Merge pull request #1623 from akohlmey/next-version

Step version string for stable release

cmake/CMakeLists.txt

@@ -133,6 +133,24 @@ foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
+######################################################
+# download and unpack support binaries for compilation
+# of windows binaries.
+######################################################
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
+  file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
+          EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
+  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+  if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
+    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
+  elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
+    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
+  endif()
+  set(OpenCL_INCLUDE_DIR "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
+endif()
+
+######################################################
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
@@ -148,6 +166,7 @@ if(PKG_USER-ADIOS)
 endif()
 
 # do MPI detection after language activation, if MPI for these language is required
+set(MPI_CXX_SKIP_MPICXX TRUE)
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 if(BUILD_MPI)
@@ -175,11 +194,13 @@ add_definitions(-DLAMMPS_${LAMMPS_SIZES})
 set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}")
 
 # posix_memalign is not available on Windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
+else()
   set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
-  if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
-    add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
-  endif()
+endif()
+if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
+  add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 endif()
 
 option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
@@ -229,6 +250,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
     enable_language(Fortran)
     file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
     add_library(linalg STATIC ${LAPACK_SOURCES})
+    set(BLAS_LIBRARIES linalg)
     set(LAPACK_LIBRARIES linalg)
   else()
     list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})

cmake/README.md

@@ -33,12 +33,17 @@ tasks, act as a reference and provide examples of typical use cases.
       * [Package-Specific Configuration Options](#package-specific-configuration-options)
          * [KSPACE Package](#kspace-package)
          * [MKL](#mkl)
-         * [FFTW2](#fftw2)
          * [FFTW3](#fftw3)
+         * [BLAS](#blas)
          * [LAPACK](#lapack)
          * [PYTHON Package](#python-package)
          * [GPU Package](#gpu-package)
+         * [MESSAGE Package](#message-package)
+         * [MSCG Package](#mscg-package)
          * [VORONOI Package](#voronoi-package)
+         * [USER-LATTE Package](#user-latte-package)
+         * [USER-PLUMED Package](#user-plumed-package)
+         * [USER-SCAFACOS Package](#user-scafacos-package)
          * [USER-SMD Package](#user-smd-package)
       * [Optional Features](#optional-features)
          * [zlib support](#zlib-support)
@@ -50,8 +55,6 @@ tasks, act as a reference and provide examples of typical use cases.
          * [Building with GNU Compilers](#building-with-gnu-compilers)
          * [Building with Intel Compilers](#building-with-intel-compilers)
          * [Building with LLVM/Clang Compilers](#building-with-llvmclang-compilers)
-      * [Examples](#examples)
-
 
