Merge pull request #1615 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})
@@ -497,37 +519,36 @@ if(BUILD_LIB)
     add_dependencies(lammps ${LAMMPS_DEPS})
   endif()
   set(LAMMPS_CXX_HEADERS
-    angle.h
-    atom.h
-    bond.h
-    citeme.h
-    comm.h
-    compute.h
-    dihedral.h
-    domain.h
-    error.h
-    fix.h
-    force.h
-    group.h
-    improper.h
-    input.h
-    kspace.h
-    lammps.h
-    lattice.h
-    lmppython.h
-    memory.h
-    modify.h
-    neighbor.h
-    neigh_list.h
-    output.h
-    pair.h
-    pointers.h
-    region.h
-    timer.h
-    universe.h
-    update.h
-    variable.h)
-  list(TRANSFORM LAMMPS_CXX_HEADERS PREPEND ${LAMMPS_SOURCE_DIR}/)
+    ${LAMMPS_SOURCE_DIR}/angle.h
+    ${LAMMPS_SOURCE_DIR}/atom.h
+    ${LAMMPS_SOURCE_DIR}/bond.h
+    ${LAMMPS_SOURCE_DIR}/citeme.h
+    ${LAMMPS_SOURCE_DIR}/comm.h
+    ${LAMMPS_SOURCE_DIR}/compute.h
+    ${LAMMPS_SOURCE_DIR}/dihedral.h
+    ${LAMMPS_SOURCE_DIR}/domain.h
+    ${LAMMPS_SOURCE_DIR}/error.h
+    ${LAMMPS_SOURCE_DIR}/fix.h
+    ${LAMMPS_SOURCE_DIR}/force.h
+    ${LAMMPS_SOURCE_DIR}/group.h
+    ${LAMMPS_SOURCE_DIR}/improper.h
+    ${LAMMPS_SOURCE_DIR}/input.h
+    ${LAMMPS_SOURCE_DIR}/kspace.h
+    ${LAMMPS_SOURCE_DIR}/lammps.h
+    ${LAMMPS_SOURCE_DIR}/lattice.h
+    ${LAMMPS_SOURCE_DIR}/lmppython.h
+    ${LAMMPS_SOURCE_DIR}/memory.h
+    ${LAMMPS_SOURCE_DIR}/modify.h
+    ${LAMMPS_SOURCE_DIR}/neighbor.h
+    ${LAMMPS_SOURCE_DIR}/neigh_list.h
+    ${LAMMPS_SOURCE_DIR}/output.h
+    ${LAMMPS_SOURCE_DIR}/pair.h
+    ${LAMMPS_SOURCE_DIR}/pointers.h
+    ${LAMMPS_SOURCE_DIR}/region.h
+    ${LAMMPS_SOURCE_DIR}/timer.h
+    ${LAMMPS_SOURCE_DIR}/universe.h
+    ${LAMMPS_SOURCE_DIR}/update.h
+    ${LAMMPS_SOURCE_DIR}/variable.h)
 
   set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
   set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})

cmake/Modules/Packages/KIM.cmake

@@ -20,9 +20,13 @@ if(PKG_KIM)
       message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
     endif()
     message(STATUS "KIM-API download requested - we will build our own")
-    enable_language(C)
-    enable_language(Fortran)
+    include(CheckLanguage)
     include(ExternalProject)
+    enable_language(C)
+    check_language(Fortran)
+    if(NOT CMAKE_Fortran_COMPILER)
+      message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
+    endif()
     ExternalProject_Add(kim_build
       URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz
       URL_MD5 6ac52e14ef52967fc7858220b208cba5

cmake/Modules/Packages/VORONOI.cmake

@@ -18,8 +18,12 @@ if(PKG_VORONOI)
     else()
       set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
     endif()
-    string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS})
-    set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    if(APPLE)
+      get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
+      set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
+    else()
+      set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    endif()
 
     ExternalProject_Add(voro_build
       URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz

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 "31 July 2019" "2019-07-31"
+.TH LAMMPS "6 August 2019" "2019-08-06"
 .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/Eqs/pair_kolmogorov_crespi_full.tex

@@ -27,7 +27,7 @@
   V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\
   \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt]
   \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot  {\bf n}_{j})^2 \\[15pt]
-  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
+  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n}
 \end{eqnarray*}
 \endgroup
 \end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="31 Jul 2019 version">
+<META NAME="docnumber" CONTENT="6 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
-31 Jul 2019 version :c,h2
+6 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/fix.txt

@@ -165,40 +165,40 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
 accelerated styles exist.
 
 "adapt"_fix_adapt.html - change a simulation parameter over time
-"adapt/fep"_fix_adapt_fep.html -
+"adapt/fep"_fix_adapt_fep.html - enhanced version of fix adapt
 "addforce"_fix_addforce.html - add a force to each atom
-"addtorque"_fix_addtorque.html -
+"addtorque"_fix_addtorque.html - add a torque to a group of atoms
 "append/atoms"_fix_append_atoms.html - append atoms to a running simulation
-"atc"_fix_atc.html -
+"atc"_fix_atc.html - initiates a coupled MD/FE simulation
 "atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
 "ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
 "ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
 "ave/correlate"_fix_ave_correlate.html - compute/output time correlations
 "ave/correlate/long"_fix_ave_correlate_long.html -
 "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
-"ave/histo/weight"_fix_ave_histo.html -
+"ave/histo/weight"_fix_ave_histo.html - weighted version of fix ave/histo
 "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
 "aveforce"_fix_aveforce.html - add an averaged force to each atom
 "balance"_fix_balance.html - perform dynamic load-balancing
-"bocs"_fix_bocs.html -
+"bocs"_fix_bocs.html - NPT style time integration with pressure correction
 "bond/break"_fix_bond_break.html - break bonds on the fly
 "bond/create"_fix_bond_create.html - create bonds on the fly
-"bond/react"_fix_bond_react.html -
+"bond/react"_fix_bond_react.html - apply topology changes to model reactions
 "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
 "box/relax"_fix_box_relax.html - relax box size during energy minimization
-"client/md"_fix_client_md.html -
-"cmap"_fix_cmap.html -
-"colvars"_fix_colvars.html -
-"controller"_fix_controller.html -
+"client/md"_fix_client_md.html - MD client for client/server simulations
+"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
+"colvars"_fix_colvars.html - interface to the collective variables “Colvars” library
+"controller"_fix_controller.html - apply control loop feedback mechanism
 "deform"_fix_deform.html - change the simulation box size/shape
 "deposit"_fix_deposit.html - add new atoms above a surface
-"dpd/energy"_fix_dpd_energy.html -
+"dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics
 "drag"_fix_drag.html - drag atoms towards a defined coordinate
-"drude"_fix_drude.html -
-"drude/transform/direct"_fix_drude_transform.html -
-"drude/transform/inverse"_fix_drude_transform.html -
+"drude"_fix_drude.html - part of Drude oscillator polarization model
+"drude/transform/direct"_fix_drude_transform.html -  part of Drude oscillator polarization model
+"drude/transform/inverse"_fix_drude_transform.html -  part of Drude oscillator polarization model
 "dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
-"edpd/source"_fix_dpd_source.html -
+"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations
 "efield"_fix_efield.html - impose electric field on system
 "ehex"_fix_ehex.html - enhanced heat exchange algorithm
 "electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
@@ -208,27 +208,26 @@ accelerated styles exist.
 "eos/table/rx"_fix_eos_table_rx.html -
 "evaporate"_fix_evaporate.html - remove atoms from simulation periodically
 "external"_fix_external.html - callback to an external driver program
-"ffl"_fix_ffl.html -
-"filter/corotate"_fix_filter_corotate.html -
-"flow/gauss"_fix_flow_gauss.html -
+"ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat
+"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA
+"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux
 "freeze"_fix_freeze.html - freeze atoms in a granular simulation
 "gcmc"_fix_gcmc.html - grand canonical insertions/deletions
-"gld"_fix_gcmc.html - generalized Langevin dynamics integrator
-"gld"_fix_gld.html -
-"gle"_fix_gle.html -
+"gld"_fix_gld.html - generalized Langevin dynamics integrator
+"gle"_fix_gle.html - generalized Langevin equation thermostat
 "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
-"grem"_fix_grem.html -
+"grem"_fix_grem.html - implements the generalized replica exchange method
 "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 -
+"imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol 
 "indent"_fix_indent.html - impose force due to an indenter
-"ipi"_fix_ipi.html -
+"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
 "langevin"_fix_langevin.html - Langevin temperature control
-"langevin/drude"_fix_langevin_drude.html -
-"langevin/eff"_fix_langevin_eff.html -
-"langevin/spin"_fix_langevin_spin.html -
+"langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators
+"langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model
+"langevin/spin"_fix_langevin_spin.html - Langevin temperature control for a spin or spin-lattice system
 "latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
 "lb/fluid"_fix_lb_fluid.html -
 "lb/momentum"_fix_lb_momentum.html -
@@ -236,64 +235,60 @@ accelerated styles exist.
 "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html -
 "lb/viscous"_fix_lb_viscous.html -
 "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 -
+"manifoldforce"_fix_manifoldforce.html - restrain atoms to a manifold during minimization
+"meso"_fix_meso.html - time integration for SPH/DPDE particles
+"meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
 "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
-"mscg"_fix_mscg.html -
+"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
 "msst"_fix_msst.html - multi-scale shock technique (MSST) integration
-"mvv/dpd"_fix_mvv_dpd.html -
-"mvv/edpd"_fix_mvv_dpd.html -
-"mvv/tdpd"_fix_mvv_dpd.html -
+"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
+"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm
+"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
 "neb"_fix_neb.html - nudged elastic band (NEB) spring forces
 "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
 "nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
-"nph/body"_fix_nph_body.html -
-"nph/body"_fix_nve_body.html - NPH for body particles
-"nph/eff"_fix_nh_eff.html -
+"nph/body"_fix_nph_body.html - NPH for body particles
+"nph/eff"_fix_nh_eff.html - NPH for  nuclei and electrons in the electron force field model
 "nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
 "nphug"_fix_nphug.html - constant-stress Hugoniostat integration
 "npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
 "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
-"npt/body"_fix_npt_body.html -
-"npt/body"_fix_nve_body.html - NPT for body particles
-"npt/eff"_fix_nh_eff.html -
+"npt/body"_fix_npt_body.html - NPT for body particles
+"npt/eff"_fix_nh_eff.html - NPT for  nuclei and electrons in the electron force field model
 "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
-"npt/uef"_fix_nh_uef.html -
+"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow
 "nve"_fix_nve.html - constant NVE time integration
 "nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces"
-"nve/awpmd"_fix_nve_awpmd.html -
+"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces
+"nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model
 "nve/body"_fix_nve_body.html - NVE for body particles
-"nve/dot"_fix_nve_dot.html -
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html -
-"nve/eff"_fix_nve_eff.html -
+"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models
+"nve/eff"_fix_nve_eff.html - NVE for  nuclei and electrons in the electron force field model
 "nve/limit"_fix_nve_limit.html - NVE with limited step length
 "nve/line"_fix_nve_line.html - NVE for line segments
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html -
 "nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
 "nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
-"nve/spin"_fix_nve_spin.html -
+"nve/spin"_fix_nve_spin.html - NVE for a spin or spin-lattice system
 "nve/tri"_fix_nve_tri.html - NVE for triangles
-"nvk"_fix_nvk.html -
-"nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover
+"nvk"_fix_nvk.html - constant kinetic energy time integration
+"nvt"_fix_nh.html - NVT time integration via Nose/Hoover
 "nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
-"nvt/body"_fix_nve_body.html - NVT for body particles
-"nvt/body"_fix_nvt_body.html -
-"nvt/eff"_fix_nh_eff.html -
+"nvt/body"_fix_nvt_body.html - NVT for body particles
+"nvt/eff"_fix_nh_eff.html - NVE for  nuclei and electrons in the electron force field model
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -
 "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html -
+"nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model
 "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
-"nvt/uef"_fix_nh_uef.html -
+"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow
 "oneway"_fix_oneway.html - constrain particles on move in one direction
 "orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
 "orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
-"phonon"_fix_phonon.html -
-"pimd"_fix_pimd.html -
+"phonon"_fix_phonon.html - calculate dynamical matrix from MD simulations
+"pimd"_fix_pimd.html - Feynman path integral molecular dynamics
 "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
@@ -302,24 +297,24 @@ accelerated styles exist.
 "press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat
 "print"_fix_print.html - print text and variables during a simulation
 "property/atom"_fix_property_atom.html - add customized per-atom values
-"python/invoke"_fix_python_invoke.html -
-"python/move"_fix_python_move.html -
-"qbmsst"_fix_qbmsst.html -
+"python/invoke"_fix_python_invoke.html - call a Python function during a simulation
+"python/move"_fix_python_move.html -  call a Python function during a simulation run
+"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator
 "qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential
 "qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method
 "qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer
 "qeq/point"_fix_qeq.html - charge equilibration via point method
-"qeq/reax"_fix_qeq_reax.html -
+"qeq/reax"_fix_qeq_reax.html - charge equilibration for ReaxFF potential
 "qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
 "qeq/slater"_fix_qeq.html - charge equilibration via Slater method
-"qmmm"_fix_qmmm.html -
-"qtb"_fix_qtb.html -
+"qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling
+"qtb"_fix_qtb.html - implement quantum thermal bath scheme
 "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
 "reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
 "reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
 "recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
 "restrain"_fix_restrain.html - constrain a bond, angle, dihedral
-"rhok"_fix_rhok.html -
+"rhok"_fix_rhok.html - add bias potential for long-range ordered systems
 "rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
 "rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
 "rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
@@ -332,11 +327,11 @@ accelerated styles exist.
 "rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
 "rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
 "rx"_fix_rx.html -
-"saed/vtk"_fix_saed_vtk.html -
+"saed/vtk"_fix_saed_vtk.html - 
 "setforce"_fix_setforce.html - set the force on each atom
 "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
-"shardlow"_fix_shardlow.html -
-"smd"_fix_smd.html -
+"shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting
+"smd"_fix_smd.html - applied a steered MD force to a group
 "smd/adjust_dt"_fix_smd_adjust_dt.html -
 "smd/integrate_tlsph"_fix_smd_integrate_tlsph.html -
 "smd/integrate_ulsph"_fix_smd_integrate_ulsph.html -
@@ -355,13 +350,13 @@ accelerated styles exist.
 "temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
 "temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
 "temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling
-"temp/rescale/eff"_fix_temp_rescale_eff.html -
+"temp/rescale/eff"_fix_temp_rescale_eff.html - temperature control by velocity rescaling in the electron force field model
 "tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
 "thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
 "ti/spring"_fix_ti_spring.html -
 "tmd"_fix_tmd.html - guide a group of atoms to a new configuration
 "ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
-"ttm/mod"_fix_ttm.html -
+"ttm/mod"_fix_ttm.html - enhanced two-temperature model with additional options
 "tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters
 "vector"_fix_vector.html - accumulate a global vector every N timesteps
 "viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation
@@ -369,7 +364,7 @@ accelerated styles exist.
 "wall/body/polygon"_fix_wall_body_polygon.html -
 "wall/body/polyhedron"_fix_wall_body_polyhedron.html -
 "wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
-"wall/ees"_fix_wall_ees.html -
+"wall/ees"_fix_wall_ees.html - wall for ellipsoidal particles
 "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
 "wall/gran/region"_fix_wall_gran_region.html -
 "wall/harmonic"_fix_wall.html - harmonic spring wall
@@ -379,7 +374,7 @@ accelerated styles exist.
 "wall/piston"_fix_wall_piston.html - moving reflective piston wall
 "wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
 "wall/region"_fix_wall_region.html - use region surface as wall
-"wall/region/ees"_fix_wall_ees.html -
+"wall/region/ees"_fix_wall_ees.html - use region surface as wall for ellipsoidal particles
 "wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
 
 [Restrictions:]

doc/src/fix_bocs.txt

@@ -47,13 +47,13 @@ or {cubic_spline}.
 
 With either spline method, the only argument that needs to follow it
 is the name of a file that contains the desired pressure correction
-as a function of volume. The file should be formatted so each line has:
+as a function of volume. The file must be formatted so each line has:
 
 Volume_i, PressureCorrection_i :pre
 
 Note both the COMMA and the SPACE separating the volume's
 value and its corresponding pressure correction. The volumes in the file
-should be uniformly spaced. Both the volumes and the pressure corrections
+must be uniformly spaced. Both the volumes and the pressure corrections
 should be provided in the proper units, e.g. if you are using {units real},
 the volumes should all be in cubic angstroms, and the pressure corrections
 should all be in atmospheres. Furthermore, the table should start/end at a

doc/src/fix_rhok.txt

@@ -39,8 +39,8 @@ An example of using the interface pinning method is located in the
 
 [Restrictions:]
 
-This fix is part of the MISC package.  It is only enabled if LAMMPS
-was built with that package.  See the "Build
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
 package"_Build_package.html doc page for more info.
 
 [Related commands:]

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/pair_coul_shield.txt

@@ -13,7 +13,7 @@ pair_style coul/shield command :h3
 pair_style coul/shield cutoff tap_flag :pre
 
 cutoff = global cutoff (distance units)
-tap_flag = 0/1 to turn off/on the taper function
+tap_flag = 0/1 to turn off/on the taper function :ul
 
 [Examples:]
 

doc/src/pair_ilp_graphene_hbn.txt

@@ -13,17 +13,17 @@ pair_style ilp/graphene/hbn command :h3
 pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre
 
 cutoff = global cutoff (distance units)
-tap_flag = 0/1 to turn off/on the taper function
+tap_flag = 0/1 to turn off/on the taper function :ul
 
 [Examples:]
 
-pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
-pair_coeff * * ilp/graphene/hbn  BNCH.ILP B N C :pre
+pair_style  hybrid/overlay ilp/graphene/hbn 16.0 1
+pair_coeff  * * ilp/graphene/hbn  BNCH.ILP B N C :pre
 
 pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-pair_coeff  * * rebo                 CH.rebo     NULL NULL C
-pair_coeff  * * tersoff              BNC.tersoff B    N    NULL
-pair_coeff  * * ilp/graphene/hbn     BNCH.ILP    B    N    C
+pair_coeff  * * rebo              CH.rebo     NULL NULL C
+pair_coeff  * * tersoff           BNC.tersoff B    N    NULL
+pair_coeff  * * ilp/graphene/hbn  BNCH.ILP    B    N    C
 pair_coeff  1 1 coul/shield 0.70
 pair_coeff  1 2 coul/shield 0.695
 pair_coeff  2 2 coul/shield 0.69 :pre
@@ -85,6 +85,22 @@ be found in "(Ouyang)"_#Ouyang.
 This potential must be used in combination with hybrid/overlay.
 Other interactions can be set to zero using pair_style {none}.
 
