ -61,15 +62,26 @@ Running multiple replicas gives an effective enhancement in the
 timescale spanned by the multiple simulations, while waiting for an
 event to occur.
 
-Each replica runs on a partition of one or more processors.  Processor
-partitions are defined at run-time using the "-partition command-line
-switch"_Run_options.html.  Note that if you have MPI installed, you
-can run a multi-replica simulation with more replicas (partitions)
-than you have physical processors, e.g you can run a 10-replica
-simulation on one or two processors.  However for PRD, this makes
-little sense, since running a replica on virtual instead of physical
-processors,offers no effective parallel speed-up in searching for
-infrequent events.  See the "Howto replica"_Howto_replica.html doc
+Both PRD and HD produce a time-accurate trajectory that effectively
+extends the timescale over which a system can be simulated, but they
+do it differently.  PRD creates Nr replicas of the system and runs
+dynamics on each independently with a normal unbiased potential until
+an event occurs in one of the replicas.  The time between events is
+reduced by a factor of Nr replicas.  HD uses a single replica of the
+system and accelerates time by biasing the interaction potential in a
+manner such that each timestep is effectively longer.  For both
+methods, per CPU second, more physical time elapses and more events
+occur.  See the "hyper"_hyper.html doc page for more info about HD.
+
+In PRD, each replica runs on a partition of one or more processors.
+Processor partitions are defined at run-time using the "-partition
+command-line switch"_Run_options.html.  Note that if you have MPI
+installed, you can run a multi-replica simulation with more replicas
+(partitions) than you have physical processors, e.g you can run a
+10-replica simulation on one or two processors.  However for PRD, this
+makes little sense, since running a replica on virtual instead of
+physical processors,offers no effective parallel speed-up in searching
+for infrequent events.  See the "Howto replica"_Howto_replica.html doc
 page for further discussion.
 
 When a PRD simulation is performed, it is assumed that each replica is
@@ -78,8 +90,8 @@ I.e. the simulation domain, the number of atoms, the interaction
 potentials, etc should be the same for every replica.
 
 A PRD run has several stages, which are repeated each time an "event"
-occurs in one of the replicas, as defined below.  The logic for a PRD
-run is as follows:
+occurs in one of the replicas, as explained below.  The logic for a
+PRD run is as follows:
 
 while (time remains):
   dephase for n_dephase*t_dephase steps
@@ -129,7 +141,8 @@ Minimization parameters may be set via the
 PRD command.  The latter are the settings that would be used with the
 "minimize"_minimize.html command.  Note that typically, you do not
 need to perform a highly-converged minimization to detect a transition
-event.
+event, though you may need to in order to prevent a set of atoms in
+the system from relaxing to a saddle point.
 
 The event check is performed by a compute with the specified
 {compute-ID}.  Currently there is only one compute that works with the
@@ -307,7 +320,7 @@ deposit"_fix_deposit.html.
 "min_modify"_min_modify.html, "min_style"_min_style.html,
 "run_style"_run_style.html, "minimize"_minimize.html,
 "velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html,
-"tad"_tad.html
+"tad"_tad.html, "hyper"_hyper.html
 
 [Default:]
 

examples/README

@@ -78,6 +78,7 @@ friction: frictional contact of spherical asperities between 2d surfaces
 gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
 granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
+hyper:    global and local hyperdynamics of diffusion on Pt surface
 indent:	  spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
 latte:    use of LATTE density-functional tight-binding quantum code

examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt

@@ -36,7 +36,7 @@ fix myrxns all bond/react stabilization yes statted_grp .03 &
   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
 
 # stable at 800K
-fix 1 statted_grp nvt temp 800 800 100
+fix 1 statted_grp_REACT nvt temp 800 800 100
 
 # in order to customize behavior of reacting atoms,
 # you can use the internally created 'bond_react_MASTER_group', like so:

examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon

@@ -36,7 +36,7 @@ fix myrxns all bond/react stabilization yes statted_grp .03 &
   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
 
-fix 1 statted_grp nvt temp 300 300 100
+fix 1 statted_grp_REACT nvt temp 300 300 100
 
 fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
 

examples/USER/plumed/in.peptide-plumed

@@ -0,0 +1,41 @@
+# 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
+
+neighbor	2.0 bin
+neigh_modify	delay 5
+
+timestep	2.0
+
+group		peptide type <= 12
+group		one id 2 4 5 6
+group		two id 80 82 83 84
+group		ref id 37
+group		colvar union one two ref
+
+fix		1 all nvt temp  275.0 275.0 100.0 tchain 1
+
+fix		2 all plumed plumedfile plumed.dat outfile p.log
+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
+
+#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
+variable        step equal step
+variable        pe equal pe
+
+run		101

examples/USER/plumed/log.24Oct18.peptide-plumed.g++.1

@@ -0,0 +1,162 @@
+LAMMPS (24 Oct 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87)
+  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		2 all plumed plumedfile plumed.dat outfile p.log
+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
+variable        step equal step
+variable        pe equal pe
+
+run		101
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../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_2 
+       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152            0 
+      10     276.9783   -5234.3057   -6348.6171    1114.3114   -6421.6171    17.024361   0.47785504 
+      20    279.08532   -5226.4036   -6349.1917    1122.7881   -6441.0169    20.764378   0.52605302 
+      30    282.32141   -5222.3866   -6358.1939    1135.8073   -6448.9785    22.945165   0.65106011 
+      40    276.34173   -5218.7623   -6330.5128    1111.7504   -6423.7566    15.655345   0.23795099 
+      50    286.12741   -5215.9248   -6367.0439    1151.1192   -6449.2655    17.420975   0.42646205 
+      60    273.01449   -5217.7381   -6316.1026    1098.3646   -6406.4709    21.800931   0.92327815 
+      70    274.67549   -5221.0246   -6326.0716     1105.047   -6409.7721     19.41235 0.0016975896 
+      80    273.74824   -5224.7613   -6326.0778    1101.3165   -6418.5055    19.206793   0.48550348 
+      90    284.32594    -5229.195   -6373.0667    1143.8717   -6461.3467    21.124789    0.5468014 
+SHAKE stats (type/ave/delta) on step 100
+  4 1.111 2.06868e-06
+  6 0.996999 2.09521e-06
+  8 1.08 1.10835e-06
+  10 1.111 2.46599e-06
+  12 1.08 8.86314e-07
+  14 0.959999 0
+  18 0.9572 9.14098e-06
+  31 104.52 0.000760401
+     100    270.40648   -5234.9604   -6322.8327    1087.8723     -6417.73    19.666404 0.0094784372 
+     101    270.99811   -5235.8295    -6326.082    1090.2525   -6418.8974    17.285816  0.086681332 
+Loop time of 2.12948 on 1 procs for 101 steps with 2004 atoms
+
+Performance: 8.196 ns/day, 2.928 hours/ns, 47.429 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    | 1.757      | 1.757      | 1.757      |   0.0 | 82.51
+Bond    | 0.0052233  | 0.0052233  | 0.0052233  |   0.0 |  0.25
+Kspace  | 0.14772    | 0.14772    | 0.14772    |   0.0 |  6.94
+Neigh   | 0.16455    | 0.16455    | 0.16455    |   0.0 |  7.73
+Comm    | 0.0083704  | 0.0083704  | 0.0083704  |   0.0 |  0.39
+Output  | 0.00031424 | 0.00031424 | 0.00031424 |   0.0 |  0.01
+Modify  | 0.044411   | 0.044411   | 0.044411   |   0.0 |  2.09
+Other   |            | 0.001851   |            |       |  0.09
+
+Nlocal:    2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11134 ave 11134 max 11134 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    707961 ave 707961 max 707961 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 707961
+Ave neighs/atom = 353.274
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 8
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/USER/plumed/log.24Oct18.peptide-plumed.g++.4

@@ -0,0 +1,162 @@
+LAMMPS (24 Oct 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87)
+  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		2 all plumed plumedfile plumed.dat outfile p.log
+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
+variable        step equal step
+variable        pe equal pe
+
+run		101
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../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_2 
+       0    282.10052    -5237.458   -6372.3766    1134.9186    -6442.768    16.557152            0 
+      10     276.9783   -5234.3057   -6348.6171    1114.3114   -6421.6171    17.024361   0.47785504 
+      20    279.08532   -5226.4036   -6349.1917    1122.7881   -6441.0169    20.764378   0.52605302 
+      30    282.32141   -5222.3866   -6358.1939    1135.8073   -6448.9785    22.945165   0.65106011 
+      40    276.34173   -5218.7623   -6330.5128    1111.7504   -6423.7566    15.655345   0.23795099 
+      50    286.12741   -5215.9248   -6367.0439    1151.1192   -6449.2655    17.420975   0.42646205 
+      60    273.01449   -5217.7381   -6316.1026    1098.3646   -6406.4709    21.800931   0.92327815 
+      70    274.67549   -5221.0246   -6326.0716     1105.047   -6409.7721     19.41235 0.0016975896 
+      80    273.74824   -5224.7613   -6326.0778    1101.3165   -6418.5055    19.206793   0.48550348 
+      90    284.32594    -5229.195   -6373.0667    1143.8717   -6461.3466    21.124789    0.5468014 
+SHAKE stats (type/ave/delta) on step 100
+  4 1.111 2.06868e-06
+  6 0.996999 2.09521e-06
+  8 1.08 1.10835e-06
+  10 1.111 2.46599e-06
+  12 1.08 8.86314e-07
+  14 0.959999 0
+  18 0.9572 9.14098e-06
+  31 104.52 0.000760401
+     100    270.40648   -5234.9604   -6322.8327    1087.8723     -6417.73    19.666404  0.009478437 
+     101    270.99811   -5235.8295    -6326.082    1090.2525   -6418.8974    17.285816  0.086681332 
+Loop time of 1.16767 on 4 procs for 101 steps with 2004 atoms
+
+Performance: 14.947 ns/day, 1.606 hours/ns, 86.497 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    | 0.84633    | 0.86651    | 0.88617    |   1.6 | 74.21
+Bond    | 0.0010614  | 0.0027132  | 0.004288   |   3.0 |  0.23
+Kspace  | 0.095008   | 0.1162     | 0.13491    |   4.3 |  9.95
+Neigh   | 0.07834    | 0.078424   | 0.078516   |   0.0 |  6.72
+Comm    | 0.03314    | 0.033299   | 0.033426   |   0.1 |  2.85
+Output  | 0.00036979 | 0.00076199 | 0.0019338  |   0.0 |  0.07
+Modify  | 0.063471   | 0.064011   | 0.065312   |   0.3 |  5.48
+Other   |            | 0.005751   |            |       |  0.49
+
+Nlocal:    501 ave 512 max 492 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Nghost:    6570.25 ave 6604 max 6529 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs:    176990 ave 181122 max 173551 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 707961
+Ave neighs/atom = 353.274
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 8
+Dangerous builds = 0
+Total wall time: 0:00:01

examples/USER/plumed/plumed.dat

@@ -0,0 +1,4 @@
+UNITS LENGTH=A ENERGY=kcal/mol
+dd: DISTANCE ATOMS=45,48 
+RESTRAINT ARG=dd KAPPA=2000 AT=6.0
+PRINT ARG=dd FILE=colvar

examples/USER/plumed/reference/colvar

@@ -0,0 +1,103 @@
+#! FIELDS time dd
+ 0.000000 5.985554
+ 0.002000 6.002880
+ 0.004000 6.022015
+ 0.006000 6.029922
+ 0.008000 6.020103
+ 0.010000 5.996906
+ 0.012000 5.972734
+ 0.014000 5.960079
+ 0.016000 5.963714
+ 0.018000 5.978140
+ 0.020000 5.991813
+ 0.022000 5.995155
+ 0.024000 5.987021
+ 0.026000 5.975340
+ 0.028000 5.971456
+ 0.030000 5.981945
+ 0.032000 6.003550
+ 0.034000 6.024743
+ 0.036000 6.032990
+ 0.038000 6.022936
+ 0.040000 6.000131
+ 0.042000 5.977800
+ 0.044000 5.968692
+ 0.046000 5.977224
+ 0.048000 5.996934
+ 0.050000 6.014800
+ 0.052000 6.019586
+ 0.054000 6.008803
+ 0.056000 5.989809
+ 0.058000 5.974484
+ 0.060000 5.971140
+ 0.062000 5.979074
+ 0.064000 5.989379
+ 0.066000 5.991356
+ 0.068000 5.980176
+ 0.070000 5.960625
+ 0.072000 5.944401
+ 0.074000 5.942614
+ 0.076000 5.958402
+ 0.078000 5.984574
+ 0.080000 6.007964
+ 0.082000 6.017667
+ 0.084000 6.011795
+ 0.086000 5.998304
+ 0.088000 5.989405
+ 0.090000 5.993275
+ 0.092000 6.008545
+ 0.094000 6.025183
+ 0.096000 6.031186
+ 0.098000 6.020651
+ 0.100000 5.997952
+ 0.102000 5.975230
+ 0.104000 5.964757
+ 0.106000 5.971150
+ 0.108000 5.988568
+ 0.110000 6.004676
+ 0.112000 6.008731
+ 0.114000 5.998481
+ 0.116000 5.981406
+ 0.118000 5.969615
+ 0.120000 5.971827
+ 0.122000 5.987658
+ 0.124000 6.007888
+ 0.126000 6.020477
+ 0.128000 6.018377
+ 0.130000 6.004046
+ 0.132000 5.987682
+ 0.134000 5.980338
+ 0.136000 5.986534
+ 0.138000 6.001303
+ 0.140000 6.013589
+ 0.142000 6.013717
+ 0.144000 6.000028
+ 0.146000 5.980283
+ 0.148000 5.966836
+ 0.150000 5.968670
+ 0.152000 5.985459
+ 0.154000 6.007612
+ 0.156000 6.022374
+ 0.158000 6.022034
+ 0.160000 6.008851
+ 0.162000 5.993355
+ 0.164000 5.987212
+ 0.166000 5.995452
+ 0.168000 6.013111
+ 0.170000 6.028386
+ 0.172000 6.030387
+ 0.174000 6.016468
+ 0.176000 5.994191
+ 0.178000 5.976616
+ 0.180000 5.973983
+ 0.182000 5.987185
+ 0.184000 6.007275
+ 0.186000 6.021338
+ 0.188000 6.020837
+ 0.190000 6.006955
+ 0.192000 5.989433
+ 0.194000 5.979796
+ 0.196000 5.983601
+ 0.198000 5.996921
+ 0.200000 6.009310
+ 0.202000 6.011114

examples/USER/plumed/reference/p.log

@@ -0,0 +1,57 @@
+PLUMED: PLUMED is starting
+PLUMED: Version: 2.4.2 (git: Unknown) compiled on Jul 11 2018 at 19:09:03
+PLUMED: Please cite this paper when using PLUMED [1]
+PLUMED: For further information see the PLUMED web page at http://www.plumed.org
+PLUMED: Root: /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2/
+PLUMED: For installed feature, see /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2//src/config/config.txt
+PLUMED: Molecular dynamics engine: LAMMPS
+PLUMED: Precision of reals: 8
+PLUMED: Running over 1 node
+PLUMED: Number of threads: 1
+PLUMED: Cache line size: 512
+PLUMED: Number of atoms: 2004
+PLUMED: File suffix: 
+PLUMED: FILE: plumed.dat
+PLUMED: Action UNITS
+PLUMED:   with label @0
+PLUMED:   length: A
+PLUMED:   energy: kcal/mol
+PLUMED:   time: ps
+PLUMED:   charge: e
+PLUMED:   mass: amu
+PLUMED:   using physical units
+PLUMED:   inside PLUMED, Boltzmann constant is 0.001987
+PLUMED: Action DISTANCE
+PLUMED:   with label dd
+PLUMED:   between atoms 45 48
+PLUMED:   using periodic boundary conditions
+PLUMED: Action RESTRAINT
+PLUMED:   with label @2
+PLUMED:   with arguments dd
+PLUMED:   added component to this action:  @2.bias 
+PLUMED:   at 6.000000
+PLUMED:   with harmonic force constant 2000.000000
+PLUMED:   and linear force constant 0.000000
+PLUMED:   added component to this action:  @2.force2 
+PLUMED: Action PRINT
+PLUMED:   with label @3
+PLUMED:   with stride 1
+PLUMED:   with arguments dd
+PLUMED:   on file colvar
+PLUMED:   with format  %f
+PLUMED: END FILE: plumed.dat
+PLUMED: Timestep: 0.002000
+PLUMED: KbT has not been set by the MD engine
+PLUMED: It should be set by hand where needed
+PLUMED: Relevant bibliography:
+PLUMED:   [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
+PLUMED: Please read and cite where appropriate!
+PLUMED: Finished setup
+PLUMED:                                               Cycles        Total      Average      Minumum      Maximum
+PLUMED:                                                    1     0.020354     0.020354     0.020354     0.020354
+PLUMED: 1 Prepare dependencies                           102     0.000256     0.000003     0.000001     0.000006
+PLUMED: 2 Sharing data                                   102     0.010002     0.000098     0.000078     0.000546
+PLUMED: 3 Waiting for data                               102     0.001398     0.000014     0.000011     0.000072
+PLUMED: 4 Calculating (forward loop)                     102     0.001797     0.000018     0.000013     0.000058
+PLUMED: 5 Applying (backward loop)                       102     0.002666     0.000026     0.000022     0.000062
+PLUMED: 6 Update                                         102     0.001126     0.000011     0.000007     0.000055

examples/USER/sdpd/2d-diffusion-in-shear-flow/in.lammps

@@ -0,0 +1,61 @@
+dimension       2
+units           micro
+atom_style      meso
+
+variable        R equal 0.5             # radius of sphere          micrometers
+variable        a equal $R/5            # lattice spacing           micrometers
+variable        Lf equal $R*3
+variable        Lb equal $R*4
+variable        wall_velocity equal 0.01                          # micrometers/microsecond
+variable        T equal 300.
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.5          # kernel function cutoff    micrometers
+variable        mass equal $a*$a*$a*${rho_0}
+variable        dt equal 1e-3           # timestep                  microseconds
+variable        skin equal 0.2*$h
+
+region          box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
+create_box      4 box
+lattice         sq $a
+
+create_atoms    1 box
+
+region          sphere sphere 0 0 0 $R units box
+set             region sphere type 2
+
+region          upper_wall block INF INF +${Lf} INF INF INF units box
+set             region upper_wall type 3
+
+region          lower_wall block INF INF INF -${Lf} INF INF units box
+set             region lower_wall type 4
+
+group           fluid type 1
+group           sphere type 2
+group           upper_wall type 3
+group           lower_wall type 4
+
+mass            * ${mass}
+set             group all meso/rho ${rho_0}
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+
+fix             1 fluid meso
+fix             2 sphere rigid/meso single
+fix             3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
+fix             4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
+
+fix             2d all enforce2d
+
+neighbor        ${skin} bin
+neigh_modify	delay 0 every 1 check yes
+timestep        ${dt}
+
+dump            dump_id all atom 100 dump.lammpstrj
+
+thermo          100
+thermo_style    custom step time nbuild ndanger
+
+run             10000

examples/USER/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1

@@ -0,0 +1,247 @@
+LAMMPS (24 Oct 2018)
+dimension       2
+units           micro
+atom_style      meso
+
+variable        R equal 0.5             # radius of sphere          micrometers
+variable        a equal $R/5            # lattice spacing           micrometers
+variable        a equal 0.5/5            
+variable        Lf equal $R*3
+variable        Lf equal 0.5*3
+variable        Lb equal $R*4
+variable        Lb equal 0.5*4
+variable        wall_velocity equal 0.01                          # micrometers/microsecond
+variable        T equal 300.
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.5          # kernel function cutoff    micrometers
+variable        h equal 0.1*4.5          
+variable        mass equal $a*$a*$a*${rho_0}
+variable        mass equal 0.1*$a*$a*${rho_0}
+variable        mass equal 0.1*0.1*$a*${rho_0}
+variable        mass equal 0.1*0.1*0.1*${rho_0}
+variable        mass equal 0.1*0.1*0.1*1
+variable        dt equal 1e-3           # timestep                  microseconds
+variable        skin equal 0.2*$h
+variable        skin equal 0.2*0.45
+
+region          box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 2 -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 2 -2 ${Lb} 0 ${a} units box
+region          box block -2 2 -2 2 0 ${a} units box
+region          box block -2 2 -2 2 0 0.1 units box
+create_box      4 box
+Created orthogonal box = (-2 -2 0) to (2 2 0.1)
+  1 by 1 by 1 MPI processor grid
+lattice         sq $a
+lattice         sq 0.1
+Lattice spacing in x,y,z = 0.1 0.1 0.1
+
+create_atoms    1 box
+Created 1600 atoms
+  Time spent = 0.00169706 secs
+
+region          sphere sphere 0 0 0 $R units box
+region          sphere sphere 0 0 0 0.5 units box
+set             region sphere type 2
+  81 settings made for type
+
+region          upper_wall block INF INF +${Lf} INF INF INF units box
+region          upper_wall block INF INF +1.5 INF INF INF units box
+set             region upper_wall type 3
+  200 settings made for type
+
+region          lower_wall block INF INF INF -${Lf} INF INF units box
+region          lower_wall block INF INF INF -1.5 INF INF units box
+set             region lower_wall type 4
+  240 settings made for type
+
+group           fluid type 1
+1079 atoms in group fluid
+group           sphere type 2
+81 atoms in group sphere
+group           upper_wall type 3
+200 atoms in group upper_wall
+group           lower_wall type 4
+240 atoms in group lower_wall
+
+mass            * ${mass}
+mass            * 0.001
+set             group all meso/rho ${rho_0}
+set             group all meso/rho 1
+  1600 settings made for meso/rho
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
+pair_style      sdpd/taitwater/isothermal 300 1 76787    
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+pair_coeff      * * 1 ${c_0} ${h}
+pair_coeff      * * 1 100 ${h}
+pair_coeff      * * 1 100 0.45
+
+fix             1 fluid meso
+fix             2 sphere rigid/meso single
+1 rigid bodies with 81 atoms
+fix             3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
+fix             3 upper_wall meso/move linear +0.01 0 0 units box
+fix             4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
+fix             4 lower_wall meso/move linear -0.01 0 0 units box
+
+fix             2d all enforce2d
+
+neighbor        ${skin} bin
+neighbor        0.09 bin
+neigh_modify	delay 0 every 1 check yes
+timestep        ${dt}
+timestep        0.001
+
+dump            dump_id all atom 100 dump.lammpstrj
+
+thermo          100
+thermo_style    custom step time nbuild ndanger
+
+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 = 0.54
+  ghost atom cutoff = 0.54
+  binsize = 0.27, bins = 15 15 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sdpd/taitwater/isothermal, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.937 | 6.937 | 6.937 Mbytes
+Step Time Nbuild Ndanger 
+       0            0        0        0 
+     100          0.1        0        0 
+     200          0.2        0        0 
+     300          0.3        0        0 
+     400          0.4        0        0 
+     500          0.5        1        0 
+     600          0.6        1        0 
+     700          0.7        2        0 
+     800          0.8        2        0 
+     900          0.9        2        0 
+    1000            1        3        0 
+    1100          1.1        3        0 
+    1200          1.2        3        0 
+    1300          1.3        4        0 
+    1400          1.4        4        0 
+    1500          1.5        4        0 
+    1600          1.6        5        0 
+    1700          1.7        5        0 
+    1800          1.8        5        0 
+    1900          1.9        6        0 
+    2000            2        6        0 
+    2100          2.1        6        0 
+    2200          2.2        7        0 
+    2300          2.3        7        0 
+    2400          2.4        7        0 
+    2500          2.5        8        0 
+    2600          2.6        8        0 
+    2700          2.7        8        0 
+    2800          2.8        9        0 
+    2900          2.9        9        0 
+    3000            3        9        0 
+    3100          3.1       10        0 
+    3200          3.2       10        0 
+    3300          3.3       10        0 
+    3400          3.4       11        0 
+    3500          3.5       11        0 
+    3600          3.6       11        0 
+    3700          3.7       12        0 
+    3800          3.8       12        0 
+    3900          3.9       12        0 
+    4000            4       13        0 
+    4100          4.1       13        0 
+    4200          4.2       14        0 
+    4300          4.3       14        0 
+    4400          4.4       14        0 
+    4500          4.5       15        0 
+    4600          4.6       15        0 
+    4700          4.7       15        0 
+    4800          4.8       16        0 
+    4900          4.9       16        0 
+    5000            5       16        0 
+    5100          5.1       17        0 
+    5200          5.2       17        0 
+    5300          5.3       17        0 
+    5400          5.4       17        0 
+    5500          5.5       18        0 
+    5600          5.6       18        0 
+    5700          5.7       19        0 
+    5800          5.8       19        0 
+    5900          5.9       19        0 
+    6000            6       20        0 
+    6100          6.1       20        0 
+    6200          6.2       21        0 
+    6300          6.3       21        0 
+    6400          6.4       21        0 
+    6500          6.5       22        0 
+    6600          6.6       22        0 
+    6700          6.7       22        0 
+    6800          6.8       23        0 
+    6900          6.9       23        0 
+    7000            7       23        0 
+    7100          7.1       24        0 
+    7200          7.2       24        0 
+    7300          7.3       25        0 
+    7400          7.4       25        0 
+    7500          7.5       25        0 
+    7600          7.6       26        0 
+    7700          7.7       26        0 
+    7800          7.8       26        0 
+    7900          7.9       27        0 
+    8000            8       27        0 
+    8100          8.1       27        0 
+    8200          8.2       28        0 
+    8300          8.3       28        0 
+    8400          8.4       28        0 
+    8500          8.5       29        0 
+    8600          8.6       29        0 
+    8700          8.7       30        0 
+    8800          8.8       30        0 
+    8900          8.9       30        0 
+    9000            9       31        0 
+    9100          9.1       31        0 
+    9200          9.2       31        0 
+    9300          9.3       32        0 
+    9400          9.4       32        0 
+    9500          9.5       32        0 
+    9600          9.6       33        0 
+    9700          9.7       33        0 
+    9800          9.8       33        0 
+    9900          9.9       34        0 
+   10000           10       34        0 
+Loop time of 144.208 on 1 procs for 10000 steps with 1600 atoms
+
+Performance: 5991348.580 ns/day, 0.000 hours/ns, 69.344 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 143.08     | 143.08     | 143.08     |   0.0 | 99.22
+Neigh   | 0.033195   | 0.033195   | 0.033195   |   0.0 |  0.02
+Comm    | 0.24139    | 0.24139    | 0.24139    |   0.0 |  0.17
+Output  | 0.11687    | 0.11687    | 0.11687    |   0.0 |  0.08
+Modify  | 0.61566    | 0.61566    | 0.61566    |   0.0 |  0.43
+Other   |            | 0.117      |            |       |  0.08
+
+Nlocal:    1600 ave 1600 max 1600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    993 ave 993 max 993 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    73236 ave 73236 max 73236 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 73236
+Ave neighs/atom = 45.7725
+Neighbor list builds = 34
+Dangerous builds = 0
+Total wall time: 0:02:24