 ## Quick Start for the Impatient
 If you want to skip ahead and just run the compilation using `cmake`, please
@@ -205,8 +208,10 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   <td>Controls if debugging symbols are added to the generated binaries</td>
   <td>
   <dl>
-  <dt><code>Release</code> (default)</dt>
+  <dt><code>RelWithDebInfo (default)</code></dt>
+  <dt><code>Release</code></dt>
   <dt><code>Debug</code></dt>
+  <dt><code>MinSizeRel</code></dt>
   </dl>
   </td>
 </tr>
@@ -249,6 +254,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
+  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>LAMMPS_MEMALIGN</code></td>
   <td>controls the alignment of blocks of memory allocated by LAMMPS</td>
@@ -271,7 +286,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
 </tr>
 <tr>
   <td><code>LAMMPS_MACHINE</code></td>
-  <td>allows appending a machine suffix to the generate LAMMPS binary</td>
+  <td>allows appending a machine suffix to the generated LAMMPS binary</td>
+  <td>
+  <dl>
+    <dt>*none*  (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_LIB_SUFFIX</code></td>
+  <td>allows appending a suffix to the generated LAMMPS library</td>
   <td>
   <dl>
     <dt>*none*  (default)</dt>
@@ -319,8 +343,8 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </td>
 </tr>
 <tr>
-  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
-  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
+  <td><code>BUILD_TOOLS</code></td>
+  <td>control whether to build LAMMPS tools</td>
   <td>
   <dl>
     <dt><code>off</code> (default)</dt>
@@ -561,23 +585,6 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </dl>
   </td>
 </tr>
-<tr>
-  <td><code>PKG_MEAM</code></td>
-  <td>
-<p>A pair style for the modified embedded atom (MEAM) potential.</p>
-
-<p><strong>Please note that the MEAM package has been superseded by the USER-MEAMC package,
-which is a direct translation of the MEAM package to C++. USER-MEAMC contains
-additional optimizations making it run faster than MEAM on most machines, while
-providing the identical features and USER interface.</strong></p>
-  </td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_MISC</code></td>
   <td>
@@ -634,21 +641,6 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
-<tr>
-  <td><code>PKG_REAX</code></td>
-  <td>
-  A pair style which wraps a Fortran library which implements the ReaxFF
-  potential, which is a universal reactive force field. See the USER-REAXC
-  package for an alternate implementation in C/C++. Also a fix reax/bonds
-  command for monitoring molecules as bonds are created and destroyed.
-  </td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_REPLICA</code></td>
   <td>
@@ -695,6 +687,16 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_SPIN</code></td>
+  <td>Model atomic magnetic spins classically, coupled to atoms moving in the usual manner via MD. Various pair, fix, and compute styles.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_SNAP</code></td>
   <td>
@@ -757,6 +759,16 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_MESSAGE</code></td>
+  <td>Commands to use LAMMPS as either a client or server and couple it to another application.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_MSCG</code></td>
   <td>
@@ -811,6 +823,18 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_VORONOI</code></td>
+  <td>
+  A compute command which calculates the Voronoi tesselation of a collection of atoms by wrapping the Voro++ library. This can be used to calculate the local volume or each atoms or its near neighbors.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -825,6 +849,16 @@ providing the identical features and USER interface.</strong></p>
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>PKG_USER-ADIOS</code></td>
+  <td>ADIOS is a high-performance I/O library. This package implements the dump “atom/adios” and dump “custom/adios” commands to write data using the ADIOS library.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-ATC</code></td>
   <td>
@@ -853,6 +887,18 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-BOCS</code></td>
+  <td>
+  This package provides fix bocs, a modified version of fix npt which includes the pressure correction to the barostat as outlined in: N. J. H. Dunn and W. G. Noid, “Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids,” J. Chem. Phys. 143, 243148 (2015).
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-CGDNA</code></td>
   <td>
@@ -1142,6 +1188,30 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-PLUMED</code></td>
+  <td>
+  The fix plumed command allows you to use the PLUMED free energy plugin for molecular dynamics to analyze and bias your LAMMPS trajectory on the fly. The PLUMED library is called from within the LAMMPS input script by using the <code>fix plumed</code> command.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PKG_USER-PTM</code></td>
+  <td>
+  A <code>compute ptm/atom</code> command that calculates local structure characterization using the Polyhedral Template Matching methodology.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-QTB</code></td>
   <td>
@@ -1197,6 +1267,33 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-SCAFACOS</code></td>
+  <td>
+  A KSpace style which wraps the ScaFaCoS Coulomb solver library to compute long-range Coulombic interactions.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PKG_USER-SDPD</code></td>
+  <td>
+  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). Also two fixes for
+  moving and rigid body integration of SPH/SDPD particles (particles of
+  <code>atom_style meso</code>).</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-SMD</code></td>
   <td>
@@ -1280,6 +1377,23 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-YAFF</code></td>
+  <td>
+  Some potentials that are also implemented in the Yet Another Force Field (YAFF) code.
+  The expressions and their use are discussed in the following papers:
+  <ul>
+    <li><a href="http://dx.doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li>
+    <li><a href="http://dx.doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
+  </ul>
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -1300,14 +1414,27 @@ providing the identical features and USER interface.</strong></p>
   <td><code>FFT</code></td>
   <td>
     <p>FFT library for KSPACE package</p>
-    <p>If either MKL or FFTW is selected <code>cmake</code> will try to locate these libraries automatically. To control which one should be used please see the options below for each FFT library.</p>
+    <p>If either MKL or FFTW is selected <code>cmake</code> will try to locate
+    these libraries automatically. To control which one should be used please see
+    the options below for each FFT library.  Otherwise it will default to KISS
+    FFT.</p>
   </td>
   <td>
   <dl>
-    <dt><code>KISS</code></dt>
     <dt><code>FFTW3</code></dt>
     <dt><code>FFTW2</code></dt>
     <dt><code>MKL</code></dt>
+    <dt><code>KISS</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>FFT_SINGLE</code></td>
+  <td>Use single-precision floating-point in FFT</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default = double precision)</dt>
+    <dt><code>on</code></dt>
   </dl>
   </td>
 </tr>
@@ -1325,60 +1452,6 @@ providing the identical features and USER interface.</strong></p>
 </tbody>
 </table>
 