+This pair style tallies a breakdown of the total interlayer potential
+energy into sub-categories, which can be accessed via the "compute
+pair"_compute_pair.html command as a vector of values of length 2.
+The 2 values correspond to the following sub-categories:
+
+{E_vdW} = vdW (attractive) energy
+{E_Rep} = Repulsive energy :ol
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+compute 0 all pair ilp/graphene/hbn
+variable Evdw  equal c_0\[1\]
+variable Erep  equal c_0\[2\]
+thermo_style custom step temp epair v_Erep v_Evdw :pre
+
 :line
 
 [Mixing, shift, table, tail correction, restart, rRESPA info]:

doc/src/pair_kolmogorov_crespi_full.txt

@@ -13,7 +13,7 @@ pair_style kolmogorov/crespi/full command :h3
 pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre
 
 cutoff = global cutoff (distance units)
-tap_flag = 0/1 to turn off/on the taper function
+tap_flag = 0/1 to turn off/on the taper function :ul
 
 [Examples:]
 
@@ -74,6 +74,22 @@ comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
 This potential must be used in combination with hybrid/overlay.
 Other interactions can be set to zero using pair_style {none}.
 
+This pair style tallies a breakdown of the total interlayer potential
+energy into sub-categories, which can be accessed via the "compute
+pair"_compute_pair.html command as a vector of values of length 2.
+The 2 values correspond to the following sub-categories:
+
+{E_vdW} = vdW (attractive) energy
+{E_Rep} = Repulsive energy :ol
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+compute 0 all pair kolmogorov/crespi/full
+variable Evdw  equal c_0\[1\]
+variable Erep  equal c_0\[2\]
+thermo_style custom step temp epair v_Erep v_Evdw :pre
+
 :line
 
 [Mixing, shift, table, tail correction, restart, rRESPA info]:

doc/utils/sphinx-config/false_positives.txt

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

examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP

@@ -1 +0,0 @@
-../../../../../potentials/BNCH-old.ILP

examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.airebo

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

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

@@ -1,61 +0,0 @@
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1
-group adsorbate type 2
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo      NULL C  # chemical
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP   C    C  # long range
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair ilp/graphene/hbn
-variable  REBO     equal c_0
-variable  ILP      equal c_1
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000

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

@@ -1,137 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
-  orthogonal box = (0 0 0) to (42.6 41.8117 100)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1
-680 atoms in group membrane
-group adsorbate type 2
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo      NULL C  # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP   C    C  # long range
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair ilp/graphene/hbn
-variable  REBO     equal c_0
-variable  ILP      equal c_1
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair rebo, perpetual, skip from (2)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes
-Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 
-     100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564 
-     200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465 
-     300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539 
-     400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113372 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709 
-     500 -5029.3985510533 -5046.0433160610 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534 
-     600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537 
-     700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274644 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955 
-     800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515 
-     900 -5029.3930414672 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839 
-    1000 -5029.3908907831 -5045.6437703691 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974 
-Loop time of 137.46 on 1 procs for 1000 steps with 1360 atoms
-
-Performance: 0.629 ns/day, 38.183 hours/ns, 7.275 timesteps/s
-95.1% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 137.33     | 137.33     | 137.33     |   0.0 | 99.90
-Bond    | 0.00071788 | 0.00071788 | 0.00071788 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.067907   | 0.067907   | 0.067907   |   0.0 |  0.05
-Output  | 0.0016029  | 0.0016029  | 0.0016029  |   0.0 |  0.00
-Modify  | 0.036542   | 0.036542   | 0.036542   |   0.0 |  0.03
-Other   |            | 0.02574    |            |       |  0.02
-
-Nlocal:    1360 ave 1360 max 1360 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    7964 ave 7964 max 7964 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  265206 ave 265206 max 265206 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 265206
-Ave neighs/atom = 195.004
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:02:17

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

@@ -1,137 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
-  orthogonal box = (0 0 0) to (42.6 41.8117 100)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1
-680 atoms in group membrane
-group adsorbate type 2
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo      NULL C  # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP   C    C  # long range
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair ilp/graphene/hbn
-variable  REBO     equal c_0
-variable  ILP      equal c_1
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair rebo, perpetual, skip from (2)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes
-Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 
-     100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564 
-     200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465 
-     300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539 
-     400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113371 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709 
-     500 -5029.3985510533 -5046.0433160611 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534 
-     600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537 
-     700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274643 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955 
-     800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515 
-     900 -5029.3930414671 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839 
-    1000 -5029.3908907831 -5045.6437703692 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974 
-Loop time of 36.0917 on 4 procs for 1000 steps with 1360 atoms
-
-Performance: 2.394 ns/day, 10.025 hours/ns, 27.707 timesteps/s
-97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 33.204     | 34.289     | 35.893     |  17.3 | 95.01
-Bond    | 0.00038719 | 0.00065947 | 0.00097609 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.1539     | 1.7595     | 2.8464     |  76.7 |  4.88
-Output  | 0.0013447  | 0.0014529  | 0.0016887  |   0.4 |  0.00
-Modify  | 0.010811   | 0.012037   | 0.013764   |   1.0 |  0.03
-Other   |            | 0.0287     |            |       |  0.08
-
-Nlocal:    340 ave 344 max 334 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-Nghost:    4628 ave 4634 max 4624 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  66301.5 ave 67860 max 63963 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-
-Total # of neighbors = 265206
-Ave neighs/atom = 195.004
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:36

examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff

@@ -1 +0,0 @@
-../../../../../potentials/BNC.tersoff

examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP

@@ -1 +0,0 @@
-../../../../../potentials/BNCH-old.ILP

examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo

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

examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN

@@ -1,71 +0,0 @@
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       gr_hBN_Cstack_2L_noH.data
-mass            1 10.8110   # boron    mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | membrane
-mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-group adsorbate type 3
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo     NULL NULL C    # chemical
-pair_coeff  * * tersoff            BNC.tersoff   B    N    NULL # chemical
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP  B    N    C    # long range
-pair_coeff  1 1 coul/shield 0.70
-pair_coeff  1 2 coul/shield 0.69498201415576216335
-pair_coeff  2 2 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair tersoff
-compute   2 all pair ilp/graphene/hbn
-compute   3 all pair coul/shield
-variable  REBO     equal  c_0
-variable  Tersoff  equal  c_1
-variable  EILP     equal  c_2
-variable  Ecoul    equal  c_3
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000

examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.1

@@ -1,171 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       gr_hBN_Cstack_2L_noH.data
-  orthogonal box = (0 0 0) to (44.583 42.9 100)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1440 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron    mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | membrane
-mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-720 atoms in group membrane
-group adsorbate type 3
-720 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo     NULL NULL C    # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * tersoff            BNC.tersoff   B    N    NULL # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP  B    N    C    # long range
-pair_coeff  1 1 coul/shield 0.70
-pair_coeff  1 2 coul/shield 0.69498201415576216335
-pair_coeff  2 2 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair tersoff
-compute   2 all pair ilp/graphene/hbn
-compute   3 all pair coul/shield
-variable  REBO     equal  c_0
-variable  Tersoff  equal  c_1
-variable  EILP     equal  c_2
-variable  Ecoul    equal  c_3
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  7 neighbor lists, perpetual/occasional/extra = 6 1 0
-  (1) pair rebo, perpetual, skip from (3)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair tersoff, perpetual, skip from (6)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (4) pair coul/shield, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton/skip
-      stencil: none
-      bin: none
-  (5) compute group/group, occasional, copy from (7)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, copy from (3)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (7) neighbor class addition, perpetual, half/full from (6)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 25.93 | 25.93 | 25.93 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -10708.4531746010 -10764.2547791975 55.8016045965 -66.8250335416 -5401.7347845703 -5322.2780762734 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755 
-     100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614 
-     200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321 
-     300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196 
-     400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799 
-     500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266 
-     600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507737 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624 
-     700 -10708.1867253590 -10736.6143955088 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688 
-     800 -10708.1733385055 -10736.0277775931 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693 
-     900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300 
-    1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943 
-Loop time of 149.449 on 1 procs for 1000 steps with 1440 atoms
-
-Performance: 0.578 ns/day, 41.514 hours/ns, 6.691 timesteps/s
-96.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 149.06     | 149.06     | 149.06     |   0.0 | 99.74
-Bond    | 0.00082946 | 0.00082946 | 0.00082946 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.068351   | 0.068351   | 0.068351   |   0.0 |  0.05
-Output  | 0.25935    | 0.25935    | 0.25935    |   0.0 |  0.17
-Modify  | 0.030915   | 0.030915   | 0.030915   |   0.0 |  0.02
-Other   |            | 0.02702    |            |       |  0.02
-
-Nlocal:    1440 ave 1440 max 1440 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    8180 ave 8180 max 8180 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    140400 ave 140400 max 140400 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  280800 ave 280800 max 280800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 280800
-Ave neighs/atom = 195
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:02:29

examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4

@@ -1,171 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       gr_hBN_Cstack_2L_noH.data
-  orthogonal box = (0 0 0) to (44.583 42.9 100)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  1440 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron    mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | membrane
-mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-720 atoms in group membrane
-group adsorbate type 3
-720 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo     NULL NULL C    # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * tersoff            BNC.tersoff   B    N    NULL # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP  B    N    C    # long range
-pair_coeff  1 1 coul/shield 0.70
-pair_coeff  1 2 coul/shield 0.69498201415576216335
-pair_coeff  2 2 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair tersoff
-compute   2 all pair ilp/graphene/hbn
-compute   3 all pair coul/shield
-variable  REBO     equal  c_0
-variable  Tersoff  equal  c_1
-variable  EILP     equal  c_2
-variable  Ecoul    equal  c_3
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  7 neighbor lists, perpetual/occasional/extra = 6 1 0
-  (1) pair rebo, perpetual, skip from (3)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair tersoff, perpetual, skip from (6)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (4) pair coul/shield, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton/skip
-      stencil: none
-      bin: none
-  (5) compute group/group, occasional, copy from (7)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, copy from (3)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (7) neighbor class addition, perpetual, half/full from (6)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 14.25 | 14.25 | 14.25 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -10708.4531746011 -10764.2547791976 55.8016045965 -66.8250335415 -5401.7347845703 -5322.2780762735 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755 
-     100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614 
-     200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321 
-     300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196 
-     400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799 
-     500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266 
-     600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507736 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624 
-     700 -10708.1867253590 -10736.6143955089 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688 
-     800 -10708.1733385055 -10736.0277775930 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693 
-     900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300 
-    1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943 
-Loop time of 39.6206 on 4 procs for 1000 steps with 1440 atoms
-
-Performance: 2.181 ns/day, 11.006 hours/ns, 25.239 timesteps/s
-98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 34.948     | 37.122     | 39.309     |  31.6 | 93.69
-Bond    | 0.00046444 | 0.0005914  | 0.00089121 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.20131    | 2.3895     | 4.565      | 124.7 |  6.03
-Output  | 0.069107   | 0.069157   | 0.069264   |   0.0 |  0.17
-Modify  | 0.010056   | 0.010403   | 0.010688   |   0.3 |  0.03
-Other   |            | 0.02875    |            |       |  0.07
-
-Nlocal:    360 ave 380 max 340 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    4716 ave 4736 max 4696 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    35100 ave 37050 max 33150 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-FullNghs:  70200 ave 74100 max 66300 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 280800
-Ave neighs/atom = 195
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:39

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

@@ -0,0 +1,51 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+group		layer2 molecule 2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo   C  C  # chemical
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair ilp/graphene/hbn
+variable  	REBO  equal c_0     # REBO energy
+variable  	ILP   equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000

examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN

@@ -0,0 +1,56 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AA_prime_stack_2L_noH.data
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group 		layer1 molecule 1
+group 		layer2 molecule 2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff B N B N  # chemical
+pair_coeff  * * ilp/graphene/hbn BNCH.ILP    B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair tersoff
+compute   	1 all pair coul/shield ecoul
+compute   	2 all pair ilp/graphene/hbn
+variable  	Tersoff  equal c_0     # Tersoff energy
+variable  	Ecoul    equal c_1     # Coulomb energy
+variable  	EILP     equal c_2     # total interlayer energy
+variable  	Evdw     equal c_2[1]  # attractive energy
+variable 	Erep     equal c_2[2]  # repulsive  energy
+
+############# Output ###############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+run 		1000

examples/USER/misc/ilp_graphene_hbn/in.grhBN

@@ -0,0 +1,56 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       gr_hBN_Cstack_2L_noH.data
+mass            1 10.8110   # boron    mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | membrane
+mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
+# Separate atom groups
+group 		hBN molecule 1
+group 		gr  molecule 2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo     NULL NULL C    # chemical
+pair_coeff  * * tersoff            BNC.tersoff B    N    NULL # chemical
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP    B    N    C    # long range
+pair_coeff  1 1 coul/shield 0.70
+pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  2 2 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair rebo
+compute   	1 all pair tersoff
+compute   	2 all pair ilp/graphene/hbn
+compute   	3 all pair coul/shield
+variable  	REBO     equal  c_0
+variable  	Tersoff  equal  c_1
+variable  	EILP     equal  c_2     # total interlayer energy
+variable  	Evdw     equal  c_2[1]  # attractive energy
+variable 	Erep     equal  c_2[2]  # repulsive  energy
+variable  	Ecoul    equal  c_3
+
+############# Output ##############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
+
+###### Run molecular dynamics ######
+run 		1000

examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn

@@ -32,14 +32,6 @@ neigh_modify    every 1
 neigh_modify    delay 0
 neigh_modify    check yes
 
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
 #### Simulation settings ####
 timestep  0.001
 #velocity  adsorbate create 300.0 12345
@@ -51,19 +43,16 @@ compute   1 all pair coul/shield ecoul
 compute   2 all pair ilp/graphene/hbn
 variable  Tersoff  equal c_0
 variable  Ecoul    equal c_1
-variable  EILP     equal c_2
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
+variable  ILP      equal c_2
+variable  Evdw     equal c_2[1]
+variable  Erep     equal c_2[2]
 
 ############################
 
 # Output
 thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
+thermo_style    custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
+thermo_modify   lost warn #ignore
 
 #dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
 #dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes

examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1

@@ -1,168 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       hBN_AB_stack_2L_noH_equi_300K.data
-  orthogonal box = (0 0 0) to (43.38 42.5773 100)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
-mass            3 10.8110   # boron mass (g/mole) | membrane
-mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-680 atoms in group membrane
-group adsorbate type 3 4
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
-####################################################################
-pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
-pair_coeff  1 3 coul/shield 0.70
-pair_coeff  1 4 coul/shield 0.69498201415576216335
-pair_coeff  2 3 coul/shield 0.69498201415576216335
-pair_coeff  2 4 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair tersoff
-compute   1 all pair coul/shield ecoul
-compute   2 all pair ilp/graphene/hbn
-variable  Tersoff  equal c_0
-variable  Ecoul    equal c_1
-variable  EILP     equal c_2
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  6 neighbor lists, perpetual/occasional/extra = 5 1 0
-  (1) pair tersoff, perpetual, skip from (5)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (3) pair coul/shield, perpetual, skip from (6)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (4) compute group/group, occasional, copy from (6)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (5) neighbor class addition, perpetual, copy from (2)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, half/full from (5)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 57.85 | 57.85 | 57.85 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] 
-       0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801 
-     100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275 
-     200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807 
-     300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614 
-     400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122 
-     500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319 
-     600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794 
-     700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989 
-     800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553 
-     900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606 
-    1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557 
-Loop time of 202.063 on 1 procs for 1000 steps with 1360 atoms
-
-Performance: 0.428 ns/day, 56.129 hours/ns, 4.949 timesteps/s
-91.0% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 201.4      | 201.4      | 201.4      |   0.0 | 99.67
-Bond    | 0.00092697 | 0.00092697 | 0.00092697 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.086005   | 0.086005   | 0.086005   |   0.0 |  0.04
-Output  | 0.50438    | 0.50438    | 0.50438    |   0.0 |  0.25
-Modify  | 0.038846   | 0.038846   | 0.038846   |   0.0 |  0.02
-Other   |            | 0.03093    |            |       |  0.02
-
-Nlocal:    1360 ave 1360 max 1360 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    7840 ave 7840 max 7840 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    249628 ave 249628 max 249628 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  253390 ave 253390 max 253390 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 253390
-Ave neighs/atom = 186.316
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:03:22

examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.4

@@ -1,168 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       hBN_AB_stack_2L_noH_equi_300K.data
-  orthogonal box = (0 0 0) to (43.38 42.5773 100)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
-mass            3 10.8110   # boron mass (g/mole) | membrane
-mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-680 atoms in group membrane
-group adsorbate type 3 4
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
-####################################################################
-pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
-pair_coeff  1 3 coul/shield 0.70
-pair_coeff  1 4 coul/shield 0.69498201415576216335
-pair_coeff  2 3 coul/shield 0.69498201415576216335
-pair_coeff  2 4 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair tersoff
-compute   1 all pair coul/shield ecoul
-compute   2 all pair ilp/graphene/hbn
-variable  Tersoff  equal c_0
-variable  Ecoul    equal c_1
-variable  EILP     equal c_2
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  6 neighbor lists, perpetual/occasional/extra = 5 1 0
-  (1) pair tersoff, perpetual, skip from (5)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (3) pair coul/shield, perpetual, skip from (6)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (4) compute group/group, occasional, copy from (6)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (5) neighbor class addition, perpetual, copy from (2)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, half/full from (5)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 30.63 | 30.63 | 30.64 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] 
-       0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801 
-     100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275 
-     200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807 
-     300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614 
-     400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122 
-     500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319 
-     600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794 
-     700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989 
-     800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553 
-     900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606 
-    1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557 
-Loop time of 53.3155 on 4 procs for 1000 steps with 1360 atoms
-
-Performance: 1.621 ns/day, 14.810 hours/ns, 18.756 timesteps/s
-97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 49.475     | 50.978     | 52.988     |  18.0 | 95.62
-Bond    | 0.00045061 | 0.00066602 | 0.00086665 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.16491    | 2.1759     | 3.679      |  87.0 |  4.08
-Output  | 0.11871    | 0.11882    | 0.11911    |   0.0 |  0.22
-Modify  | 0.012956   | 0.013504   | 0.01387    |   0.3 |  0.03
-Other   |            | 0.02828    |            |       |  0.05
-
-Nlocal:    340 ave 346 max 336 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-Nghost:    4537.5 ave 4540 max 4534 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Neighs:    62407 ave 62413 max 62402 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-FullNghs:  63347.5 ave 65585 max 61866 min
-Histogram: 1 1 0 1 0 0 0 0 0 1
-
-Total # of neighbors = 253926
-Ave neighs/atom = 186.71
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:53