examples/USER/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4

@@ -0,0 +1,247 @@
+LAMMPS (24 Oct 2018)
+dimension       2
+units           micro
+atom_style      meso
+
+variable        R equal 0.5             # radius of sphere          micrometers
+variable        a equal $R/5            # lattice spacing           micrometers
+variable        a equal 0.5/5            
+variable        Lf equal $R*3
+variable        Lf equal 0.5*3
+variable        Lb equal $R*4
+variable        Lb equal 0.5*4
+variable        wall_velocity equal 0.01                          # micrometers/microsecond
+variable        T equal 300.
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.5          # kernel function cutoff    micrometers
+variable        h equal 0.1*4.5          
+variable        mass equal $a*$a*$a*${rho_0}
+variable        mass equal 0.1*$a*$a*${rho_0}
+variable        mass equal 0.1*0.1*$a*${rho_0}
+variable        mass equal 0.1*0.1*0.1*${rho_0}
+variable        mass equal 0.1*0.1*0.1*1
+variable        dt equal 1e-3           # timestep                  microseconds
+variable        skin equal 0.2*$h
+variable        skin equal 0.2*0.45
+
+region          box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 2 -${Lb} ${Lb} 0 ${a} units box
+region          box block -2 2 -2 ${Lb} 0 ${a} units box
+region          box block -2 2 -2 2 0 ${a} units box
+region          box block -2 2 -2 2 0 0.1 units box
+create_box      4 box
+Created orthogonal box = (-2 -2 0) to (2 2 0.1)
+  2 by 2 by 1 MPI processor grid
+lattice         sq $a
+lattice         sq 0.1
+Lattice spacing in x,y,z = 0.1 0.1 0.1
+
+create_atoms    1 box
+Created 1600 atoms
+  Time spent = 0.000589566 secs
+
+region          sphere sphere 0 0 0 $R units box
+region          sphere sphere 0 0 0 0.5 units box
+set             region sphere type 2
+  81 settings made for type
+
+region          upper_wall block INF INF +${Lf} INF INF INF units box
+region          upper_wall block INF INF +1.5 INF INF INF units box
+set             region upper_wall type 3
+  200 settings made for type
+
+region          lower_wall block INF INF INF -${Lf} INF INF units box
+region          lower_wall block INF INF INF -1.5 INF INF units box
+set             region lower_wall type 4
+  240 settings made for type
+
+group           fluid type 1
+1079 atoms in group fluid
+group           sphere type 2
+81 atoms in group sphere
+group           upper_wall type 3
+200 atoms in group upper_wall
+group           lower_wall type 4
+240 atoms in group lower_wall
+
+mass            * ${mass}
+mass            * 0.001
+set             group all meso/rho ${rho_0}
+set             group all meso/rho 1
+  1600 settings made for meso/rho
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
+pair_style      sdpd/taitwater/isothermal 300 1 76787    
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+pair_coeff      * * 1 ${c_0} ${h}
+pair_coeff      * * 1 100 ${h}
+pair_coeff      * * 1 100 0.45
+
+fix             1 fluid meso
+fix             2 sphere rigid/meso single
+1 rigid bodies with 81 atoms
+fix             3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
+fix             3 upper_wall meso/move linear +0.01 0 0 units box
+fix             4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
+fix             4 lower_wall meso/move linear -0.01 0 0 units box
+
+fix             2d all enforce2d
+
+neighbor        ${skin} bin
+neighbor        0.09 bin
+neigh_modify	delay 0 every 1 check yes
+timestep        ${dt}
+timestep        0.001
+
+dump            dump_id all atom 100 dump.lammpstrj
+
+thermo          100
+thermo_style    custom step time nbuild ndanger
+
+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 = 0.54
+  ghost atom cutoff = 0.54
+  binsize = 0.27, bins = 15 15 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sdpd/taitwater/isothermal, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.854 | 6.854 | 6.854 Mbytes
+Step Time Nbuild Ndanger 
+       0            0        0        0 
+     100          0.1        0        0 
+     200          0.2        0        0 
+     300          0.3        0        0 
+     400          0.4        1        0 
+     500          0.5        1        0 
+     600          0.6        1        0 
+     700          0.7        2        0 
+     800          0.8        2        0 
+     900          0.9        2        0 
+    1000            1        3        0 
+    1100          1.1        3        0 
+    1200          1.2        4        0 
+    1300          1.3        4        0 
+    1400          1.4        4        0 
+    1500          1.5        4        0 
+    1600          1.6        5        0 
+    1700          1.7        5        0 
+    1800          1.8        5        0 
+    1900          1.9        6        0 
+    2000            2        6        0 
+    2100          2.1        6        0 
+    2200          2.2        6        0 
+    2300          2.3        7        0 
+    2400          2.4        7        0 
+    2500          2.5        7        0 
+    2600          2.6        8        0 
+    2700          2.7        8        0 
+    2800          2.8        8        0 
+    2900          2.9        9        0 
+    3000            3        9        0 
+    3100          3.1        9        0 
+    3200          3.2       10        0 
+    3300          3.3       10        0 
+    3400          3.4       10        0 
+    3500          3.5       11        0 
+    3600          3.6       11        0 
+    3700          3.7       11        0 
+    3800          3.8       12        0 
+    3900          3.9       12        0 
+    4000            4       12        0 
+    4100          4.1       13        0 
+    4200          4.2       13        0 
+    4300          4.3       13        0 
+    4400          4.4       14        0 
+    4500          4.5       14        0 
+    4600          4.6       15        0 
+    4700          4.7       15        0 
+    4800          4.8       15        0 
+    4900          4.9       16        0 
+    5000            5       16        0 
+    5100          5.1       17        0 
+    5200          5.2       17        0 
+    5300          5.3       17        0 
+    5400          5.4       17        0 
+    5500          5.5       18        0 
+    5600          5.6       18        0 
+    5700          5.7       18        0 
+    5800          5.8       19        0 
+    5900          5.9       19        0 
+    6000            6       20        0 
+    6100          6.1       20        0 
+    6200          6.2       20        0 
+    6300          6.3       21        0 
+    6400          6.4       21        0 
+    6500          6.5       21        0 
+    6600          6.6       22        0 
+    6700          6.7       22        0 
+    6800          6.8       22        0 
+    6900          6.9       23        0 
+    7000            7       23        0 
+    7100          7.1       23        0 
+    7200          7.2       24        0 
+    7300          7.3       24        0 
+    7400          7.4       25        0 
+    7500          7.5       25        0 
+    7600          7.6       25        0 
+    7700          7.7       25        0 
+    7800          7.8       26        0 
+    7900          7.9       26        0 
+    8000            8       26        0 
+    8100          8.1       27        0 
+    8200          8.2       27        0 
+    8300          8.3       27        0 
+    8400          8.4       28        0 
+    8500          8.5       28        0 
+    8600          8.6       28        0 
+    8700          8.7       29        0 
+    8800          8.8       29        0 
+    8900          8.9       29        0 
+    9000            9       30        0 
+    9100          9.1       30        0 
+    9200          9.2       31        0 
+    9300          9.3       31        0 
+    9400          9.4       31        0 
+    9500          9.5       32        0 
+    9600          9.6       32        0 
+    9700          9.7       32        0 
+    9800          9.8       32        0 
+    9900          9.9       33        0 
+   10000           10       33        0 
+Loop time of 63.2372 on 4 procs for 10000 steps with 1600 atoms
+
+Performance: 13662841.706 ns/day, 0.000 hours/ns, 158.135 timesteps/s
+94.3% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 51.576     | 53.662     | 55.484     |  23.9 | 84.86
+Neigh   | 0.011519   | 0.012395   | 0.013405   |   0.7 |  0.02
+Comm    | 6.8389     | 8.5423     | 10.517     |  56.1 | 13.51
+Output  | 0.12342    | 0.12513    | 0.1302     |   0.8 |  0.20
+Modify  | 0.58708    | 0.69128    | 0.78806    |  11.3 |  1.09
+Other   |            | 0.2038     |            |       |  0.32
+
+Nlocal:    400 ave 411 max 388 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:    552.25 ave 567 max 539 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:    18298.8 ave 18781 max 17829 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 73195
+Ave neighs/atom = 45.7469
+Neighbor list builds = 33
+Dangerous builds = 0
+Total wall time: 0:01:03

examples/USER/sdpd/2d-diffusion/in.lammps

@@ -0,0 +1,49 @@
+dimension       2
+units           micro
+atom_style      meso
+
+variable        R equal 0.5             # radius of sphere          micrometers
+variable        a equal $R/5            # lattice spacing           micrometers
+variable        L equal $R*3
+variable        T equal 300.
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.5          # kernel function cutoff    micrometers
+variable        mass equal $a*$a*$a*${rho_0}
+variable        dt equal 1e-3           # timestep                  microseconds
+variable        skin equal 0.2*$h
+
+region          box block -$L $L -$L $L 0 $a units box
+create_box      2 box
+lattice         sq $a
+
+create_atoms    1 box
+
+region          sphere sphere 0 0 0 $R units box
+set             region sphere type 2
+
+group           fluid type 1
+group           sphere type 2
+
+mass            * ${mass}
+set             group all meso/rho ${rho_0}
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+
+fix             1 fluid meso
+fix             2 sphere rigid/meso single
+
+fix             2d all enforce2d
+
+neighbor        ${skin} bin
+neigh_modify	delay 0 every 1 check yes
+timestep        ${dt}
+
+dump            dump_id all atom 100 dump.lammpstrj
+
+thermo          100
+thermo_style    custom step time nbuild ndanger
+
+run             10000

examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.1

@@ -0,0 +1,226 @@
+LAMMPS (24 Oct 2018)
+dimension       2
+units           micro
+atom_style      meso
+
+variable        R equal 0.5             # radius of sphere          micrometers
+variable        a equal $R/5            # lattice spacing           micrometers
+variable        a equal 0.5/5            
+variable        L equal $R*3
+variable        L equal 0.5*3
+variable        T equal 300.
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.5          # kernel function cutoff    micrometers
+variable        h equal 0.1*4.5          
+variable        mass equal $a*$a*$a*${rho_0}
+variable        mass equal 0.1*$a*$a*${rho_0}
+variable        mass equal 0.1*0.1*$a*${rho_0}
+variable        mass equal 0.1*0.1*0.1*${rho_0}
+variable        mass equal 0.1*0.1*0.1*1
+variable        dt equal 1e-3           # timestep                  microseconds
+variable        skin equal 0.2*$h
+variable        skin equal 0.2*0.45
+
+region          box block -$L $L -$L $L 0 $a units box
+region          box block -1.5 $L -$L $L 0 $a units box
+region          box block -1.5 1.5 -$L $L 0 $a units box
+region          box block -1.5 1.5 -1.5 $L 0 $a units box
+region          box block -1.5 1.5 -1.5 1.5 0 $a units box
+region          box block -1.5 1.5 -1.5 1.5 0 0.1 units box
+create_box      2 box
+Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
+  1 by 1 by 1 MPI processor grid
+lattice         sq $a
+lattice         sq 0.1
+Lattice spacing in x,y,z = 0.1 0.1 0.1
+
+create_atoms    1 box
+Created 900 atoms
+  Time spent = 0.0015769 secs
+
+region          sphere sphere 0 0 0 $R units box
+region          sphere sphere 0 0 0 0.5 units box
+set             region sphere type 2
+  81 settings made for type
+
+group           fluid type 1
+819 atoms in group fluid
+group           sphere type 2
+81 atoms in group sphere
+
+mass            * ${mass}
+mass            * 0.001
+set             group all meso/rho ${rho_0}
+set             group all meso/rho 1
+  900 settings made for meso/rho
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
+pair_style      sdpd/taitwater/isothermal 300 1 76787    
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+pair_coeff      * * 1 ${c_0} ${h}
+pair_coeff      * * 1 100 ${h}
+pair_coeff      * * 1 100 0.45
+
+fix             1 fluid meso
+fix             2 sphere rigid/meso single
+1 rigid bodies with 81 atoms
+
+fix             2d all enforce2d
+
+neighbor        ${skin} bin
+neighbor        0.09 bin
+neigh_modify	delay 0 every 1 check yes
+timestep        ${dt}
+timestep        0.001
+
+dump            dump_id all atom 100 dump.lammpstrj
+
+thermo          100
+thermo_style    custom step time nbuild ndanger
+
+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 = 0.54
+  ghost atom cutoff = 0.54
+  binsize = 0.27, bins = 12 12 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sdpd/taitwater/isothermal, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.137 | 6.137 | 6.137 Mbytes
+Step Time Nbuild Ndanger 
+       0            0        0        0 
+     100          0.1        0        0 
+     200          0.2        0        0 
+     300          0.3        0        0 
+     400          0.4        1        0 
+     500          0.5        1        0 
+     600          0.6        1        0 
+     700          0.7        2        0 
+     800          0.8        2        0 
+     900          0.9        2        0 
+    1000            1        3        0 
+    1100          1.1        3        0 
+    1200          1.2        3        0 
+    1300          1.3        4        0 
+    1400          1.4        4        0 
+    1500          1.5        4        0 
+    1600          1.6        5        0 
+    1700          1.7        5        0 
+    1800          1.8        6        0 
+    1900          1.9        6        0 
+    2000            2        6        0 
+    2100          2.1        7        0 
+    2200          2.2        7        0 
+    2300          2.3        7        0 
+    2400          2.4        7        0 
+    2500          2.5        8        0 
+    2600          2.6        8        0 
+    2700          2.7        8        0 
+    2800          2.8        9        0 
+    2900          2.9        9        0 
+    3000            3       10        0 
+    3100          3.1       10        0 
+    3200          3.2       10        0 
+    3300          3.3       11        0 
+    3400          3.4       11        0 
+    3500          3.5       11        0 
+    3600          3.6       12        0 
+    3700          3.7       12        0 
+    3800          3.8       12        0 
+    3900          3.9       13        0 
+    4000            4       13        0 
+    4100          4.1       13        0 
+    4200          4.2       14        0 
+    4300          4.3       14        0 
+    4400          4.4       14        0 
+    4500          4.5       15        0 
+    4600          4.6       15        0 
+    4700          4.7       15        0 
+    4800          4.8       16        0 
+    4900          4.9       16        0 
+    5000            5       17        0 
+    5100          5.1       17        0 
+    5200          5.2       17        0 
+    5300          5.3       17        0 
+    5400          5.4       18        0 
+    5500          5.5       18        0 
+    5600          5.6       18        0 
+    5700          5.7       19        0 
+    5800          5.8       19        0 
+    5900          5.9       19        0 
+    6000            6       19        0 
+    6100          6.1       20        0 
+    6200          6.2       20        0 
+    6300          6.3       20        0 
+    6400          6.4       21        0 
+    6500          6.5       21        0 
+    6600          6.6       21        0 
+    6700          6.7       21        0 
+    6800          6.8       22        0 
+    6900          6.9       22        0 
+    7000            7       22        0 
+    7100          7.1       23        0 
+    7200          7.2       23        0 
+    7300          7.3       23        0 
+    7400          7.4       24        0 
+    7500          7.5       24        0 
+    7600          7.6       24        0 
+    7700          7.7       25        0 
+    7800          7.8       25        0 
+    7900          7.9       26        0 
+    8000            8       26        0 
+    8100          8.1       26        0 
+    8200          8.2       26        0 
+    8300          8.3       27        0 
+    8400          8.4       27        0 
+    8500          8.5       27        0 
+    8600          8.6       28        0 
+    8700          8.7       28        0 
+    8800          8.8       28        0 
+    8900          8.9       29        0 
+    9000            9       29        0 
+    9100          9.1       29        0 
+    9200          9.2       30        0 
+    9300          9.3       30        0 
+    9400          9.4       30        0 
+    9500          9.5       30        0 
+    9600          9.6       31        0 
+    9700          9.7       31        0 
+    9800          9.8       32        0 
+    9900          9.9       32        0 
+   10000           10       32        0 
+Loop time of 80.9456 on 1 procs for 10000 steps with 900 atoms
+
+Performance: 10673829.855 ns/day, 0.000 hours/ns, 123.540 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 80.306     | 80.306     | 80.306     |   0.0 | 99.21
+Neigh   | 0.017418   | 0.017418   | 0.017418   |   0.0 |  0.02
+Comm    | 0.16939    | 0.16939    | 0.16939    |   0.0 |  0.21
+Output  | 0.070281   | 0.070281   | 0.070281   |   0.0 |  0.09
+Modify  | 0.3154     | 0.3154     | 0.3154     |   0.0 |  0.39
+Other   |            | 0.067      |            |       |  0.08
+
+Nlocal:    900 ave 900 max 900 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    762 ave 762 max 762 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    40697 ave 40697 max 40697 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 40697
+Ave neighs/atom = 45.2189
+Neighbor list builds = 32
+Dangerous builds = 0
+Total wall time: 0:01:20

examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.4

@@ -0,0 +1,226 @@
+LAMMPS (24 Oct 2018)
+dimension       2
+units           micro
+atom_style      meso
+
+variable        R equal 0.5             # radius of sphere          micrometers
+variable        a equal $R/5            # lattice spacing           micrometers
+variable        a equal 0.5/5            
+variable        L equal $R*3
+variable        L equal 0.5*3
+variable        T equal 300.
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 100.          # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.5          # kernel function cutoff    micrometers
+variable        h equal 0.1*4.5          
+variable        mass equal $a*$a*$a*${rho_0}
+variable        mass equal 0.1*$a*$a*${rho_0}
+variable        mass equal 0.1*0.1*$a*${rho_0}
+variable        mass equal 0.1*0.1*0.1*${rho_0}
+variable        mass equal 0.1*0.1*0.1*1
+variable        dt equal 1e-3           # timestep                  microseconds
+variable        skin equal 0.2*$h
+variable        skin equal 0.2*0.45
+
+region          box block -$L $L -$L $L 0 $a units box
+region          box block -1.5 $L -$L $L 0 $a units box
+region          box block -1.5 1.5 -$L $L 0 $a units box
+region          box block -1.5 1.5 -1.5 $L 0 $a units box
+region          box block -1.5 1.5 -1.5 1.5 0 $a units box
+region          box block -1.5 1.5 -1.5 1.5 0 0.1 units box
+create_box      2 box
+Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
+  2 by 2 by 1 MPI processor grid
+lattice         sq $a
+lattice         sq 0.1
+Lattice spacing in x,y,z = 0.1 0.1 0.1
+
+create_atoms    1 box
+Created 900 atoms
+  Time spent = 0.0010246 secs
+
+region          sphere sphere 0 0 0 $R units box
+region          sphere sphere 0 0 0 0.5 units box
+set             region sphere type 2
+  81 settings made for type
+
+group           fluid type 1
+819 atoms in group fluid
+group           sphere type 2
+81 atoms in group sphere
+
+mass            * ${mass}
+mass            * 0.001
+set             group all meso/rho ${rho_0}
+set             group all meso/rho 1
+  900 settings made for meso/rho
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
+pair_style      sdpd/taitwater/isothermal 300 1 76787    
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+pair_coeff      * * 1 ${c_0} ${h}
+pair_coeff      * * 1 100 ${h}
+pair_coeff      * * 1 100 0.45
+
+fix             1 fluid meso
+fix             2 sphere rigid/meso single
+1 rigid bodies with 81 atoms
+
+fix             2d all enforce2d
+
+neighbor        ${skin} bin
+neighbor        0.09 bin
+neigh_modify	delay 0 every 1 check yes
+timestep        ${dt}
+timestep        0.001
+
+dump            dump_id all atom 100 dump.lammpstrj
+
+thermo          100
+thermo_style    custom step time nbuild ndanger
+
+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 = 0.54
+  ghost atom cutoff = 0.54
+  binsize = 0.27, bins = 12 12 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sdpd/taitwater/isothermal, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.087 | 6.087 | 6.087 Mbytes
+Step Time Nbuild Ndanger 
+       0            0        0        0 
+     100          0.1        0        0 
+     200          0.2        0        0 
+     300          0.3        0        0 
+     400          0.4        1        0 
+     500          0.5        1        0 
+     600          0.6        1        0 
+     700          0.7        2        0 
+     800          0.8        2        0 
+     900          0.9        2        0 
+    1000            1        3        0 
+    1100          1.1        3        0 
+    1200          1.2        3        0 
+    1300          1.3        4        0 
+    1400          1.4        4        0 
+    1500          1.5        5        0 
+    1600          1.6        5        0 
+    1700          1.7        5        0 
+    1800          1.8        6        0 
+    1900          1.9        6        0 
+    2000            2        6        0 
+    2100          2.1        7        0 
+    2200          2.2        7        0 
+    2300          2.3        7        0 
+    2400          2.4        8        0 
+    2500          2.5        8        0 
+    2600          2.6        8        0 
+    2700          2.7        9        0 
+    2800          2.8        9        0 
+    2900          2.9        9        0 
+    3000            3        9        0 
+    3100          3.1       10        0 
+    3200          3.2       10        0 
+    3300          3.3       10        0 
+    3400          3.4       11        0 
+    3500          3.5       11        0 
+    3600          3.6       11        0 
+    3700          3.7       12        0 
+    3800          3.8       12        0 
+    3900          3.9       12        0 
+    4000            4       13        0 
+    4100          4.1       13        0 
+    4200          4.2       13        0 
+    4300          4.3       14        0 
+    4400          4.4       14        0 
+    4500          4.5       15        0 
+    4600          4.6       15        0 
+    4700          4.7       15        0 
+    4800          4.8       16        0 
+    4900          4.9       16        0 
+    5000            5       16        0 
+    5100          5.1       16        0 
+    5200          5.2       17        0 
+    5300          5.3       17        0 
+    5400          5.4       18        0 
+    5500          5.5       18        0 
+    5600          5.6       19        0 
+    5700          5.7       19        0 
+    5800          5.8       19        0 
+    5900          5.9       20        0 
+    6000            6       20        0 
+    6100          6.1       20        0 
+    6200          6.2       21        0 
+    6300          6.3       21        0 
+    6400          6.4       21        0 
+    6500          6.5       22        0 
+    6600          6.6       22        0 
+    6700          6.7       22        0 
+    6800          6.8       23        0 
+    6900          6.9       23        0 
+    7000            7       23        0 
+    7100          7.1       24        0 
+    7200          7.2       24        0 
+    7300          7.3       24        0 
+    7400          7.4       25        0 
+    7500          7.5       25        0 
+    7600          7.6       25        0 
+    7700          7.7       26        0 
+    7800          7.8       26        0 
+    7900          7.9       26        0 
+    8000            8       27        0 
+    8100          8.1       27        0 
+    8200          8.2       27        0 
+    8300          8.3       28        0 
+    8400          8.4       28        0 
+    8500          8.5       28        0 
+    8600          8.6       28        0 
+    8700          8.7       29        0 
+    8800          8.8       29        0 
+    8900          8.9       29        0 
+    9000            9       30        0 
+    9100          9.1       30        0 
+    9200          9.2       31        0 
+    9300          9.3       31        0 
+    9400          9.4       31        0 
+    9500          9.5       31        0 
+    9600          9.6       32        0 
+    9700          9.7       32        0 
+    9800          9.8       32        0 
+    9900          9.9       33        0 
+   10000           10       33        0 
+Loop time of 69.01 on 4 procs for 10000 steps with 900 atoms
+
+Performance: 12519931.275 ns/day, 0.000 hours/ns, 144.907 timesteps/s
+48.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 56.528     | 57.936     | 58.729     |  11.0 | 83.95
+Neigh   | 0.013157   | 0.013382   | 0.013551   |   0.1 |  0.02
+Comm    | 8.9594     | 9.7555     | 11.113     |  26.7 | 14.14
+Output  | 0.14644    | 0.15009    | 0.15809    |   1.2 |  0.22
+Modify  | 0.72913    | 0.91574    | 1.0524     |  12.4 |  1.33
+Other   |            | 0.2389     |            |       |  0.35
+
+Nlocal:    225 ave 229 max 223 min
+Histogram: 1 2 0 0 0 0 0 0 0 1
+Nghost:    442 ave 444 max 439 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Neighs:    10188.8 ave 10437 max 9932 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+
+Total # of neighbors = 40755
+Ave neighs/atom = 45.2833
+Neighbor list builds = 33
+Dangerous builds = 0
+Total wall time: 0:01:09