-### MKL
-
-<table>
-<thead>
-<tr>
-  <th>Option</th>
-  <th>Description</th>
-  <th>Values</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-  <td><code>MKL_INCLUDE_DIRS</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-<tr>
-  <td><code>MKL_LIBRARIES</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-</tbody>
-</table>
-
-TODO static vs dynamic linking
-
-### FFTW2
-
-<table>
-<thead>
-<tr>
-  <th>Option</th>
-  <th>Description</th>
-  <th>Values</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-  <td><code>FFTW2_INCLUDE_DIRS</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-<tr>
-  <td><code>FFTW2_LIBRARIES</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-</tbody>
-</table>
-
 ### FFTW3
 
 <table>
@@ -1392,24 +1465,57 @@ TODO static vs dynamic linking
 <tbody>
 <tr>
   <td><code>FFTW3_INCLUDE_DIRS</code></td>
-  <td></td>
+  <td>path to FFTW3 include files</td>
   <td>
   </td>
 </tr>
 <tr>
   <td><code>FFTW3_LIBRARIES</code></td>
-  <td></td>
+  <td>list of paths to FFTW3 libraries</td>
   <td>
   </td>
 </tr>
 </tbody>
 </table>
 
+### MKL
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>MKL_INCLUDE_DIRS</code></td>
+  <td>path to MKL include files</td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>MKL_LIBRARIES</code></td>
+  <td>list of paths to MKL libraries</td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### BLAS
+
+See [FindBLAS documentation](https://cmake.org/cmake/help/latest/module/FindBLAS.html)
+
 ### LAPACK
-TODO
+
+See [FindLAPACK documentation](https://cmake.org/cmake/help/latest/module/FindLAPACK.html)
 
 ### PYTHON Package
 
+See [FindPYTHON documentation](https://cmake.org/cmake/help/latest/module/FindPython.html)
+
 ### USER-INTEL Package
 
 <table>
@@ -1499,10 +1605,11 @@ target API.
   <td>
   <dl>
     <dt><code>sm_20</code> (Fermi)</dt>
-    <dt><code>sm_30</code> (Kepler)</dt>
+    <dt><code>sm_30</code> (Kepler) (default)</dt>
     <dt><code>sm_50</code> (Maxwell)</dt>
     <dt><code>sm_60</code> (Pascal)</dt>
     <dt><code>sm_70</code> (Volta)</dt>
+    <dt><code>sm_75</code> (Turing)</dt>
   </dl>
   </td>
 </tr>
@@ -1534,13 +1641,14 @@ target API.
 </tbody>
 </table>
 
-### VORONOI Package
+### KIM Package
 
-TODO
+Requires installation of the KIM library with API v2
 
-### USER-SMD Package
-
-Requires a Eigen3 installation
+If `DOWNLOAD_KIM` is set, the KIM library will be downloaded and built inside
+the CMake build directory. If the KIM library is already on your system (in a
+location CMake cannot find it), set the `PKG_CONFIG_PATH` environment variable
+so that `libkim-api` can be found.
 