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.1

@@ -0,0 +1,127 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (42.6 41.8117 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000290871 secs
+  read_data CPU = 0.00159073 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+680 atoms in group layer1
+group		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo   C  C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair ilp/graphene/hbn
+variable  	REBO  equal c_0     # REBO energy
+variable  	ILP   equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual, copy from (1)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
+Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp 
+       0   -10037.285   -10089.985    52.699361   -10057.189   -32.795185    43.640104   -76.435288          300 
+     100   -10037.034   -10064.765     27.73131   -10032.181    -32.58421    34.730868   -67.315078    157.86516 
+     200   -10036.963   -10061.144     24.18111   -10028.856   -32.288132    28.179936   -60.468068    137.65505 
+     300   -10037.003     -10063.5    26.496726   -10030.823   -32.677105    34.923849   -67.600954    150.83708 
+     400   -10037.032   -10064.389    27.356526   -10031.853   -32.535415    44.242347   -76.777762    155.73164 
+     500   -10037.023   -10064.114    27.090279   -10031.431   -32.682418    37.229232    -69.91165    154.21598 
+     600   -10037.003   -10063.657    26.653718   -10031.327   -32.329664    28.509073   -60.838737    151.73078 
+     700   -10037.004    -10063.35    26.345697   -10030.801   -32.549231    32.564686   -65.113917    149.97732 
+     800   -10037.025   -10064.219    27.194765   -10031.766   -32.453653    43.381557    -75.83521    154.81078 
+     900   -10037.028   -10064.668    27.639127   -10032.167   -32.500121     39.99345   -72.493571    157.34039 
+    1000   -10037.003   -10063.662    26.658825   -10031.337   -32.325053    29.573578   -61.898631    151.75986 
+Loop time of 149.887 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 0.576 ns/day, 41.635 hours/ns, 6.672 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    | 149.75     | 149.75     | 149.75     |   0.0 | 99.91
+Bond    | 0.00024772 | 0.00024772 | 0.00024772 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.086328   | 0.086328   | 0.086328   |   0.0 |  0.06
+Output  | 0.00036383 | 0.00036383 | 0.00036383 |   0.0 |  0.00
+Modify  | 0.028636   | 0.028636   | 0.028636   |   0.0 |  0.02
+Other   |            | 0.01708    |            |       |  0.01
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7964 ave 7964 max 7964 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.037e+06 ave 1.037e+06 max 1.037e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037000
+Ave neighs/atom = 762.5
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:02:30

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.4

@@ -0,0 +1,127 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (42.6 41.8117 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000157118 secs
+  read_data CPU = 0.00145698 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+680 atoms in group layer1
+group		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo   C  C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair ilp/graphene/hbn
+variable  	REBO  equal c_0     # REBO energy
+variable  	ILP   equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual, copy from (1)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.879 | 9.879 | 9.879 Mbytes
+Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp 
+       0   -10037.285   -10089.985    52.699361   -10057.189   -32.795185    43.640104   -76.435288          300 
+     100   -10037.034   -10064.765     27.73131   -10032.181    -32.58421    34.730868   -67.315078    157.86516 
+     200   -10036.963   -10061.144     24.18111   -10028.856   -32.288132    28.179936   -60.468068    137.65505 
+     300   -10037.003     -10063.5    26.496726   -10030.823   -32.677105    34.923849   -67.600954    150.83708 
+     400   -10037.032   -10064.389    27.356526   -10031.853   -32.535415    44.242347   -76.777762    155.73164 
+     500   -10037.023   -10064.114    27.090279   -10031.431   -32.682418    37.229232    -69.91165    154.21598 
+     600   -10037.003   -10063.657    26.653718   -10031.327   -32.329664    28.509073   -60.838737    151.73078 
+     700   -10037.004    -10063.35    26.345697   -10030.801   -32.549231    32.564686   -65.113917    149.97732 
+     800   -10037.025   -10064.219    27.194765   -10031.766   -32.453653    43.381557    -75.83521    154.81078 
+     900   -10037.028   -10064.668    27.639127   -10032.167   -32.500121     39.99345   -72.493571    157.34039 
+    1000   -10037.003   -10063.662    26.658825   -10031.337   -32.325053    29.573578   -61.898631    151.75986 
+Loop time of 44.6551 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 1.935 ns/day, 12.404 hours/ns, 22.394 timesteps/s
+93.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 40.304     | 41.221     | 41.998     |   9.5 | 92.31
+Bond    | 0.00027633 | 0.00029379 | 0.00031424 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 2.5678     | 3.3334     | 4.2403     |  32.9 |  7.46
+Output  | 0.0051446  | 0.0054518  | 0.0059683  |   0.4 |  0.01
+Modify  | 0.0088317  | 0.009002   | 0.0090654  |   0.1 |  0.02
+Other   |            | 0.08586    |            |       |  0.19
+
+Nlocal:    340 ave 340 max 340 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    4628 ave 4628 max 4628 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  259250 ave 259250 max 259250 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037000
+Ave neighs/atom = 762.5
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:44

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.1

@@ -0,0 +1,142 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AA_prime_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000375509 secs
+  read_data CPU = 0.00181293 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group 		layer1 molecule 1
+680 atoms in group layer1
+group 		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff B N B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH.ILP    B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair tersoff
+compute   	1 all pair coul/shield ecoul
+compute   	2 all pair ilp/graphene/hbn
+variable  	Tersoff  equal c_0     # Tersoff energy
+variable  	Ecoul    equal c_1     # Coulomb energy
+variable  	EILP     equal c_2     # total interlayer energy
+variable  	Evdw     equal c_2[1]  # attractive energy
+variable 	Erep     equal c_2[2]  # repulsive  energy
+
+############# Output ###############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  4 neighbor lists, perpetual/occasional/extra = 4 0 0
+  (1) pair tersoff, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (4)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10193.138   -10245.837    52.699361   -77.557069    -10208.73   -36.776483    40.780586   -77.557069  -0.33075117          300 
+     100   -10192.814   -10215.193     22.37957   -80.997619   -10177.878   -36.967736    44.029884   -80.997619  -0.34809915    127.39947 
+     200   -10192.922   -10221.807    28.884855   -86.370319   -10184.251   -37.168986    49.201334   -86.370319  -0.38644764    164.43191 
+     300   -10192.878   -10219.029    26.151464   -83.063924   -10182.349    -36.30412    46.759804   -83.063924  -0.37660157    148.87162 
+     400   -10192.892   -10218.834    25.942229   -78.394242   -10181.398   -37.110968    41.283274   -78.394242  -0.32494569    147.68051 
+     500   -10192.909   -10221.331    28.422213   -81.768531    -10184.03   -36.946226    44.822304   -81.768531  -0.35489965    161.79824 
+     600   -10192.886   -10219.371     26.48495   -86.278335   -10182.669    -36.29515    49.983185   -86.278335  -0.40636253    150.77004 
+     700   -10192.902    -10220.95    28.048108    -82.28873   -10183.208    -37.39374     44.89499    -82.28873  -0.34777958    159.66859 
+     800    -10192.88    -10218.51    25.630186   -78.011019   -10181.427   -36.754209    41.256811   -78.011019  -0.32904942    145.90415 
+     900   -10192.894    -10220.56    27.665437   -82.474379   -10183.801   -36.381157    46.093222   -82.474379  -0.37703328    157.49017 
+    1000   -10192.897    -10219.01     26.11313   -87.125683   -10181.252   -37.361898    49.763785   -87.125683  -0.39607952    148.65339 
+Loop time of 211.527 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 0.408 ns/day, 58.757 hours/ns, 4.728 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 211.4      | 211.4      | 211.4      |   0.0 | 99.94
+Bond    | 0.00018859 | 0.00018859 | 0.00018859 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.082034   | 0.082034   | 0.082034   |   0.0 |  0.04
+Output  | 0.00037289 | 0.00037289 | 0.00037289 |   0.0 |  0.00
+Modify  | 0.027928   | 0.027928   | 0.027928   |   0.0 |  0.01
+Other   |            | 0.0159     |            |       |  0.01
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7836 ave 7836 max 7836 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    249560 ave 249560 max 249560 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.00504e+06 ave 1.00504e+06 max 1.00504e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1005040
+Ave neighs/atom = 739
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:03:31

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.4

@@ -0,0 +1,142 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AA_prime_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000224352 secs
+  read_data CPU = 0.00160909 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group 		layer1 molecule 1
+680 atoms in group layer1
+group 		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff B N B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH.ILP    B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair tersoff
+compute   	1 all pair coul/shield ecoul
+compute   	2 all pair ilp/graphene/hbn
+variable  	Tersoff  equal c_0     # Tersoff energy
+variable  	Ecoul    equal c_1     # Coulomb energy
+variable  	EILP     equal c_2     # total interlayer energy
+variable  	Evdw     equal c_2[1]  # attractive energy
+variable 	Erep     equal c_2[2]  # repulsive  energy
+
+############# Output ###############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  4 neighbor lists, perpetual/occasional/extra = 4 0 0
+  (1) pair tersoff, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (4)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 18.99 | 18.99 | 18.99 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10193.138   -10245.837    52.699361   -77.557069    -10208.73   -36.776483    40.780586   -77.557069  -0.33075117          300 
+     100   -10192.814   -10215.193     22.37957   -80.997619   -10177.878   -36.967736    44.029884   -80.997619  -0.34809915    127.39947 
+     200   -10192.922   -10221.807    28.884855   -86.370319   -10184.251   -37.168986    49.201334   -86.370319  -0.38644764    164.43191 
+     300   -10192.878   -10219.029    26.151464   -83.063924   -10182.349    -36.30412    46.759804   -83.063924  -0.37660157    148.87162 
+     400   -10192.892   -10218.834    25.942229   -78.394242   -10181.398   -37.110968    41.283274   -78.394242  -0.32494569    147.68051 
+     500   -10192.909   -10221.331    28.422213   -81.768531    -10184.03   -36.946226    44.822304   -81.768531  -0.35489965    161.79824 
+     600   -10192.886   -10219.371     26.48495   -86.278335   -10182.669    -36.29515    49.983185   -86.278335  -0.40636253    150.77004 
+     700   -10192.902    -10220.95    28.048108    -82.28873   -10183.208    -37.39374     44.89499    -82.28873  -0.34777958    159.66859 
+     800    -10192.88    -10218.51    25.630186   -78.011019   -10181.427   -36.754209    41.256811   -78.011019  -0.32904942    145.90415 
+     900   -10192.894    -10220.56    27.665437   -82.474379   -10183.801   -36.381157    46.093222   -82.474379  -0.37703328    157.49017 
+    1000   -10192.897    -10219.01     26.11313   -87.125683   -10181.252   -37.361898    49.763785   -87.125683  -0.39607952    148.65339 
+Loop time of 68.3631 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 1.264 ns/day, 18.990 hours/ns, 14.628 timesteps/s
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 64.58      | 66.38      | 67.402     |  13.2 | 97.10
+Bond    | 0.0001719  | 0.00021869 | 0.00024033 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.93767    | 1.9601     | 3.76       |  77.0 |  2.87
+Output  | 0.00033593 | 0.00061601 | 0.0014501  |   0.0 |  0.00
+Modify  | 0.0085733  | 0.0089303  | 0.0093236  |   0.4 |  0.01
+Other   |            | 0.01285    |            |       |  0.02
+
+Nlocal:    340 ave 340 max 340 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    4536 ave 4536 max 4536 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    62390 ave 62390 max 62390 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  251260 ave 251260 max 251260 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1005040
+Ave neighs/atom = 739
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:08

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.1

@@ -0,0 +1,153 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       gr_hBN_Cstack_2L_noH.data
+  orthogonal box = (0 0 0) to (44.583 42.9 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1440 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000282049 secs
+  read_data CPU = 0.00159025 secs
+mass            1 10.8110   # boron    mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | membrane
+mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
+# Separate atom groups
+group 		hBN molecule 1
+720 atoms in group hBN
+group 		gr  molecule 2
+720 atoms in group gr
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo     NULL NULL C    # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * tersoff            BNC.tersoff B    N    NULL # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP    B    N    C    # long range
+pair_coeff  1 1 coul/shield 0.70
+pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  2 2 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair rebo
+compute   	1 all pair tersoff
+compute   	2 all pair ilp/graphene/hbn
+compute   	3 all pair coul/shield
+variable  	REBO     equal  c_0
+variable  	Tersoff  equal  c_1
+variable  	EILP     equal  c_2     # total interlayer energy
+variable  	Evdw     equal  c_2[1]  # attractive energy
+variable 	Erep     equal  c_2[2]  # repulsive  energy
+variable  	Ecoul    equal  c_3
+
+############# Output ##############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair rebo, perpetual, skip from (3)
+      attributes: full, newton on, ghost
+      pair build: skip/ghost
+      stencil: none
+      bin: none
+  (2) pair tersoff, perpetual, skip from (5)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (4) pair coul/shield, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton/skip
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, copy from (3)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) neighbor class addition, perpetual, half/full from (5)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 22.52 | 22.52 | 22.52 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10707.284   -10763.085    55.801605   -75.247726   -5401.7348   -5322.2781   -39.072409    36.175318   -75.247726            0          300 
+     100   -10707.074   -10737.127     30.05353   -73.217322   -5389.9568   -5309.2004   -37.970102     35.24722   -73.217322            0    161.57347 
+     200   -10707.016   -10734.932     27.91576   -71.603097   -5389.1294   -5307.7455   -38.056875    33.546222   -71.603097            0    150.08042 
+     300   -10707.013   -10734.987    27.973705   -75.082134   -5388.9196   -5308.1165   -37.950947    37.131186   -75.082134            0    150.39194 
+     400   -10707.012   -10735.498    28.486171   -76.339871   -5389.1657    -5308.153   -38.179442    38.160429   -76.339871            0    153.14706 
+     500   -10707.007   -10734.681    27.674101   -73.312354   -5388.7261   -5307.7384   -38.216944     35.09541   -73.312354            0    148.78121 
+     600   -10707.018   -10735.833    28.815132   -71.927763   -5389.0798    -5308.596   -38.157333     33.77043   -71.927763            0    154.91561 
+     700    -10707.02   -10735.656    28.635377   -74.679371   -5389.2971   -5308.1866   -38.172002    36.507368   -74.679371            0    153.94921 
+     800   -10707.004   -10734.352    27.347425   -76.371288   -5388.5923   -5307.7206   -38.038736    38.332552   -76.371288            0    147.02494 
+     900   -10707.014   -10735.832    28.817405   -73.699332   -5388.9674   -5308.7964   -38.068078    35.631254   -73.699332            0    154.92783 
+    1000   -10706.995   -10733.562     26.56615   -71.439868   -5388.0186   -5307.4414   -38.101452    33.338415   -71.439868            0    142.82466 
+Loop time of 152.66 on 1 procs for 1000 steps with 1440 atoms
+
+Performance: 0.566 ns/day, 42.406 hours/ns, 6.550 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    | 152.52     | 152.52     | 152.52     |   0.0 | 99.91
+Bond    | 0.00023174 | 0.00023174 | 0.00023174 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.087147   | 0.087147   | 0.087147   |   0.0 |  0.06
+Output  | 0.0004189  | 0.0004189  | 0.0004189  |   0.0 |  0.00
+Modify  | 0.029972   | 0.029972   | 0.029972   |   0.0 |  0.02
+Other   |            | 0.02057    |            |       |  0.01
+
+Nlocal:    1440 ave 1440 max 1440 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    8180 ave 8180 max 8180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    140400 ave 140400 max 140400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  280800 ave 280800 max 280800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 280800
+Ave neighs/atom = 195
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:02:32

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.4

@@ -0,0 +1,153 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       gr_hBN_Cstack_2L_noH.data
+  orthogonal box = (0 0 0) to (44.583 42.9 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1440 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.00012207 secs
+  read_data CPU = 0.00357461 secs
+mass            1 10.8110   # boron    mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | membrane
+mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
+# Separate atom groups
+group 		hBN molecule 1
+720 atoms in group hBN
+group 		gr  molecule 2
+720 atoms in group gr
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo     NULL NULL C    # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * tersoff            BNC.tersoff B    N    NULL # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP    B    N    C    # long range
+pair_coeff  1 1 coul/shield 0.70
+pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  2 2 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair rebo
+compute   	1 all pair tersoff
+compute   	2 all pair ilp/graphene/hbn
+compute   	3 all pair coul/shield
+variable  	REBO     equal  c_0
+variable  	Tersoff  equal  c_1
+variable  	EILP     equal  c_2     # total interlayer energy
+variable  	Evdw     equal  c_2[1]  # attractive energy
+variable 	Erep     equal  c_2[2]  # repulsive  energy
+variable  	Ecoul    equal  c_3
+
+############# Output ##############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair rebo, perpetual, skip from (3)
+      attributes: full, newton on, ghost
+      pair build: skip/ghost
+      stencil: none
+      bin: none
+  (2) pair tersoff, perpetual, skip from (5)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (4) pair coul/shield, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton/skip
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, copy from (3)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) neighbor class addition, perpetual, half/full from (5)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10707.284   -10763.085    55.801605   -75.247726   -5401.7348   -5322.2781   -39.072409    36.175318   -75.247726            0          300 
+     100   -10707.074   -10737.127     30.05353   -73.217322   -5389.9568   -5309.2004   -37.970102     35.24722   -73.217322            0    161.57347 
+     200   -10707.016   -10734.932     27.91576   -71.603097   -5389.1294   -5307.7455   -38.056875    33.546222   -71.603097            0    150.08042 
+     300   -10707.013   -10734.987    27.973705   -75.082134   -5388.9196   -5308.1165   -37.950947    37.131186   -75.082134            0    150.39194 
+     400   -10707.012   -10735.498    28.486171   -76.339871   -5389.1657    -5308.153   -38.179442    38.160429   -76.339871            0    153.14706 
+     500   -10707.007   -10734.681    27.674101   -73.312354   -5388.7261   -5307.7384   -38.216944     35.09541   -73.312354            0    148.78121 
+     600   -10707.018   -10735.833    28.815132   -71.927763   -5389.0798    -5308.596   -38.157333     33.77043   -71.927763            0    154.91561 
+     700    -10707.02   -10735.656    28.635377   -74.679371   -5389.2971   -5308.1866   -38.172002    36.507368   -74.679371            0    153.94921 
+     800   -10707.004   -10734.352    27.347425   -76.371288   -5388.5923   -5307.7206   -38.038736    38.332552   -76.371288            0    147.02494 
+     900   -10707.014   -10735.832    28.817405   -73.699332   -5388.9674   -5308.7964   -38.068078    35.631254   -73.699332            0    154.92783 
+    1000   -10706.995   -10733.562     26.56615   -71.439868   -5388.0186   -5307.4414   -38.101452    33.338415   -71.439868            0    142.82466 
+Loop time of 54.095 on 4 procs for 1000 steps with 1440 atoms
+
+Performance: 1.597 ns/day, 15.026 hours/ns, 18.486 timesteps/s
+84.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 42.138     | 45.531     | 49.106     |  42.0 | 84.17
+Bond    | 0.0003159  | 0.00037384 | 0.000489   |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 4.71       | 8.2803     | 11.682     |  98.3 | 15.31
+Output  | 0.0021999  | 0.0055975  | 0.013382   |   6.0 |  0.01
+Modify  | 0.0092845  | 0.010981   | 0.012538   |   1.3 |  0.02
+Other   |            | 0.2673     |            |       |  0.49
+
+Nlocal:    360 ave 380 max 340 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    4716 ave 4736 max 4696 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    35100 ave 37050 max 33150 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+FullNghs:  70200 ave 74100 max 66300 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 280800
+Ave neighs/atom = 195
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:54