examples/USER/sdpd/README

@@ -0,0 +1,24 @@
+Smoothed Dissipative Particle Dynamics examples
+
+equipartition-verification:
+  This example verifies the equipartition theorem.
+  It simulates a periodic box of water with no solid bodies.
+  If equipartition theorem holds true, the average of each component of
+  translational kinetic energy should be equal to k_B T, and therefore
+  vx_sq_check, vy_sq_check, and vz_sq_check should fluctuate near 1.
+
+2d-diffusion:
+  This example demonstrates the free diffusion of a disk in 2D.
+  The 3D simulation is similar but takes much longer to complete.
+  As with other statistical experiments you need an ensemble to
+  extract meaningful average quantities.
+  For a more realistic simulation you should increase the resolution
+  of the disk/sphere which also necessitates reduction of timestep.
+
+2d-diffusion-in-shear-flow:
+  This example demonstrates the diffusion of a disk in shear flow in 2D.
+  The 3D simulation is similar but takes much longer to complete.
+  As with other statistical experiments you need an ensemble to
+  extract meaningful average quantities.
+  For a more realistic simulation you should increase the resolution
+  of the disk/sphere which also necessitates reduction of timestep.

examples/USER/sdpd/equipartition-verification/in.lammps

@@ -0,0 +1,45 @@
+dimension       3
+units           micro
+atom_style      meso
+
+variable        a equal 0.1             # lattice spacing         micrometers
+variable        L equal $a*10
+variable        T equal 300.
+variable        kB equal 1.3806504e-8   # picogram-micrometer^2/(microsecond^2-Kelvin)
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 10.           # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.0          # kernel function cutoff    micrometers
+variable        mass equal $a*$a*$a*${rho_0}
+variable        dt equal 5e-4           # timestep                  microseconds
+variable        skin equal 0.1*$h
+
+region          box block -$L $L -$L $L -$L $L units box
+create_box      1 box
+lattice         sc $a
+
+create_atoms    1 box
+
+mass            * ${mass}
+set             group all meso/rho ${rho_0}
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+
+variable        vx_sq atom vx*vx
+variable        vy_sq atom vy*vy
+variable        vz_sq atom vz*vz
+compute         v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
+variable        vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
+variable        vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
+variable        vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
+
+fix             1 all meso
+
+neighbor        ${skin} bin
+timestep        ${dt}
+
+thermo          10
+thermo_style    custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
+
+run             200

examples/USER/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.1

@@ -0,0 +1,146 @@
+LAMMPS (24 Oct 2018)
+dimension       3
+units           micro
+atom_style      meso
+
+variable        a equal 0.1             # lattice spacing         micrometers
+variable        L equal $a*10
+variable        L equal 0.1*10
+variable        T equal 300.
+variable        kB equal 1.3806504e-8   # picogram-micrometer^2/(microsecond^2-Kelvin)
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 10.           # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.0          # kernel function cutoff    micrometers
+variable        h equal 0.1*4.0          
+variable        mass equal $a*$a*$a*${rho_0}
+variable        mass equal 0.1*$a*$a*${rho_0}
+variable        mass equal 0.1*0.1*$a*${rho_0}
+variable        mass equal 0.1*0.1*0.1*${rho_0}
+variable        mass equal 0.1*0.1*0.1*1
+variable        dt equal 5e-4           # timestep                  microseconds
+variable        skin equal 0.1*$h
+variable        skin equal 0.1*0.4
+
+region          box block -$L $L -$L $L -$L $L units box
+region          box block -1 $L -$L $L -$L $L units box
+region          box block -1 1 -$L $L -$L $L units box
+region          box block -1 1 -1 $L -$L $L units box
+region          box block -1 1 -1 1 -$L $L units box
+region          box block -1 1 -1 1 -1 $L units box
+region          box block -1 1 -1 1 -1 1 units box
+create_box      1 box
+Created orthogonal box = (-1 -1 -1) to (1 1 1)
+  1 by 1 by 1 MPI processor grid
+lattice         sc $a
+lattice         sc 0.1
+Lattice spacing in x,y,z = 0.1 0.1 0.1
+
+create_atoms    1 box
+Created 8000 atoms
+  Time spent = 0.00285411 secs
+
+mass            * ${mass}
+mass            * 0.001
+set             group all meso/rho ${rho_0}
+set             group all meso/rho 1
+  8000 settings made for meso/rho
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
+pair_style      sdpd/taitwater/isothermal 300 1 76787    
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+pair_coeff      * * 1 ${c_0} ${h}
+pair_coeff      * * 1 10 ${h}
+pair_coeff      * * 1 10 0.4
+
+variable        vx_sq atom vx*vx
+variable        vy_sq atom vy*vy
+variable        vz_sq atom vz*vz
+compute         v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
+variable        vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
+variable        vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T
+variable        vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T
+variable        vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300
+variable        vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
+variable        vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T
+variable        vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T
+variable        vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300
+variable        vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
+variable        vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
+variable        vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
+variable        vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
+
+fix             1 all meso
+
+neighbor        ${skin} bin
+neighbor        0.04 bin
+timestep        ${dt}
+timestep        0.0005
+
+thermo          10
+thermo_style    custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
+
+run             200
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0.44
+  ghost atom cutoff = 0.44
+  binsize = 0.22, bins = 10 10 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sdpd/taitwater/isothermal, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.54 | 13.54 | 13.54 Mbytes
+Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check 
+       0            0            0            0            0 
+      10        0.005   0.70973271   0.71495693   0.71910087 
+      20         0.01   0.90418096   0.88845437   0.89659567 
+      30        0.015    0.9590736   0.97880338    0.9619016 
+      40         0.02   0.98533774   0.96057682   0.95600448 
+      50        0.025   0.96433662   0.96650071   0.95509683 
+      60         0.03   0.96598029   0.96373656   0.96734888 
+      70        0.035   0.95433045   0.98004764   0.96255924 
+      80         0.04   0.97872906   0.95987289   0.96623598 
+      90        0.045   0.99913888   0.99255731   0.95616142 
+     100         0.05   0.98872675   0.97141018   0.95338841 
+     110        0.055   0.97794592   0.97389258   0.98473719 
+     120         0.06   0.98389266   0.96716284   0.95504862 
+     130        0.065   0.98572886   0.96680923   0.95599065 
+     140         0.07   0.97602684   0.97580081    0.9886878 
+     150        0.075   0.99172003   0.95027467   0.96028033 
+     160         0.08   0.96793247   0.94590928   0.95644301 
+     170        0.085   0.94167619   0.98048861   0.93439426 
+     180         0.09   0.97277934   0.97383622   0.96900866 
+     190        0.095   0.96647288    1.0027643   0.96230782 
+     200          0.1   0.94864291   0.95902585   0.96398175 
+Loop time of 60.1095 on 1 procs for 200 steps with 8000 atoms
+
+Performance: 143737.595 ns/day, 0.000 hours/ns, 3.327 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 59.92      | 59.92      | 59.92      |   0.0 | 99.68
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.11154    | 0.11154    | 0.11154    |   0.0 |  0.19
+Output  | 0.0063498  | 0.0063498  | 0.0063498  |   0.0 |  0.01
+Modify  | 0.043546   | 0.043546   | 0.043546   |   0.0 |  0.07
+Other   |            | 0.02811    |            |       |  0.05
+
+Nlocal:    8000 ave 8000 max 8000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    16389 ave 16389 max 16389 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.456e+06 ave 1.456e+06 max 1.456e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1456000
+Ave neighs/atom = 182
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:00

examples/USER/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.4

@@ -0,0 +1,146 @@
+LAMMPS (24 Oct 2018)
+dimension       3
+units           micro
+atom_style      meso
+
+variable        a equal 0.1             # lattice spacing         micrometers
+variable        L equal $a*10
+variable        L equal 0.1*10
+variable        T equal 300.
+variable        kB equal 1.3806504e-8   # picogram-micrometer^2/(microsecond^2-Kelvin)
+variable        rho_0 equal 1.          # density                   picograms/micrometer^3
+variable        c_0 equal 10.           # speed of sound            micrometers/microsecond
+variable        mu equal 1.             # dynamic viscosity         picogram/(micrometer-microsecond)
+variable        h equal $a*4.0          # kernel function cutoff    micrometers
+variable        h equal 0.1*4.0          
+variable        mass equal $a*$a*$a*${rho_0}
+variable        mass equal 0.1*$a*$a*${rho_0}
+variable        mass equal 0.1*0.1*$a*${rho_0}
+variable        mass equal 0.1*0.1*0.1*${rho_0}
+variable        mass equal 0.1*0.1*0.1*1
+variable        dt equal 5e-4           # timestep                  microseconds
+variable        skin equal 0.1*$h
+variable        skin equal 0.1*0.4
+
+region          box block -$L $L -$L $L -$L $L units box
+region          box block -1 $L -$L $L -$L $L units box
+region          box block -1 1 -$L $L -$L $L units box
+region          box block -1 1 -1 $L -$L $L units box
+region          box block -1 1 -1 1 -$L $L units box
+region          box block -1 1 -1 1 -1 $L units box
+region          box block -1 1 -1 1 -1 1 units box
+create_box      1 box
+Created orthogonal box = (-1 -1 -1) to (1 1 1)
+  1 by 2 by 2 MPI processor grid
+lattice         sc $a
+lattice         sc 0.1
+Lattice spacing in x,y,z = 0.1 0.1 0.1
+
+create_atoms    1 box
+Created 8000 atoms
+  Time spent = 0.00252754 secs
+
+mass            * ${mass}
+mass            * 0.001
+set             group all meso/rho ${rho_0}
+set             group all meso/rho 1
+  8000 settings made for meso/rho
+
+pair_style      sdpd/taitwater/isothermal $T ${mu} 76787    # temperature viscosity random_seed
+pair_style      sdpd/taitwater/isothermal 300 ${mu} 76787    
+pair_style      sdpd/taitwater/isothermal 300 1 76787    
+pair_coeff      * * ${rho_0} ${c_0} ${h}
+pair_coeff      * * 1 ${c_0} ${h}
+pair_coeff      * * 1 10 ${h}
+pair_coeff      * * 1 10 0.4
+
+variable        vx_sq atom vx*vx
+variable        vy_sq atom vy*vy
+variable        vz_sq atom vz*vz
+compute         v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
+variable        vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
+variable        vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T
+variable        vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T
+variable        vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300
+variable        vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
+variable        vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T
+variable        vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T
+variable        vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300
+variable        vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
+variable        vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
+variable        vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
+variable        vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
+
+fix             1 all meso
+
+neighbor        ${skin} bin
+neighbor        0.04 bin
+timestep        ${dt}
+timestep        0.0005
+
+thermo          10
+thermo_style    custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
+
+run             200
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 0.44
+  ghost atom cutoff = 0.44
+  binsize = 0.22, bins = 10 10 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair sdpd/taitwater/isothermal, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes
+Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check 
+       0            0            0            0            0 
+      10        0.005   0.71224819   0.71470372    0.7008956 
+      20         0.01   0.90627589   0.90683966   0.90116506 
+      30        0.015     0.938505   0.95884272   0.93337542 
+      40         0.02   0.94394649   0.93668038   0.96468004 
+      50        0.025   0.97152309   0.97546161   0.95107762 
+      60         0.03   0.94710871   0.95678322   0.97285504 
+      70        0.035   0.96253148   0.95838642   0.95450883 
+      80         0.04   0.97581495   0.95278681   0.95099478 
+      90        0.045   0.96251614    0.9740684   0.96081505 
+     100         0.05   0.94191275   0.97137523   0.94084858 
+     110        0.055     0.953406   0.95739684   0.98574522 
+     120         0.06   0.99001614   0.99608287    0.9839996 
+     130        0.065   0.96575225   0.94309655   0.92847798 
+     140         0.07   0.97642687   0.97458638   0.94696406 
+     150        0.075   0.99316381   0.96876814   0.95440106 
+     160         0.08   0.94589744   0.95264791   0.95495169 
+     170        0.085   0.97599092   0.95336014   0.97687718 
+     180         0.09   0.97214242    0.9726305    0.9726035 
+     190        0.095   0.97577583   0.96523645    0.9756968 
+     200          0.1   0.96386053   0.97268854   0.94582436 
+Loop time of 32.5247 on 4 procs for 200 steps with 8000 atoms
+
+Performance: 265644.515 ns/day, 0.000 hours/ns, 6.149 timesteps/s
+73.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.385     | 28.409     | 28.761     |  11.1 | 87.34
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 3.582      | 3.9343     | 4.9531     |  29.7 | 12.10
+Output  | 0.022267   | 0.026073   | 0.033141   |   2.7 |  0.08
+Modify  | 0.031714   | 0.033134   | 0.034367   |   0.6 |  0.10
+Other   |            | 0.1226     |            |       |  0.38
+
+Nlocal:    2000 ave 2000 max 2000 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    8469 ave 8469 max 8469 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    364000 ave 376628 max 351184 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+
+Total # of neighbors = 1456000
+Ave neighs/atom = 182
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:32

examples/hyper/adatoms.list.37K

@@ -0,0 +1,184 @@
+create_atoms 1 single 27.5 9.5 4
+create_atoms 1 single 16 9 4
+create_atoms 1 single 10 12 4
+create_atoms 1 single 31 44 4
+create_atoms 1 single 13 17 4
+create_atoms 1 single 8.5 28.5 4
+create_atoms 1 single 23 26 4
+create_atoms 1 single 38 27 4
+create_atoms 1 single 37.5 4.5 4
+create_atoms 1 single 41.5 47.5 4
+create_atoms 1 single 20.5 37.5 4
+create_atoms 1 single 5 8 4
+create_atoms 1 single 2.5 16.5 4
+create_atoms 1 single 38.5 45.5 4
+create_atoms 1 single 9 0 4
+create_atoms 1 single 39 32 4
+create_atoms 1 single 45.5 11.5 4
+create_atoms 1 single 40 0 4
+create_atoms 1 single 44.5 2.5 4
+create_atoms 1 single 4.5 44.5 4
+create_atoms 1 single 24.5 13.5 4
+create_atoms 1 single 47.5 23.5 4
+create_atoms 1 single 1 20 4
+create_atoms 1 single 38.5 31.5 4
+create_atoms 1 single 12.5 12.5 4
+create_atoms 1 single 2 27 4
+create_atoms 1 single 21 5 4
+create_atoms 1 single 47 12 4
+create_atoms 1 single 32.5 46.5 4
+create_atoms 1 single 9.5 40.5 4
+create_atoms 1 single 8.5 2.5 4
+create_atoms 1 single 41.5 22.5 4
+create_atoms 1 single 29 11 4
+create_atoms 1 single 3.5 3.5 4
+create_atoms 1 single 5 21 4
+create_atoms 1 single 46.5 31.5 4
+create_atoms 1 single 35 46 4
+create_atoms 1 single 40.5 41.5 4
+create_atoms 1 single 10 22 4
+create_atoms 1 single 43.5 14.5 4
+create_atoms 1 single 42 42 4
+create_atoms 1 single 4 26 4
+create_atoms 1 single 19 34 4
+create_atoms 1 single 33 9 4
+create_atoms 1 single 0.5 45.5 4
+create_atoms 1 single 30.5 32.5 4
+create_atoms 1 single 25.5 5.5 4
+create_atoms 1 single 47.5 39.5 4
+create_atoms 1 single 15 13 4
+create_atoms 1 single 21 21 4
+create_atoms 1 single 14 28 4
+create_atoms 1 single 9 34 4
+create_atoms 1 single 7 38 4
+create_atoms 1 single 11 35 4
+create_atoms 1 single 20.5 45.5 4
+create_atoms 1 single 30.5 31.5 4
+create_atoms 1 single 32.5 2.5 4
+create_atoms 1 single 21.5 3.5 4
+create_atoms 1 single 23 12 4
+create_atoms 1 single 4.5 33.5 4
+create_atoms 1 single 46 43 4
+create_atoms 1 single 42.5 45.5 4
+create_atoms 1 single 4.5 10.5 4
+create_atoms 1 single 33.5 15.5 4
+create_atoms 1 single 24 5 4
+create_atoms 1 single 13 16 4
+create_atoms 1 single 16.5 23.5 4
+create_atoms 1 single 45.5 28.5 4
+create_atoms 1 single 44.5 5.5 4
+create_atoms 1 single 27.5 46.5 4
+create_atoms 1 single 44.5 12.5 4
+create_atoms 1 single 12 41 4
+create_atoms 1 single 6 4 4
+create_atoms 1 single 31.5 10.5 4
+create_atoms 1 single 1 44 4
+create_atoms 1 single 31 4 4
+create_atoms 1 single 21 33 4
+create_atoms 1 single 3 33 4
+create_atoms 1 single 15 10 4
+create_atoms 1 single 28.5 22.5 4
+create_atoms 1 single 43 1 4
+create_atoms 1 single 3.5 0.5 4
+create_atoms 1 single 41 37 4
+create_atoms 1 single 18.5 43.5 4
+create_atoms 1 single 17 27 4
+create_atoms 1 single 3 5 4
+create_atoms 1 single 18.5 23.5 4
+create_atoms 1 single 31.5 14.5 4
+create_atoms 1 single 41 31 4
+create_atoms 1 single 22 3 4
+create_atoms 1 single 14.5 40.5 4
+create_atoms 1 single 9 38 4
+create_atoms 1 single 36 42 4
+create_atoms 1 single 33 22 4
+create_atoms 1 single 15.5 47.5 4
+create_atoms 1 single 3 0 4
+create_atoms 1 single 25.5 27.5 4
+create_atoms 1 single 2.5 28.5 4
+create_atoms 1 single 29.5 28.5 4
+create_atoms 1 single 44.5 18.5 4
+create_atoms 1 single 26 40 4
+create_atoms 1 single 41 27 4
+create_atoms 1 single 39.5 5.5 4
+create_atoms 1 single 3 38 4
+create_atoms 1 single 35 29 4
+create_atoms 1 single 11 19 4
+create_atoms 1 single 18 1 4
+create_atoms 1 single 39.5 40.5 4
+create_atoms 1 single 46 17 4
+create_atoms 1 single 1.5 23.5 4
+create_atoms 1 single 28.5 23.5 4
+create_atoms 1 single 10 28 4
+create_atoms 1 single 19 47 4
+create_atoms 1 single 10.5 16.5 4
+create_atoms 1 single 38 45 4
+create_atoms 1 single 42.5 41.5 4
+create_atoms 1 single 47.5 42.5 4
+create_atoms 1 single 38 7 4
+create_atoms 1 single 10 44 4
+create_atoms 1 single 29.5 27.5 4
+create_atoms 1 single 45 30 4
+create_atoms 1 single 3 9 4
+create_atoms 1 single 8.5 35.5 4
+create_atoms 1 single 24 44 4
+create_atoms 1 single 47 4 4
+create_atoms 1 single 7.5 8.5 4
+create_atoms 1 single 32.5 41.5 4
+create_atoms 1 single 0.5 34.5 4
+create_atoms 1 single 11 8 4
+create_atoms 1 single 2 40 4
+create_atoms 1 single 25 24 4
+create_atoms 1 single 47.5 6.5 4
+create_atoms 1 single 39.5 28.5 4
+create_atoms 1 single 17 21 4
+create_atoms 1 single 32 43 4
+create_atoms 1 single 16.5 29.5 4
+create_atoms 1 single 34 34 4
+create_atoms 1 single 11.5 3.5 4
+create_atoms 1 single 39 22 4
+create_atoms 1 single 24.5 36.5 4
+create_atoms 1 single 33 31 4
+create_atoms 1 single 35.5 35.5 4
+create_atoms 1 single 14.5 34.5 4
+create_atoms 1 single 34 28 4
+create_atoms 1 single 37 41 4
+create_atoms 1 single 33 46 4
+create_atoms 1 single 27.5 28.5 4
+create_atoms 1 single 40.5 22.5 4
+create_atoms 1 single 27.5 1.5 4
+create_atoms 1 single 12 2 4
+create_atoms 1 single 36 43 4
+create_atoms 1 single 28.5 9.5 4
+create_atoms 1 single 20.5 25.5 4
+create_atoms 1 single 3 3 4
+create_atoms 1 single 38 33 4
+create_atoms 1 single 3 20 4
+create_atoms 1 single 35 11 4
+create_atoms 1 single 5 25 4
+create_atoms 1 single 36.5 6.5 4
+create_atoms 1 single 19.5 24.5 4
+create_atoms 1 single 27 41 4
+create_atoms 1 single 39.5 11.5 4
+create_atoms 1 single 21.5 2.5 4
+create_atoms 1 single 46.5 15.5 4
+create_atoms 1 single 13 24 4
+create_atoms 1 single 11 37 4
+create_atoms 1 single 11.5 31.5 4
+create_atoms 1 single 47 0 4
+create_atoms 1 single 25.5 17.5 4
+create_atoms 1 single 32 11 4
+create_atoms 1 single 8 17 4
+create_atoms 1 single 27.5 12.5 4
+create_atoms 1 single 25 7 4
+create_atoms 1 single 25.5 37.5 4
+create_atoms 1 single 12 15 4
+create_atoms 1 single 1 7 4
+create_atoms 1 single 18.5 47.5 4
+create_atoms 1 single 5 38 4
+create_atoms 1 single 42 19 4
+create_atoms 1 single 30.5 7.5 4
+create_atoms 1 single 42.5 7.5 4
+create_atoms 1 single 26.5 18.5 4
+create_atoms 1 single 18.5 1.5 4
+create_atoms 1 single 41.5 10.5 4