 <table>
 <thead>
@@ -1551,9 +1659,323 @@ Requires a Eigen3 installation
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>DOWNLOAD_KIM</code></td>
+  <td>Download KIM API v2 and compile it as part of the build.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### MESSAGE Package
+
+This package can optionally include support for messaging via sockets, using the open-source [ZeroMQ library](http://zeromq.org/), which must be installed on your system.
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>MESSAGE_ZMQ</code></td>
+  <td>Build with ZeroMQ support</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ZMQ_LIBRARY</code></td>
+  <td>
+    ZMQ library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>ZMG_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing ZMQ installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### MSCG Package
+
+Requires installation of the MSCG library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_MSCG</code></td>
+  <td>Download MSCG and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>MSCG_LIBRARY</code></td>
+  <td>
+    MSCG library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>MSCG_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing MSCG installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### VORONOI Package
+
+Requires installation of the Voro++ library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_VORO</code></td>
+  <td>Download Voro++ and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>VORO_LIBRARY</code></td>
+  <td>
+    Voro++ library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>VORO_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing Voro++ installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-LATTE Package
+
+Requires installation of the LATTE library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_LATTE</code></td>
+  <td>Download LATTE and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LATTE_LIBRARY</code></td>
+  <td>
+    LATTE library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-PLUMED Package
+
+Requires installation of the PLUMED library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_PLUMED</code></td>
+  <td>Download PLUMED and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PLUMED_MODE</code></td>
+  <td>
+    Determines the linkage mode for the PLUMED library.
+  </td>
+  <td>
+  <dl>
+    <dt><code>static</code> (default)</dt>
+    <dt><code>shared</code></dt>
+    <dt><code>runtime</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-LATTE Package
+
+Requires installation of the LATTE library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_LATTE</code></td>
+  <td>Download LATTE and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LATTE_LIBRARY</code></td>
+  <td>
+    LATTE library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-SMD Package
+
+Requires installation of the Eigen3 library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_EIGEN3</code></td>
+  <td>Download Eigen3 and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>EIGEN3_INCLUDE_DIR</code></td>
-  <td></td>
+  <td>
+    Provide include directory of existing Eigen3 installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+
+### USER-SCAFACOS Package
+
+To build with this package, you must download and build the [ScaFaCoS Coulomb solver library](http://www.scafacos.de/)
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_SCAFACOS</code></td>
+  <td>Download SCAFACOS and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>SCAFACOS_LIBRARY</code></td>
+  <td>
+    SCAFACOS library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>SCAFACOS_INCLUDE_DIR</code></td>
+  <td>
+    SCAFACOS include directory (only needed if at custom location)
+  </td>
   <td>
   </td>
 </tr>
@@ -1791,5 +2213,82 @@ cmake -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc -D CMAKE_Fortran_COMPIL
 cmake -D CMAKE_C_COMPILER=clang -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_Fortran_COMPILER=flang ../cmake
 ```
 
+## LAMMPS Developer Options
 
-## Examples
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>ENABLE_TESTING</code></td>
+  <td>Control wheather to add tests via CTest</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_TESTING_SOURCE_DIR</code></td>
+  <td>Custom location of lammps-testing repository (optional). If not specified it will download it via Git</td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_TESTING_GIT_TAG</code></td>
+  <td>If lammps-testing repository is cloned, this is the tag/commit that will be checked out</td>
+  <td>
+  <dl>
+    <dt><code>master</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_COVERAGE</code></td>
+  <td>Enables code coverage support via gcov and adds a gcovr build target to generate a coverage report.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_ADDRESS</code></td>