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.1

@@ -0,0 +1,154 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AB_stack_2L_noH_equi_300K.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  reading velocities ...
+  1360 velocities
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000251532 secs
+  read_data CPU = 0.00451231 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group membrane  type 1 2
+680 atoms in group membrane
+group adsorbate type 3 4
+680 atoms in group adsorbate
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  0.001
+#velocity  adsorbate create 300.0 12345
+fix       subf membrane setforce 0.0 0.0 0.0
+fix       thermostat all nve
+
+compute   0 all pair tersoff
+compute   1 all pair coul/shield ecoul
+compute   2 all pair ilp/graphene/hbn
+variable  Tersoff  equal c_0
+variable  Ecoul    equal c_1
+variable  ILP      equal c_2
+variable  Evdw     equal c_2[1]
+variable  Erep     equal c_2[2]
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
+thermo_modify   lost warn #ignore
+
+#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
+#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
+
+###### Run molecular dynamics ######
+run 1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair tersoff, perpetual, skip from (4)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (5)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, half/full from (4)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 54.59 | 54.59 | 54.59 Mbytes
+Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp 
+       0   -5114.6628   -5127.8586    13.195828   -5091.4121   -36.083114  -0.36343598    38.918674   -75.001787    75.119474 
+     100   -5114.6621   -5127.6958    13.033777   -5091.2408    -36.09276  -0.36228286    38.769906   -74.862666    74.196973 
+     200   -5114.6631   -5127.5945     12.93145   -5091.1508   -36.086669  -0.35708801     38.20076   -74.287429    73.614462 
+     300   -5114.6694   -5128.3286     13.65924   -5091.8646   -36.110786  -0.35328159    37.758284    -73.86907    77.757528 
+     400   -5114.6614   -5127.6424    12.980975   -5091.2348   -36.049634  -0.35794328    38.247252   -74.296886    73.896389 
+     500     -5114.66   -5127.4098    12.749794   -5090.9285   -36.119571  -0.36174976    38.745548   -74.865119    72.580351 
+     600   -5114.6673   -5128.0913    13.424021   -5091.6339    -36.09384  -0.36356991    38.927401   -75.021241    76.418503 
+     700    -5114.661   -5127.7467    13.085707   -5091.2811   -36.106639  -0.35892399    38.332616   -74.439255    74.492596 
+     800   -5114.6623    -5128.013    13.350778   -5091.5694   -36.089718  -0.35392503    37.851602    -73.94132    76.001554 
+     900   -5114.6675   -5128.1497    13.482146   -5091.6704   -36.124679  -0.35462869    37.885183   -74.009861    76.749392 
+    1000   -5114.6683   -5128.3365    13.668146    -5091.937   -36.037596  -0.36184347    38.709718   -74.747314    77.808228 
+Loop time of 207.028 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 0.417 ns/day, 57.508 hours/ns, 4.830 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 206.9      | 206.9      | 206.9      |   0.0 | 99.94
+Bond    | 0.00019169 | 0.00019169 | 0.00019169 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.081397   | 0.081397   | 0.081397   |   0.0 |  0.04
+Output  | 0.00036597 | 0.00036597 | 0.00036597 |   0.0 |  0.00
+Modify  | 0.033408   | 0.033408   | 0.033408   |   0.0 |  0.02
+Other   |            | 0.01615    |            |       |  0.01
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7840 ave 7840 max 7840 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    249628 ave 249628 max 249628 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  253390 ave 253390 max 253390 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 253390
+Ave neighs/atom = 186.316
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:03:27

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.4

@@ -0,0 +1,154 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AB_stack_2L_noH_equi_300K.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  reading velocities ...
+  1360 velocities
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000332117 secs
+  read_data CPU = 0.00270581 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group membrane  type 1 2
+680 atoms in group membrane
+group adsorbate type 3 4
+680 atoms in group adsorbate
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  0.001
+#velocity  adsorbate create 300.0 12345
+fix       subf membrane setforce 0.0 0.0 0.0
+fix       thermostat all nve
+
+compute   0 all pair tersoff
+compute   1 all pair coul/shield ecoul
+compute   2 all pair ilp/graphene/hbn
+variable  Tersoff  equal c_0
+variable  Ecoul    equal c_1
+variable  ILP      equal c_2
+variable  Evdw     equal c_2[1]
+variable  Erep     equal c_2[2]
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
+thermo_modify   lost warn #ignore
+
+#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
+#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
+
+###### Run molecular dynamics ######
+run 1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair tersoff, perpetual, skip from (4)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (5)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, half/full from (4)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 28.9 | 28.9 | 28.9 Mbytes
+Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp 
+       0   -5114.6628   -5127.8586    13.195828   -5091.4121   -36.083114  -0.36343598    38.918674   -75.001787    75.119474 
+     100   -5114.6621   -5127.6958    13.033777   -5091.2408    -36.09276  -0.36228286    38.769906   -74.862666    74.196973 
+     200   -5114.6631   -5127.5945     12.93145   -5091.1508   -36.086669  -0.35708801     38.20076   -74.287429    73.614462 
+     300   -5114.6694   -5128.3286     13.65924   -5091.8646   -36.110786  -0.35328159    37.758284    -73.86907    77.757528 
+     400   -5114.6614   -5127.6424    12.980975   -5091.2348   -36.049634  -0.35794328    38.247252   -74.296886    73.896389 
+     500     -5114.66   -5127.4098    12.749794   -5090.9285   -36.119571  -0.36174976    38.745548   -74.865119    72.580351 
+     600   -5114.6673   -5128.0913    13.424021   -5091.6339    -36.09384  -0.36356991    38.927401   -75.021241    76.418503 
+     700    -5114.661   -5127.7467    13.085707   -5091.2811   -36.106639  -0.35892399    38.332616   -74.439255    74.492596 
+     800   -5114.6623    -5128.013    13.350778   -5091.5694   -36.089718  -0.35392503    37.851602    -73.94132    76.001554 
+     900   -5114.6675   -5128.1497    13.482146   -5091.6704   -36.124679  -0.35462869    37.885183   -74.009861    76.749392 
+    1000   -5114.6683   -5128.3365    13.668146    -5091.937   -36.037596  -0.36184347    38.709718   -74.747314    77.808228 
+Loop time of 65.9005 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 1.311 ns/day, 18.306 hours/ns, 15.174 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 63.244     | 64.208     | 65.281     |  10.1 | 97.43
+Bond    | 0.00013971 | 0.00017679 | 0.00022101 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.58237    | 1.6612     | 2.6292     |  63.1 |  2.52
+Output  | 0.0003171  | 0.00062358 | 0.0015192  |   0.0 |  0.00
+Modify  | 0.010251   | 0.010509   | 0.01075    |   0.2 |  0.02
+Other   |            | 0.02025    |            |       |  0.03
+
+Nlocal:    340 ave 346 max 336 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Nghost:    4537.5 ave 4540 max 4534 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs:    62407 ave 62413 max 62402 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+FullNghs:  63347.5 ave 65585 max 61866 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 253926
+Ave neighs/atom = 186.71
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:06

examples/USER/misc/kolmogorov_crespi_full/CH.KC

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

examples/USER/misc/kolmogorov_crespi_full/CH_taper.KC

@@ -0,0 +1 @@
+../../../../potentials/CH_taper.KC

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

@@ -5,21 +5,22 @@ atom_style      full
 processors      * * 1     # domain decomposition over x and y
 
 # System and atom definition
-# we use 2 atom types so that inter- and intra-layer
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
 # interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
+
+read_data       Bi_gr_AB_stack_2L_noH.data
 mass            1 12.0107   # carbon mass (g/mole) | membrane
 mass            2 12.0107   # carbon mass (g/mole) | adsorbate
 # Separate atom groups
-group membrane  type 1
-group adsorbate type 2
+group		layer1 molecule 1
+group		layer2 molecule 2
 
 ######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  kolmogorov/crespi/full 16.0
+pair_style  hybrid/overlay  rebo  kolmogorov/crespi/full 16.0 1
 ####################################################################
-pair_coeff  * * rebo                     CH.rebo      NULL C  # chemical
-pair_coeff  * * kolmogorov/crespi/full   CC.KC-full     C    C  # long range
+pair_coeff  * * rebo               	 CH.rebo      C  C  # chemical
+pair_coeff  * * kolmogorov/crespi/full   CH_taper.KC  C  C  # long range
 ####################################################################
 # Neighbor update settings
 neighbor        2.0 bin
@@ -27,34 +28,25 @@ neigh_modify    every 1
 neigh_modify    delay 0
 neigh_modify    check yes
 
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
 #### Simulation settings ####
-timestep  0.001
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
+timestep	0.001
+velocity	all create 300.0 12345
 
-compute   0 all pair rebo
-compute   1 all pair kolmogorov/crespi/full
-variable  REBO     equal c_0
-variable  KC       equal c_1
+compute   	0 all pair rebo
+compute  	1 all pair kolmogorov/crespi/full
+variable  	REBO  equal c_0     # REBO energy
+variable  	KC    equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
 
 ############################
 
 # Output
 thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
+thermo_style    custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
+thermo_modify   line one format float %.16f
+thermo_modify   flush yes norm no lost warn
 
 ###### Run molecular dynamics ######
-run 1000
+fix       	thermostat all nve
+run 	  	1000

examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.1

@@ -0,0 +1,129 @@
+LAMMPS (5 Jun 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (42.6 41.8117 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000143357 secs
+  read_data CPU = 0.00128686 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+680 atoms in group layer1
+group		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  kolmogorov/crespi/full 16.0 1
+####################################################################
+pair_coeff  * * rebo               	 CH.rebo      C  C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * kolmogorov/crespi/full   CH_taper.KC  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair kolmogorov/crespi/full
+variable  	REBO  equal c_0     # REBO energy
+variable  	KC    equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
+thermo_modify   line one format float %.16f
+thermo_modify   flush yes norm no lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair kolmogorov/crespi/full, perpetual, copy from (1)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
+Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp 
+       0 0.0000000000000000 -10037.7640583248121402 -10090.4634194413119985 52.6993611164999436 -10057.1894932863488066 -33.2739261549639664 35.9559834316876348 -69.2299095866357561 299.9999999999996589 
+     100 5.3877589240437374 -10037.5122858156355505 -10065.4637593850693520 27.9514735694345475 -10032.2132655062632693 -33.2504938788055995 25.2100699045900747 -58.4605637833913789 159.1184768311149185 
+     200 10.7755050340201706 -10037.4414086674350983 -10061.6271012692632212 24.1856926018286202 -10028.9093252939674130 -32.7177759752951403 18.5366534598604176 -51.2544294351563394 137.6811336385792970 
+     300 16.1665089030284435 -10037.4824653300311184 -10064.2845326005663082 26.8020672705344225 -10030.9195389405322203 -33.3649936600345924 26.3639208740001152 -59.7289145340284122 152.5752876469470891 
+     400 21.5454839280573651 -10037.5105626329259394 -10064.8769084956420556 27.3663458627154164 -10031.8478821022799821 -33.0290263933626349 36.6142885774199272 -69.6433149707719963 155.7875386888538571 
+     500 26.9370588400634006 -10037.5010433785082569 -10064.8363209936451312 27.3352776151367571 -10031.4417172103931080 -33.3946037832518243 26.2980262321670750 -59.6926300154142595 155.6106774503846850 
+     600 32.4204196080099791 -10037.4817772372425679 -10064.1925798287738871 26.7108025915316247 -10031.4376178099264507 -32.7549620188478201 18.5745873777024606 -51.3295493965519327 152.0557480714992380 
+     700 37.8001567909959704 -10037.4834430268438155 -10064.1291975032218033 26.6457544763788299 -10030.8722888097800023 -33.2569086934421492 25.2322818106646771 -58.4891905041015008 151.6854507067418467 
+     800 43.1622281169984490 -10037.5047888097760733 -10064.8671187128948077 27.3623299031188978 -10031.9815058608437539 -32.8856128520517217 36.5236695083771536 -69.4092823604148350 155.7646771616279011 
+     900 48.5261204120470211 -10037.5068323940176924 -10065.3998155271074211 27.8929831330889542 -10032.1734374829957233 -33.2263780441125931 27.7314849391008309 -60.9578629832065317 158.7855101588076820 
+    1000 53.8888844919856638 -10037.4811494880468672 -10064.0099109142265661 26.5287614261789670 -10031.3325267421259923 -32.6773841721003464 18.9005970229871600 -51.5779811950879434 151.0194480396057202 
+Loop time of 53.8889 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 1.603 ns/day, 14.969 hours/ns, 18.557 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 53.836     | 53.836     | 53.836     |   0.0 | 99.90
+Bond    | 0.00043479 | 0.00043479 | 0.00043479 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.032452   | 0.032452   | 0.032452   |   0.0 |  0.06
+Output  | 0.00058326 | 0.00058326 | 0.00058326 |   0.0 |  0.00
+Modify  | 0.0094135  | 0.0094135  | 0.0094135  |   0.0 |  0.02
+Other   |            | 0.009815   |            |       |  0.02
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7964 ave 7964 max 7964 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.037e+06 ave 1.037e+06 max 1.037e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037000
+Ave neighs/atom = 762.5
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:54

examples/USER/misc/kolmogorov_crespi_full/log.5Jun19.bilayer-graphene.icc.4

@@ -0,0 +1,129 @@
+LAMMPS (5 Jun 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (42.6 41.8117 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000245051 secs
+  read_data CPU = 0.00257704 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+680 atoms in group layer1
+group		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  kolmogorov/crespi/full 16.0 1
+####################################################################
+pair_coeff  * * rebo               	 CH.rebo      C  C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * kolmogorov/crespi/full   CH_taper.KC  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair kolmogorov/crespi/full
+variable  	REBO  equal c_0     # REBO energy
+variable  	KC    equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
+thermo_modify   line one format float %.16f
+thermo_modify   flush yes norm no lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair kolmogorov/crespi/full, perpetual, copy from (1)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.878 | 9.878 | 9.878 Mbytes
+Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp 
+       0 0.0000000000000000 -10037.7640583250176860 -10090.4634194415175443 52.6993611164999933 -10057.1894932866325689 -33.2739261548851388 35.9559834317043467 -69.2299095866038954 299.9999999999999432 
+     100 1.5180600649910048 -10037.5122858156355505 -10065.4637593850711710 27.9514735694348637 -10032.2132655062741833 -33.2504938787968172 25.2100699046001573 -58.4605637833912795 159.1184768311167090 
+     200 3.0089348420733586 -10037.4414086674296414 -10061.6271012692577642 24.1856926018279914 -10028.9093252939601371 -32.7177759752976272 18.5366534598677504 -51.2544294351567515 137.6811336385757158 
+     300 4.5315427089808509 -10037.4824653300020145 -10064.2845326005372044 26.8020672705348311 -10030.9195389405158494 -33.3649936600211205 26.3639208740115549 -59.7289145340278722 152.5752876469494197 
+     400 6.0353655620710924 -10037.5105626329095685 -10064.8769084956238657 27.3663458627148124 -10031.8478821022818011 -33.0290263933414394 36.6142885774347562 -69.6433149707726074 155.7875386888504181 
+     500 7.5396006110822782 -10037.5010433784900670 -10064.8363209936269413 27.3352776151361780 -10031.4417172103858320 -33.3946037832416351 26.2980262321774489 -59.6926300154146787 155.6106774503813881 
+     600 9.2617433650884777 -10037.4817772372534819 -10064.1925798287848011 26.7108025915320830 -10031.4376178099319077 -32.7549620188514226 18.5745873777100208 -51.3295493965524017 152.0557480715018528 
+     700 10.7484918619738892 -10037.4834430268347205 -10064.1291975032127084 26.6457544763787268 -10030.8722888097836403 -33.2569086934306739 25.2322818106757047 -58.4891905041008613 151.6854507067412499 
+     800 12.2509897360578179 -10037.5047888097869873 -10064.8671187129039026 27.3623299031166667 -10031.9815058608728577 -32.8856128520297801 36.5236695083899718 -69.4092823604150908 155.7646771616151966 
+     900 13.7584852169966325 -10037.5068323939758557 -10065.3998155270637653 27.8929831330881477 -10032.1734374829648004 -33.2263780440982259 27.7314849391120788 -60.9578629832060841 158.7855101588031062 
+    1000 15.2755981830414385 -10037.4811494880432292 -10064.0099109142211091 26.5287614261777058 -10031.3325267421205353 -32.6773841721017888 18.9005970229946634 -51.5779811950868776 151.0194480395985295 
+Loop time of 15.2757 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 5.656 ns/day, 4.243 hours/ns, 65.464 timesteps/s
+99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 13.985     | 14.446     | 14.823     |   7.9 | 94.57
+Bond    | 0.00040979 | 0.00042456 | 0.00046059 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.43692    | 0.81428    | 1.2749     |  33.2 |  5.33
+Output  | 0.00028016 | 0.00037143 | 0.00063561 |   0.0 |  0.00
+Modify  | 0.0045586  | 0.0046468  | 0.0047903  |   0.1 |  0.03
+Other   |            | 0.01041    |            |       |  0.07
+
+Nlocal:    340 ave 340 max 340 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    4628 ave 4628 max 4628 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  259250 ave 259250 max 259250 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037000
+Ave neighs/atom = 762.5
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:15