examples/hyper/in.hyper.global

@@ -0,0 +1,95 @@
+# 3d EAM surface for global HD
+
+# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
+# hop event on (100) surface is same distance
+# exchange event is 2 atoms moving same distance
+
+variable        Tequil index 500.0
+variable        Vmax index 0.5
+variable        qfactor index 0.3
+variable        cutbond index 3.2
+variable        cutevent index 1.1
+variable        steps index 100000
+variable        nevent index 1000
+variable        zoom index 1.8
+
+units           metal
+atom_style	atomic
+atom_modify     map array
+boundary        p p p
+
+lattice		fcc 3.92
+region		box block 0 6 0 6 0 4
+create_box	3 box
+create_atoms	1 box
+
+mass            * 1.0
+
+change_box      all z final -0.1 5.0 boundary p p f 
+create_atoms    2 single 3.5 3.5 4
+
+# define frozen substrate and mobile atoms
+
+group           adatom type 2
+region          base block INF INF INF INF 0 1.8
+set             region base type 3
+group           base type 3
+group           mobile type 1 2
+
+# pair style
+
+pair_style	eam/alloy
+pair_coeff	* * ptvoterlammps.eam Pt Pt Pt
+
+neighbor	0.5 bin
+neigh_modify    every 1 delay 5 check yes
+
+fix		1 mobile nve
+fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 858872873 zero yes
+
+timestep	0.005
+
+compute         tmobile mobile temp
+
+thermo		100
+thermo_modify   temp tmobile
+
+# thermal equilibration
+
+run             1000
+reset_timestep  0
+
+# pin base so will not move during quenches
+
+fix             freeze base setforce 0.0 0.0 0.0
+
+# event detection
+
+compute         event all event/displace ${cutevent}
+
+# hyper/global
+
+fix             HG mobile hyper/global ${cutbond} ${qfactor} ${Vmax} ${Tequil}
+
+# thermo output
+
+thermo_style    custom step temp pe f_HG f_HG[*]
+
+thermo_modify   lost ignore
+thermo_modify   temp tmobile
+
+thermo          ${nevent}
+
+# dump output options
+
+region          substrate block INF INF INF INF 1.8 3.8
+region          adatoms block INF INF INF INF 3.8 INF
+variable        acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)
+
+dump		1 all image 1000000 global.*.jpg v_acolor type &
+		zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
+dump_modify	1 pad 6 amap 1 3 sa 1 3 blue red green
+
+# run
+
+hyper           ${steps} ${nevent} HG event min 1.0e-6 1.0e-6 100 100 dump 1

examples/hyper/in.hyper.local

@@ -0,0 +1,112 @@
+# 3d EAM surface for local HD
+
+# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
+# hop event on (100) surface is same distance
+# exchange event is 2 atoms moving same distance
+
+variable        Tequil index 400.0
+variable        Vmax index 0.4
+variable        qfactor index 0.3
+variable        cutbond index 3.2
+variable        Dcut index 10.0
+variable        cutevent index 1.1
+variable        alpha index 200.0
+variable        boost index 4000.0
+variable        ghostcut index 12.0
+variable        steps index 1500
+variable        nevent index 100
+variable        nx index 8
+variable        ny index 8
+variable        zoom index 1.8
+variable        seed index 826626413
+variable        tol index 1.0e-15
+variable        add index 37K
+
+units           metal
+atom_style	atomic
+atom_modify     map array
+boundary        p p p
+comm_modify     cutoff ${ghostcut}
+
+lattice		fcc 3.92
+region		box block 0 6 0 6 0 4
+create_box	2 box
+create_atoms	1 box
+
+mass            * 1.0
+
+change_box      all z final -0.1 5.0 boundary p p f 
+
+# replicate in xy
+
+replicate       ${nx} ${ny} 1
+
+# add adatoms
+
+include         adatoms.list.${add}
+
+# define frozen substrate and mobile atoms
+
+region          base block INF INF INF INF 0 1.8
+set             region base type 2
+group           base type 2
+group           mobile type 1
+
+# pair style
+
+pair_style	eam/alloy
+pair_coeff	* * ptvoterlammps.eam Pt Pt
+
+neighbor	0.5 bin
+neigh_modify    every 1 delay 5 check yes
+
+fix		1 mobile nve
+fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
+
+timestep	0.005
+
+compute         tmobile mobile temp
+
+thermo		100
+thermo_modify   temp tmobile
+
+# thermal equilibration
+
+run             1000
+reset_timestep  0
+
+# pin base so will not move during quenches
+
+fix             freeze base setforce 0.0 0.0 0.0
+
+# event detection
+
+compute         event all event/displace ${cutevent}
+
+# hyper/local
+    
+fix             HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil} &
+                ${Dcut} ${alpha} ${boost}
+
+# thermo output
+
+thermo_style    custom step temp pe f_HL f_HL[*]
+
+thermo_modify   lost ignore
+thermo_modify   temp tmobile
+
+thermo          ${nevent}
+
+# dump
+
+region          substrate block INF INF INF INF 1.8 3.8
+region          adatoms block INF INF INF INF 3.8 INF
+variable        acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)
+
+dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 &
+		zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
+dump_modify	1 pad 6 amap 1 3 sa 1 3 blue red green
+
+# run
+
+hyper           ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1