+  <td>Enables Address Sanitizer support when compiling using GCC or Clang for detecting memory leaks in binaries while running them. See https://clang.llvm.org/docs/AddressSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_UNDEFINED</code></td>
+  <td>Enables Undefined Behavior Sanitizer support when compiling using GCC or Clang for detecting code that is running into undefined behavior of the language. See https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_THREAD</code></td>
+  <td>Enables Thread Sanitizer support when compiling using GCC or Clang for detecting data races in binaries while running them. See https://clang.llvm.org/docs/ThreadSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>

cmake/presets/mingw-cross.cmake

@@ -3,9 +3,9 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
                  REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
                  USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
                  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
-                 USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-MOLFILE USER-OMP
-                 USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD USER-SMD
-                 USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
+                 USER-MEAMC USER-MESO USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE
+                 USER-OMP USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD
+                 USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
 
 foreach(PKG ${WIN_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -14,4 +14,4 @@ endforeach()
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
-set(INTEL_LRT_MODE "none" CACHE STRING "" FORCE)
+set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "2 August 2019" "2019-08-02"
+.TH LAMMPS "7 August 2019" "2019-08-07"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build.txt

@@ -29,6 +29,7 @@ as described on the "Install"_Install.html doc page.
    Build_package
    Build_extras
    Build_windows
+   Build_development
 
 END_RST -->
 
@@ -41,7 +42,8 @@ END_RST -->
 "Optional build settings"_Build_settings.html
 "Include packages in build"_Build_package.html
 "Packages with extra build options"_Build_extras.html
-"Notes for building LAMMPS on Windows"_Build_windows.html  :all(b)
+"Notes for building LAMMPS on Windows"_Build_windows.html
+"Development build options (CMake only)"_Build_development.html  :all(b)
 
 If you have problems building LAMMPS, it is often due to software
 issues on your local machine.  If you can, find a local expert to

doc/src/Build_basics.txt

@@ -235,12 +235,16 @@ running LAMMPS from Python via its library interface.
 
 -D BUILD_EXE=value           # yes (default) or no
 -D BUILD_LIB=value           # yes or no (default)
--D BUILD_SHARED_LIBS=value   # yes or no (default) :pre
+-D BUILD_SHARED_LIBS=value   # yes or no (default)
+-D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc
+                             # no default value :pre
+
 
 Setting BUILD_EXE=no will not produce an executable.  Setting
 BUILD_LIB=yes will produce a static library named liblammps.a.
 Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a
-shared library named liblammps.so.
+shared library named liblammps.so. If LAMMPS_LIB_SUFFIX is set the generated
+libraries will be named liblammps_name.a or liblammps_name.so instead.
 
 [Traditional make]:
 
@@ -310,6 +314,30 @@ current LAMMPS version (HTML and PDF files), from the website
 
 :line
 
+Build LAMMPS tools :h4,link(tools)
+
+Some tools described in "Auxiliary tools"_Tools.html can be built directly
+using CMake or Make.
+
+[CMake variable]:
+
+-D BUILD_TOOLS=value       # yes or no (default) :pre
+
+The generated binaries will also become part of the LAMMPS installation (see below)
+
+[Traditional make]:
+
+cd lammps/tools
+make all              # build all binaries of tools
+make binary2txt       # build only binary2txt tool
+make chain            # build only chain tool
+make micelle2d        # build only micelle2d tool
+make thermo_extract   # build only thermo_extract tool
+:pre
+
+:line
+
+
 Install LAMMPS after a build :h4,link(install)
 
 After building LAMMPS, you may wish to copy the LAMMPS executable of

doc/src/Build_cmake.txt

@@ -120,7 +120,7 @@ The argument can be preceeded or followed by various CMake
 command-line options.  Several useful ones are:
 
 -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
--D CMAKE_BUILD_TYPE=type      # type = Release or Debug
+-D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
 -G output                     # style of output CMake generates
 -DVARIABLE=value              # setting for a LAMMPS feature to enable
 -D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir

doc/src/Build_development.txt

@@ -0,0 +1,86 @@