lib/colvars/Makefile.common

@@ -34,6 +34,7 @@ COLVARS_SRCS = \
         colvarcomp_coordnums.cpp \
         colvarcomp.cpp \
         colvarcomp_distances.cpp \
+        colvarcomp_gpath.cpp \
         colvarcomp_protein.cpp \
         colvarcomp_rotations.cpp \
         colvar.cpp \

lib/colvars/colvar.cpp

@@ -791,6 +791,11 @@ int colvar::init_components(std::string const &conf)
     "inertia", "inertia");
   error_code |= init_components_type<inertia_z>(conf, "moment of inertia around an axis", "inertiaZ");
   error_code |= init_components_type<eigenvector>(conf, "eigenvector", "eigenvector");
+  error_code |= init_components_type<gspath>(conf, "geometrical path collective variables (s)", "gspath");
+  error_code |= init_components_type<gzpath>(conf, "geometrical path collective variables (z)", "gzpath");
+  error_code |= init_components_type<linearCombination>(conf, "linear combination of other collective variables", "subColvar");
+  error_code |= init_components_type<gspathCV>(conf, "geometrical path collective variables (s) for other CVs", "gspathCV");
+  error_code |= init_components_type<gzpathCV>(conf, "geometrical path collective variables (z) for other CVs", "gzpathCV");
 
   if (!cvcs.size() || (error_code != COLVARS_OK)) {
     cvm::error("Error: no valid components were provided "
@@ -1495,6 +1500,8 @@ int colvar::calc_colvar_properties()
     // calculate the velocity by finite differences
     if (cvm::step_relative() == 0) {
       x_old = x;
+      v_fdiff.reset(); // Do not pretend we know anything about the actual velocity
+      // eg. upon restarting. That would require saving v_fdiff or x_old to the state file
     } else {
       v_fdiff = fdiff_velocity(x_old, x);
       v_reported = v_fdiff;
@@ -1516,8 +1523,9 @@ int colvar::calc_colvar_properties()
       x_ext = prev_x_ext;
       v_ext = prev_v_ext;
     }
-
     // report the restraint center as "value"
+    // These position and velocities come from integration at the _previous timestep_ in update_forces_energy()
+    // But we report values at the beginning of the timestep (value at t=0 on the first timestep)
     x_reported = x_ext;
     v_reported = v_ext;
     // the "total force" with the extended Lagrangian is
@@ -1651,8 +1659,6 @@ cvm::real colvar::update_forces_energy()
       // is equal to the actual coordinate
       x_ext = x;
     }
-    // Report extended value
-    x_reported = x_ext;
   }
 
   // Now adding the force on the actual colvar (for those biases that
@@ -1975,9 +1981,8 @@ std::istream & colvar::read_restart(std::istream &is)
   }
 
   if (is_enabled(f_cv_extended_Lagrangian)) {
-
     if ( !(get_keyval(conf, "extended_x", x_ext,
-                      colvarvalue(x.type()), colvarparse::parse_silent)) &&
+                      colvarvalue(x.type()), colvarparse::parse_silent)) ||
          !(get_keyval(conf, "extended_v", v_ext,
                       colvarvalue(x.type()), colvarparse::parse_silent)) ) {
       cvm::log("Error: restart file does not contain "
@@ -2079,11 +2084,11 @@ std::ostream & colvar::write_restart(std::ostream &os) {
     os << "  extended_x "
        << std::setprecision(cvm::cv_prec)
        << std::setw(cvm::cv_width)
-       << x_ext << "\n"
+       << x_reported << "\n"
        << "  extended_v "
        << std::setprecision(cvm::cv_prec)
        << std::setw(cvm::cv_width)
-       << v_ext << "\n";
+       << v_reported << "\n";
   }
 
   os << "}\n\n";
@@ -2150,7 +2155,6 @@ std::ostream & colvar::write_traj_label(std::ostream & os)
 std::ostream & colvar::write_traj(std::ostream &os)
 {
   os << " ";
-
   if (is_enabled(f_cv_output_value)) {
 
     if (is_enabled(f_cv_extended_Lagrangian)) {

lib/colvars/colvar.h

@@ -569,6 +569,14 @@ public:
   class alpha_dihedrals;
   class alpha_angles;
   class dihedPC;
+  class componentDisabled;
+  class CartesianBasedPath;
+  class gspath;
+  class gzpath;
+  class linearCombination;
+  class CVBasedPath;
+  class gspathCV;
+  class gzpathCV;
 
   // non-scalar components
   class distance_vec;

lib/colvars/colvar_geometricpath.h

@@ -0,0 +1,270 @@
+#ifndef GEOMETRICPATHCV_H
+#define GEOMETRICPATHCV_H
+// This file is part of the Collective Variables module (Colvars).
+// The original version of Colvars and its updates are located at:
+// https://github.com/colvars/colvars
+// Please update all Colvars source files before making any changes.
+// If you wish to distribute your changes, please submit them to the
+// Colvars repository at GitHub.
+
+
+#include <vector>
+#include <cmath>
+#include <iostream>
+#include <algorithm>
+#include <string>
+#include <map>
+
+namespace GeometricPathCV {
+
+enum path_sz {S, Z};
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+class GeometricPathBase {
+private:
+    struct doCompareFrameDistance {
+        doCompareFrameDistance(const GeometricPathBase& obj): m_obj(obj) {}
+        const GeometricPathBase& m_obj;
+        bool operator()(const size_t& i1, const size_t& i2) {
+            return m_obj.frame_distances[i1] < m_obj.frame_distances[i2];
+        }
+    };
+protected:
+    scalar_type v1v1;
+    scalar_type v2v2;
+    scalar_type v3v3;
+    scalar_type v4v4;
+    scalar_type v1v3;
+    scalar_type v1v4;
+    scalar_type f;
+    scalar_type dx;
+    scalar_type s;
+    scalar_type z;
+    scalar_type zz;
+    std::vector<element_type> v1;
+    std::vector<element_type> v2;
+    std::vector<element_type> v3;
+    std::vector<element_type> v4;
+    std::vector<element_type> dfdv1;
+    std::vector<element_type> dfdv2;
+    std::vector<element_type> dzdv1;
+    std::vector<element_type> dzdv2;
+    std::vector<scalar_type> frame_distances;
+    std::vector<size_t> frame_index;
+    bool use_second_closest_frame;
+    bool use_third_closest_frame;
+    bool use_z_square;
+    long min_frame_index_1;
+    long min_frame_index_2;
+    long min_frame_index_3;
+    long sign;
+    double M;
+    double m;
+public:
+    GeometricPathBase(size_t vector_size, const element_type& element = element_type(), size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
+    GeometricPathBase(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
+    GeometricPathBase() {}
+    virtual ~GeometricPathBase() {}
+    virtual void initialize(size_t vector_size, const element_type& element = element_type(), size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
+    virtual void initialize(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
+    virtual void prepareVectors();
+    virtual void updateReferenceDistances();
+    virtual void compute();
+    virtual void determineClosestFrames();
+    virtual void computeValue();
+    virtual void computeDerivatives();
+};
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+GeometricPathBase<element_type, scalar_type, path_type>::GeometricPathBase(size_t vector_size, const element_type& element, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
+    initialize(vector_size, element, total_frames, p_use_second_closest_frame, p_use_third_closest_frame, p_use_z_square);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+GeometricPathBase<element_type, scalar_type, path_type>::GeometricPathBase(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
+    initialize(vector_size, elements, total_frames, p_use_second_closest_frame, p_use_third_closest_frame, p_use_z_square);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::initialize(size_t vector_size, const element_type& element, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
+    v1v1 = scalar_type();
+    v2v2 = scalar_type();
+    v3v3 = scalar_type();
+    v4v4 = scalar_type();
+    v1v3 = scalar_type();
+    v1v4 = scalar_type();
+    f = scalar_type();
+    dx = scalar_type();
+    z = scalar_type();
+    zz = scalar_type();
+    sign = 0;
+    v1.resize(vector_size, element);
+    v2.resize(vector_size, element);
+    v3.resize(vector_size, element);
+    v4.resize(vector_size, element);
+    dfdv1.resize(vector_size, element);
+    dfdv2.resize(vector_size, element);
+    dzdv1.resize(vector_size, element);
+    dzdv2.resize(vector_size, element);
+    frame_distances.resize(total_frames);
+    frame_index.resize(total_frames);
+    for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
+        frame_index[i_frame] = i_frame;
+    }
+    use_second_closest_frame = p_use_second_closest_frame;
+    use_third_closest_frame = p_use_third_closest_frame;
+    use_z_square = p_use_z_square;
+    M = static_cast<scalar_type>(total_frames - 1);
+    m = static_cast<scalar_type>(1.0);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::initialize(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
+    v1v1 = scalar_type();
+    v2v2 = scalar_type();
+    v3v3 = scalar_type();
+    v4v4 = scalar_type();
+    v1v3 = scalar_type();
+    v1v4 = scalar_type();
+    f = scalar_type();
+    dx = scalar_type();
+    z = scalar_type();
+    zz = scalar_type();
+    sign = 0;
+    v1 = elements;
+    v2 = elements;
+    v3 = elements;
+    v4 = elements;
+    dfdv1 = elements;
+    dfdv2 = elements;
+    dzdv1 = elements;
+    dzdv2 = elements;
+    frame_distances.resize(total_frames);
+    frame_index.resize(total_frames);
+    for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
+        frame_index[i_frame] = i_frame;
+    }
+    use_second_closest_frame = p_use_second_closest_frame;
+    use_third_closest_frame = p_use_third_closest_frame;
+    use_z_square = p_use_z_square;
+    M = static_cast<scalar_type>(total_frames - 1);
+    m = static_cast<scalar_type>(1.0);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::prepareVectors() {
+    std::cout << "Warning: you should not call the prepareVectors() in base class!\n";
+    std::cout << std::flush;
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::updateReferenceDistances() {
+    std::cout << "Warning: you should not call the updateReferenceDistances() in base class!\n";
+    std::cout << std::flush;
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::compute() {
+    computeValue();
+    computeDerivatives();
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::determineClosestFrames() {
+    // Find the closest and the second closest frames
+    std::sort(frame_index.begin(), frame_index.end(), doCompareFrameDistance(*this));
+    // Determine the sign
+    sign = static_cast<long>(frame_index[0]) - static_cast<long>(frame_index[1]);
+    if (sign > 1) {
+        // sigma(z) is on the left side of the closest frame
+        sign = 1;
+    } else if (sign < -1) {
+        // sigma(z) is on the right side of the closest frame
+        sign = -1;
+    }
+    if (std::abs(static_cast<long>(frame_index[0]) - static_cast<long>(frame_index[1])) > 1) {
+        std::cout << "Warning: Geometrical pathCV relies on the assumption that the second closest frame is the neighbouring frame\n";
+        std::cout << "         Please check your configuration or increase restraint on z(σ)\n";
+        for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
+            std::cout << "Frame index: " << frame_index[i_frame] << " ; optimal RMSD = " << frame_distances[frame_index[i_frame]] << "\n";
+        }
+    }
+    min_frame_index_1 = frame_index[0];                                                         // s_m
+    min_frame_index_2 = use_second_closest_frame ? frame_index[1] : min_frame_index_1 - sign;   // s_(m-1)
+    min_frame_index_3 = use_third_closest_frame ? frame_index[2] : min_frame_index_1 + sign;    // s_(m+1)
+    m = static_cast<double>(frame_index[0]);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::computeValue() {
+    updateReferenceDistances();
+    determineClosestFrames();
+    prepareVectors();
+    v1v1 = scalar_type();
+    v2v2 = scalar_type();
+    v3v3 = scalar_type();
+    v1v3 = scalar_type();
+    if (path_type == Z) {
+        v1v4 = scalar_type();
+        v4v4 = scalar_type();
+    }
+    for (size_t i_elem = 0; i_elem < v1.size(); ++i_elem) {
+        v1v1 += v1[i_elem] * v1[i_elem];
+        v2v2 += v2[i_elem] * v2[i_elem];
+        v3v3 += v3[i_elem] * v3[i_elem];
+        v1v3 += v1[i_elem] * v3[i_elem];
+        if (path_type == Z) {
+            v1v4 += v1[i_elem] * v4[i_elem];
+            v4v4 += v4[i_elem] * v4[i_elem];
+        }
+    }
+    f = (std::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)) - v1v3) / v3v3;
+    if (path_type == Z) {
+        dx = 0.5 * (f - 1);
+        zz = v1v1 + 2 * dx * v1v4 + dx * dx * v4v4;
+        if (use_z_square) {
+            z = zz;
+        } else {
+            z = std::sqrt(std::fabs(zz));
+        }
+    }
+    if (path_type == S) {
+        s = m/M + static_cast<double>(sign) * ((f - 1) / (2 * M));
+    }
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void GeometricPathBase<element_type, scalar_type, path_type>::computeDerivatives() {
+    const scalar_type factor1 = 1.0 / (2.0 * v3v3 * std::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)));
+    const scalar_type factor2 = 1.0 / v3v3;
+    for (size_t i_elem = 0; i_elem < v1.size(); ++i_elem) {
+        // Compute the derivative of f with vector v1
+        dfdv1[i_elem] = factor1 * (2.0 * v1v3 * v3[i_elem] - 2.0 * v3v3 * v1[i_elem]) - factor2 * v3[i_elem];
+        // Compute the derivative of f with respect to vector v2
+        dfdv2[i_elem] = factor1 * (2.0 * v3v3 * v2[i_elem]);
+        // dZ(v1(r), v2(r), v3) / dr = ∂Z/∂v1 * dv1/dr + ∂Z/∂v2 * dv2/dr
+        // dv1/dr = [fitting matrix 1][-1, ..., -1]
+        // dv2/dr = [fitting matrix 2][1, ..., 1]
+        // ∂Z/∂v1 = 1/(2*z) * (2v1 + (f-1)v4 + (v1⋅v4)∂f/∂v1 + v4^2 * 1/4 * 2(f-1) * ∂f/∂v1)
+        // ∂Z/∂v2 = 1/(2*z) * ((v1⋅v4)∂f/∂v2 + v4^2 * 1/4 * 2(f-1) * ∂f/∂v2)
+        if (path_type == Z) {
+            if (use_z_square) {
+                dzdv1[i_elem] = 2.0 * v1[i_elem] + (f-1) * v4[i_elem] + v1v4 * dfdv1[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv1[i_elem];
+                dzdv2[i_elem] = v1v4 * dfdv2[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv2[i_elem];
+            } else {
+                if (z > static_cast<scalar_type>(0)) {
+                    dzdv1[i_elem] = (1.0 / (2.0 * z)) * (2.0 * v1[i_elem] + (f-1) * v4[i_elem] + v1v4 * dfdv1[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv1[i_elem]);
+                    dzdv2[i_elem] = (1.0 / (2.0 * z)) * (v1v4 * dfdv2[i_elem] + v4v4 * 0.25 * 2.0 * (f-1) * dfdv2[i_elem]);
+                } else {
+                    // workaround at z = 0
+                    dzdv1[i_elem] = 0;
+                    dzdv2[i_elem] = 0;
+                }
+            }
+        }
+    }
+}
+
+}
+
+#endif // GEOMETRICPATHCV_H

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/colvarbias_meta.cpp

@@ -37,7 +37,6 @@ colvarbias_meta::colvarbias_meta(char const *key)
 {
   new_hills_begin = hills.end();
   hills_traj_os = NULL;
-  replica_hills_os = NULL;
 
   ebmeta_equil_steps = 0L;
 }
@@ -203,23 +202,37 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
     target_dist = new colvar_grid_scalar();
     target_dist->init_from_colvars(colvars);
     std::string target_dist_file;
-    get_keyval(conf, "targetdistfile", target_dist_file);
+    get_keyval(conf, "targetDistFile", target_dist_file);
     std::ifstream targetdiststream(target_dist_file.c_str());
     target_dist->read_multicol(targetdiststream);
     cvm::real min_val = target_dist->minimum_value();
+    cvm::real max_val = target_dist->maximum_value();
     if(min_val<0){
-      cvm::error("Error: Target distribution of ebMeta "
+      cvm::error("Error: Target distribution of EBMetaD "
                  "has negative values!.\n", INPUT_ERROR);
     }
-    cvm::real min_pos_val = target_dist->minimum_pos_value();
-    if(min_pos_val<=0){
-      cvm::error("Error: Target distribution of ebMeta has negative "
-                 "or zero minimum positive value!.\n", INPUT_ERROR);
-    }
-    if(min_val==0){
-      cvm::log("WARNING: Target distribution has zero values.\n");
-      cvm::log("Zeros will be converted to the minimum positive value.\n");
-      target_dist->remove_zeros(min_pos_val);
+    cvm::real target_dist_min_val;
+    get_keyval(conf, "targetDistMinVal", target_dist_min_val, 1/1000000.0);
+    if(target_dist_min_val>0 && target_dist_min_val<1){
+      target_dist_min_val=max_val*target_dist_min_val;
+      target_dist->remove_small_values(target_dist_min_val);
+    } else {
+      if (target_dist_min_val==0) {
+        cvm::log("NOTE: targetDistMinVal is set to zero, the minimum value of the target \n");
+        cvm::log(" distribution will be set as the minimum positive value.\n");
+        cvm::real min_pos_val = target_dist->minimum_pos_value();
+        if(min_pos_val<=0){
+          cvm::error("Error: Target distribution of EBMetaD has negative "
+                     "or zero minimum positive value!.\n", INPUT_ERROR);
+        }
+        if(min_val==0){
+          cvm::log("WARNING: Target distribution has zero values.\n");
+          cvm::log("Zeros will be converted to the minimum positive value.\n");
+          target_dist->remove_small_values(min_pos_val);
+        }
+      } else {
+          cvm::error("Error: targetDistMinVal must be a value between 0 and 1!.\n", INPUT_ERROR);
+      }
     }
     // normalize target distribution and multiply by effective volume = exp(differential entropy)
     target_dist->multiply_constant(1.0/target_dist->integral());
@@ -235,14 +248,14 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf)
 colvarbias_meta::~colvarbias_meta()
 {
   colvarbias_meta::clear_state_data();
+  colvarproxy *proxy = cvm::proxy;
 