examples/hyper/log.10Oct18.hyper.local.g++.16

@@ -0,0 +1,993 @@
+LAMMPS (10 Oct 2018)
+# 3d EAM surface for local HD
+
+# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
+# hop event on (100) surface is same distance
+# exchange event is 2 atoms moving same distance
+
+variable        Tequil index 400.0
+variable        Vmax index 0.4
+variable        qfactor index 0.3
+variable        cutbond index 3.2
+variable        Dcut index 10.0
+variable        cutevent index 1.1
+variable        alpha index 200.0
+variable        boost index 4000.0
+variable        ghostcut index 12.0
+variable        steps index 1500
+variable        nevent index 100
+variable        nx index 8
+variable        ny index 8
+variable        zoom index 1.8
+variable        seed index 826626413
+variable        tol index 1.0e-15
+variable        add index 37K
+
+units           metal
+atom_style	atomic
+atom_modify     map array
+boundary        p p p
+comm_modify     cutoff ${ghostcut}
+comm_modify     cutoff 12.0
+
+lattice		fcc 3.92
+Lattice spacing in x,y,z = 3.92 3.92 3.92
+region		box block 0 6 0 6 0 4
+create_box	2 box
+Created orthogonal box = (0 0 0) to (23.52 23.52 15.68)
+  2 by 4 by 2 MPI processor grid
+create_atoms	1 box
+Created 576 atoms
+  Time spent = 0.00108504 secs
+
+mass            * 1.0
+
+change_box      all z final -0.1 5.0 boundary p p f
+  orthogonal box = (0 0 -0.392) to (23.52 23.52 19.6)
+
+# replicate in xy
+
+replicate       ${nx} ${ny} 1
+replicate       8 ${ny} 1
+replicate       8 8 1
+  orthogonal box = (0 0 -0.392) to (188.16 188.16 19.6)
+  4 by 4 by 1 MPI processor grid
+  36864 atoms
+  Time spent = 0.0028758 secs
+
+# add adatoms
+
+include         adatoms.list.${add}
+include         adatoms.list.37K
+create_atoms 1 single 27.5 9.5 4
+Created 1 atoms
+  Time spent = 0.000183105 secs
+create_atoms 1 single 16 9 4
+Created 1 atoms
+  Time spent = 0.000178099 secs
+create_atoms 1 single 10 12 4
+Created 1 atoms
+  Time spent = 0.000179768 secs
+create_atoms 1 single 31 44 4
+Created 1 atoms
+  Time spent = 0.000184059 secs
+create_atoms 1 single 13 17 4
+Created 1 atoms
+  Time spent = 0.000173807 secs
+create_atoms 1 single 8.5 28.5 4
+Created 1 atoms
+  Time spent = 0.000167847 secs
+create_atoms 1 single 23 26 4
+Created 1 atoms
+  Time spent = 0.000179052 secs
+create_atoms 1 single 38 27 4
+Created 1 atoms
+  Time spent = 0.000169992 secs
+create_atoms 1 single 37.5 4.5 4
+Created 1 atoms
+  Time spent = 0.000166178 secs
+create_atoms 1 single 41.5 47.5 4
+Created 1 atoms
+  Time spent = 0.000172138 secs
+create_atoms 1 single 20.5 37.5 4
+Created 1 atoms
+  Time spent = 0.000165939 secs
+create_atoms 1 single 5 8 4
+Created 1 atoms
+  Time spent = 0.00018096 secs
+create_atoms 1 single 2.5 16.5 4
+Created 1 atoms
+  Time spent = 0.000165939 secs
+create_atoms 1 single 38.5 45.5 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 9 0 4
+Created 1 atoms
+  Time spent = 0.000168085 secs
+create_atoms 1 single 39 32 4
+Created 1 atoms
+  Time spent = 0.000170946 secs
+create_atoms 1 single 45.5 11.5 4
+Created 1 atoms
+  Time spent = 0.00018096 secs
+create_atoms 1 single 40 0 4
+Created 1 atoms
+  Time spent = 0.000168085 secs
+create_atoms 1 single 44.5 2.5 4
+Created 1 atoms
+  Time spent = 0.000165939 secs
+create_atoms 1 single 4.5 44.5 4
+Created 1 atoms
+  Time spent = 0.000168085 secs
+create_atoms 1 single 24.5 13.5 4
+Created 1 atoms
+  Time spent = 0.000165939 secs
+create_atoms 1 single 47.5 23.5 4
+Created 1 atoms
+  Time spent = 0.00018096 secs
+create_atoms 1 single 1 20 4
+Created 1 atoms
+  Time spent = 0.000166893 secs
+create_atoms 1 single 38.5 31.5 4
+Created 1 atoms
+  Time spent = 0.000168085 secs
+create_atoms 1 single 12.5 12.5 4
+Created 1 atoms
+  Time spent = 0.000169992 secs
+create_atoms 1 single 2 27 4
+Created 1 atoms
+  Time spent = 0.000188828 secs
+create_atoms 1 single 21 5 4
+Created 1 atoms
+  Time spent = 0.000174999 secs
+create_atoms 1 single 47 12 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 32.5 46.5 4
+Created 1 atoms
+  Time spent = 0.000165939 secs
+create_atoms 1 single 9.5 40.5 4
+Created 1 atoms
+  Time spent = 0.000166893 secs
+create_atoms 1 single 8.5 2.5 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 41.5 22.5 4
+Created 1 atoms
+  Time spent = 0.000174046 secs
+create_atoms 1 single 29 11 4
+Created 1 atoms
+  Time spent = 0.000166893 secs
+create_atoms 1 single 3.5 3.5 4
+Created 1 atoms
+  Time spent = 0.000165224 secs
+create_atoms 1 single 5 21 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 46.5 31.5 4
+Created 1 atoms
+  Time spent = 0.000166178 secs
+create_atoms 1 single 35 46 4
+Created 1 atoms
+  Time spent = 0.000183105 secs
+create_atoms 1 single 40.5 41.5 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 10 22 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 43.5 14.5 4
+Created 1 atoms
+  Time spent = 0.000169992 secs
+create_atoms 1 single 42 42 4
+Created 1 atoms
+  Time spent = 0.000165939 secs
+create_atoms 1 single 4 26 4
+Created 1 atoms
+  Time spent = 0.000174999 secs
+create_atoms 1 single 19 34 4
+Created 1 atoms
+  Time spent = 0.000163078 secs
+create_atoms 1 single 33 9 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 0.5 45.5 4
+Created 1 atoms
+  Time spent = 0.000163078 secs
+create_atoms 1 single 30.5 32.5 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 25.5 5.5 4
+Created 1 atoms
+  Time spent = 0.000178099 secs
+create_atoms 1 single 47.5 39.5 4
+Created 1 atoms
+  Time spent = 0.000165939 secs
+create_atoms 1 single 15 13 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 21 21 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 14 28 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 9 34 4
+Created 1 atoms
+  Time spent = 0.000174999 secs
+create_atoms 1 single 7 38 4
+Created 1 atoms
+  Time spent = 0.000175953 secs
+create_atoms 1 single 11 35 4
+Created 1 atoms
+  Time spent = 0.000154972 secs
+create_atoms 1 single 20.5 45.5 4
+Created 1 atoms
+  Time spent = 0.000156879 secs
+create_atoms 1 single 30.5 31.5 4
+Created 1 atoms
+  Time spent = 0.000159979 secs
+create_atoms 1 single 32.5 2.5 4
+Created 1 atoms
+  Time spent = 0.000166178 secs
+create_atoms 1 single 21.5 3.5 4
+Created 1 atoms
+  Time spent = 0.000157833 secs
+create_atoms 1 single 23 12 4
+Created 1 atoms
+  Time spent = 0.000155926 secs
+create_atoms 1 single 4.5 33.5 4
+Created 1 atoms
+  Time spent = 0.000156879 secs
+create_atoms 1 single 46 43 4
+Created 1 atoms
+  Time spent = 0.000155926 secs
+create_atoms 1 single 42.5 45.5 4
+Created 1 atoms
+  Time spent = 0.000156879 secs
+create_atoms 1 single 4.5 10.5 4
+Created 1 atoms
+  Time spent = 0.000158072 secs
+create_atoms 1 single 33.5 15.5 4
+Created 1 atoms
+  Time spent = 0.000157833 secs
+create_atoms 1 single 24 5 4
+Created 1 atoms
+  Time spent = 0.000154018 secs
+create_atoms 1 single 13 16 4
+Created 1 atoms
+  Time spent = 0.000158072 secs
+create_atoms 1 single 16.5 23.5 4
+Created 1 atoms
+  Time spent = 0.000156164 secs
+create_atoms 1 single 45.5 28.5 4
+Created 1 atoms
+  Time spent = 0.000247002 secs
+create_atoms 1 single 44.5 5.5 4
+Created 1 atoms
+  Time spent = 0.000156164 secs
+create_atoms 1 single 27.5 46.5 4
+Created 1 atoms
+  Time spent = 0.000155926 secs
+create_atoms 1 single 44.5 12.5 4
+Created 1 atoms
+  Time spent = 0.000157833 secs
+create_atoms 1 single 12 41 4
+Created 1 atoms
+  Time spent = 0.000156879 secs
+create_atoms 1 single 6 4 4
+Created 1 atoms
+  Time spent = 0.0001688 secs
+create_atoms 1 single 31.5 10.5 4
+Created 1 atoms
+  Time spent = 0.00015521 secs
+create_atoms 1 single 1 44 4
+Created 1 atoms
+  Time spent = 0.000154972 secs
+create_atoms 1 single 31 4 4
+Created 1 atoms
+  Time spent = 0.000156879 secs
+create_atoms 1 single 21 33 4
+Created 1 atoms
+  Time spent = 0.000156879 secs
+create_atoms 1 single 3 33 4
+Created 1 atoms
+  Time spent = 0.000164032 secs
+create_atoms 1 single 15 10 4
+Created 1 atoms
+  Time spent = 0.0001719 secs
+create_atoms 1 single 28.5 22.5 4
+Created 1 atoms
+  Time spent = 0.000153065 secs
+create_atoms 1 single 43 1 4
+Created 1 atoms
+  Time spent = 0.000155926 secs
+create_atoms 1 single 3.5 0.5 4
+Created 1 atoms
+  Time spent = 0.000154972 secs
+create_atoms 1 single 41 37 4
+Created 1 atoms
+  Time spent = 0.000153065 secs
+create_atoms 1 single 18.5 43.5 4
+Created 1 atoms
+  Time spent = 0.000213146 secs
+create_atoms 1 single 17 27 4
+Created 1 atoms
+  Time spent = 0.000159979 secs
+create_atoms 1 single 3 5 4
+Created 1 atoms
+  Time spent = 0.000153065 secs
+create_atoms 1 single 18.5 23.5 4
+Created 1 atoms
+  Time spent = 0.000154972 secs
+create_atoms 1 single 31.5 14.5 4
+Created 1 atoms
+  Time spent = 0.000154972 secs
+create_atoms 1 single 41 31 4
+Created 1 atoms
+  Time spent = 0.000155926 secs
+create_atoms 1 single 22 3 4
+Created 1 atoms
+  Time spent = 0.00015521 secs
+create_atoms 1 single 14.5 40.5 4
+Created 1 atoms
+  Time spent = 0.000154018 secs
+create_atoms 1 single 9 38 4
+Created 1 atoms
+  Time spent = 0.000154018 secs
+create_atoms 1 single 36 42 4
+Created 1 atoms
+  Time spent = 0.000155926 secs
+create_atoms 1 single 33 22 4
+Created 1 atoms
+  Time spent = 0.000163078 secs
+create_atoms 1 single 15.5 47.5 4
+Created 1 atoms
+  Time spent = 0.000154972 secs
+create_atoms 1 single 3 0 4
+Created 1 atoms
+  Time spent = 0.000154972 secs
+create_atoms 1 single 25.5 27.5 4
+Created 1 atoms
+  Time spent = 0.000176907 secs
+create_atoms 1 single 2.5 28.5 4
+Created 1 atoms
+  Time spent = 0.000154972 secs
+create_atoms 1 single 29.5 28.5 4
+Created 1 atoms
+  Time spent = 0.000162125 secs
+create_atoms 1 single 44.5 18.5 4
+Created 1 atoms
+  Time spent = 0.000152826 secs
+create_atoms 1 single 26 40 4
+Created 1 atoms
+  Time spent = 0.000155926 secs
+create_atoms 1 single 41 27 4
+Created 1 atoms
+  Time spent = 0.000158072 secs
+create_atoms 1 single 39.5 5.5 4
+Created 1 atoms
+  Time spent = 0.000155926 secs
+create_atoms 1 single 3 38 4
+Created 1 atoms
+  Time spent = 0.000152826 secs
+create_atoms 1 single 35 29 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 11 19 4
+Created 1 atoms
+  Time spent = 0.000164986 secs
+create_atoms 1 single 18 1 4
+Created 1 atoms
+  Time spent = 0.000146866 secs
+create_atoms 1 single 39.5 40.5 4
+Created 1 atoms
+  Time spent = 0.000146866 secs
+create_atoms 1 single 46 17 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 1.5 23.5 4
+Created 1 atoms
+  Time spent = 0.000154018 secs
+create_atoms 1 single 28.5 23.5 4
+Created 1 atoms
+  Time spent = 0.000145912 secs
+create_atoms 1 single 10 28 4
+Created 1 atoms
+  Time spent = 0.000159979 secs
+create_atoms 1 single 19 47 4
+Created 1 atoms
+  Time spent = 0.000148058 secs
+create_atoms 1 single 10.5 16.5 4
+Created 1 atoms
+  Time spent = 0.000147104 secs
+create_atoms 1 single 38 45 4
+Created 1 atoms
+  Time spent = 0.000144958 secs
+create_atoms 1 single 42.5 41.5 4
+Created 1 atoms
+  Time spent = 0.000161886 secs
+create_atoms 1 single 47.5 42.5 4
+Created 1 atoms
+  Time spent = 0.000147104 secs
+create_atoms 1 single 38 7 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 10 44 4
+Created 1 atoms
+  Time spent = 0.000145912 secs
+create_atoms 1 single 29.5 27.5 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 45 30 4
+Created 1 atoms
+  Time spent = 0.000145912 secs
+create_atoms 1 single 3 9 4
+Created 1 atoms
+  Time spent = 0.000154018 secs
+create_atoms 1 single 8.5 35.5 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 24 44 4
+Created 1 atoms
+  Time spent = 0.000145912 secs
+create_atoms 1 single 47 4 4
+Created 1 atoms
+  Time spent = 0.000144958 secs
+create_atoms 1 single 7.5 8.5 4
+Created 1 atoms
+  Time spent = 0.000144958 secs
+create_atoms 1 single 32.5 41.5 4
+Created 1 atoms
+  Time spent = 0.000157833 secs
+create_atoms 1 single 0.5 34.5 4
+Created 1 atoms
+  Time spent = 0.000145912 secs
+create_atoms 1 single 11 8 4
+Created 1 atoms
+  Time spent = 0.000147104 secs
+create_atoms 1 single 2 40 4
+Created 1 atoms
+  Time spent = 0.000144958 secs
+create_atoms 1 single 25 24 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 47.5 6.5 4
+Created 1 atoms
+  Time spent = 0.000147104 secs
+create_atoms 1 single 39.5 28.5 4
+Created 1 atoms
+  Time spent = 0.000154972 secs
+create_atoms 1 single 17 21 4
+Created 1 atoms
+  Time spent = 0.000164032 secs
+create_atoms 1 single 32 43 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 16.5 29.5 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 34 34 4
+Created 1 atoms
+  Time spent = 0.000145912 secs
+create_atoms 1 single 11.5 3.5 4
+Created 1 atoms
+  Time spent = 0.000154018 secs
+create_atoms 1 single 39 22 4
+Created 1 atoms
+  Time spent = 0.000144958 secs
+create_atoms 1 single 24.5 36.5 4
+Created 1 atoms
+  Time spent = 0.000144958 secs
+create_atoms 1 single 33 31 4
+Created 1 atoms
+  Time spent = 0.000144958 secs
+create_atoms 1 single 35.5 35.5 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 14.5 34.5 4
+Created 1 atoms
+  Time spent = 0.000146866 secs
+create_atoms 1 single 34 28 4
+Created 1 atoms
+  Time spent = 0.000153065 secs
+create_atoms 1 single 37 41 4
+Created 1 atoms
+  Time spent = 0.000145912 secs
+create_atoms 1 single 33 46 4
+Created 1 atoms
+  Time spent = 0.000144958 secs
+create_atoms 1 single 27.5 28.5 4
+Created 1 atoms
+  Time spent = 0.000145197 secs
+create_atoms 1 single 40.5 22.5 4
+Created 1 atoms
+  Time spent = 0.000150919 secs
+create_atoms 1 single 27.5 1.5 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 12 2 4
+Created 1 atoms
+  Time spent = 0.000151873 secs
+create_atoms 1 single 36 43 4
+Created 1 atoms
+  Time spent = 0.000144005 secs
+create_atoms 1 single 28.5 9.5 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 20.5 25.5 4
+Created 1 atoms
+  Time spent = 0.000144958 secs
+create_atoms 1 single 3 3 4
+Created 1 atoms
+  Time spent = 0.000144005 secs
+create_atoms 1 single 38 33 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 3 20 4
+Created 1 atoms
+  Time spent = 0.000154972 secs
+create_atoms 1 single 35 11 4
+Created 1 atoms
+  Time spent = 0.000145912 secs
+create_atoms 1 single 5 25 4
+Created 1 atoms
+  Time spent = 0.000144005 secs
+create_atoms 1 single 36.5 6.5 4
+Created 1 atoms
+  Time spent = 0.000144005 secs
+create_atoms 1 single 19.5 24.5 4
+Created 1 atoms
+  Time spent = 0.000236988 secs
+create_atoms 1 single 27 41 4
+Created 1 atoms
+  Time spent = 0.000169992 secs
+create_atoms 1 single 39.5 11.5 4
+Created 1 atoms
+  Time spent = 0.000138998 secs
+create_atoms 1 single 21.5 2.5 4
+Created 1 atoms
+  Time spent = 0.000136852 secs
+create_atoms 1 single 46.5 15.5 4
+Created 1 atoms
+  Time spent = 0.000138998 secs
+create_atoms 1 single 13 24 4
+Created 1 atoms
+  Time spent = 0.000137091 secs
+create_atoms 1 single 11 37 4
+Created 1 atoms
+  Time spent = 0.000144005 secs
+create_atoms 1 single 11.5 31.5 4
+Created 1 atoms
+  Time spent = 0.000144958 secs
+create_atoms 1 single 47 0 4
+Created 1 atoms
+  Time spent = 0.000138044 secs
+create_atoms 1 single 25.5 17.5 4
+Created 1 atoms
+  Time spent = 0.00014019 secs
+create_atoms 1 single 32 11 4
+Created 1 atoms
+  Time spent = 0.000138044 secs
+create_atoms 1 single 8 17 4
+Created 1 atoms
+  Time spent = 0.000138044 secs
+create_atoms 1 single 27.5 12.5 4
+Created 1 atoms
+  Time spent = 0.000137806 secs
+create_atoms 1 single 25 7 4
+Created 1 atoms
+  Time spent = 0.000146151 secs
+create_atoms 1 single 25.5 37.5 4
+Created 1 atoms
+  Time spent = 0.000139952 secs
+create_atoms 1 single 12 15 4
+Created 1 atoms
+  Time spent = 0.000138044 secs
+create_atoms 1 single 1 7 4
+Created 1 atoms
+  Time spent = 0.000138998 secs
+create_atoms 1 single 18.5 47.5 4
+Created 1 atoms
+  Time spent = 0.000138044 secs
+create_atoms 1 single 5 38 4
+Created 1 atoms
+  Time spent = 0.000136852 secs
+create_atoms 1 single 42 19 4
+Created 1 atoms
+  Time spent = 0.000149012 secs
+create_atoms 1 single 30.5 7.5 4
+Created 1 atoms
+  Time spent = 0.000138044 secs
+create_atoms 1 single 42.5 7.5 4
+Created 1 atoms
+  Time spent = 0.000138998 secs
+create_atoms 1 single 26.5 18.5 4
+Created 1 atoms
+  Time spent = 0.000153065 secs
+create_atoms 1 single 18.5 1.5 4
+Created 1 atoms
+  Time spent = 0.000137091 secs
+create_atoms 1 single 41.5 10.5 4
+Created 1 atoms
+  Time spent = 0.000140905 secs
+
+# define frozen substrate and mobile atoms
+
+region          base block INF INF INF INF 0 1.8
+set             region base type 2
+  18432 settings made for type
+group           base type 2
+18432 atoms in group base
+group           mobile type 1
+18616 atoms in group mobile
+
+# pair style
+
+pair_style	eam/alloy
+pair_coeff	* * ptvoterlammps.eam Pt Pt
+
+neighbor	0.5 bin
+neigh_modify    every 1 delay 5 check yes
+
+fix		1 mobile nve
+fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
+fix		2 mobile langevin 400.0 ${Tequil} 1.0 ${seed} zero yes
+fix		2 mobile langevin 400.0 400.0 1.0 ${seed} zero yes
+fix		2 mobile langevin 400.0 400.0 1.0 826626413 zero yes
+
+timestep	0.005
+
+compute         tmobile mobile temp
+
+thermo		100
+thermo_modify   temp tmobile
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
+
+# thermal equilibration
+
+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 = 6.07583
+  ghost atom cutoff = 12
+  binsize = 3.03792, bins = 62 62 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair eam/alloy, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.359 | 3.359 | 3.36 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -206220.22            0   -206220.22   -52155.664 
+     100    188.18127   -206044.43            0   -205591.63    -25068.83 
+     200    274.34464   -205860.78            0   -205200.66   -40191.797 
+     300    325.66286   -205750.01            0    -204966.4   -31510.222 
+     400    352.48242   -205675.42            0   -204827.28   -35058.064 
+     500    370.88571   -205619.66            0   -204727.25   -32735.022 
+     600    388.62129   -205592.87            0   -204657.78   -33904.556 
+     700    389.54874   -205579.73            0    -204642.4   -32769.852 
+     800    395.56074   -205576.82            0   -204625.03   -33755.948 
+     900    398.03458   -205564.48            0   -204606.74   -32777.103 
+    1000    401.24089   -205562.85            0    -204597.4   -33785.341 
+Loop time of 4.3687 on 16 procs for 1000 steps with 37048 atoms
+
+Performance: 98.885 ns/day, 0.243 hours/ns, 228.901 timesteps/s
+98.4% CPU use with 16 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.2988     | 3.3828     | 3.4667     |   2.3 | 77.43
+Neigh   | 0.20856    | 0.23127    | 0.24382    |   1.9 |  5.29
+Comm    | 0.33313    | 0.45075    | 0.55485    |   9.2 | 10.32
+Output  | 0.00042987 | 0.00044042 | 0.00049591 |   0.0 |  0.01
+Modify  | 0.18811    | 0.28363    | 0.36798    |   9.7 |  6.49
+Other   |            | 0.01983    |            |       |  0.45
+
+Nlocal:    2315.5 ave 2332 max 2297 min
+Histogram: 2 0 0 3 4 0 2 1 2 2
+Nghost:    3186.31 ave 3205 max 3170 min
+Histogram: 2 1 3 0 2 3 2 1 0 2
+Neighs:    55590.9 ave 56174 max 55103 min
+Histogram: 2 2 1 1 4 1 3 0 0 2
+
+Total # of neighbors = 889454
+Ave neighs/atom = 24.0082
+Neighbor list builds = 105
+Dangerous builds = 0
+reset_timestep  0
+
+# pin base so will not move during quenches
+
+fix             freeze base setforce 0.0 0.0 0.0
+
+# event detection
+
+compute         event all event/displace ${cutevent}
+compute         event all event/displace 1.1
+
+# hyper/local
+
+fix             HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 ${qfactor} ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 0.3 ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 0.3 0.4 ${Tequil}                 ${Dcut} ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 ${Dcut} ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 ${alpha} ${boost}
+fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 200.0 ${boost}
+fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 200.0 4000.0
+
+# thermo output
+
+thermo_style    custom step temp pe f_HL f_HL[*]
+WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:705)
+
+thermo_modify   lost ignore
+thermo_modify   temp tmobile
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
+
+thermo          ${nevent}
+thermo          100
+
+# dump
+
+region          substrate block INF INF INF INF 1.8 3.8
+region          adatoms block INF INF INF INF 3.8 INF
+variable        acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)
+
+dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 		zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
+dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 		zoom 1.8 adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
+dump_modify	1 pad 6 amap 1 3 sa 1 3 blue red green
+
+# run
+
+hyper           ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
+hyper           1500 ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
+hyper           1500 100 HL event min ${tol} ${tol} 1000 1000 dump 1
+hyper           1500 100 HL event min 1.0e-15 ${tol} 1000 1000 dump 1
+hyper           1500 100 HL event min 1.0e-15 1.0e-15 1000 1000 dump 1
+WARNING: Resetting reneighboring criteria during hyper (../hyper.cpp:133)
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.07583
+  ghost atom cutoff = 12
+  binsize = 3.03792, bins = 62 62 7
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair eam/alloy, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix hyper/local, occasional
+      attributes: full, newton on, cut 10
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.566 | 7.567 | 7.567 Mbytes
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+       0    401.24089   -205562.85            0            0            0            1            0            0            0            0            0            0            0            0        4e+19            0            0            0            0            0            0            0            0            0            0            0 
+      77    401.24089   -206534.96            0            0            0            1            0            0            0            0            0            0            0            0        4e+19            0            0            0            0            0            0            0         1540            0            0            0 
+Loop time of 0.540347 on 16 procs for 77 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+       0    401.24089   -205562.85    23.271302           74   0.18753621            1    6.0138739    703.62325            0   0.55802338    3.5350432            0            0            0        4e+19    10.115141    10.115141            0            0            0            0            0            0            0            0            0 
+     100    399.15639   -205546.21    22.904368           90   0.32935524   0.39929142    6.0138739    703.62325  0.026229865   0.91517139    3.9968927        91.88    0.3995539    0.4009724   0.39695676    10.262823    10.262823            0            0            0            0            0         2000            0            0            0 
+Loop time of 0.579085 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     100    399.15639   -205546.21    22.904368           90   0.32935524   0.39929142    6.0138739    703.62325  0.026229865   0.91517139    3.9968927        91.88    0.3995539    0.4009724   0.39695676    10.262823    10.262823            0            0            0            0            0         2000            0            0            0 
+     184    399.15639   -206534.96    22.904368           90   0.32935524   0.39929142    6.0138739    703.62325  0.026229865   0.91517139    3.9968927    49.934783   0.21714886    0.4009724   0.39695676    10.262823    10.262823            0            0            0            0            0         3680            0            0            0 
+Loop time of 0.556056 on 16 procs for 84 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     100    399.15639   -205546.21    22.903938           90   0.32935524   0.39929142    6.0138739    703.62325  0.026229865   0.91517139    3.9968927        91.88    0.3995539    0.4009724   0.39695676    10.262823    10.262823            0            0            0            0            0         2000            0            0            0 
+     200    403.01717   -205543.17    20.844359           90    0.3291605   0.39888693    6.0138739    703.62325  0.039527213   0.94418421    4.0368484        90.95   0.39930574    0.4019706   0.39554353    10.262823    10.262823            0            0            0            0            0         4000            0            0            0 
+Loop time of 0.581214 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     200    403.01717   -205543.17    20.844359           90    0.3291605   0.39888693    6.0138739    703.62325  0.039527213   0.94418421    4.0368484        90.95   0.39930574    0.4019706   0.39554353    10.262823    10.262823            0            0            0            0            0         4000            0            0            0 
+     275    403.01717   -206534.96    20.844359           90    0.3291605   0.39888693    6.0138739    703.62325  0.039527213   0.94418421    4.0368484    66.145455   0.29040418    0.4019706   0.39554353    10.262823    10.262823            0            0            0            0            0         5500            0            0            0 
+Loop time of 0.481812 on 16 procs for 75 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     200    403.01717   -205543.17    21.115577           91    0.3291605   0.39888693    6.0138739    703.62325  0.039527213   0.94418421    4.0368484        90.95   0.39930574    0.4019706   0.39554353    10.262823    10.262823            0            0            0            0            0         4000            0            0            0 
+     300    399.01963   -205541.46    19.137336           85   0.32442182   0.39862755    6.0138739    703.62325  0.046873868   0.94776891    4.0368484        92.02   0.39912484   0.40296919   0.39497622    10.288936    10.288936            0            0            0            0            0         6000            0            0            0 
+Loop time of 0.5757 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     300    399.01963   -205541.46    19.137336           85   0.32442182   0.39862755    6.0138739    703.62325  0.046873868   0.94776891    4.0368484        92.02   0.39912484   0.40296919   0.39497622    10.288936    10.288936            0            0            0            0            0         6000            0            0            0 
+     377    399.01963   -206534.96    19.137336           85   0.32442182   0.39862755    6.0138739    703.62325  0.046873868   0.94776891    4.0368484    73.225464   0.31760598   0.40296919   0.39497622    10.288936    10.288936            0            0            0            0            0         7540            0            0            0 
+Loop time of 0.514907 on 16 procs for 77 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     300    399.01963   -205541.46    19.137003           85   0.32442182   0.39862755    6.0138739    703.62325  0.046873868   0.94776891    4.0368484        92.02   0.39912484   0.40296919   0.39497622    10.288936    10.288936            0            0            0            0            0         6000            0            0            0 
+     400    398.15351   -205544.87    20.470844           93   0.34589451   0.39828754    6.0138739    703.62325  0.049952465   0.94776891    4.0779385      92.0375   0.39894967   0.40395328    0.3932824    10.307052    10.307052            0            0            0            0            0         8000            0            0            0 
+Loop time of 0.577371 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     400    398.15351   -205544.87    20.470844           93   0.34589451   0.39828754    6.0138739    703.62325  0.049952465   0.94776891    4.0779385      92.0375   0.39894967   0.40395328    0.3932824    10.307052    10.307052            0            0            0            0            0         8000            0            0            0 
+     471    398.15351   -206534.96    20.470844           93   0.34589451   0.39828754    6.0138739    703.62325  0.049952465   0.94776891    4.0779385    78.163482   0.33881076   0.40395328    0.3932824    10.307052    10.307052            0            0            0            0            0         9420            0            0            0 
+Loop time of 0.465473 on 16 procs for 71 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     400    398.15351   -205544.87    20.470689           93   0.34589451   0.39828754    6.0138739    703.62325  0.049952465   0.94776891    4.0779385      92.0375   0.39894967   0.40395328    0.3932824    10.307052    10.307052            0            0            0            0            0         8000            0            0            0 
+     500    400.29399   -205544.98    17.051242           83   0.42140172   0.39805251    6.0138739    703.62325  0.056986933    1.0907861    4.0779385       91.986   0.39879563   0.40493836   0.39165573    10.307052    10.307052            0            0            0            0            0        10000            0            0            0 
+Loop time of 0.579188 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     500    400.29399   -205544.98    17.051242           83   0.42140172   0.39805251    6.0138739    703.62325  0.056986933    1.0907861    4.0779385       91.986   0.39879563   0.40493836   0.39165573    10.307052    10.307052            0            0            0            0            0        10000            0            0            0 
+     577    400.29399   -206534.96    17.051242           83   0.42140172   0.39805251    6.0138739    703.62325  0.056986933    1.0910651    4.0779385    79.710572    0.3455768   0.40493836   0.39165573    10.307052    10.307052            0            0            0            0            0        11540            0            0            0 
+Loop time of 0.502193 on 16 procs for 77 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     500    400.29399   -205544.98    17.051107           83   0.42140172   0.39805251    6.0138739    703.62325  0.056986933    1.0910651    4.0779385       91.986   0.39879563   0.40493836   0.39165573    10.307052    10.307052            0            0            0            0            0        10000            0            0            0 
+     600    400.96099   -205544.56    20.904479           91   0.41219484   0.39780769    6.0138739    703.62325  0.061331691    1.1358732    4.0779385    92.013333   0.39864794   0.40593806   0.39067432    10.307052    10.307052            0            0            0            0            0        12000            0            0            0 
+Loop time of 0.694955 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     600    400.96099   -205544.56    20.904479           91   0.41219484   0.39780769    6.0138739    703.62325  0.061331691    1.1358732    4.0779385    92.013333   0.39864794   0.40593806   0.39067432    10.307052    10.307052            0            0            0            0            0        12000            0            0            0 
+     680    400.96099   -206534.96    20.904479           91   0.41219484   0.39780769    6.0138739    703.62325  0.061331691    1.1358732    4.0779385    81.188235   0.35174818   0.40593806   0.39067432    10.307052    10.307052            0            0            0            0            0        13600            0            0            0 
+Loop time of 0.529041 on 16 procs for 80 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     600    400.96099   -205544.56    20.904088           91   0.41219484   0.39780769    6.0138739    703.62325  0.061331691    1.1358732    4.0779385    92.013333   0.39864794   0.40593806   0.39067432    10.307052    10.307052            0            0            0            0            0        12000            0            0            0 
+     700    397.78618   -205534.96    20.361513           95   0.54466603   0.39757442    6.0138739    703.62325  0.061146951    1.1853748    4.1995704        92.12   0.39850836   0.40693553   0.38981834    10.307052    10.307052            0            0            0            0            0        14000            0            0            0 
+Loop time of 0.590093 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     700    397.78618   -205534.96    20.361513           95   0.54466603   0.39757442    6.0138739    703.62325  0.061146951    1.2139704    4.1995704        92.12   0.39850836   0.40693553   0.38981834    10.307052    10.307052            0            0            0            0            0        14000            0            0            0 
+     790    397.78618   -206534.96    20.361513           95   0.54466603   0.39757442    6.0138739    703.62325  0.061146951    2.2107138    4.1995704    81.625316   0.35310868   0.40693553   0.38981834    10.307052    10.307052            0            0            0            0            0        15800            0            0            0 
+Loop time of 0.594281 on 16 procs for 90 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     700    397.78618   -205534.96    20.236364           94   0.51088027   0.39757442    6.0138739    703.62325  0.061146951    2.2107138     4.205089        92.12   0.39850836   0.40693553   0.38981834    10.307052    10.307052            0            0            0            0            0        14000            1            2            6 
+     800    399.66919   -205547.44    21.285461           94   0.56079766   0.39739855    6.0138739    703.62325   0.06556778    2.2107138    4.3041291     92.36625    0.3983806   0.40793368      0.38875    10.307052    10.385797            0            0            0            0            0        16000            1            2            6 
+Loop time of 0.583824 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     800    399.66919   -205547.44    21.285461           94   0.56079766   0.39739855    6.0138739    703.62325   0.06556778    2.2107138    4.3041291     92.36625    0.3983806   0.40793368      0.38875    10.307052    10.385797            0            0            0            0            0        16000            1            2            6 
+     872    399.66919   -206535.54    21.285461           94   0.56079766   0.39739855    6.0138739    703.62325   0.06556778    2.3177682    4.3041291    84.739679   0.36548679   0.40793368      0.38875    10.307052    10.385797            0            0            0            0            0        17440            1            2            6 
+Loop time of 0.46886 on 16 procs for 72 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     800    399.66919   -205547.44      21.2852           94   0.44964213   0.39739855    6.0138739    703.62325   0.06556778    2.3177682    4.3041291     92.36625    0.3983806   0.40793368      0.38875    10.307052    10.385797            0            0            0            0            0        16000            2            4           13 
+     900     401.5853   -205544.22    19.308189           94   0.47610389   0.39719191    6.0138739    703.62325  0.066991886    2.3177682    4.3041291    92.017778   0.39825974   0.40893337    0.3878576    10.307052    10.385797            0            0            0            0            0        18000            2            4           13 
+Loop time of 0.585137 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     900     401.5853   -205544.22    19.308189           94   0.47610389   0.39719191    6.0138739    703.62325  0.066991886    2.3177682    4.3041291    92.017778   0.39825974   0.40893337    0.3878576    10.307052    10.385797            0            0            0            0            0        18000            2            4           13 
+     975     401.5853   -206535.54    19.308189           94   0.47610389   0.39719191    6.0138739    703.62325  0.066991886    2.3177682    4.3041291    84.939487   0.36762438   0.40893337    0.3878576    10.307052    10.385797            0            0            0            0            0        19500            2            4           13 
+Loop time of 0.502012 on 16 procs for 75 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+     900     401.5853   -205544.22    19.307938           94   0.47610389   0.39719191    6.0138739    703.62325  0.066991886    2.3177682    4.3041291    92.017778   0.39825974   0.40893337    0.3878576    10.307052    10.385797            0            0            0            0            0        18000            2            4           13 
+    1000    395.06218   -205526.35    17.514295           91   0.42044925   0.39716259    6.0138739    703.62325  0.067937867    2.3177682    4.3041291       92.511   0.39814962   0.40993184    0.3867545    10.307052    10.385797            0            0            0            0            0        20000            2            4           13 
+Loop time of 0.588597 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1000    395.06218   -205526.35    17.514295           91   0.42044925   0.39716259    6.0138739    703.62325  0.067937867    2.3177682    4.3041291       92.511   0.39814962   0.40993184    0.3867545    10.307052    10.385797            0            0            0            0            0        20000            2            4           13 
+    1083    395.06218   -206535.54    17.514295           91   0.42044925   0.39716259    6.0138739    703.62325  0.067937867    2.3177682    4.3041291    85.421053   0.36763584   0.40993184    0.3867545    10.307052    10.385797            0            0            0            0            0        21660            2            4           13 
+Loop time of 0.543222 on 16 procs for 83 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1000    395.06218   -205526.35    17.514191           91   0.42044925   0.39716259    6.0138739    703.62325  0.067937867    2.3177682    4.3041291       92.511   0.39814962   0.40993184    0.3867545    10.307052    10.385797            0            0            0            0            0        20000            2            4           13 
+    1100    400.04484   -205545.92     19.52012           89   0.58919981   0.39704631    6.0138739    703.62325  0.069136967    2.3177682    4.4265979    92.517273   0.39805636   0.41093134   0.38574293    10.307052    10.385797            0            0            0            0            0        22000            2            4           13 
+Loop time of 0.590075 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1100    400.04484   -205545.92     19.52012           89   0.58919981   0.39704631    6.0138739    703.62325  0.069136967    2.3177682    4.4265979    92.517273   0.39805636   0.41093134   0.38574293    10.307052    10.385797            0            0            0            0            0        22000            2            4           13 
+    1177    400.04484   -206535.53     19.52012           89   0.58919981   0.39704631    6.0138739    703.62325  0.069136967    2.3177682    4.4265979    86.464741   0.37201529   0.41093134   0.38574293    10.307052    10.385797            0            0            0            0            0        23540            2            4           13 
+Loop time of 0.500839 on 16 procs for 77 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1100    400.04484   -205545.92    19.518413           89     0.429675   0.39705701    6.0137119     703.6043  0.069136967    2.3177682    4.4265979    92.517273   0.39805636   0.41093134   0.38574293    10.307052    10.385797            0            0            0            0            0        22000            3            6           19 
+    1200     400.7462    -205543.2    21.169548           91   0.32511134   0.39679665    6.0137119     703.6043   0.06750442    2.3177682    4.4265979    92.376667   0.39796198   0.41191655    0.3846039    10.307052    10.385797            0            0            0            0            0        24000            3            6           19 
+Loop time of 0.583971 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1200     400.7462    -205543.2    21.169548           91   0.32511134   0.39679665    6.0137119     703.6043   0.06750442    2.3177682    4.4265979    92.376667   0.39796198   0.41191655    0.3846039    10.307052    10.385797            0            0            0            0            0        24000            3            6           19 
+    1277     400.7462   -206535.53    21.169548           91   0.32511134   0.39679665    6.0137119     703.6043   0.06750442    2.3177682    4.4265979    86.806578   0.37396584   0.41191655    0.3846039    10.307052    10.385797            0            0            0            0            0        25540            3            6           19 
+Loop time of 0.509118 on 16 procs for 77 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1200     400.7462    -205543.2    21.169281           91   0.32511134   0.39679665    6.0137119     703.6043   0.06750442    2.3177682    4.4265979    92.376667   0.39796198   0.41191655    0.3846039    10.307052    10.385797            0            0            0            0            0        24000            3            6           19 
+    1300    398.53702   -205539.33     21.35815           94   0.38773898   0.39659935    6.0137119     703.6043  0.067808168    2.3177682    4.4265979    92.500769   0.39786514   0.41289519    0.3846039    10.307052    10.385797            0            0            0            0            0        26000            3            6           19 
+Loop time of 0.587306 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1300    398.53702   -205539.33     21.35815           94   0.38773898   0.39659935    6.0137119     703.6043  0.067808168    2.3177682    4.4265979    92.500769   0.39786514   0.41289519    0.3846039    10.307052    10.385797            0            0            0            0            0        26000            3            6           19 
+    1375    398.53702   -206535.53     21.35815           94   0.38773898   0.39659935    6.0137119     703.6043  0.067808168    2.3177682    4.4265979    87.455273   0.37616341   0.41289519    0.3846039    10.307052    10.385797            0            0            0            0            0        27500            3            6           19 
+Loop time of 0.483781 on 16 procs for 75 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1300    398.53702   -205539.33     21.35787           94   0.38773898   0.39659935    6.0137119     703.6043  0.067808168    2.3177682    4.4265979    92.500769   0.39786514   0.41289519    0.3846039    10.307052    10.385797            0            0            0            0            0        26000            3            6           19 
+    1400    402.80537    -205549.3    19.481887           95   0.32554201   0.39648737    6.0137119     703.6043  0.069550538    2.3177682    4.4265979    92.666429   0.39776836   0.41389491   0.38420043    10.307052    10.385797            0            0            0            0            0        28000            3            6           19 
+Loop time of 0.586411 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1400    402.80537    -205549.3    19.481887           95   0.32554201   0.39648737    6.0137119     703.6043  0.069550538    2.3177682    4.4265979    92.666429   0.39776836   0.41389491   0.38420043    10.307052    10.385797            0            0            0            0            0        28000            3            6           19 
+    1471    402.80537   -206535.53    19.481887           95   0.32554201   0.39648737    6.0137119     703.6043  0.069550538    2.3177682    4.4265979    88.193746   0.37856948   0.41389491   0.38420043    10.307052    10.385797            0            0            0            0            0        29420            3            6           19 
+Loop time of 0.473799 on 16 procs for 71 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1400    402.80537    -205549.3    19.481632           95   0.32554201   0.39648737    6.0137119     703.6043  0.069550538    2.3177682    4.4265979    92.666429   0.39776836   0.41389491   0.38420043    10.307052    10.385797            0            0            0            0            0        28000            3            6           19 
+    1500     402.0803    -205537.7    20.903964           99    0.3340498   0.39635609    6.0137119     703.6043  0.070409086    2.3177682    4.4265979    92.857333   0.39767858   0.41489448   0.38372784    10.333041    10.385797            0            0            0            0            0        30000            3            6           19 
+Loop time of 0.587342 on 16 procs for 100 steps with 37048 atoms
+
+Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
+    1500     402.0803    -205537.7    20.903964           99    0.3340498   0.39635609    6.0137119     703.6043  0.070409086    2.3177682    4.4265979    92.857333   0.39767858   0.41489448   0.38372784    10.333041    10.385797            0            0            0            0            0        30000            3            6           19 
+    1574     402.0803   -206535.53    20.903964           99    0.3340498   0.39635609    6.0137119     703.6043  0.070409086    2.3177682    4.4265979    88.491741   0.37898213   0.41489448   0.38372784    10.333041    10.385797            0            0            0            0            0        31480            3            6           19 
+Loop time of 0.493982 on 16 procs for 74 steps with 37048 atoms
+
+Final hyper stats ...
+
+Cummulative quantities for fix hyper:
+  hyper time = 30000
+  event timesteps = 3
+  # of atoms in events = 6
+Quantities for this hyper run:
+  event timesteps = 3
+  # of atoms in events = 6
+  max length of any bond = 4.4266
+  max drift distance of any atom = 2.31777
+  fraction of steps & bonds with zero bias = 0.0704091
+Current quantities:
+  ave bonds/atom = 6.01371
+Cummulative quantities specific tofix hyper/local:
+  # of new bonds formed = 19
+  max bonds/atom = 13
+Quantities for this hyper run specific to fix hyper/local:
+  ave boosted bonds/step = 92.8573
+  ave boost coeff of all bonds = 0.397679
+  max boost coeff of any bond = 0.414894
+  min boost coeff of any bond = 0.383728
+  max dist from my box of any non-maxstrain bond ghost atom = 10.333
+  max dist from my box of any bond ghost atom = 10.3858
+  count of ghost bond neighbors not found on reneighbor steps = 0
+  lost bond partners = 0
+  ave bias coeff for lost bond partners = 0
+  bias overlaps = 0
+  non-matching bias coeffs = 0
+  CPU time for bond builds = 0.044807
+Current quantities specific to fix hyper/local:
+  neighbor bonds/bond = 703.604
+  ave boost coeff for all bonds = 0.396356
+
+Loop time of 17.9972 on 16 procs for 1500 steps with 37048 atoms
+
+Performance: 36.006 ns/day, 0.667 hours/ns, 83.346 timesteps/s
+120.7% CPU use with 16 MPI tasks x no OpenMP threads
+
+Hyper stats:
+  Dynamics time (%) = 8.87027 (49.2869)
+  Quench   time (%) = 8.15972 (45.3388)
+  Other    time (%) = 1.2212 (6.78552)
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.6       | 11.848     | 12.043     |   3.9 | 65.83
+Neigh   | 0.50025    | 0.52638    | 0.55163    |   2.1 |  2.92
+Comm    | 0.34528    | 0.49905    | 0.66742    |  13.3 |  2.77
+Output  | 0.0021305  | 0.0021461  | 0.0022686  |   0.1 |  0.01
+Modify  | 3.7498     | 3.9009     | 3.9786     |   2.8 | 21.67
+Other   |            | 1.221      |            |       |  6.79
+
+Nlocal:    2315.5 ave 2361 max 2267 min
+Histogram: 1 1 0 4 2 1 3 3 0 1
+Nghost:    3187.88 ave 3236 max 3141 min
+Histogram: 1 0 3 2 2 1 4 1 1 1
+Neighs:    53950.6 ave 54989 max 53049 min
+Histogram: 2 0 3 2 1 2 4 1 0 1
+FullNghs:  542951 ave 554654 max 533224 min
+Histogram: 1 2 3 1 2 2 2 2 0 1
+
+Total # of neighbors = 8687214
+Ave neighs/atom = 234.485
+Neighbor list builds = 165
+Dangerous builds = 0
+Total wall time: 0:00:22