+"Higher level section"_Build.html - "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
+
+Development build options (CMake only) :h3
+
+The CMake build of LAMMPS has a few extra options which are useful during
+development,  testing or debugging.
+
+:line
+
+Verify compilation flags :h4,link(compilation)
+
+Sometimes it is necessary to verify the complete sequence of compilation flags
+generated by the CMake build. To enable a more verbose output during
+compilation you can use the following option.
+
+-D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes :pre
+
+Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+
+make VERBOSE=1 :pre
+
+:line
+
+Address, Undefined Behavior, and Thread Sanitizer Support :h4,link(sanitizer)
+
+Compilers such as GCC and Clang support generating binaries which use different
+sanitizers to detect problems in code during run-time. They can detect "memory leaks"_https://clang.llvm.org/docs/AddressSanitizer.html,
+code that runs into "undefined behavior"_https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html of the
+language and "data races"_https://clang.llvm.org/docs/ThreadSanitizer.html in threaded code.
+
+The following settings allow you enable these features if your compiler supports
+it. Please note that they come with a performance hit. However, they are
+usually faster than using tools like Valgrind.
+
+-D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
+-D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
+-D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes
+:pre
+
+:line
+
+Code Coverage and Testing :h4,link(testing)
+
+We do extensive regression testing of the LAMMPS code base on a continuous
+basis. Some of the logic to do this has been added to the CMake build so
+developers can run the tests directly on their workstation. 
+
+NOTE: this is incomplete and only represents a small subset of tests that we run
+
+-D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
+-D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
+-D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
+:pre
+
+If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
+
+make test
+:pre
+
+The test cases used come from the lammps-testing repository. They are
+derivatives of the examples folder with some modifications to make the run
+faster.
+
+You can also collect code coverage metrics while running the tests by enabling
+coverage support during building.
+
+-D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes :pre
+
+This will also add the following targets to generate coverage reports after running the LAMMPS executable:
+
+make test               # run tests first!
+make gen_coverage_html  # generate coverage report in HTML format
+make gen_coverage_xml   # generate coverage report in XML format
+:pre
+
+These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
+
+pip install git+https://github.com/gcovr/gcovr.git :pre
+:pre

doc/src/Build_extras.txt

@@ -88,7 +88,7 @@ which GPU hardware to build for.
                           # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
 -D GPU_ARCH=value         # primary GPU hardware choice for GPU_API=cuda
                           # value = sm_XX, see below
-                          # default is Cuda-compiler dependent, but typically sm_20
+                          # default is sm_30
 -D CUDPP_OPT=value        # optimization setting for GPU_API=cuda
                           # enables CUDA Performance Primitives Optimizations
                           # value = yes (default) or no
@@ -354,6 +354,9 @@ be installed on your system.
 [CMake build]:
 
 -D MESSAGE_ZMQ=value    # build with ZeroMQ support, value = no (default) or yes
+-D ZMQ_LIBRARY=path     # ZMQ library file (only needed if a custom location)
+-D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)
+:pre
 
 [Traditional make]:
 
@@ -366,6 +369,7 @@ simply invoke the lib/message/Install.py script with the specified args:
 make lib-message               # print help message
 make lib-message args="-m -z"  # build with MPI and socket (ZMQ) support
 make lib-message args="-s"     # build as serial lib with no ZMQ support
+:pre
 
 The build should produce two files: lib/message/cslib/src/libmessage.a
 and lib/message/Makefile.lammps.  The latter is copied from an

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="2 Aug 2019 version">
+<META NAME="docnumber" CONTENT="7 Aug 2019 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-2 Aug 2019 version :c,h2
+7 Aug 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -1191,7 +1191,7 @@ USER-PLUMED package :link(PKG-USER-PLUMED),h4
 The fix plumed command allows you to use the PLUMED free energy plugin
 for molecular dynamics to analyze 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.
+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

doc/src/kim_commands.txt