-  if (replica_hills_os) {
-    cvm::proxy->close_output_stream(replica_hills_file);
-    replica_hills_os = NULL;
+  if (proxy->get_output_stream(replica_hills_file)) {
+    proxy->close_output_stream(replica_hills_file);
   }
 
   if (hills_traj_os) {
-    cvm::proxy->close_output_stream(hills_traj_file_name());
+    proxy->close_output_stream(hills_traj_file_name());
     hills_traj_os = NULL;
   }
 
@@ -523,6 +536,8 @@ int colvarbias_meta::update_bias()
 
     case multiple_replicas:
       create_hill(hill(hill_weight*hills_scale, colvars, hill_width, replica_id));
+      std::ostream *replica_hills_os =
+        cvm::proxy->get_output_stream(replica_hills_file);
       if (replica_hills_os) {
         *replica_hills_os << hills.back();
       } else {
@@ -921,13 +936,16 @@ void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter  h_first
 
 int colvarbias_meta::replica_share()
 {
+  colvarproxy *proxy = cvm::proxy;
   // sync with the other replicas (if needed)
   if (comm == multiple_replicas) {
     // reread the replicas registry
     update_replicas_registry();
     // empty the output buffer
+    std::ostream *replica_hills_os =
+      proxy->get_output_stream(replica_hills_file);
     if (replica_hills_os) {
-      cvm::proxy->flush_output_stream(replica_hills_os);
+      proxy->flush_output_stream(replica_hills_os);
     }
     read_replica_files();
   }
@@ -1089,11 +1107,7 @@ void colvarbias_meta::read_replica_files()
                (replicas[ir])->replica_state_file+"\".\n");
 
       std::ifstream is((replicas[ir])->replica_state_file.c_str());
-      if (! (replicas[ir])->read_state(is)) {
-        cvm::log("Reading from file \""+(replicas[ir])->replica_state_file+
-                 "\" failed or incomplete: will try again in "+
-                 cvm::to_str(replica_update_freq)+" steps.\n");
-      } else {
+      if ((replicas[ir])->read_state(is)) {
         // state file has been read successfully
         (replicas[ir])->replica_state_file_in_sync = true;
         (replicas[ir])->update_status = 0;
@@ -1550,15 +1564,11 @@ int colvarbias_meta::setup_output()
     // for the others to read
 
     // open the "hills" buffer file
-    if (!replica_hills_os) {
-      cvm::proxy->backup_file(replica_hills_file);
-      replica_hills_os = cvm::proxy->output_stream(replica_hills_file);
-      if (!replica_hills_os) return cvm::get_error();
-      replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
-    }
+    reopen_replica_buffer_file();
 
     // write the state file (so that there is always one available)
     write_replica_state_file();
+
     // schedule to read the state files of the other replicas
     for (size_t ir = 0; ir < replicas.size(); ir++) {
       (replicas[ir])->replica_state_file_in_sync = false;
@@ -1661,15 +1671,16 @@ std::ostream & colvarbias_meta::write_state_data(std::ostream& os)
 
 int colvarbias_meta::write_state_to_replicas()
 {
+  int error_code = COLVARS_OK;
   if (comm != single_replica) {
-    write_replica_state_file();
-    // schedule to reread the state files of the other replicas (they
-    // have also rewritten them)
+    error_code |= write_replica_state_file();
+    error_code |= reopen_replica_buffer_file();
+    // schedule to reread the state files of the other replicas
     for (size_t ir = 0; ir < replicas.size(); ir++) {
       (replicas[ir])->replica_state_file_in_sync = false;
     }
   }
-  return COLVARS_OK;
+  return error_code;
 }
 
 
@@ -1693,6 +1704,20 @@ void colvarbias_meta::write_pmf()
     // output the PMF from this instance or replica
     pmf->reset();
     pmf->add_grid(*hills_energy);
+
+    if (ebmeta) {
+      int nt_points=pmf->number_of_points();
+      for (int i = 0; i < nt_points; i++) {
+         cvm:: real pmf_val=0.0;
+         cvm:: real target_val=target_dist->value(i);
+         if (target_val>0) {
+           pmf_val=pmf->value(i);
+           pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * std::log(target_val);
+         }
+         pmf->set_value(i,pmf_val);
+      }
+    }
+
     cvm::real const max = pmf->maximum_value();
     pmf->add_constant(-1.0 * max);
     pmf->multiply_constant(-1.0);
@@ -1716,10 +1741,24 @@ void colvarbias_meta::write_pmf()
   if (comm != single_replica) {
     // output the combined PMF from all replicas
     pmf->reset();
-    pmf->add_grid(*hills_energy);
+    // current replica already included in the pools of replicas
     for (size_t ir = 0; ir < replicas.size(); ir++) {
       pmf->add_grid(*(replicas[ir]->hills_energy));
     }
+
+    if (ebmeta) {
+      int nt_points=pmf->number_of_points();
+      for (int i = 0; i < nt_points; i++) {
+         cvm:: real pmf_val=0.0;
+         cvm:: real target_val=target_dist->value(i);
+         if (target_val>0) {
+           pmf_val=pmf->value(i);
+           pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * std::log(target_val);
+         }
+         pmf->set_value(i,pmf_val);
+      }
+    }
+
     cvm::real const max = pmf->maximum_value();
     pmf->add_constant(-1.0 * max);
     pmf->multiply_constant(-1.0);
@@ -1744,74 +1783,47 @@ void colvarbias_meta::write_pmf()
 
 int colvarbias_meta::write_replica_state_file()
 {
+  colvarproxy *proxy = cvm::proxy;
+
   if (cvm::debug()) {
     cvm::log("Writing replica state file for bias \""+name+"\"\n");
   }
-  // write down also the restart for the other replicas
-  cvm::backup_file(replica_state_file.c_str());
-  std::ostream *rep_state_os = cvm::proxy->output_stream(replica_state_file);
-  if (rep_state_os == NULL) {
-    cvm::error("Error: in opening file \""+
-               replica_state_file+"\" for writing.\n", FILE_ERROR);
-    return FILE_ERROR;
+
+  int error_code = COLVARS_OK;
+
+  // Write to temporary state file
+  std::string const tmp_state_file(replica_state_file+".tmp");
+  error_code |= proxy->remove_file(tmp_state_file);
+  std::ostream *rep_state_os = cvm::proxy->output_stream(tmp_state_file);
+  if (rep_state_os) {
+    if (!write_state(*rep_state_os)) {
+      error_code |= cvm::error("Error: in writing to temporary file \""+
+                               tmp_state_file+"\".\n", FILE_ERROR);
+    }
   }
+  error_code |= proxy->close_output_stream(tmp_state_file);
 
-  rep_state_os->setf(std::ios::scientific, std::ios::floatfield);
+  error_code |= proxy->rename_file(tmp_state_file, replica_state_file);
 
-  if (!write_state(*rep_state_os)) {
-    cvm::error("Error: in writing to file \""+
-               replica_state_file+"\".\n", FILE_ERROR);
-    cvm::proxy->close_output_stream(replica_state_file);
-    return FILE_ERROR;
+  return error_code;
+}
+
+
+int colvarbias_meta::reopen_replica_buffer_file()
+{
+  int error_code = COLVARS_OK;
+  colvarproxy *proxy = cvm::proxy;
+  if (proxy->get_output_stream(replica_hills_file) != NULL) {
+    error_code |= proxy->close_output_stream(replica_hills_file);
   }
-
-  cvm::proxy->close_output_stream(replica_state_file);
-
-  // rep_state_os.setf(std::ios::scientific, std::ios::floatfield);
-  // rep_state_os << "\n"
-  //              << "metadynamics {\n"
-  //              << "  configuration {\n"
-  //              << "    name " << this->name << "\n"
-  //              << "    step " << cvm::step_absolute() << "\n";
-  // if (this->comm != single_replica) {
-  //   rep_state_os << "    replicaID " << this->replica_id << "\n";
-  // }
-  // rep_state_os << "  }\n\n";
-  // rep_state_os << "  hills_energy\n";
-  // rep_state_os << std::setprecision(cvm::cv_prec)
-  //              << std::setw(cvm::cv_width);
-  // hills_energy->write_restart(rep_state_os);
-  // rep_state_os << "  hills_energy_gradients\n";
-  // rep_state_os << std::setprecision(cvm::cv_prec)
-  //              << std::setw(cvm::cv_width);
-  // hills_energy_gradients->write_restart(rep_state_os);
-
-  // if ( (!use_grids) || keep_hills ) {
-  //   // write all hills currently in memory
-  //   for (std::list<hill>::const_iterator h = this->hills.begin();
-  //        h != this->hills.end();
-  //        h++) {
-  //     rep_state_os << *h;
-  //   }
-  // } else {
-  //   // write just those that are near the grid boundaries
-  //   for (std::list<hill>::const_iterator h = this->hills_off_grid.begin();
-  //        h != this->hills_off_grid.end();
-  //        h++) {
-  //     rep_state_os << *h;
-  //   }
-  // }
-  // rep_state_os << "}\n\n";
-  // rep_state_os.close();
-
-  // reopen the hills file
-  cvm::proxy->close_output_stream(replica_hills_file);
-  cvm::proxy->backup_file(replica_hills_file);
-  replica_hills_os = cvm::proxy->output_stream(replica_hills_file);
-  if (!replica_hills_os) return cvm::get_error();
-  replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
-
-  return COLVARS_OK;
+  error_code |= proxy->remove_file(replica_hills_file);
+  std::ostream *replica_hills_os = proxy->output_stream(replica_hills_file);
+  if (replica_hills_os) {
+    replica_hills_os->setf(std::ios::scientific, std::ios::floatfield);
+  } else {
+    error_code |= FILE_ERROR;
+  }
+  return error_code;
 }
 
 
@@ -1883,5 +1895,3 @@ std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h)
 
   return os;
 }
-
-

lib/colvars/colvarbias_meta.h

@@ -215,9 +215,12 @@ protected:
   /// \brief Read new data from replicas' files
   virtual void read_replica_files();
 
-  /// \brief Write data to other replicas
+  /// Write full state information to be read by other replicas
   virtual int write_replica_state_file();
 
+  /// Call this after write_replica_state_file()
+  virtual int reopen_replica_buffer_file();
+
   /// \brief Additional, "mirror" metadynamics biases, to collect info
   /// from the other replicas
   ///
@@ -251,9 +254,6 @@ protected:
   /// This file becomes empty after replica_state_file is rewritten
   std::string            replica_hills_file;
 
-  /// \brief Output stream corresponding to replica_hills_file
-  std::ostream          *replica_hills_os;
-
   /// Position within replica_hills_file (when reading it)
   int                    replica_hills_file_pos;
 

lib/colvars/colvarbias_restraint.cpp

@@ -1295,7 +1295,8 @@ colvarvalue const colvarbias_restraint_linear::restraint_force(size_t i) const
 
 cvm::real colvarbias_restraint_linear::d_restraint_potential_dk(size_t i) const
 {
-  return 1.0 / variables(i)->width * (variables(i)->value() - colvar_centers[i]);
+  return 1.0 / variables(i)->width * (variables(i)->value() -
+                                      colvar_centers[i]).sum();
 }
 
 

lib/colvars/colvarcomp.cpp

@@ -7,6 +7,8 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
+#include <algorithm>
+
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvar.h"

lib/colvars/colvarcomp.h

@@ -24,6 +24,13 @@
 #include "colvar.h"
 #include "colvaratoms.h"
 
+#if (__cplusplus >= 201103L)
+#include "colvar_geometricpath.h"
+#include <functional>
+#endif // C++11 checking
+
+#include <map>
+
 
 /// \brief Colvar component (base class for collective variables)
 ///
@@ -688,9 +695,6 @@ protected:
   /// Reference coordinates
   std::vector<cvm::atom_pos>  ref_pos;
 
-  /// Geometric center of the reference coordinates
-  cvm::atom_pos                ref_pos_center;
-
   /// Eigenvector (of a normal or essential mode): will always have zero center
   std::vector<cvm::rvector>   eigenvec;
 
@@ -883,9 +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;
@@ -937,9 +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);
+
 };
 
 
@@ -1383,6 +1389,222 @@ public:
 };
 
 
+
+class colvar::componentDisabled
+  : public colvar::cvc
+{
+public:
+    componentDisabled(std::string const &conf) {
+        cvm::error("Error: this component is not enabled in the current build; please see https://colvars.github.io/README-c++11.html");
+    }
+    virtual ~componentDisabled() {}
+    virtual void calc_value() {}
+    virtual void calc_gradients() {}
+    virtual void apply_force(colvarvalue const &force) {}
+};
+
+
+
+#if (__cplusplus >= 201103L)
+class colvar::CartesianBasedPath
+  : public colvar::cvc
+{
+protected:
+    virtual void computeReferenceDistance(std::vector<cvm::real>& result);
+    /// Selected atoms
+    cvm::atom_group *atoms;
+    /// Fitting options
+    bool has_user_defined_fitting;
+    /// Reference frames
+    std::vector<std::vector<cvm::atom_pos>> reference_frames;
+    std::vector<std::vector<cvm::atom_pos>> reference_fitting_frames;
+    /// Atom groups for RMSD calculation together with reference frames
+    std::vector<cvm::atom_group*> comp_atoms;
+    /// Total number of reference frames
+    size_t total_reference_frames;
+public:
+    CartesianBasedPath(std::string const &conf);
+    virtual ~CartesianBasedPath();
+    virtual void calc_value() = 0;
+    virtual void apply_force(colvarvalue const &force) = 0;
+};
+
+/// \brief Colvar component: alternative path collective variable using geometry, variable s
+/// For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html
+/// Díaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601.
+class colvar::gspath
+  : public colvar::CartesianBasedPath, public GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::S>
+{
+private:
+    // Optimal rotation for compute v3
+    cvm::rotation rot_v3;
+protected:
+    virtual void prepareVectors();
+    virtual void updateReferenceDistances();
+public:
+    gspath(std::string const &conf);
+    virtual ~gspath() {}
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+
+
+/// \brief Colvar component: alternative path collective variable using geometry, variable z
+/// This should be merged with gspath in the same class by class inheritance or something else
+class colvar::gzpath
+  : public colvar::CartesianBasedPath, public GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::Z>
+{
+private:
+    // Optimal rotation for compute v3, v4
+    cvm::rotation rot_v3;
+    cvm::rotation rot_v4;
+protected:
+    virtual void prepareVectors();
+    virtual void updateReferenceDistances();
+public:
+    gzpath(std::string const &conf);
+    virtual ~gzpath() {}
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+/// Current only linear combination of sub-CVCs is available
+class colvar::linearCombination
+  : public colvar::cvc
+{
+protected:
+    /// Map from string to the types of colvar components
+    std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> string_cv_map;
+    /// Sub-colvar components
+    std::vector<colvar::cvc*> cv;
+    /// If all sub-cvs use explicit gradients then we also use it
+    bool use_explicit_gradients;
+protected:
+    cvm::real getPolynomialFactorOfCVGradient(size_t i_cv) const;
+public:
+    linearCombination(std::string const &conf);
+    virtual ~linearCombination();
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+
+class colvar::CVBasedPath
+  : public colvar::cvc
+{
+protected:
+    /// Map from string to the types of colvar components
+    std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>> string_cv_map;
+    /// Sub-colvar components
+    std::vector<colvar::cvc*> cv;
+    /// Refernce colvar values from path
+    std::vector<std::vector<colvarvalue>> ref_cv;
+    /// If all sub-cvs use explicit gradients then we also use it
+    bool use_explicit_gradients;
+    /// Total number of reference frames
+    size_t total_reference_frames;
+protected:
+    virtual void computeReferenceDistance(std::vector<cvm::real>& result);
+    cvm::real getPolynomialFactorOfCVGradient(size_t i_cv) const;
+public:
+    CVBasedPath(std::string const &conf);
+    virtual ~CVBasedPath();
+    virtual void calc_value() = 0;
+    virtual void apply_force(colvarvalue const &force) = 0;
+};
+
+
+/// \brief Colvar component: alternative path collective variable using geometry, variable s
+/// Allow any combination of existing (scalar) CVs
+/// For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html
+/// Díaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601.
+class colvar::gspathCV
+  : public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>
+{
+protected:
+    virtual void updateReferenceDistances();
+    virtual void prepareVectors();
+public:
+    gspathCV(std::string const &conf);
+    virtual ~gspathCV();
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+
+
+class colvar::gzpathCV
+  : public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::Z>
+{
+protected:
+    virtual void updateReferenceDistances();
+    virtual void prepareVectors();
+public:
+    gzpathCV(std::string const &conf);
+    virtual ~gzpathCV();
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+#else // if the compiler doesn't support C++11
+
+class colvar::linearCombination
+  : public colvar::componentDisabled
+{
+public:
+    linearCombination(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::CartesianBasedPath
+  : public colvar::componentDisabled
+{
+public:
+    CartesianBasedPath(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::CVBasedPath
+  : public colvar::componentDisabled
+{
+public:
+    CVBasedPath(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::gspath
+  : public colvar::componentDisabled
+{
+public:
+    gspath(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::gzpath
+  : public colvar::componentDisabled
+{
+public:
+    gzpath(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::gspathCV
+  : public colvar::componentDisabled
+{
+public:
+    gspathCV(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::gzpathCV
+  : public colvar::componentDisabled
+{
+public:
+    gzpathCV(std::string const &conf) : componentDisabled(conf) {}
+};
+
+#endif // C++11 checking
+
 // metrics functions for cvc implementations
 
 // simple definitions of the distance functions; these are useful only

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/colvarcomp_distances.cpp

@@ -1013,8 +1013,7 @@ colvar::rmsd::rmsd(std::string const &conf)
                   cvm::to_str(atoms->size())+").\n");
       return;
     }
-  }
-  {
+  } else { // Only look for ref pos file if ref positions not already provided
     std::string ref_pos_file;
     if (get_keyval(conf, "refPositionsFile", ref_pos_file, std::string(""))) {
 