lib/colvars/colvar.cpp

@@ -426,8 +426,8 @@ int colvar::init_custom_function(std::string const &conf)
 
   if (x.size() != value_evaluators.size()) {
     cvm::error("Error: based on custom function type, expected "
-        + cvm::to_str(x.size()) + " scalar expressions, but "
-        + cvm::to_str(value_evaluators.size() + " were found.\n"));
+               + cvm::to_str(x.size()) + " scalar expressions, but "
+               + cvm::to_str(value_evaluators.size()) + " were found.\n");
     return INPUT_ERROR;
   }
 
@@ -455,36 +455,42 @@ int colvar::init_grid_parameters(std::string const &conf)
   }
 
   lower_boundary.type(value());
-
   upper_boundary.type(value());
-  upper_wall.type(value());
 
   if (is_enabled(f_cv_scalar)) {
 
     if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) {
       enable(f_cv_lower_boundary);
     }
-    std::string lw_conf, uw_conf;
-
-    if (get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0, parse_silent)) {
-      cvm::log("Warning: lowerWallConstant and lowerWall are deprecated, "
-               "please define a harmonicWalls bias instead.\n");
-      lower_wall.type(value());
-      get_keyval(conf, "lowerWall", lower_wall, lower_boundary);
-      lw_conf = std::string("\n\
-    lowerWallConstant "+cvm::to_str(lower_wall_k*width*width)+"\n\
-    lowerWalls "+cvm::to_str(lower_wall)+"\n");
-    }
 
     if (get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary)) {
       enable(f_cv_upper_boundary);
     }
 
-    if (get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0, parse_silent)) {
-      cvm::log("Warning: upperWallConstant and upperWall are deprecated, "
-               "please define a harmonicWalls bias instead.\n");
+    std::string lw_conf, uw_conf;
+    if (get_keyval(conf, "lowerWallConstant", lower_wall_k, 0.0,
+                   parse_silent)) {
+      cvm::log("Reading legacy options lowerWall and lowerWallConstant: "
+               "consider using a harmonicWalls restraint.\n");
+      lower_wall.type(value());
+      if (!get_keyval(conf, "lowerWall", lower_wall, lower_boundary)) {
+        cvm::log("Warning: lowerWall will need to be "
+                 "defined explicitly in the next release.\n");
+      }
+      lw_conf = std::string("\n\
+    lowerWallConstant "+cvm::to_str(lower_wall_k*width*width)+"\n\
+    lowerWalls "+cvm::to_str(lower_wall)+"\n");
+    }
+
+    if (get_keyval(conf, "upperWallConstant", upper_wall_k, 0.0,
+                   parse_silent)) {
+      cvm::log("Reading legacy options upperWall and upperWallConstant: "
+               "consider using a harmonicWalls restraint.\n");
       upper_wall.type(value());
-      get_keyval(conf, "upperWall", upper_wall, upper_boundary);
+      if (!get_keyval(conf, "upperWall", upper_wall, upper_boundary)) {
+        cvm::log("Warning: upperWall will need to be "
+                 "defined explicitly in the next release.\n");
+      }
       uw_conf = std::string("\n\
     upperWallConstant "+cvm::to_str(upper_wall_k*width*width)+"\n\
     upperWalls "+cvm::to_str(upper_wall)+"\n");
@@ -677,6 +683,7 @@ template<typename def_class_name> int colvar::init_components_type(std::string c
     if (cvcp != NULL) {
       cvcs.push_back(cvcp);
       cvcp->check_keywords(def_conf, def_config_key);
+      cvcp->config_key = def_config_key;
       if (cvm::get_error()) {
         cvm::error("Error: in setting up component \""+
                    std::string(def_config_key)+"\".\n", INPUT_ERROR);
@@ -1022,13 +1029,13 @@ int colvar::calc()
 
 int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
 {
-  colvarproxy *proxy = cvm::main()->proxy;
-
-  int error_code = COLVARS_OK;
   if (cvm::debug())
     cvm::log("Calculating colvar \""+this->name+"\", components "+
              cvm::to_str(first_cvc)+" through "+cvm::to_str(first_cvc+num_cvcs)+".\n");
 
+  colvarproxy *proxy = cvm::main()->proxy;
+  int error_code = COLVARS_OK;
+
   error_code |= check_cvc_range(first_cvc, num_cvcs);
   if (error_code != COLVARS_OK) {
     return error_code;
@@ -1059,9 +1066,10 @@ int colvar::collect_cvc_data()
   if (cvm::debug())
     cvm::log("Calculating colvar \""+this->name+"\"'s properties.\n");
 
+  colvarproxy *proxy = cvm::main()->proxy;
   int error_code = COLVARS_OK;
 
-  if (cvm::step_relative() > 0) {
+  if ((cvm::step_relative() > 0) && (!proxy->total_forces_same_step())){
     // Total force depends on Jacobian derivative from previous timestep
     // collect_cvc_total_forces() uses the previous value of jd
     error_code |= collect_cvc_total_forces();
@@ -1069,6 +1077,10 @@ int colvar::collect_cvc_data()
   error_code |= collect_cvc_values();
   error_code |= collect_cvc_gradients();
   error_code |= collect_cvc_Jacobians();
+  if (proxy->total_forces_same_step()){
+    // Use Jacobian derivative from this timestep
+    error_code |= collect_cvc_total_forces();
+  }
   error_code |= calc_colvar_properties();
 
   if (cvm::debug())
@@ -1394,6 +1406,13 @@ int colvar::calc_colvar_properties()
       vr.reset(); // (already 0; added for clarity)
     }
 
+    // Special case of a repeated timestep (eg. multiple NAMD "run" statements)
+    // revert values of the extended coordinate and velocity prior to latest integration
+    if (cvm::step_relative() == prev_timestep) {
+      xr = prev_xr;
+      vr = prev_vr;
+    }
+
     // report the restraint center as "value"
     x_reported = xr;
     v_reported = vr;
@@ -1450,7 +1469,6 @@ cvm::real colvar::update_forces_energy()
   // extended variable if there is one
 
   if (is_enabled(f_cv_extended_Lagrangian)) {
-
     if (cvm::debug()) {
       cvm::log("Updating extended-Lagrangian degree of freedom.\n");
     }
@@ -1502,6 +1520,11 @@ cvm::real colvar::update_forces_energy()
       ft_reported = f_ext;
     }
 
+    // backup in case we need to revert this integration timestep
+    // if the same MD timestep is re-run
+    prev_xr = xr;
+    prev_vr = vr;
+
     // leapfrog: starting from x_i, f_i, v_(i-1/2)
     vr  += (0.5 * dt) * f_ext / ext_mass;
     // Because of leapfrog, kinetic energy at time i is approximate
@@ -1638,18 +1661,26 @@ int colvar::set_cvc_flags(std::vector<bool> const &flags)
 }
 
 
+void colvar::update_active_cvc_square_norm()
+{
+  active_cvc_square_norm = 0.0;
+  for (size_t i = 0; i < cvcs.size(); i++) {
+    if (cvcs[i]->is_enabled()) {
+      active_cvc_square_norm += cvcs[i]->sup_coeff * cvcs[i]->sup_coeff;
+    }
+  }
+}
+
+
 int colvar::update_cvc_flags()
 {
   // Update the enabled/disabled status of cvcs if necessary
   if (cvc_flags.size()) {
     n_active_cvcs = 0;
-    active_cvc_square_norm = 0.;
-
     for (size_t i = 0; i < cvcs.size(); i++) {
       cvcs[i]->set_enabled(f_cvc_active, cvc_flags[i]);
       if (cvcs[i]->is_enabled()) {
         n_active_cvcs++;
-        active_cvc_square_norm += cvcs[i]->sup_coeff * cvcs[i]->sup_coeff;
       }
     }
     if (!n_active_cvcs) {
@@ -1657,12 +1688,49 @@ int colvar::update_cvc_flags()
       return COLVARS_ERROR;
     }
     cvc_flags.clear();
+
+    update_active_cvc_square_norm();
   }
 
   return COLVARS_OK;
 }
 
 
+int colvar::update_cvc_config(std::vector<std::string> const &confs)
+{
+  cvm::log("Updating configuration for colvar \""+name+"\"");
+
+  if (confs.size() != cvcs.size()) {
+    return cvm::error("Error: Wrong number of CVC config strings.  "
+                      "For those CVCs that are not being changed, try passing "
+                      "an empty string.", INPUT_ERROR);
+  }
+
+  int error_code = COLVARS_OK;
+  int num_changes = 0;
+  for (size_t i = 0; i < cvcs.size(); i++) {
+    if (confs[i].size()) {
+      std::string conf(confs[i]);
+      cvm::increase_depth();
+      error_code |= cvcs[i]->colvar::cvc::init(conf);
+      error_code |= cvcs[i]->check_keywords(conf,
+                                            cvcs[i]->config_key.c_str());
+      cvm::decrease_depth();
+      num_changes++;
+    }
+  }
+
+  if (num_changes == 0) {
+    cvm::log("Warning: no changes were applied through modifycvcs; "
+             "please check that its argument is a list of strings.\n");
+  }
+
+  update_active_cvc_square_norm();
+
+  return error_code;
+}
+
+
 // ******************** METRIC FUNCTIONS ********************
 // Use the metrics defined by \link cvc \endlink objects
 

lib/colvars/colvar.h

@@ -171,8 +171,12 @@ protected:
   // Options for extended_lagrangian
   /// Restraint center
   colvarvalue xr;
+  /// Previous value of the restraint center;
+  colvarvalue prev_xr;
   /// Velocity of the restraint center
   colvarvalue vr;
+  /// Previous velocity of the restraint center
+  colvarvalue prev_vr;
   /// Mass of the restraint center
   cvm::real ext_mass;
   /// Restraint force constant
@@ -352,6 +356,9 @@ public:
   /// \brief Updates the flags in the CVC objects, and their number
   int update_cvc_flags();
 
+  /// \brief Modify the configuration of CVCs (currently, only base class data)
+  int update_cvc_config(std::vector<std::string> const &confs);
+
 protected:
   /// \brief Number of CVC objects with an active flag
   size_t n_active_cvcs;
@@ -359,10 +366,17 @@ protected:
   /// Sum of square coefficients for active cvcs
   cvm::real active_cvc_square_norm;
 
+  /// Update the sum of square coefficients for active cvcs
+  void update_active_cvc_square_norm();
+
   /// \brief Absolute timestep number when this colvar was last updated
   int prev_timestep;
 
 public:
+
+  /// \brief Return the number of CVC objects defined
+  inline size_t num_cvcs() const { return cvcs.size(); }
+
   /// \brief Return the number of CVC objects with an active flag (as set by update_cvc_flags)
   inline size_t num_active_cvcs() const { return n_active_cvcs; }
 
@@ -371,21 +385,21 @@ public:
   ///
   /// Handles correctly symmetries and periodic boundary conditions
   cvm::real dist2(colvarvalue const &x1,
-                   colvarvalue const &x2) const;
+                  colvarvalue const &x2) const;
 
   /// \brief Use the internal metrics (as from \link cvc
   /// \endlink objects) to calculate square distances and gradients
   ///
   /// Handles correctly symmetries and periodic boundary conditions
   colvarvalue dist2_lgrad(colvarvalue const &x1,
-                           colvarvalue const &x2) const;
+                          colvarvalue const &x2) const;
 
   /// \brief Use the internal metrics (as from \link cvc
   /// \endlink objects) to calculate square distances and gradients
   ///
   /// Handles correctly symmetries and periodic boundary conditions
   colvarvalue dist2_rgrad(colvarvalue const &x1,
-                           colvarvalue const &x2) const;
+                          colvarvalue const &x2) const;
 
   /// \brief Use the internal metrics (as from \link cvc
   /// \endlink objects) to wrap a value into a standard interval

lib/colvars/colvaratoms.cpp

@@ -21,6 +21,8 @@ cvm::atom::atom()
 {
   index = -1;
   id = -1;
+  mass = 1.0;
+  charge = 1.0;
   reset_data();
 }
 
@@ -395,7 +397,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
       }
 
       // NOTE: calls to add_atom() and/or add_atom_id() are in the proxy-implemented function
-      cvm::load_atoms(atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
+      parse_error |= cvm::load_atoms(atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
     }
   }
 

lib/colvars/colvaratoms.h

@@ -90,7 +90,7 @@ public:
   /// Destructor
   ~atom();
 
-  /// Set mutable data (everything except id and mass) to zero; update mass
+  /// Set mutable data (everything except id and mass) to zero
   inline void reset_data()
   {
     pos = cvm::atom_pos(0.0);

lib/colvars/colvarbias_abf.cpp

@@ -564,6 +564,8 @@ int colvarbias_abf::replica_share() {
   return COLVARS_OK;
 }
 
+
+
 void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool append)
 {
   std::string  samples_out_name = prefix + ".count";
@@ -572,10 +574,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
 
   std::ostream *samples_os =
     cvm::proxy->output_stream(samples_out_name, mode);
-  if (!samples_os) {
-    cvm::error("Error opening ABF samples file " + samples_out_name + " for writing");
-    return;
-  }
+  if (!samples_os) return;
   samples->write_multicol(*samples_os);
   cvm::proxy->close_output_stream(samples_out_name);
 
@@ -583,10 +582,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
   if (num_variables() > 2) {
     std::string  samples_dx_out_name = prefix + ".count.dx";
     std::ostream *samples_dx_os = cvm::proxy->output_stream(samples_dx_out_name, mode);
-    if (!samples_os) {
-      cvm::error("Error opening samples file " + samples_dx_out_name + " for writing");
-      return;
-    }
+    if (!samples_os) return;
     samples->write_opendx(*samples_dx_os);
     *samples_dx_os << std::endl;
     cvm::proxy->close_output_stream(samples_dx_out_name);
@@ -594,10 +590,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
 
   std::ostream *gradients_os =
     cvm::proxy->output_stream(gradients_out_name, mode);
-  if (!gradients_os) {
-    cvm::error("Error opening ABF gradient file " + gradients_out_name + " for writing");
-    return;
-  }
+  if (!gradients_os) return;
   gradients->write_multicol(*gradients_os);
   cvm::proxy->close_output_stream(gradients_out_name);
 
@@ -609,20 +602,14 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
 
     std::string  pmf_out_name = prefix + ".pmf";
     std::ostream *pmf_os = cvm::proxy->output_stream(pmf_out_name, mode);
-    if (!pmf_os) {
-      cvm::error("Error opening pmf file " + pmf_out_name + " for writing");
-      return;
-    }
+    if (!pmf_os) return;
     pmf->write_multicol(*pmf_os);
 
     // In dimension higher than 2, dx is easier to handle and visualize
     if (num_variables() > 2) {
       std::string  pmf_dx_out_name = prefix + ".pmf.dx";
       std::ostream *pmf_dx_os = cvm::proxy->output_stream(pmf_dx_out_name, mode);
-      if (!pmf_dx_os) {
-        cvm::error("Error opening pmf file " + pmf_dx_out_name + " for writing");
-        return;
-      }
+      if (!pmf_dx_os) return;
       pmf->write_opendx(*pmf_dx_os);
       *pmf_dx_os << std::endl;
       cvm::proxy->close_output_stream(pmf_dx_out_name);
@@ -639,10 +626,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
 
     std::ostream *z_samples_os =
       cvm::proxy->output_stream(z_samples_out_name, mode);
-    if (!z_samples_os) {
-      cvm::error("Error opening eABF z-histogram file " + z_samples_out_name + " for writing");
-      return;
-    }
+    if (!z_samples_os) return;
     z_samples->write_multicol(*z_samples_os);
     cvm::proxy->close_output_stream(z_samples_out_name);
 
@@ -651,10 +635,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
 
       std::ostream *z_gradients_os =
         cvm::proxy->output_stream(z_gradients_out_name, mode);
-      if (!z_gradients_os) {
-        cvm::error("Error opening eABF z-gradient file " + z_gradients_out_name + " for writing");
-        return;
-      }
+      if (!z_gradients_os) return;
       z_gradients->write_multicol(*z_gradients_os);
       cvm::proxy->close_output_stream(z_gradients_out_name);
     }
@@ -672,10 +653,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
 
     std::ostream *czar_gradients_os =
       cvm::proxy->output_stream(czar_gradients_out_name, mode);
-    if (!czar_gradients_os) {
-      cvm::error("Error opening CZAR gradient file " + czar_gradients_out_name + " for writing");
-      return;
-    }
+    if (!czar_gradients_os) return;
     czar_gradients->write_multicol(*czar_gradients_os);
     cvm::proxy->close_output_stream(czar_gradients_out_name);
 
@@ -688,20 +666,14 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
 
       std::string  czar_pmf_out_name = prefix + ".czar.pmf";
       std::ostream *czar_pmf_os = cvm::proxy->output_stream(czar_pmf_out_name, mode);
-      if (!czar_pmf_os) {
-        cvm::error("Error opening CZAR pmf file " + czar_pmf_out_name + " for writing");
-        return;
-      }
+      if (!czar_pmf_os) return;
       czar_pmf->write_multicol(*czar_pmf_os);
 
       // In dimension higher than 2, dx is easier to handle and visualize
       if (num_variables() > 2) {
         std::string  czar_pmf_dx_out_name = prefix + ".czar.pmf.dx";
         std::ostream *czar_pmf_dx_os = cvm::proxy->output_stream(czar_pmf_dx_out_name, mode);
-        if (!czar_pmf_dx_os) {
-          cvm::error("Error opening CZAR pmf file " + czar_pmf_dx_out_name + " for writing");
-          return;
-        }
+        if (!czar_pmf_dx_os) return;
         czar_pmf->write_opendx(*czar_pmf_dx_os);
         *czar_pmf_dx_os << std::endl;
         cvm::proxy->close_output_stream(czar_pmf_dx_out_name);
@@ -854,3 +826,9 @@ std::istream & colvarbias_abf::read_state_data(std::istream& is)
 
   return is;
 }
+
+int colvarbias_abf::write_output_files()
+{
+  write_gradients_samples(output_prefix);
+  return COLVARS_OK;
+}

lib/colvars/colvarbias_abf.h

@@ -136,13 +136,13 @@ private:
 
   /// Write human-readable FE gradients and sample count, and DX file in dim > 2
   void write_gradients_samples(const std::string &prefix, bool append = false);
-  void write_last_gradients_samples(const std::string &prefix, bool append = false);
 
   /// Read human-readable FE gradients and sample count (if not using restart)
   void read_gradients_samples();
 
-  std::istream& read_state_data(std::istream&);
-  std::ostream& write_state_data(std::ostream&);
+  virtual std::istream& read_state_data(std::istream&);
+  virtual std::ostream& write_state_data(std::ostream&);
+  virtual int write_output_files();
 };
 
 #endif

lib/colvars/colvarbias_restraint.cpp

@@ -996,11 +996,16 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
   if ((lower_walls.size() > 0) && (upper_walls.size() > 0)) {
     for (i = 0; i < num_variables(); i++) {
       if (lower_walls[i] >= upper_walls[i]) {
-        cvm::error("Error: one upper wall, "+
-                   cvm::to_str(upper_walls[i])+
-                   ", is not higher than the lower wall, "+
-                   cvm::to_str(lower_walls[i])+".\n",
-                   INPUT_ERROR);
+        return cvm::error("Error: one upper wall, "+
+                          cvm::to_str(upper_walls[i])+
+                          ", is not higher than the lower wall, "+
+                          cvm::to_str(lower_walls[i])+".\n",
+                          INPUT_ERROR);
+      }
+      if (variables(i)->dist2(lower_walls[i], upper_walls[i]) < 1.0e-12) {
+        return cvm::error("Error: lower wall and upper wall are equal "
+                          "in the domain of the variable \""+
+                          variables(i)->name+"\".\n", INPUT_ERROR);
       }
     }
     if (lower_wall_k * upper_wall_k == 0.0) {
@@ -1279,13 +1284,16 @@ cvm::real colvarbias_restraint_linear::energy_difference(std::string const &conf
 
 cvm::real colvarbias_restraint_linear::restraint_potential(size_t i) const
 {
-  return force_k / variables(i)->width * (variables(i)->value() - colvar_centers[i]);
+  return force_k / variables(i)->width * (variables(i)->value() -
+                                          colvar_centers[i]).sum();
 }
 
 
 colvarvalue const colvarbias_restraint_linear::restraint_force(size_t i) const
 {
-  return -1.0 * force_k / variables(i)->width;
+  colvarvalue dummy(variables(i)->value());
+  dummy.set_ones();
+  return -1.0 * force_k / variables(i)->width * dummy;
 }
 