@@ -365,7 +365,7 @@ an array of one or more comma-separated items in brackets.
 The list of supported keywords and the type and format of their values
 depend on the query function used. The current list of query functions
 is available on the OpenKIM webpage at
-"https://openkim.org/doc/repository/kim-query"_https://openkim.org/doc/repository/kim-query.
+"https://openkim.org/doc/usage/kim-query"_https://openkim.org/doc/usage/kim-query.
 
 NOTE: All query functions require the {model} keyword, which identifies
 the IM whose predictions are being queried. This keyword is automatically

doc/src/replicate.txt

@@ -14,7 +14,8 @@ replicate nx ny nz {keyword} :pre
 
 nx,ny,nz = replication factors in each dimension :ulb
 optional {keyword} = {bbox} :l
-  {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule
+  {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :pre
+:ule
 
 [Examples:]
 
@@ -45,11 +46,13 @@ file that crosses a periodic boundary should be between two atoms with
 image flags that differ by 1.  This will allow the bond to be
 unwrapped appropriately.
 
-The optional keyword {bbox} uses a bounding box to only check atoms
-in replicas that overlap with a processor's sub-domain when assigning
-atoms to processors, and thus can result in substantial speedups for
-calculations using a large number of processors. It does require
-temporarily using more memory.
+The optional keyword {bbox} uses a bounding box to only check atoms in
+replicas that overlap with a processor's sub-domain when assigning
+atoms to processors.  It typically results in a substantial speedup
+when using the replicate command on a large number of processors.  It
+does require temporary use of more memory, specifically that each
+processor can store all atoms in the entire system before it is
+replicated.
 
 [Restrictions:]
 

doc/utils/sphinx-config/false_positives.txt

@@ -2443,6 +2443,8 @@ Salles
 sandia
 Sandia
 sandybrown
+Sanitizer
+sanitizers
 sc
 scafacos
 SCAFACOS

lib/colvars/colvaratoms.cpp

@@ -178,6 +178,31 @@ int cvm::atom_group::remove_atom(cvm::atom_iter ai)
 }
 
 
+int cvm::atom_group::set_dummy()
+{
+  if (atoms_ids.size() > 0) {
+    return cvm::error("Error: setting group with keyword \""+key+
+                      "\" and name \""+name+"\" as dummy, but it already "
+                      "contains atoms.\n", INPUT_ERROR);
+  }
+  b_dummy = true;
+  return COLVARS_OK;
+}
+
+
+int cvm::atom_group::set_dummy_pos(cvm::atom_pos const &pos)
+{
+  if (b_dummy) {
+    dummy_atom_pos = pos;
+  } else {
+    return cvm::error("Error: setting dummy position for group with keyword \""+
+                      key+"\" and name \""+name+
+                      "\", but it is not dummy.\n", INPUT_ERROR);
+  }
+  return COLVARS_OK;
+}
+
+
 int cvm::atom_group::init()
 {
   if (!key.size()) key = "unnamed";
@@ -469,20 +494,15 @@ int cvm::atom_group::parse(std::string const &group_conf)
   // checks of doubly-counted atoms have been handled by add_atom() already
 
   if (get_keyval(group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos())) {
-    b_dummy = true;
-    // note: atoms_ids.size() is used here in lieu of atoms.size(),
-    // which can be empty for scalable groups
-    if (atoms_ids.size()) {
-      cvm::error("Error: cannot set up group \""+
-                 key+"\" as a dummy atom "
-                 "and provide it with atom definitions.\n", INPUT_ERROR);
-    }
+
+    parse_error |= set_dummy();
+    parse_error |= set_dummy_pos(dummy_atom_pos);
+
   } else {
-    b_dummy = false;
 
     if (!(atoms_ids.size())) {
-      cvm::error("Error: no atoms defined for atom group \""+
-                 key+"\".\n", INPUT_ERROR);
+      parse_error |= cvm::error("Error: no atoms defined for atom group \""+
+                                key+"\".\n", INPUT_ERROR);
     }
 
     // whether these atoms will ever receive forces or not

lib/colvars/colvaratoms.h

@@ -207,6 +207,12 @@ public:
   /// \brief Remove an atom object from this group
   int remove_atom(cvm::atom_iter ai);
 
+  /// Set this group as a dummy group (no actual atoms)
+  int set_dummy();
+
+  /// If this group is dummy, set the corresponding position
+  int set_dummy_pos(cvm::atom_pos const &pos);
+
   /// \brief Print the updated the total mass and charge of a group.
   /// This is needed in case the hosting MD code has an option to
   /// change atom masses after their initialization.

lib/colvars/colvarcomp.h

@@ -887,9 +887,8 @@ protected:
   /// Integer exponent of the function denominator
   int ed;
 
-  /// \brief If true, group2 will be treated as a single atom, stored in this
-  /// accessory group
-  cvm::atom_group *group2_center;
+  /// If true, group2 will be treated as a single atom
+  bool b_group2_center_only;
 
   /// Tolerance for the pair list
   cvm::real tolerance;
@@ -941,9 +940,12 @@ public:
                                       bool **pairlist_elem,
                                       cvm::real tolerance);
 
-  /// Main workhorse function
+  /// Workhorse function
   template<int flags> int compute_coordnum();
 
+  /// Workhorse function
+  template<int flags> void main_loop(bool **pairlist_elem);
+
 };
 
 

lib/colvars/colvarcomp_coordnums.cpp

@@ -91,7 +91,7 @@ cvm::real colvar::coordnum::switching_function(cvm::real const &r0,
 
 
 colvar::coordnum::coordnum(std::string const &conf)
-  : cvc(conf), b_anisotropic(false), group2_center(NULL), pairlist(NULL)
+  : cvc(conf), b_anisotropic(false), pairlist(NULL)
 
 {
   function_type = "coordnum";
@@ -156,14 +156,7 @@ 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) {
@@ -185,7 +178,7 @@ colvar::coordnum::coordnum(std::string const &conf)
 
 
 colvar::coordnum::coordnum()
-  : b_anisotropic(false), group2_center(NULL), pairlist(NULL)
+  : b_anisotropic(false), pairlist(NULL)
 {
   function_type = "coordnum";
   x.type(colvarvalue::type_scalar);
@@ -197,69 +190,60 @@ colvar::coordnum::~coordnum()
   if (pairlist != NULL) {
     delete [] pairlist;
   }
-  if (group2_center != NULL) {
-    delete group2_center;
+}
+
+
+template<int flags> void colvar::coordnum::main_loop(bool **pairlist_elem)
+{
+  if (b_group2_center_only) {
+    cvm::atom group2_com_atom;
+    group2_com_atom.pos = group2->center_of_mass();
+    for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) {
+      x.real_value += switching_function<flags>(r0, r0_vec, en, ed,
+                                                *ai1, group2_com_atom,
+                                                pairlist_elem,
+                                                tolerance);
+    }
+    if (b_group2_center_only) {
+      group2->set_weighted_gradient(group2_com_atom.grad);
+    }
+  } 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<flags>(r0, r0_vec, en, ed,
+                                                  *ai1, *ai2,
+                                                  pairlist_elem,
+                                                  tolerance);
+      }
+    }
   }
 }
 
 
 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;
-
   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);
-          }
-        }
-
+        main_loop<flags>(&pairlist_elem);
       } 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);
-          }
-        }
+        main_loop<flags>(&pairlist_elem);
       }
 
-    } else { // if (use_pairlist) {
+    } else {
 
       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);
-        }
-      }
+      main_loop<flags>(NULL);
     }
 
   } else {
@@ -267,46 +251,17 @@ template<int compute_flags> int colvar::coordnum::compute_coordnum()
     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);
-          }
-        }
-
+        main_loop<flags>(&pairlist_elem);
       } 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);
-          }
-        }
+        main_loop<flags>(&pairlist_elem);
       }
 
-    } else { // if (use_pairlist) {
+    } else {
 
       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);
+      main_loop<flags>(NULL);
     }
   }
 

lib/colvars/colvars_version.h

@@ -1,5 +1,5 @@
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2019-08-01"
+#define COLVARS_VERSION "2019-08-05"
 // 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/kim/Install.py

@@ -18,7 +18,7 @@ parser = ArgumentParser(prog='Install.py',
 # settings
 
 thisdir = fullpath('.')
-version = "kim-api-2.1.1"
+version = "kim-api-2.1.2"
 
 # help message
 

src/USER-INTEL/verlet_lrt_intel.cpp

@@ -102,18 +102,20 @@ void VerletLRTIntel::setup(int flag)
   }
 
   #if defined(_LMP_INTEL_LRT_PTHREAD)
+  #if defined(__linux)
   if (comm->me == 0) {
     cpu_set_t cpuset;
     sched_getaffinity(0, sizeof(cpuset), &cpuset);
     int my_cpu_count = CPU_COUNT(&cpuset);
     if (my_cpu_count < comm->nthreads + 1) {
       char str[128];
-      sprintf(str,"Using %d threads per MPI, but only %d core(s) allocated"
-                  " per MPI",
+      sprintf(str,"Using %d threads per MPI rank, but only %d core(s)"
+                  " allocated for each MPI rank",
               comm->nthreads + 1, my_cpu_count);
       error->warning(FLERR, str);
     }
   }
+  #endif
 
   _kspace_ready = 0;
   _kspace_done = 0;

src/fix_ave_histo_weight.cpp

@@ -33,7 +33,7 @@ using namespace FixConst;
 enum{X,V,F,COMPUTE,FIX,VARIABLE};
 enum{ONE,RUNNING};
 enum{SCALAR,VECTOR,WINDOW};
-enum{GLOBAL,PERATOM,LOCAL};
+enum{DEFAULT,GLOBAL,PERATOM,LOCAL};
 enum{IGNORE,END,EXTRA};
 enum{SINGLE,VALUE};
 

src/info.cpp

@@ -60,7 +60,7 @@
 #include <sys/utsname.h>
 #endif
 
-#if defined __linux
+#if defined(__linux)
 #include <malloc.h>
 #endif
 

src/version.h

@@ -1 +1 @@
-#define LAMMPS_VERSION "2 Aug 2019"
+#define LAMMPS_VERSION "7 Aug 2019"