@@ -1041,12 +1040,15 @@ colvar::rmsd::rmsd(std::string const &conf)
 
       cvm::load_coords(ref_pos_file.c_str(), &ref_pos, atoms,
                        ref_pos_col, ref_pos_col_value);
+    } else {
+      cvm::error("Error: no reference positions for RMSD; use either refPositions of refPositionsFile.");
+      return;
     }
   }
 
   if (ref_pos.size() != atoms->size()) {
     cvm::error("Error: found " + cvm::to_str(ref_pos.size()) +
-                    " reference positions; expected " + cvm::to_str(atoms->size()));
+                    " reference positions for RMSD; expected " + cvm::to_str(atoms->size()));
     return;
   }
 

lib/colvars/colvarcomp_gpath.cpp

@@ -0,0 +1,910 @@
+#if (__cplusplus >= 201103L)
+
+// This file is part of the Collective Variables module (Colvars).
+// The original version of Colvars and its updates are located at:
+// https://github.com/colvars/colvars
+// Please update all Colvars source files before making any changes.
+// If you wish to distribute your changes, please submit them to the
+// Colvars repository at GitHub.
+
+#include <numeric>
+#include <algorithm>
+#include <cmath>
+#include <cstdlib>
+#include <limits>
+
+#include "colvarmodule.h"
+#include "colvarvalue.h"
+#include "colvarparse.h"
+#include "colvar.h"
+#include "colvarcomp.h"
+
+namespace GeometricPathCV {
+void init_string_cv_map(std::map<std::string, std::function<colvar::cvc* (const std::string& conf)>>& string_cv_map);
+}
+
+bool compareColvarComponent(colvar::cvc *i, colvar::cvc *j)
+{
+    return i->name < j->name;
+}
+
+colvar::CartesianBasedPath::CartesianBasedPath(std::string const &conf): cvc(conf), atoms(nullptr), reference_frames(0) {
+    // Parse selected atoms
+    atoms = parse_group(conf, "atoms");
+    has_user_defined_fitting = false;
+    std::string fitting_conf;
+    if (key_lookup(conf, "fittingAtoms", &fitting_conf)) {
+        has_user_defined_fitting = true;
+    }
+    // Lookup reference column of PDB
+    // Copied from the RMSD class
+    std::string reference_column;
+    double reference_column_value;
+    if (get_keyval(conf, "refPositionsCol", reference_column, std::string(""))) {
+        bool found = get_keyval(conf, "refPositionsColValue", reference_column_value, 0.0);
+        if (found && reference_column_value == 0.0) {
+          cvm::error("Error: refPositionsColValue, "
+                     "if provided, must be non-zero.\n");
+          return;
+        }
+    }
+    // Lookup all reference frames
+    bool has_frames = true;
+    total_reference_frames = 0;
+    while (has_frames) {
+        std::string reference_position_file_lookup = "refPositionsFile" + cvm::to_str(total_reference_frames + 1);
+        if (key_lookup(conf, reference_position_file_lookup.c_str())) {
+            std::string reference_position_filename;
+            get_keyval(conf, reference_position_file_lookup.c_str(), reference_position_filename, std::string(""));
+            std::vector<cvm::atom_pos> reference_position(atoms->size());
+            cvm::load_coords(reference_position_filename.c_str(), &reference_position, atoms, reference_column, reference_column_value);
+            reference_frames.push_back(reference_position);
+            ++total_reference_frames;
+        } else {
+            has_frames = false;
+        }
+    }
+    // Setup alignment to compute RMSD with respect to reference frames
+    for (size_t i_frame = 0; i_frame < reference_frames.size(); ++i_frame) {
+        cvm::atom_group* tmp_atoms = parse_group(conf, "atoms");
+        if (!has_user_defined_fitting) {
+            // Swipe from the rmsd class
+            tmp_atoms->b_center = true;
+            tmp_atoms->b_rotate = true;
+            tmp_atoms->ref_pos = reference_frames[i_frame];
+            tmp_atoms->center_ref_pos();
+            tmp_atoms->enable(f_ag_fit_gradients);
+            tmp_atoms->rot.request_group1_gradients(tmp_atoms->size());
+            tmp_atoms->rot.request_group2_gradients(tmp_atoms->size());
+            comp_atoms.push_back(tmp_atoms);
+        } else {
+            // parse a group of atoms for fitting
+            std::string fitting_group_name = std::string("fittingAtoms") + cvm::to_str(i_frame);
+            cvm::atom_group* tmp_fitting_atoms = new cvm::atom_group(fitting_group_name.c_str());
+            tmp_fitting_atoms->parse(fitting_conf);
+            tmp_fitting_atoms->disable(f_ag_scalable);
+            tmp_fitting_atoms->disable(f_ag_scalable_com);
+            tmp_fitting_atoms->fit_gradients.assign(tmp_fitting_atoms->size(), cvm::atom_pos(0.0, 0.0, 0.0));
+            std::string reference_position_file_lookup = "refPositionsFile" + cvm::to_str(i_frame + 1);
+            std::string reference_position_filename;
+            get_keyval(conf, reference_position_file_lookup.c_str(), reference_position_filename, std::string(""));
+            std::vector<cvm::atom_pos> reference_fitting_position(tmp_fitting_atoms->size());
+            cvm::load_coords(reference_position_filename.c_str(), &reference_fitting_position, tmp_fitting_atoms, reference_column, reference_column_value);
+            // setup the atom group for calculating
+            tmp_atoms->b_center = true;
+            tmp_atoms->b_rotate = true;
+            tmp_atoms->b_user_defined_fit = true;
+            tmp_atoms->disable(f_ag_scalable);
+            tmp_atoms->disable(f_ag_scalable_com);
+            tmp_atoms->ref_pos = reference_fitting_position;
+            tmp_atoms->center_ref_pos();
+            tmp_atoms->enable(f_ag_fit_gradients);
+            tmp_atoms->enable(f_ag_fitting_group);
+            tmp_atoms->fitting_group = tmp_fitting_atoms;
+            tmp_atoms->rot.request_group1_gradients(tmp_fitting_atoms->size());
+            tmp_atoms->rot.request_group2_gradients(tmp_fitting_atoms->size());
+            reference_fitting_frames.push_back(reference_fitting_position);
+            comp_atoms.push_back(tmp_atoms);
+        }
+    }
+    x.type(colvarvalue::type_scalar);
+    // Don't use implicit gradient
+    enable(f_cvc_explicit_gradient);
+}
+
+colvar::CartesianBasedPath::~CartesianBasedPath() {
+    for (auto it_comp_atoms = comp_atoms.begin(); it_comp_atoms != comp_atoms.end(); ++it_comp_atoms) {
+        if (*it_comp_atoms != nullptr) {
+            delete (*it_comp_atoms);
+            (*it_comp_atoms) = nullptr;
+        }
+    }
+}
+
+void colvar::CartesianBasedPath::computeReferenceDistance(std::vector<cvm::real>& result) {
+    for (size_t i_frame = 0; i_frame < reference_frames.size(); ++i_frame) {
+        cvm::real frame_rmsd = 0.0;
+        for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            frame_rmsd += ((*(comp_atoms[i_frame]))[i_atom].pos - reference_frames[i_frame][i_atom]).norm2();
+        }
+        frame_rmsd /= cvm::real(atoms->size());
+        frame_rmsd = cvm::sqrt(frame_rmsd);
+        result[i_frame] = frame_rmsd;
+    }
+}
+
+colvar::gspath::gspath(std::string const &conf): CartesianBasedPath(conf) {
+    function_type = "gspath";
+    get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
+    if (use_second_closest_frame == true) {
+        cvm::log(std::string("Geometric path s(σ) will use the second closest frame to compute s_(m-1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m-1)\n"));
+    }
+    get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
+    if (use_third_closest_frame == true) {
+        cvm::log(std::string("Geometric path s(σ) will use the third closest frame to compute s_(m+1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n"));
+    }
+    GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::S>::initialize(atoms->size(), cvm::atom_pos(), total_reference_frames, use_second_closest_frame, use_third_closest_frame);
+    cvm::log(std::string("Geometric pathCV(s) is initialized.\n"));
+    cvm::log(std::string("Geometric pathCV(s) loaded ") + cvm::to_str(reference_frames.size()) + std::string(" frames.\n"));
+}
+
+void colvar::gspath::updateReferenceDistances() {
+    computeReferenceDistance(frame_distances);
+}
+
+void colvar::gspath::prepareVectors() {
+    size_t i_atom;
+    for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        // v1 = s_m - z
+        v1[i_atom] = reference_frames[min_frame_index_1][i_atom] - (*(comp_atoms[min_frame_index_1]))[i_atom].pos;
+        // v2 = z - s_(m-1)
+        v2[i_atom] = (*(comp_atoms[min_frame_index_2]))[i_atom].pos - reference_frames[min_frame_index_2][i_atom];
+    }
+    if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
+        cvm::atom_pos reference_cog_1, reference_cog_2;
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            reference_cog_1 += reference_frames[min_frame_index_1][i_atom];
+            reference_cog_2 += reference_frames[min_frame_index_2][i_atom];
+        }
+        reference_cog_1 /= reference_frames[min_frame_index_1].size();
+        reference_cog_2 /= reference_frames[min_frame_index_2].size();
+        std::vector<cvm::atom_pos> tmp_reference_frame_1(reference_frames[min_frame_index_1].size());
+        std::vector<cvm::atom_pos> tmp_reference_frame_2(reference_frames[min_frame_index_2].size());
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1;
+            tmp_reference_frame_2[i_atom] = reference_frames[min_frame_index_2][i_atom] - reference_cog_2;
+        }
+        if (has_user_defined_fitting) {
+            cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_2;
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+                reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom];
+                reference_fitting_cog_2 += reference_fitting_frames[min_frame_index_2][i_atom];
+            }
+            reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size();
+            reference_fitting_cog_2 /= reference_fitting_frames[min_frame_index_2].size();
+            std::vector<cvm::atom_pos> tmp_reference_fitting_frame_1(reference_fitting_frames[min_frame_index_1].size());
+            std::vector<cvm::atom_pos> tmp_reference_fitting_frame_2(reference_fitting_frames[min_frame_index_2].size());
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+                tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1;
+                tmp_reference_fitting_frame_2[i_atom] = reference_fitting_frames[min_frame_index_2][i_atom] - reference_fitting_cog_2;
+            }
+            rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_2);
+        } else {
+            rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_2);
+        }
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            v3[i_atom] = rot_v3.q.rotate(tmp_reference_frame_1[i_atom]) - tmp_reference_frame_2[i_atom];
+        }
+    } else {
+        cvm::atom_pos reference_cog_1, reference_cog_3;
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            reference_cog_1 += reference_frames[min_frame_index_1][i_atom];
+            reference_cog_3 += reference_frames[min_frame_index_3][i_atom];
+        }
+        reference_cog_1 /= reference_frames[min_frame_index_1].size();
+        reference_cog_3 /= reference_frames[min_frame_index_3].size();
+        std::vector<cvm::atom_pos> tmp_reference_frame_1(reference_frames[min_frame_index_1].size());
+        std::vector<cvm::atom_pos> tmp_reference_frame_3(reference_frames[min_frame_index_3].size());
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1;
+            tmp_reference_frame_3[i_atom] = reference_frames[min_frame_index_3][i_atom] - reference_cog_3;
+        }
+        if (has_user_defined_fitting) {
+            cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_3;
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+                reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom];
+                reference_fitting_cog_3 += reference_fitting_frames[min_frame_index_3][i_atom];
+            }
+            reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size();
+            reference_fitting_cog_3 /= reference_fitting_frames[min_frame_index_3].size();
+            std::vector<cvm::atom_pos> tmp_reference_fitting_frame_1(reference_fitting_frames[min_frame_index_1].size());
+            std::vector<cvm::atom_pos> tmp_reference_fitting_frame_3(reference_fitting_frames[min_frame_index_3].size());
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+                tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1;
+                tmp_reference_fitting_frame_3[i_atom] = reference_fitting_frames[min_frame_index_3][i_atom] - reference_fitting_cog_3;
+            }
+            rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_3);
+        } else {
+            rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_3);
+        }
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            // v3 = s_(m+1) - s_m
+            v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_v3.q.rotate(tmp_reference_frame_1[i_atom]);
+        }
+    }
+}
+
+void colvar::gspath::calc_value() {
+    computeValue();
+    x = s;
+}
+
+void colvar::gspath::calc_gradients() {
+    computeDerivatives();
+    cvm::rvector tmp_atom_grad_v1, tmp_atom_grad_v2;
+    // dS(v1, v2(r), v3) / dr = ∂S/∂v1 * dv1/dr + ∂S/∂v2 * dv2/dr
+    // dv1/dr = [fitting matrix 1][-1, ..., -1]
+    // dv2/dr = [fitting matrix 2][1, ..., 1]
+    // ∂S/∂v1 = ± (∂f/∂v1) / (2M)
+    // ∂S/∂v2 = ± (∂f/∂v2) / (2M)
+    // dS(v1, v2(r), v3) / dr = -1.0 * ± (∂f/∂v1) / (2M) + ± (∂f/∂v2) / (2M)
+    for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        tmp_atom_grad_v1[0] = -1.0 * sign * 0.5 * dfdv1[i_atom][0] / M;
+        tmp_atom_grad_v1[1] = -1.0 * sign * 0.5 * dfdv1[i_atom][1] / M;
+        tmp_atom_grad_v1[2] = -1.0 * sign * 0.5 * dfdv1[i_atom][2] / M;
+        tmp_atom_grad_v2[0] = sign * 0.5 * dfdv2[i_atom][0] / M;
+        tmp_atom_grad_v2[1] = sign * 0.5 * dfdv2[i_atom][1] / M;
+        tmp_atom_grad_v2[2] = sign * 0.5 * dfdv2[i_atom][2] / M;
+        (*(comp_atoms[min_frame_index_1]))[i_atom].grad += tmp_atom_grad_v1;
+        (*(comp_atoms[min_frame_index_2]))[i_atom].grad += tmp_atom_grad_v2;
+    }
+}
+
+void colvar::gspath::apply_force(colvarvalue const &force) {
+    // The force applied to this CV is scalar type
+    cvm::real const &F = force.real_value;
+    (*(comp_atoms[min_frame_index_1])).apply_colvar_force(F);
+    (*(comp_atoms[min_frame_index_2])).apply_colvar_force(F);
+}
+
+colvar::gzpath::gzpath(std::string const &conf): CartesianBasedPath(conf) {
+    function_type = "gzpath";
+    get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
+    if (use_second_closest_frame == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the second closest frame to compute s_(m-1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m-1)\n"));
+    }
+    get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
+    if (use_third_closest_frame == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the third closest frame to compute s_(m+1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m+1)\n"));
+    }
+    bool b_use_z_square = false;
+    get_keyval(conf, "useZsquare", b_use_z_square, false);
+    if (b_use_z_square == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n"));
+    }
+    GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::Z>::initialize(atoms->size(), cvm::atom_pos(), total_reference_frames, use_second_closest_frame, use_third_closest_frame, b_use_z_square);
+    // Logging
+    cvm::log(std::string("Geometric pathCV(z) is initialized.\n"));
+    cvm::log(std::string("Geometric pathCV(z) loaded ") + cvm::to_str(reference_frames.size()) + std::string(" frames.\n"));
+}
+
+void colvar::gzpath::updateReferenceDistances() {
+    computeReferenceDistance(frame_distances);
+}
+
+void colvar::gzpath::prepareVectors() {
+    cvm::atom_pos reference_cog_1, reference_cog_2;
+    size_t i_atom;
+    for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        reference_cog_1 += reference_frames[min_frame_index_1][i_atom];
+        reference_cog_2 += reference_frames[min_frame_index_2][i_atom];
+    }
+    reference_cog_1 /= reference_frames[min_frame_index_1].size();
+    reference_cog_2 /= reference_frames[min_frame_index_2].size();
+    std::vector<cvm::atom_pos> tmp_reference_frame_1(reference_frames[min_frame_index_1].size());
+    std::vector<cvm::atom_pos> tmp_reference_frame_2(reference_frames[min_frame_index_2].size());
+    for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        tmp_reference_frame_1[i_atom] = reference_frames[min_frame_index_1][i_atom] - reference_cog_1;
+        tmp_reference_frame_2[i_atom] = reference_frames[min_frame_index_2][i_atom] - reference_cog_2;
+    }
+    std::vector<cvm::atom_pos> tmp_reference_fitting_frame_1;
+    std::vector<cvm::atom_pos> tmp_reference_fitting_frame_2;
+    if (has_user_defined_fitting) {
+        cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_2;
+        for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+            reference_fitting_cog_1 += reference_fitting_frames[min_frame_index_1][i_atom];
+            reference_fitting_cog_2 += reference_fitting_frames[min_frame_index_2][i_atom];
+        }
+        reference_fitting_cog_1 /= reference_fitting_frames[min_frame_index_1].size();
+        reference_fitting_cog_2 /= reference_fitting_frames[min_frame_index_2].size();
+        tmp_reference_fitting_frame_1.resize(reference_fitting_frames[min_frame_index_1].size());
+        tmp_reference_fitting_frame_2.resize(reference_fitting_frames[min_frame_index_2].size());
+        for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_1].size(); ++i_atom) {
+            tmp_reference_fitting_frame_1[i_atom] = reference_fitting_frames[min_frame_index_1][i_atom] - reference_fitting_cog_1;
+            tmp_reference_fitting_frame_2[i_atom] = reference_fitting_frames[min_frame_index_2][i_atom] - reference_fitting_cog_2;
+        }
+        rot_v4.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_2);
+    } else {
+        rot_v4.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_2);
+    }
+    for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        v1[i_atom] = reference_frames[min_frame_index_1][i_atom] - (*(comp_atoms[min_frame_index_1]))[i_atom].pos;
+        v2[i_atom] = (*(comp_atoms[min_frame_index_2]))[i_atom].pos - reference_frames[min_frame_index_2][i_atom];
+        // v4 only computes in gzpath
+        // v4 = s_m - s_(m-1)
+        v4[i_atom] = rot_v4.q.rotate(tmp_reference_frame_1[i_atom]) - tmp_reference_frame_2[i_atom];
+    }
+    if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
+        v3 = v4;
+    } else {
+        cvm::atom_pos reference_cog_3;
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            reference_cog_3 += reference_frames[min_frame_index_3][i_atom];
+        }
+        reference_cog_3 /= reference_frames[min_frame_index_3].size();
+        std::vector<cvm::atom_pos> tmp_reference_frame_3(reference_frames[min_frame_index_3].size());
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            tmp_reference_frame_3[i_atom] = reference_frames[min_frame_index_3][i_atom] - reference_cog_3;
+        }
+        if (has_user_defined_fitting) {