 

lib/colvars/colvarcomp.cpp

@@ -43,16 +43,27 @@ colvar::cvc::cvc(std::string const &conf)
 
 int colvar::cvc::init(std::string const &conf)
 {
-  int error_code = COLVARS_OK;
   if (cvm::debug())
     cvm::log("Initializing cvc base object.\n");
 
-  get_keyval(conf, "name", this->name, this->name);
+  std::string const old_name(name);
+
   if (name.size() > 0) {
-    // Temporary description until child object is initialized
-    description = "cvc " + name;
-  } else {
-    description = "uninitialized cvc";
+    cvm::log("Updating configuration for component \""+name+"\"");
+  }
+
+  if (get_keyval(conf, "name", name, name)) {
+    if (name.size() > 0) {
+      description = "cvc \"" + name + "\" of type " + function_type;
+    } else {
+      description = "unnamed cvc";
+    }
+    if ((name != old_name) && (old_name.size() > 0)) {
+      cvm::error("Error: cannot rename component \""+old_name+
+                 "\" after initialization (new name = \""+name+"\")",
+                 INPUT_ERROR);
+      name = old_name;
+    }
   }
 
   get_keyval(conf, "componentCoeff", sup_coeff, sup_coeff);
@@ -78,7 +89,7 @@ int colvar::cvc::init(std::string const &conf)
   if (cvm::debug())
     cvm::log("Done initializing cvc base object.\n");
 
-  return error_code;
+  return cvm::get_error();
 }
 
 

lib/colvars/colvarcomp.h

@@ -82,6 +82,9 @@ public:
   /// this variable definition should be set within the constructor.
   std::string function_type;
 
+  /// Keyword used in the input to denote this CVC
+  std::string config_key;
+
   /// \brief Coefficient in the polynomial combination (default: 1.0)
   cvm::real sup_coeff;
   /// \brief Exponent in the polynomial combination (default: 1)
@@ -834,49 +837,70 @@ protected:
   cvm::real     r0;
   /// \brief "Cutoff vector" for anisotropic calculation
   cvm::rvector  r0_vec;
-  /// \brief Wheter dist/r0 or \vec{dist}*\vec{1/r0_vec} should ne be
-  /// used
+  /// \brief Whether r/r0 or \vec{r}*\vec{1/r0_vec} should be used
   bool b_anisotropic;
   /// Integer exponent of the function numerator
   int en;
   /// Integer exponent of the function denominator
   int ed;
-  /// \brief If true, group2 will be treated as a single atom
-  /// (default: loop over all pairs of atoms in group1 and group2)
-  bool b_group2_center_only;
+
+  /// \brief If true, group2 will be treated as a single atom, stored in this
+  /// accessory group
+  cvm::atom_group *group2_center;
+
+  /// Tolerance for the pair list
+  cvm::real tolerance;
+
+  /// Frequency of update of the pair list
+  int pairlist_freq;
+
+  /// Pair list
+  bool *pairlist;
+
 public:
-  /// Constructor
+
   coordnum(std::string const &conf);
   coordnum();
-  virtual ~coordnum() {}
+  ~coordnum();
+
   virtual void calc_value();
   virtual void calc_gradients();
   virtual void apply_force(colvarvalue const &force);
-  template<bool b_gradients>
-  /// \brief Calculate a coordination number through the function
-  /// (1-x**n)/(1-x**m), x = |A1-A2|/r0 \param r0 "cutoff" for the
-  /// coordination number \param exp_num \i n exponent \param exp_den
-  /// \i m exponent \param A1 atom \param A2 atom
-  static cvm::real switching_function(cvm::real const &r0,
-                                      int const &exp_num, int const &exp_den,
-                                      cvm::atom &A1, cvm::atom &A2);
-
-  template<bool b_gradients>
-  /// \brief Calculate a coordination number through the function
-  /// (1-x**n)/(1-x**m), x = |(A1-A2)*(r0_vec)^-|1 \param r0_vec
-  /// vector of different cutoffs in the three directions \param
-  /// exp_num \i n exponent \param exp_den \i m exponent \param A1
-  /// atom \param A2 atom
-  static cvm::real switching_function(cvm::rvector const &r0_vec,
-                                      int const &exp_num, int const &exp_den,
-                                      cvm::atom &A1, cvm::atom &A2);
-
   virtual cvm::real dist2(colvarvalue const &x1,
                           colvarvalue const &x2) const;
   virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
                                   colvarvalue const &x2) const;
   virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
                                   colvarvalue const &x2) const;
+
+  enum {
+    ef_null = 0,
+    ef_gradients = 1,
+    ef_anisotropic = (1<<8),
+    ef_use_pairlist = (1<<9),
+    ef_rebuild_pairlist = (1<<10)
+  };
+
+  /// \brief Calculate a coordination number through the function
+  /// (1-x**n)/(1-x**m), where x = |A1-A2|/r0 \param r0, r0_vec "cutoff" for
+  /// the coordination number (scalar or vector depending on user choice)
+  /// \param en Numerator exponent \param ed Denominator exponent \param First
+  /// atom \param Second atom \param pairlist_elem pointer to pair flag for
+  /// this pair \param tolerance A pair is defined as having a larger
+  /// coordination than this number
+  template<int flags>
+  static cvm::real switching_function(cvm::real const &r0,
+                                      cvm::rvector const &r0_vec,
+                                      int en,
+                                      int ed,
+                                      cvm::atom &A1,
+                                      cvm::atom &A2,
+                                      bool **pairlist_elem,
+                                      cvm::real tolerance);
+
+  /// Main workhorse function
+  template<int flags> int compute_coordnum();
+
 };
 
 
@@ -887,7 +911,8 @@ class colvar::selfcoordnum
   : public colvar::cvc
 {
 protected:
-  /// First atom group
+
+  /// Selected atoms
   cvm::atom_group  *group1;
   /// \brief "Cutoff" for isotropic calculation (default)
   cvm::real     r0;
@@ -895,22 +920,18 @@ protected:
   int en;
   /// Integer exponent of the function denominator
   int ed;
+  cvm::real tolerance;
+  int pairlist_freq;
+  bool *pairlist;
+
 public:
-  /// Constructor
+
   selfcoordnum(std::string const &conf);
   selfcoordnum();
-  virtual ~selfcoordnum() {}
+  ~selfcoordnum();
   virtual void calc_value();
   virtual void calc_gradients();
   virtual void apply_force(colvarvalue const &force);
-  template<bool b_gradients>
-  /// \brief Calculate a coordination number through the function
-  /// (1-x**n)/(1-x**m), x = |A1-A2|/r0 \param r0 "cutoff" for the
-  /// coordination number \param exp_num \i n exponent \param exp_den
-  /// \i m exponent \param A1 atom \param A2 atom
-  static cvm::real switching_function(cvm::real const &r0,
-                                      int const &exp_num, int const &exp_den,
-                                      cvm::atom &A1, cvm::atom &A2);
 
   virtual cvm::real dist2(colvarvalue const &x1,
                           colvarvalue const &x2) const;
@@ -918,6 +939,9 @@ public:
                                   colvarvalue const &x2) const;
   virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
                                   colvarvalue const &x2) const;
+
+  /// Main workhorse function
+  template<int flags> int compute_selfcoordnum();
 };
 
 
@@ -947,26 +971,6 @@ public:
   virtual void calc_value();
   virtual void calc_gradients();
   virtual void apply_force(colvarvalue const &force);
-  template<bool b_gradients>
-  /// \brief Calculate a coordination number through the function
-  /// (1-x**n)/(1-x**m), x = |A1-A2|/r0 \param r0 "cutoff" for the
-  /// coordination number \param exp_num \i n exponent \param exp_den
-  /// \i m exponent \param A1 atom \param A2 atom
-  static cvm::real switching_function(cvm::real const &r0,
-                                      int const &exp_num, int const &exp_den,
-                                      cvm::atom &A1, cvm::atom &A2);
-
-  /*
-  template<bool b_gradients>
-  /// \brief Calculate a coordination number through the function
-  /// (1-x**n)/(1-x**m), x = |(A1-A2)*(r0_vec)^-|1 \param r0_vec
-  /// vector of different cutoffs in the three directions \param
-  /// exp_num \i n exponent \param exp_den \i m exponent \param A1
-  /// atom \param A2 atom
-  static cvm::real switching_function(cvm::rvector const &r0_vec,
-                                      int const &exp_num, int const &exp_den,
-                                      cvm::atom &A1, cvm::atom &A2);
-  */
 
   virtual cvm::real dist2(colvarvalue const &x1,
                           colvarvalue const &x2) const;

lib/colvars/colvarcomp_coordnums.cpp

@@ -18,45 +18,36 @@
 
 
 
-
-template<bool calculate_gradients>
+template<int flags>
 cvm::real colvar::coordnum::switching_function(cvm::real const &r0,
-                                               int const &en,
-                                               int const &ed,
+                                               cvm::rvector const &r0_vec,
+                                               int en,
+                                               int ed,
                                                cvm::atom &A1,
-                                               cvm::atom &A2)
+                                               cvm::atom &A2,
+                                               bool **pairlist_elem,
+                                               cvm::real pairlist_tol)
 {
-  cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
-  cvm::real const l2 = diff.norm2()/(r0*r0);
-
-  // Assume en and ed are even integers, and avoid sqrt in the following
-  int const en2 = en/2;
-  int const ed2 = ed/2;
-
-  cvm::real const xn = cvm::integer_power(l2, en2);
-  cvm::real const xd = cvm::integer_power(l2, ed2);
-  cvm::real const func = (1.0-xn)/(1.0-xd);
-
-  if (calculate_gradients) {
-    cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
-    cvm::rvector const dl2dx = (2.0/(r0*r0))*diff;
-    A1.grad += (-1.0)*dFdl2*dl2dx;
-    A2.grad +=        dFdl2*dl2dx;
+  if ((flags & ef_use_pairlist) && !(flags & ef_rebuild_pairlist)) {
+    bool const within = **pairlist_elem;
+    (*pairlist_elem)++;
+    if (!within) {
+      return 0.0;
+    }
   }
 
-  return func;
-}
+  cvm::rvector const r0sq_vec(r0_vec.x*r0_vec.x,
+                              r0_vec.y*r0_vec.y,
+                              r0_vec.z*r0_vec.z);
 
-
-template<bool calculate_gradients>
-cvm::real colvar::coordnum::switching_function(cvm::rvector const &r0_vec,
-                                               int const &en,
-                                               int const &ed,
-                                               cvm::atom &A1,
-                                               cvm::atom &A2)
-{
   cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
-  cvm::rvector const scal_diff(diff.x/r0_vec.x, diff.y/r0_vec.y, diff.z/r0_vec.z);
+
+  cvm::rvector const scal_diff(diff.x/((flags & ef_anisotropic) ?
+                                       r0_vec.x : r0),
+                               diff.y/((flags & ef_anisotropic) ?
+                                       r0_vec.y : r0),
+                               diff.z/((flags & ef_anisotropic) ?
+                                       r0_vec.z : r0));
   cvm::real const l2 = scal_diff.norm2();
 
   // Assume en and ed are even integers, and avoid sqrt in the following
@@ -65,22 +56,45 @@ cvm::real colvar::coordnum::switching_function(cvm::rvector const &r0_vec,
 
   cvm::real const xn = cvm::integer_power(l2, en2);
   cvm::real const xd = cvm::integer_power(l2, ed2);
-  cvm::real const func = (1.0-xn)/(1.0-xd);
+  //The subtraction and division stretches the function back to the range of [0,1] from [pairlist_tol,1]
+  cvm::real const func = (((1.0-xn)/(1.0-xd)) - pairlist_tol) / (1.0-pairlist_tol);
 
-  if (calculate_gradients) {
-    cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
-    cvm::rvector const dl2dx((2.0/(r0_vec.x*r0_vec.x))*diff.x,
-                             (2.0/(r0_vec.y*r0_vec.y))*diff.y,
-                             (2.0/(r0_vec.z*r0_vec.z))*diff.z);
+  if (flags & ef_rebuild_pairlist) {
+    //Particles just outside of the cutoff also are considered if they come near.
+    **pairlist_elem = (func > (-pairlist_tol * 0.5)) ? true : false;
+    (*pairlist_elem)++;
+  }
+  //If the value is too small, we need to exclude it, rather than let it contribute to the sum or the gradients.
+  if (func < 0)
+    return 0;
+
+  if (flags & ef_gradients) {
+    //This is the old, completely correct expression for dFdl2:
+    //cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) -
+    //                                        func*ed2*(xd/l2))*(-1.0);
+    //This can become:
+    //cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2)*(1.0-xn)/(1.0-xn) -
+    //                                        func*ed2*(xd/l2))*(-1.0);
+    //Recognizing that func = (1.0-xn)/(1.0-xd), we can group together the "func" and get a version of dFdl2 that is 0
+    //when func=0, which lets us skip this gradient calculation when func=0.
+    cvm::real const dFdl2 = func * ((ed2*xd/((1.0-xd)*l2)) - (en2*xn/((1.0-xn)*l2)));
+    cvm::rvector const dl2dx((2.0/((flags & ef_anisotropic) ? r0sq_vec.x :
+                                   r0*r0)) * diff.x,
+                             (2.0/((flags & ef_anisotropic) ? r0sq_vec.y :
+                                   r0*r0)) * diff.y,
+                             (2.0/((flags & ef_anisotropic) ? r0sq_vec.z :
+                                   r0*r0)) * diff.z);
     A1.grad += (-1.0)*dFdl2*dl2dx;
     A2.grad +=        dFdl2*dl2dx;
   }
+
   return func;
 }
 
 
 colvar::coordnum::coordnum(std::string const &conf)
-  : cvc(conf), b_anisotropic(false), b_group2_center_only(false)
+  : cvc(conf), b_anisotropic(false), group2_center(NULL), pairlist(NULL)
+
 {
   function_type = "coordnum";
   x.type(colvarvalue::type_scalar);
@@ -90,23 +104,26 @@ colvar::coordnum::coordnum(std::string const &conf)
 
   if (int atom_number = cvm::atom_group::overlap(*group1, *group2)) {
     cvm::error("Error: group1 and group2 share a common atom (number: " +
-      cvm::to_str(atom_number) + ")\n");
+               cvm::to_str(atom_number) + ")\n", INPUT_ERROR);
     return;
   }
 
   if (group1->b_dummy) {
-    cvm::error("Error: only group2 is allowed to be a dummy atom\n");
+    cvm::error("Error: only group2 is allowed to be a dummy atom\n",
+               INPUT_ERROR);
     return;
   }
 
   bool const b_isotropic = get_keyval(conf, "cutoff", r0,
                                       cvm::real(4.0 * cvm::unit_angstrom()));
 
-  if (get_keyval(conf, "cutoff3", r0_vec, cvm::rvector(4.0 * cvm::unit_angstrom(),
-                                                       4.0 * cvm::unit_angstrom(),
-                                                       4.0 * cvm::unit_angstrom()))) {
+  if (get_keyval(conf, "cutoff3", r0_vec,
+                 cvm::rvector(4.0 * cvm::unit_angstrom(),
+                              4.0 * cvm::unit_angstrom(),
+                              4.0 * cvm::unit_angstrom()))) {
     if (b_isotropic) {
-      cvm::error("Error: cannot specify \"cutoff\" and \"cutoff3\" at the same time.\n",
+      cvm::error("Error: cannot specify \"cutoff\" and \"cutoff3\" "
+                 "at the same time.\n",
                  INPUT_ERROR);
       return;
     }
@@ -135,86 +152,178 @@ colvar::coordnum::coordnum(std::string const &conf)
     cvm::log("Warning: only minimum-image distances are used by this variable.\n");
   }
 
+  bool b_group2_center_only = false;
   get_keyval(conf, "group2CenterOnly", b_group2_center_only, group2->b_dummy);
+  if (b_group2_center_only) {
+    if (!group2_center) {
+      group2_center = new cvm::atom_group();
+      group2_center->add_atom(cvm::atom());
+    }
+  }
+
+  get_keyval(conf, "tolerance", tolerance, 0.0);
+  if (tolerance > 0) {
+    get_keyval(conf, "pairListFrequency", pairlist_freq, 100);
+    if ( ! (pairlist_freq > 0) ) {
+      cvm::error("Error: non-positive pairlistfrequency provided.\n",
+                 INPUT_ERROR);
+      return; // and do not allocate the pairlists below
+    }
+    if (b_group2_center_only) {
+      pairlist = new bool[group1->size()];
+    }
+    else {
+      pairlist = new bool[group1->size() * group2->size()];
+    }
+  }
+
 }
 
 
 colvar::coordnum::coordnum()
-  : b_anisotropic(false), b_group2_center_only(false)
+  : b_anisotropic(false), group2_center(NULL), pairlist(NULL)
 {
   function_type = "coordnum";
   x.type(colvarvalue::type_scalar);
 }
 
 
-void colvar::coordnum::calc_value()
+colvar::coordnum::~coordnum()
 {
-  x.real_value = 0.0;
+  if (pairlist != NULL) {
+    delete [] pairlist;
+  }
+  if (group2_center != NULL) {
+    delete group2_center;
+  }
+}
 
-  if (b_group2_center_only) {
 
-    // create a fake atom to hold the group2 com coordinates
-    cvm::atom group2_com_atom;
-    group2_com_atom.pos = group2->center_of_mass();
+template<int compute_flags> int colvar::coordnum::compute_coordnum()
+{
+  if (group2_center) {
+    (*group2_center)[0].pos = group2->center_of_mass();
+    group2_center->calc_required_properties();
+  }
+  cvm::atom_group *group2p = group2_center ? group2_center : group2;
 
-    if (b_anisotropic) {
-      for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
-        x.real_value += switching_function<false>(r0_vec, en, ed, *ai1, group2_com_atom);
-    } else {
-      for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
-        x.real_value += switching_function<false>(r0, en, ed, *ai1, group2_com_atom);
+  bool const use_pairlist = (pairlist != NULL);
+  bool const rebuild_pairlist = (pairlist != NULL) &&
+    (cvm::step_relative() % pairlist_freq == 0);
+
+  bool *pairlist_elem = use_pairlist ? pairlist : NULL;
+  cvm::atom_iter ai1 = group1->begin(), ai2 = group2p->begin();
+  cvm::atom_iter const ai1_end = group1->end();
+  cvm::atom_iter const ai2_end = group2p->end();
+
+  if (b_anisotropic) {
+
+    if (use_pairlist) {
+
+      if (rebuild_pairlist) {
+
+        int const flags = compute_flags | ef_anisotropic | ef_use_pairlist |
+          ef_rebuild_pairlist;
+        for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
+          for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
+            x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
+                                                      *ai1, *ai2,
+                                                      &pairlist_elem,
+                                                      tolerance);
+          }
+        }
+
+      } else {
+
+        int const flags = compute_flags | ef_anisotropic | ef_use_pairlist;
+        for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
+          for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
+            x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
+                                                      *ai1, *ai2,
+                                                      &pairlist_elem,
+                                                      tolerance);
+          }
+        }
+      }
+
+    } else { // if (use_pairlist) {
+
+      int const flags = compute_flags | ef_anisotropic;
+      for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
+        for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
+          x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
+                                                    *ai1, *ai2,
+                                                    NULL, 0.0);
+        }
+      }
     }
 
   } else {
 
-    if (b_anisotropic) {
-      for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
-        for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
-          x.real_value += switching_function<false>(r0_vec, en, ed, *ai1, *ai2);
+    if (use_pairlist) {
+
+      if (rebuild_pairlist) {
+
+        int const flags = compute_flags | ef_use_pairlist | ef_rebuild_pairlist;
+        for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
+          for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
+            x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
+                                                      *ai1, *ai2,
+                                                      &pairlist_elem,
+                                                      tolerance);
+          }
         }
-    } else {
-      for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
-        for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
-          x.real_value += switching_function<false>(r0, en, ed, *ai1, *ai2);
+
+      } else {
+
+        int const flags = compute_flags | ef_use_pairlist;
+        for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
+          for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
+            x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
+                                                      *ai1, *ai2,
+                                                      &pairlist_elem,
+                                                      tolerance);
+          }
         }
+      }
+
+    } else { // if (use_pairlist) {
+
+      int const flags = compute_flags;
+      for (ai1 = group1->begin(); ai1 != ai1_end; ai1++) {
+        for (ai2 = group2->begin(); ai2 != ai2_end; ai2++) {
+          x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
+                                                    *ai1, *ai2,
+                                                    NULL, 0.0);
+        }
+      }
     }
   }
+
+  if (compute_flags & ef_gradients) {
+    if (group2_center) {
+      group2->set_weighted_gradient((*group2_center)[0].grad);
+    }
+  }
+
+  return COLVARS_OK;
+}
+
+
+void colvar::coordnum::calc_value()
+{
+  x.real_value = 0.0;
+  if (is_enabled(f_cvc_gradient)) {
+    compute_coordnum<ef_gradients>();
+  } else {
+    compute_coordnum<ef_null>();
+  }
 }
 
 
 void colvar::coordnum::calc_gradients()
 {
-  if (b_group2_center_only) {
-
-    // create a fake atom to hold the group2 com coordinates
-    cvm::atom group2_com_atom;
-    group2_com_atom.pos = group2->center_of_mass();
-
-
-    if (b_anisotropic) {
-      for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
-        switching_function<true>(r0_vec, en, ed, *ai1, group2_com_atom);
-    } else {
-      for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
-        switching_function<true>(r0, en, ed, *ai1, group2_com_atom);
-    }
-
-    group2->set_weighted_gradient(group2_com_atom.grad);
-
-  } else {
-
-    if (b_anisotropic) {
-      for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
-        for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
-          switching_function<true>(r0_vec, en, ed, *ai1, *ai2);
-        }
-    } else {
-      for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++)
-        for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
-          switching_function<true>(r0, en, ed, *ai1, *ai2);
-        }
-    }
-  }
+  // Gradients are computed by calc_value() if f_cvc_gradients is enabled
 }
 
 
@@ -235,7 +344,7 @@ simple_scalar_dist_functions(coordnum)
 // h_bond member functions
 
 colvar::h_bond::h_bond(std::string const &conf)
-  : cvc(conf)
+: cvc(conf)
 {
   if (cvm::debug())
     cvm::log("Initializing h_bond object.\n");
@@ -307,13 +416,24 @@ colvar::h_bond::~h_bond()
 
 void colvar::h_bond::calc_value()
 {
-  x.real_value = colvar::coordnum::switching_function<false>(r0, en, ed, (*atom_groups[0])[0], (*atom_groups[0])[1]);
+  int const flags = coordnum::ef_null;
+  cvm::rvector const r0_vec(0.0); // TODO enable the flag?
+  x.real_value =
+    coordnum::switching_function<flags>(r0, r0_vec, en, ed,
+                                        (*atom_groups[0])[0],
+                                        (*atom_groups[0])[1],
+                                        NULL, 0.0);
 }
 
 
 void colvar::h_bond::calc_gradients()
 {
-  colvar::coordnum::switching_function<true>(r0, en, ed, (*atom_groups[0])[0], (*atom_groups[0])[1]);
+  int const flags = coordnum::ef_gradients;
+  cvm::rvector const r0_vec(0.0); // TODO enable the flag?
+  coordnum::switching_function<flags>(r0, r0_vec, en, ed,
+                                      (*atom_groups[0])[0],
+                                      (*atom_groups[0])[1],
+                                      NULL, 0.0);
 }
 
 
@@ -328,7 +448,7 @@ simple_scalar_dist_functions(h_bond)
 
 
 colvar::selfcoordnum::selfcoordnum(std::string const &conf)
-  : cvc(conf)
+  : cvc(conf), pairlist(NULL)
 {
   function_type = "selfcoordnum";
   x.type(colvarvalue::type_scalar);
@@ -353,36 +473,115 @@ colvar::selfcoordnum::selfcoordnum(std::string const &conf)
   if (!is_enabled(f_cvc_pbc_minimum_image)) {
     cvm::log("Warning: only minimum-image distances are used by this variable.\n");
   }
+
+  get_keyval(conf, "tolerance", tolerance, 0.0);
+  if (tolerance > 0) {
+    get_keyval(conf, "pairListFrequency", pairlist_freq, 100);
+    if ( ! (pairlist_freq > 0) ) {
+      cvm::error("Error: non-positive pairlistfrequency provided.\n",
+                 INPUT_ERROR);
+      return;
+    }
+    pairlist = new bool[(group1->size()-1) * (group1->size()-1)];
+  }
 }
 
 
 colvar::selfcoordnum::selfcoordnum()
+  : pairlist(NULL)
 {
   function_type = "selfcoordnum";
   x.type(colvarvalue::type_scalar);
 }
 
 
+colvar::selfcoordnum::~selfcoordnum()
+{
+  if (pairlist != NULL) {
+    delete [] pairlist;
+  }
+}
+
+
+template<int compute_flags> int colvar::selfcoordnum::compute_selfcoordnum()
+{
+  cvm::rvector const r0_vec(0.0); // TODO enable the flag?
+
+  bool const use_pairlist = (pairlist != NULL);
+  bool const rebuild_pairlist = (pairlist != NULL) &&
+    (cvm::step_relative() % pairlist_freq == 0);
+
+  bool *pairlist_elem = use_pairlist ? pairlist : NULL;
+  size_t i = 0, j = 0;
+  size_t const n = group1->size();
+
+  // Always isotropic (TODO: enable the ellipsoid?)
+
+  if (use_pairlist) {
+
+    if (rebuild_pairlist) {
+      int const flags = compute_flags | coordnum::ef_use_pairlist |
+        coordnum::ef_rebuild_pairlist;
+      for (i = 0; i < n - 1; i++) {
+        for (j = i + 1; j < n; j++) {
+          x.real_value +=
+            coordnum::switching_function<flags>(r0, r0_vec, en, ed,
+                                                (*group1)[i],
+                                                (*group1)[j],
+                                                &pairlist_elem,
+                                                tolerance);
+        }
+      }
+    } else {
+      int const flags = compute_flags | coordnum::ef_use_pairlist;
+      for (i = 0; i < n - 1; i++) {
+        for (j = i + 1; j < n; j++) {
+          x.real_value +=
+            coordnum::switching_function<flags>(r0, r0_vec, en, ed,
+                                                (*group1)[i],
+                                                (*group1)[j],
+                                                &pairlist_elem,
+                                                tolerance);
+        }
+      }
+    }
+
+  } else { // if (use_pairlist) {
+
+    int const flags = compute_flags | coordnum::ef_null;
+    for (i = 0; i < n - 1; i++) {
+      for (j = i + 1; j < n; j++) {
+        x.real_value +=
+          coordnum::switching_function<flags>(r0, r0_vec, en, ed,
+                                              (*group1)[i],
+                                              (*group1)[j],
+                                              &pairlist_elem,
+                                              tolerance);
+      }
+    }
+  }
+
+  return COLVARS_OK;
+}
+
+
 void colvar::selfcoordnum::calc_value()
 {
   x.real_value = 0.0;
-  for (size_t i = 0; i < group1->size() - 1; i++) {
-    for (size_t j = i + 1; j < group1->size(); j++) {
-      x.real_value += colvar::coordnum::switching_function<false>(r0, en, ed, (*group1)[i], (*group1)[j]);
-    }
+  if (is_enabled(f_cvc_gradient)) {
+    compute_selfcoordnum<coordnum::ef_gradients>();
+  } else {
+    compute_selfcoordnum<coordnum::ef_null>();
   }
 }
 
 
 void colvar::selfcoordnum::calc_gradients()
 {
-  for (size_t i = 0; i < group1->size() - 1; i++) {
-    for (size_t j = i + 1; j < group1->size(); j++) {
-      colvar::coordnum::switching_function<true>(r0, en, ed, (*group1)[i], (*group1)[j]);
-    }
-  }
+  // Gradients are computed by calc_value() if f_cvc_gradients is enabled
 }
 
+
 void colvar::selfcoordnum::apply_force(colvarvalue const &force)
 {
   if (!group1->noforce) {
@@ -394,6 +593,7 @@ void colvar::selfcoordnum::apply_force(colvarvalue const &force)
 simple_scalar_dist_functions(selfcoordnum)
 
 
+
 // groupcoordnum member functions
 colvar::groupcoordnum::groupcoordnum(std::string const &conf)
   : distance(conf), b_anisotropic(false)
@@ -415,7 +615,7 @@ colvar::groupcoordnum::groupcoordnum(std::string const &conf)
 
     if (b_scale) {
       cvm::error("Error: cannot specify \"scale\" and "
-                       "\"scale3\" at the same time.\n");
+                 "\"scale3\" at the same time.\n");
       return;
     }
     b_anisotropic = true;
@@ -453,95 +653,56 @@ colvar::groupcoordnum::groupcoordnum()
 }
 
 
-template<bool calculate_gradients>
-cvm::real colvar::groupcoordnum::switching_function(cvm::real const &r0,
-                                                    int const &en,
-                                                    int const &ed,
-                                                    cvm::atom &A1,
-                                                    cvm::atom &A2)
-{
-  cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
-  cvm::real const l2 = diff.norm2()/(r0*r0);
-
-  // Assume en and ed are even integers, and avoid sqrt in the following
-  int const en2 = en/2;
-  int const ed2 = ed/2;
-
-  cvm::real const xn = cvm::integer_power(l2, en2);
-  cvm::real const xd = cvm::integer_power(l2, ed2);
-  cvm::real const func = (1.0-xn)/(1.0-xd);
-
-  if (calculate_gradients) {
-    cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
-    cvm::rvector const dl2dx = (2.0/(r0*r0))*diff;
-    A1.grad += (-1.0)*dFdl2*dl2dx;
-    A2.grad +=        dFdl2*dl2dx;
-  }
-
-  return func;
-}
-
-
-#if 0  // AMG: I don't think there's any reason to support anisotropic,
-       //      and I don't have those flags below in calc_value, but
-       //      if I need them, I'll also need to uncomment this method
-template<bool calculate_gradients>
-cvm::real colvar::groupcoordnum::switching_function(cvm::rvector const &r0_vec,
-                                                    int const &en,
-                                                    int const &ed,
-                                                    cvm::atom &A1,
-                                                    cvm::atom &A2)
-{
-  cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
-  cvm::rvector const scal_diff(diff.x/r0_vec.x, diff.y/r0_vec.y, diff.z/r0_vec.z);
-  cvm::real const l2 = scal_diff.norm2();
-
-  // Assume en and ed are even integers, and avoid sqrt in the following
-  int const en2 = en/2;
-  int const ed2 = ed/2;
-
-  cvm::real const xn = cvm::integer_power(l2, en2);
-  cvm::real const xd = cvm::integer_power(l2, ed2);
-  cvm::real const func = (1.0-xn)/(1.0-xd);
-
-  if (calculate_gradients) {
-    cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
-    cvm::rvector const dl2dx((2.0/(r0_vec.x*r0_vec.x))*diff.x,
-                             (2.0/(r0_vec.y*r0_vec.y))*diff.y,
-                             (2.0/(r0_vec.z*r0_vec.z))*diff.z);
-    A1.grad += (-1.0)*dFdl2*dl2dx;
-    A2.grad +=        dFdl2*dl2dx;
-  }
-  return func;
-}
-#endif
-
-
 void colvar::groupcoordnum::calc_value()
 {
+  cvm::rvector const r0_vec(0.0); // TODO enable the flag?
 
   // create fake atoms to hold the com coordinates
   cvm::atom group1_com_atom;
   cvm::atom group2_com_atom;
   group1_com_atom.pos = group1->center_of_mass();
   group2_com_atom.pos = group2->center_of_mass();
-
-  x.real_value = coordnum::switching_function<false>(r0, en, ed,
-                                                     group1_com_atom, group2_com_atom);
+  if (b_anisotropic) {
+    int const flags = coordnum::ef_anisotropic;
+    x.real_value = coordnum::switching_function<flags>(r0, r0_vec, en, ed,
+                                                       group1_com_atom,
+                                                       group2_com_atom,
+                                                       NULL, 0.0);
+  } else {
+    int const flags = coordnum::ef_null;
+    x.real_value = coordnum::switching_function<flags>(r0, r0_vec, en, ed,
+                                                       group1_com_atom,
+                                                       group2_com_atom,
+                                                       NULL, 0.0);
+  }
 }
 
 
 void colvar::groupcoordnum::calc_gradients()
 {
+  cvm::rvector const r0_vec(0.0); // TODO enable the flag?
+
   cvm::atom group1_com_atom;
   cvm::atom group2_com_atom;
   group1_com_atom.pos = group1->center_of_mass();
   group2_com_atom.pos = group2->center_of_mass();
 
-  coordnum::switching_function<true>(r0, en, ed, group1_com_atom, group2_com_atom);
+  if (b_anisotropic) {
+    int const flags = coordnum::ef_gradients | coordnum::ef_anisotropic;
+    coordnum::switching_function<flags>(r0, r0_vec, en, ed,
+                                        group1_com_atom,
+                                        group2_com_atom,
+                                        NULL, 0.0);
+  } else {
+    int const flags = coordnum::ef_gradients;
+    coordnum::switching_function<flags>(r0, r0_vec, en, ed,
+                                        group1_com_atom,
+                                        group2_com_atom,
+                                        NULL, 0.0);
+  }
+
   group1->set_weighted_gradient(group1_com_atom.grad);
   group2->set_weighted_gradient(group2_com_atom.grad);
-
 }
 
 

lib/colvars/colvarcomp_distances.cpp

@@ -939,7 +939,7 @@ colvar::rmsd::rmsd(std::string const &conf)
 
   bool b_Jacobian_derivative = true;
   if (atoms->fitting_group != NULL && b_Jacobian_derivative) {
-    cvm::log("The option \"refPositionsGroup\" (alternative group for fitting) was enabled: "
+    cvm::log("The option \"fittingGroup\" (alternative group for fitting) was enabled: "
               "Jacobian derivatives of the RMSD will not be calculated.\n");
     b_Jacobian_derivative = false;
   }

lib/colvars/colvarmodule.cpp

@@ -139,7 +139,7 @@ int colvarmodule::read_config_file(char const  *config_filename)
   // read the config file into a string
   std::string conf = "";
   std::string line;
-  while (colvarparse::getline_nocomments(config_s, line)) {
+  while (parse->read_config_line(config_s, line)) {
     // Delete lines that contain only white space after removing comments
     if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
       conf.append(line+"\n");
@@ -159,11 +159,12 @@ int colvarmodule::read_config_string(std::string const &config_str)
   // strip the comments away
   std::string conf = "";
   std::string line;
-  while (colvarparse::getline_nocomments(config_s, line)) {
+  while (parse->read_config_line(config_s, line)) {
     // Delete lines that contain only white space after removing comments
     if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
       conf.append(line+"\n");
   }
+
   return parse_config(conf);
 }
 
@@ -191,6 +192,12 @@ int colvarmodule::parse_config(std::string &conf)
 {
   extra_conf.clear();
 
+  // Check that the input has matching braces
+  if (colvarparse::check_braces(conf, 0) != COLVARS_OK) {
+    return cvm::error("Error: unmatched curly braces in configuration.\n",
+                      INPUT_ERROR);
+  }
+
   // Parse global options
   if (catch_input_errors(parse_global_params(conf))) {
     return get_error();
@@ -235,6 +242,12 @@ int colvarmodule::parse_config(std::string &conf)
 }
 
 
+std::string const & colvarmodule::get_config() const
+{
+  return parse->get_config();
+}
+
+
 int colvarmodule::append_new_config(std::string const &new_conf)
 {
   extra_conf += new_conf;
@@ -246,9 +259,13 @@ int colvarmodule::parse_global_params(std::string const &conf)
 {
   colvarmodule *cvm = cvm::main();
 
-  std::string index_file_name;
-  if (parse->get_keyval(conf, "indexFile", index_file_name)) {
-    cvm->read_index_file(index_file_name.c_str());
+  {
+    std::string index_file_name;
+    size_t pos = 0;
+    while (parse->key_lookup(conf, "indexFile", &index_file_name, &pos)) {
+      cvm->read_index_file(index_file_name.c_str());
+      index_file_name.clear();
+    }
   }
 
   if (parse->get_keyval(conf, "smp", proxy->b_smp_active, proxy->b_smp_active)) {
@@ -1073,10 +1090,10 @@ colvarmodule::~colvarmodule()
 
 int colvarmodule::reset()
 {
-  parse->init();
-
   cvm::log("Resetting the Collective Variables module.\n");
 
+  parse->init();
+
   // Iterate backwards because we are deleting the elements as we go
   for (std::vector<colvarbias *>::reverse_iterator bi = biases.rbegin();
        bi != biases.rend();

lib/colvars/colvarmodule.h

@@ -131,7 +131,7 @@ public:
 
   /// Module-wide error state
   /// see constants at the top of this file
-protected:
+private:
 
   static int errorCode;
 
@@ -274,6 +274,9 @@ public:
   /// \brief Parse a "clean" config string (no comments)
   int parse_config(std::string &conf);
 
+  /// Get the configuration string read so far (includes comments)
+  std::string const & get_config() const;
+
   // Parse functions (setup internal data based on a string)
 
   /// Allow reading from Windows text files using using std::getline
@@ -296,6 +299,9 @@ public:
 
 private:
 
+  /// Configuration string read so far by the module (includes comments)
+  std::string config_string;
+
   /// Auto-generated configuration during parsing (e.g. to implement
   /// back-compatibility)
   std::string extra_conf;

lib/colvars/colvarparse.cpp

@@ -43,9 +43,10 @@ template<typename TYPE> bool colvarparse::_get_keyval_scalar_(std::string const
     }
   } while (b_found);
 
-  if (found_count > 1)
-    cvm::log("Warning: found more than one instance of \""+
-             std::string(key)+"\".\n");
+  if (found_count > 1) {
+    cvm::error("Error: found more than one instance of \""+
+               std::string(key)+"\".\n", INPUT_ERROR);
+  }
 
   if (data.size()) {
     std::istringstream is(data);
@@ -98,9 +99,10 @@ bool colvarparse::_get_keyval_scalar_string_(std::string const &conf,
     }
   } while (b_found);
 
-  if (found_count > 1)
-    cvm::log("Warning: found more than one instance of \""+
-             std::string(key)+"\".\n");
+  if (found_count > 1) {
+    cvm::error("Error: found more than one instance of \""+
+               std::string(key)+"\".\n", INPUT_ERROR);
+  }
 
   if (data.size()) {
     std::istringstream is(data);
@@ -162,9 +164,10 @@ template<typename TYPE> bool colvarparse::_get_keyval_vector_(std::string const
     }
   } while (b_found);
 
-  if (found_count > 1)
-    cvm::log("Warning: found more than one instance of \""+
-             std::string(key)+"\".\n");
+  if (found_count > 1) {
+    cvm::error("Error: found more than one instance of \""+
+               std::string(key)+"\".\n", INPUT_ERROR);
+  }
 
   if (data.size()) {
     std::istringstream is(data);
@@ -319,9 +322,10 @@ bool colvarparse::get_keyval(std::string const &conf,
     }
   } while (b_found);
 
-  if (found_count > 1)
-    cvm::log("Warning: found more than one instance of \""+
-             std::string(key)+"\".\n");
+  if (found_count > 1) {
+    cvm::error("Error: found more than one instance of \""+
+               std::string(key)+"\".\n", INPUT_ERROR);
+  }
 
   if (data.size()) {
     if ( (data == std::string("on")) ||
@@ -535,6 +539,19 @@ int colvarparse::check_keywords(std::string &conf, char const *key)
 }
 
 
+std::istream & colvarparse::read_config_line(std::istream &is,
+                                             std::string &line)
+{
+  cvm::getline(is, line);
+  config_string += line+'\n';
+  size_t const comment = line.find('#');
+  if (comment != std::string::npos) {
+    line.erase(comment);
+  }
+  return is;
+}
+
+
 std::istream & colvarparse::getline_nocomments(std::istream &is,
                                                std::string &line)
 {
@@ -607,7 +624,7 @@ bool colvarparse::key_lookup(std::string const &conf,
     }
 
     // check that there are matching braces between here and the end of conf
-    bool const b_not_within_block = brace_check(conf, pos);
+    bool const b_not_within_block = (check_braces(conf, pos) == COLVARS_OK);
 
     bool const b_isolated = (b_isolated_left && b_isolated_right &&
                              b_not_within_block);
@@ -781,19 +798,15 @@ std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb)
 }
 
 
-bool colvarparse::brace_check(std::string const &conf,
+int colvarparse::check_braces(std::string const &conf,
                               size_t const start_pos)
 {
-  size_t brace_count = 0;
+  int brace_count = 0;
   size_t brace = start_pos;
-  while ( (brace = conf.find_first_of("{}", brace)) != std::string::npos) {
+  while ((brace = conf.find_first_of("{}", brace)) != std::string::npos) {
     if (conf[brace] == '{') brace_count++;
     if (conf[brace] == '}') brace_count--;
     brace++;
   }
-
-  if (brace_count != 0)
-    return false;
-  else
-    return true;
+  return (brace_count != 0) ? INPUT_ERROR : COLVARS_OK;
 }

lib/colvars/colvarparse.h

@@ -24,7 +24,7 @@
 /// need to parse input inherit from this
 class colvarparse {
 
-private:
+protected:
 
   /// \brief List of legal keywords for this object: this is updated
   /// by each call to colvarparse::get_keyval() or
@@ -47,7 +47,7 @@ private:
   /// \brief Remove all the values from the config string
   void strip_values(std::string &conf);
 
-  /// \brief Configuration string of the object
+  /// \brief Configuration string of the object (includes comments)
   std::string config_string;
 
 public:
@@ -72,7 +72,7 @@ public:
   }
 
   /// Set a new config string for this object
-  inline void init(const std::string& conf)
+  inline void init(std::string const &conf)
   {
     if (! config_string.size()) {
       init();
@@ -80,7 +80,8 @@ public:
     }
   }
 
-  inline const std::string& get_config()
+  /// Get the configuration string (includes comments)
+  inline std::string const & get_config() const
   {
     return config_string;
   }
@@ -284,14 +285,19 @@ public:
                   std::string *data = NULL,
                   size_t *save_pos = NULL);
 
+  /// \brief Reads a configuration line, adds it to config_string, and returns
+  /// the stream \param is Input stream \param s String that will hold the
+  /// configuration line, with comments stripped
+  std::istream & read_config_line(std::istream &is, std::string &line);
+
   /// \brief Works as std::getline() but also removes everything
   /// between a comment character and the following newline
-  static std::istream & getline_nocomments(std::istream &is,
-                                           std::string &s);
+  static std::istream & getline_nocomments(std::istream &is, std::string &s);
 
-  /// Check if the content of the file has matching braces
-  bool brace_check(std::string const &conf,
-                   size_t const start_pos = 0);
+  /// \brief Check if the content of a config string has matching braces
+  /// \param conf The configuration string \param start_pos Start the count
+  /// from this position
+  static int check_braces(std::string const &conf, size_t const start_pos);
 
 };
 

lib/colvars/colvarproxy.cpp

@@ -289,13 +289,23 @@ colvarproxy_smp::colvarproxy_smp()
   omp_lock_state = NULL;
 #if defined(_OPENMP)
   if (smp_thread_id() == 0) {
+    omp_lock_state = reinterpret_cast<void *>(new omp_lock_t);
     omp_init_lock(reinterpret_cast<omp_lock_t *>(omp_lock_state));
   }
 #endif
 }
 
 
-colvarproxy_smp::~colvarproxy_smp() {}
+colvarproxy_smp::~colvarproxy_smp()
+{
+#if defined(_OPENMP)
+  if (smp_thread_id() == 0) {
+    if (omp_lock_state) {
+      delete reinterpret_cast<omp_lock_t *>(omp_lock_state);
+    }
+  }
+#endif
+}
 
 
 int colvarproxy_smp::smp_enabled()
@@ -499,6 +509,14 @@ char const *colvarproxy_script::script_obj_to_str(unsigned char *obj)
 }
 
 
+std::vector<std::string> colvarproxy_script::script_obj_to_str_vector(unsigned char *obj)
+{
+  cvm::error("Error: trying to print a script object without a scripting "
+             "language interface.\n", BUG_ERROR);
+  return std::vector<std::string>();
+}
+
+
 int colvarproxy_script::run_force_callback()
 {
   return COLVARS_NOT_IMPLEMENTED;

lib/colvars/colvarproxy.h

@@ -461,6 +461,9 @@ public:
   /// Convert a script object (Tcl or Python call argument) to a C string
   virtual char const *script_obj_to_str(unsigned char *obj);
 
+  /// Convert a script object (Tcl or Python call argument) to a vector of strings
+  virtual std::vector<std::string> script_obj_to_str_vector(unsigned char *obj);
+
   /// Pointer to the scripting interface object
   /// (does not need to be allocated in a new interface)
   colvarscript *script;

lib/colvars/colvars_version.h

@@ -1,5 +1,5 @@
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2018-04-29"
+#define COLVARS_VERSION "2018-10-16"
 // This file is part of the Collective Variables module (Colvars).
 // The original version of Colvars and its updates are located at:
 // https://github.com/colvars/colvars

lib/colvars/colvarscript.cpp

@@ -82,6 +82,14 @@ int colvarscript::run(int objc, unsigned char *const objv[])
 
   int error_code = COLVARS_OK;
 
+  // If command is found in map, execute it
+  std::string const cmd_key("cv_"+cmd);
+  if (comm_str_map.count(cmd_key) > 0) {
+    error_code |= (*(comm_fns[comm_str_map[cmd_key]]))(
+                      reinterpret_cast<void *>(this), objc, objv);
+    return error_code;
+  }
+
   if (cmd == "colvar") {
     if (objc < 3) {
       result = "Missing parameters\n" + help_string();
@@ -295,11 +303,12 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[])
   }
 
   if (subcmd == "delete") {
-    size_t i;
-    for (i = 0; i < cv->biases.size(); i++) {
+    while (cv->biases.size() > 0) {
+      size_t i = cv->biases.size()-1;
+      cvm::log("Warning: before deleting colvar " + cv->name
+        + ", deleting parent bias " + cv->biases[i]->name);
       delete cv->biases[i];
     }
-    cv->biases.clear();
     // colvar destructor is tasked with the cleanup
     delete cv;
     // TODO this could be done by the destructors
@@ -373,6 +382,23 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[])
     return COLVARS_OK;
   }
 
+  if (subcmd == "modifycvcs") {
+    if (objc < 4) {
+      result = "cvcflags: missing parameter: vector of strings";
+      return COLVARSCRIPT_ERROR;
+    }
+    std::vector<std::string> const confs(proxy->script_obj_to_str_vector(objv[3]));
+    cvm::increase_depth();
+    int res = cv->update_cvc_config(confs);
+    cvm::decrease_depth();
+    if (res != COLVARS_OK) {
+      result = "Error setting CVC flags";
+      return COLVARSCRIPT_ERROR;
+    }
+    result = "0";
+    return COLVARS_OK;
+  }
+
   if ((subcmd == "get") || (subcmd == "set") || (subcmd == "state")) {
     return proc_features(cv, objc, objv);
   }
@@ -547,6 +573,8 @@ std::string colvarscript::help_string() const
 Managing the Colvars module:\n\
   configfile <file name>      -- read configuration from a file\n\
   config <string>             -- read configuration from the given string\n\
+  getconfig                   -- get the module's configuration string\n\
+  resetindexgroups            -- clear the index groups loaded so far\n\
   reset                       -- delete all internal configuration\n\
   delete                      -- delete this Colvars module instance\n\
   version                     -- return version of Colvars code\n\
@@ -579,6 +607,7 @@ Accessing collective variables:\n\
   colvar <name> gettotalforce -- return total force of colvar <name>\n\
   colvar <name> getconfig     -- return config string of colvar <name>\n\
   colvar <name> cvcflags <fl> -- enable or disable cvcs according to 0/1 flags\n\
+  colvar <name> modifycvcs <str> -- pass new config strings to each CVC\n\
   colvar <name> get <f>       -- get the value of the colvar feature <f>\n\
   colvar <name> set <f> <val> -- set the value of the colvar feature <f>\n\
 \n\