+            cvm::atom_pos reference_fitting_cog_3;
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_3].size(); ++i_atom) {
+                reference_fitting_cog_3 += reference_fitting_frames[min_frame_index_3][i_atom];
+            }
+            reference_fitting_cog_3 /= reference_fitting_frames[min_frame_index_3].size();
+            std::vector<cvm::atom_pos> tmp_reference_fitting_frame_3(reference_fitting_frames[min_frame_index_3].size());
+            for (i_atom = 0; i_atom < reference_fitting_frames[min_frame_index_3].size(); ++i_atom) {
+                tmp_reference_fitting_frame_3[i_atom] =  reference_fitting_frames[min_frame_index_3][i_atom] - reference_fitting_cog_3;
+            }
+            rot_v3.calc_optimal_rotation(tmp_reference_fitting_frame_1, tmp_reference_fitting_frame_3);
+        } else {
+            rot_v3.calc_optimal_rotation(tmp_reference_frame_1, tmp_reference_frame_3);
+        }
+        for (i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+            // v3 = s_(m+1) - s_m
+            v3[i_atom] = tmp_reference_frame_3[i_atom] - rot_v3.q.rotate(tmp_reference_frame_1[i_atom]);
+        }
+    }
+}
+
+void colvar::gzpath::calc_value() {
+    computeValue();
+    x = z;
+}
+
+void colvar::gzpath::calc_gradients() {
+    computeDerivatives();
+    cvm::rvector tmp_atom_grad_v1, tmp_atom_grad_v2;
+    for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) {
+        tmp_atom_grad_v1 = -1.0 * dzdv1[i_atom];
+        tmp_atom_grad_v2 = dzdv2[i_atom];
+        (*(comp_atoms[min_frame_index_1]))[i_atom].grad += tmp_atom_grad_v1;
+        (*(comp_atoms[min_frame_index_2]))[i_atom].grad += tmp_atom_grad_v2;
+    }
+}
+
+void colvar::gzpath::apply_force(colvarvalue const &force) {
+    // The force applied to this CV is scalar type
+    cvm::real const &F = force.real_value;
+    (*(comp_atoms[min_frame_index_1])).apply_colvar_force(F);
+    (*(comp_atoms[min_frame_index_2])).apply_colvar_force(F);
+}
+
+colvar::linearCombination::linearCombination(std::string const &conf): cvc(conf) {
+    GeometricPathCV::init_string_cv_map(string_cv_map);
+    // Lookup all available sub-cvcs
+    for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) {
+        if (key_lookup(conf, it_cv_map->first.c_str())) {
+            std::vector<std::string> sub_cvc_confs;
+            get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
+            for (auto it_sub_cvc_conf = sub_cvc_confs.begin(); it_sub_cvc_conf != sub_cvc_confs.end(); ++it_sub_cvc_conf) {
+                cv.push_back((it_cv_map->second)(*(it_sub_cvc_conf)));
+            }
+        }
+    }
+    // Sort all sub CVs by their names
+    std::sort(cv.begin(), cv.end(), compareColvarComponent);
+    for (auto it_sub_cv = cv.begin(); it_sub_cv != cv.end(); ++it_sub_cv) {
+        for (auto it_atom_group = (*it_sub_cv)->atom_groups.begin(); it_atom_group != (*it_sub_cv)->atom_groups.end(); ++it_atom_group) {
+            register_atom_group(*it_atom_group);
+        }
+    }
+    x.type(cv[0]->value());
+    x.reset();
+    use_explicit_gradients = true;
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
+            use_explicit_gradients = false;
+        }
+    }
+    if (!use_explicit_gradients) {
+        disable(f_cvc_explicit_gradient);
+    }
+}
+
+cvm::real colvar::linearCombination::getPolynomialFactorOfCVGradient(size_t i_cv) const {
+    cvm::real factor_polynomial = 1.0;
+    if (cv[i_cv]->value().type() == colvarvalue::type_scalar) {
+        factor_polynomial = cv[i_cv]->sup_coeff * cv[i_cv]->sup_np * cvm::pow(cv[i_cv]->value().real_value, cv[i_cv]->sup_np - 1);
+    } else {
+        factor_polynomial = cv[i_cv]->sup_coeff;
+    }
+    return factor_polynomial;
+}
+
+colvar::linearCombination::~linearCombination() {
+    for (auto it = cv.begin(); it != cv.end(); ++it) {
+        delete (*it);
+    }
+}
+
+void colvar::linearCombination::calc_value() {
+    x.reset();
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        cv[i_cv]->calc_value();
+        colvarvalue current_cv_value(cv[i_cv]->value());
+        // polynomial combination allowed
+        if (current_cv_value.type() == colvarvalue::type_scalar) {
+            x += cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np));
+        } else {
+            x += cv[i_cv]->sup_coeff * current_cv_value;
+        }
+    }
+}
+
+void colvar::linearCombination::calc_gradients() {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        cv[i_cv]->calc_gradients();
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
+                for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                    for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
+                        (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad;
+                    }
+                }
+            }
+        }
+    }
+}
+
+void colvar::linearCombination::apply_force(colvarvalue const &force) {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // If this CV us explicit gradients, then atomic gradients is already calculated
+        // We can apply the force to atom groups directly
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)
+        ) {
+            for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
+            }
+        } else {
+            // Compute factors for polynomial combinations
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            colvarvalue cv_force = force.real_value * factor_polynomial;
+            cv[i_cv]->apply_force(cv_force);
+        }
+    }
+}
+
+colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
+    GeometricPathCV::init_string_cv_map(string_cv_map);
+    // Lookup all available sub-cvcs
+    for (auto it_cv_map = string_cv_map.begin(); it_cv_map != string_cv_map.end(); ++it_cv_map) {
+        if (key_lookup(conf, it_cv_map->first.c_str())) {
+            std::vector<std::string> sub_cvc_confs;
+            get_key_string_multi_value(conf, it_cv_map->first.c_str(), sub_cvc_confs);
+            for (auto it_sub_cvc_conf = sub_cvc_confs.begin(); it_sub_cvc_conf != sub_cvc_confs.end(); ++it_sub_cvc_conf) {
+                cv.push_back((it_cv_map->second)(*(it_sub_cvc_conf)));
+            }
+        }
+    }
+    // Sort all sub CVs by their names
+    std::sort(cv.begin(), cv.end(), compareColvarComponent);
+    // Register atom groups and determine the colvar type for reference
+    std::vector<colvarvalue> tmp_cv;
+    for (auto it_sub_cv = cv.begin(); it_sub_cv != cv.end(); ++it_sub_cv) {
+        for (auto it_atom_group = (*it_sub_cv)->atom_groups.begin(); it_atom_group != (*it_sub_cv)->atom_groups.end(); ++it_atom_group) {
+            register_atom_group(*it_atom_group);
+        }
+        colvarvalue tmp_i_cv((*it_sub_cv)->value());
+        tmp_i_cv.reset();
+        tmp_cv.push_back(tmp_i_cv);
+    }
+    // Read path file
+    // Lookup all reference CV values
+    std::string path_filename;
+    get_keyval(conf, "pathFile", path_filename);
+    cvm::log(std::string("Reading path file: ") + path_filename + std::string("\n"));
+    std::ifstream ifs_path(path_filename);
+    if (!ifs_path.is_open()) {
+        cvm::error("Error: failed to open path file.\n");
+    }
+    std::string line;
+    const std::string token(" ");
+    total_reference_frames = 0;
+    while (std::getline(ifs_path, line)) {
+        std::vector<std::string> fields;
+        split_string(line, token, fields);
+        size_t num_value_required = 0;
+        for (size_t i_cv = 0; i_cv < tmp_cv.size(); ++i_cv) {
+            const size_t value_size = tmp_cv[i_cv].size();
+            num_value_required += value_size;
+            cvm::log(std::string("Reading CV ") + cv[i_cv]->name + std::string(" with ") + cvm::to_str(value_size) + std::string(" value(s)\n"));
+            if (num_value_required <= fields.size()) {
+                size_t start_index = num_value_required - value_size;
+                for (size_t i = start_index; i < num_value_required; ++i) {
+                    tmp_cv[i_cv][i] = std::atof(fields[i].c_str());
+                    cvm::log(fields[i] + std::string(" "));
+                }
+                cvm::log(std::string("\n"));
+            } else {
+                cvm::error("Error: incorrect format of path file.\n");
+            }
+        }
+        if (!fields.empty()) {
+            ref_cv.push_back(tmp_cv);
+            ++total_reference_frames;
+        }
+    }
+    x.type(colvarvalue::type_scalar);
+    use_explicit_gradients = true;
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
+            use_explicit_gradients = false;
+        }
+    }
+    if (!use_explicit_gradients) {
+        disable(f_cvc_explicit_gradient);
+    }
+}
+
+void colvar::CVBasedPath::computeReferenceDistance(std::vector<cvm::real>& result) {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        cv[i_cv]->calc_value();
+    }
+    for (size_t i_frame = 0; i_frame < ref_cv.size(); ++i_frame) {
+        cvm::real rmsd_i = 0.0;
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            colvarvalue ref_cv_value(ref_cv[i_frame][i_cv]);
+            colvarvalue current_cv_value(cv[i_cv]->value());
+            // polynomial combination allowed
+            if (current_cv_value.type() == colvarvalue::type_scalar) {
+                // wrapping is already in dist2
+                rmsd_i += cv[i_cv]->dist2(cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)), ref_cv_value.real_value);
+            } else {
+                rmsd_i += cv[i_cv]->dist2(cv[i_cv]->sup_coeff * current_cv_value, ref_cv_value);
+            }
+        }
+        rmsd_i /= cvm::real(cv.size());
+        rmsd_i = cvm::sqrt(rmsd_i);
+        result[i_frame] = rmsd_i;
+    }
+}
+
+cvm::real colvar::CVBasedPath::getPolynomialFactorOfCVGradient(size_t i_cv) const {
+    cvm::real factor_polynomial = 1.0;
+    if (cv[i_cv]->value().type() == colvarvalue::type_scalar) {
+        factor_polynomial = cv[i_cv]->sup_coeff * cv[i_cv]->sup_np * cvm::pow(cv[i_cv]->value().real_value, cv[i_cv]->sup_np - 1);
+    } else {
+        factor_polynomial = cv[i_cv]->sup_coeff;
+    }
+    return factor_polynomial;
+}
+
+colvar::CVBasedPath::~CVBasedPath() {
+    for (auto it = cv.begin(); it != cv.end(); ++it) {
+        delete (*it);
+    }
+}
+
+colvar::gspathCV::gspathCV(std::string const &conf): CVBasedPath(conf) {
+    function_type = "gspathCV";
+    cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
+    // Initialize variables for future calculation
+    get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
+    if (use_second_closest_frame == true) {
+        cvm::log(std::string("Geometric path s(σ) will use the second closest frame to compute s_(m-1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m-1)\n"));
+    }
+    get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
+    if (use_third_closest_frame == true) {
+        cvm::log(std::string("Geometric path s(σ) will use the third closest frame to compute s_(m+1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n"));
+    }
+    GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame);
+    x.type(colvarvalue::type_scalar);
+    use_explicit_gradients = true;
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
+            use_explicit_gradients = false;
+        }
+    }
+    if (!use_explicit_gradients) {
+        cvm::log("Geometric path s(σ) will use implicit gradients.\n");
+        disable(f_cvc_explicit_gradient);
+    }
+}
+
+colvar::gspathCV::~gspathCV() {}
+
+void colvar::gspathCV::updateReferenceDistances() {
+    computeReferenceDistance(frame_distances);
+}
+
+void colvar::gspathCV::prepareVectors() {
+    // Compute v1, v2 and v3
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // values of sub-cvc are computed in update_distances
+        // cv[i_cv]->calc_value();
+        colvarvalue f1_ref_cv_i_value(ref_cv[min_frame_index_1][i_cv]);
+        colvarvalue f2_ref_cv_i_value(ref_cv[min_frame_index_2][i_cv]);
+        colvarvalue current_cv_value(cv[i_cv]->value());
+        // polynomial combination allowed
+        if (current_cv_value.type() == colvarvalue::type_scalar) {
+            v1[i_cv] = f1_ref_cv_i_value.real_value - cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np));
+            v2[i_cv] = cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)) - f2_ref_cv_i_value.real_value;
+        } else {
+            v1[i_cv] = f1_ref_cv_i_value - cv[i_cv]->sup_coeff * current_cv_value;
+            v2[i_cv] = cv[i_cv]->sup_coeff * current_cv_value - f2_ref_cv_i_value;
+        }
+        cv[i_cv]->wrap(v1[i_cv]);
+        cv[i_cv]->wrap(v2[i_cv]);
+    }
+    if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            v3[i_cv] = ref_cv[min_frame_index_1][i_cv] - ref_cv[min_frame_index_2][i_cv];
+            cv[i_cv]->wrap(v3[i_cv]);
+        }
+    } else {
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            v3[i_cv] = ref_cv[min_frame_index_3][i_cv] - ref_cv[min_frame_index_1][i_cv];
+            cv[i_cv]->wrap(v3[i_cv]);
+        }
+    }
+}
+
+void colvar::gspathCV::calc_value() {
+    computeValue();
+    x = s;
+}
+
+void colvar::gspathCV::calc_gradients() {
+    computeDerivatives();
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // No matter whether the i-th cv uses implicit gradient, compute it first.
+        cv[i_cv]->calc_gradients();
+        // If the gradient is not implicit, then add the gradients to its atom groups
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
+            // Temporary variables storing gradients
+            colvarvalue tmp_cv_grad_v1(cv[i_cv]->value());
+            colvarvalue tmp_cv_grad_v2(cv[i_cv]->value());
+            // Compute factors for polynomial combinations
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            // Loop over all elements of the corresponding colvar value
+            for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
+                // ds/dz, z = vector of CVs
+                tmp_cv_grad_v1[j_elem] = -1.0 * sign * 0.5 * dfdv1[i_cv][j_elem] / M;
+                tmp_cv_grad_v2[j_elem] = sign * 0.5 * dfdv2[i_cv][j_elem] / M;
+                // Apply the gradients to the atom groups in i-th cv
+                // Loop over all atom groups
+                for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                    // Loop over all atoms in the k-th atom group
+                    for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
+                        // Chain rule
+                        (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * ((*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v1[j_elem] + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v2[j_elem]);
+                    }
+                }
+            }
+        }
+    }
+}
+
+void colvar::gspathCV::apply_force(colvarvalue const &force) {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // If this CV us explicit gradients, then atomic gradients is already calculated
+        // We can apply the force to atom groups directly
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)
+        ) {
+            for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
+            }
+        } else {
+            // Temporary variables storing gradients
+            colvarvalue tmp_cv_grad_v1(cv[i_cv]->value());
+            colvarvalue tmp_cv_grad_v2(cv[i_cv]->value());
+            // Compute factors for polynomial combinations
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
+                // ds/dz, z = vector of CVs
+                tmp_cv_grad_v1[j_elem] = -1.0 * sign * 0.5 * dfdv1[i_cv][j_elem] / M;
+                tmp_cv_grad_v2[j_elem] = sign * 0.5 * dfdv2[i_cv][j_elem] / M;
+            }
+            colvarvalue cv_force = force.real_value * factor_polynomial * (tmp_cv_grad_v1 + tmp_cv_grad_v2);
+            cv[i_cv]->apply_force(cv_force);
+        }
+    }
+}
+
+colvar::gzpathCV::gzpathCV(std::string const &conf): CVBasedPath(conf) {
+    function_type = "gzpathCV";
+    cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
+    // Initialize variables for future calculation
+    M = cvm::real(total_reference_frames - 1);
+    m = 1.0;
+    get_keyval(conf, "useSecondClosestFrame", use_second_closest_frame, true);
+    if (use_second_closest_frame == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the second closest frame to compute s_(m-1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m-1)\n"));
+    }
+    get_keyval(conf, "useThirdClosestFrame", use_third_closest_frame, false);
+    if (use_third_closest_frame == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the third closest frame to compute s_(m+1)\n"));
+    } else {
+        cvm::log(std::string("Geometric path z(σ) will use the neighbouring frame to compute s_(m+1)\n"));
+    }
+    bool b_use_z_square = false;
+    get_keyval(conf, "useZsquare", b_use_z_square, false);
+    if (b_use_z_square == true) {
+        cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n"));
+    }
+    GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::Z>::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame, b_use_z_square);
+    x.type(colvarvalue::type_scalar);
+    use_explicit_gradients = true;
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
+            use_explicit_gradients = false;
+        }
+    }
+    if (!use_explicit_gradients) {
+        cvm::log("Geometric path z(σ) will use implicit gradients.\n");
+        disable(f_cvc_explicit_gradient);
+    }
+}
+
+colvar::gzpathCV::~gzpathCV() {
+}
+
+void colvar::gzpathCV::updateReferenceDistances() {
+    computeReferenceDistance(frame_distances);
+}
+
+void colvar::gzpathCV::prepareVectors() {
+    // Compute v1, v2 and v3
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // values of sub-cvc are computed in update_distances
+        // cv[i_cv]->calc_value();
+        colvarvalue f1_ref_cv_i_value(ref_cv[min_frame_index_1][i_cv]);
+        colvarvalue f2_ref_cv_i_value(ref_cv[min_frame_index_2][i_cv]);
+        colvarvalue current_cv_value(cv[i_cv]->value());
+        // polynomial combination allowed
+        if (current_cv_value.type() == colvarvalue::type_scalar) {
+            v1[i_cv] = f1_ref_cv_i_value.real_value - cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np));
+            v2[i_cv] = cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)) - f2_ref_cv_i_value.real_value;
+        } else {
+            v1[i_cv] = f1_ref_cv_i_value - cv[i_cv]->sup_coeff * current_cv_value;
+            v2[i_cv] = cv[i_cv]->sup_coeff * current_cv_value - f2_ref_cv_i_value;
+        }
+        v4[i_cv] = f1_ref_cv_i_value - f2_ref_cv_i_value;
+        cv[i_cv]->wrap(v1[i_cv]);
+        cv[i_cv]->wrap(v2[i_cv]);
+        cv[i_cv]->wrap(v4[i_cv]);
+    }
+    if (min_frame_index_3 < 0 || min_frame_index_3 > M) {
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            v3[i_cv] = ref_cv[min_frame_index_1][i_cv] - ref_cv[min_frame_index_2][i_cv];
+            cv[i_cv]->wrap(v3[i_cv]);
+        }
+    } else {
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            v3[i_cv] = ref_cv[min_frame_index_3][i_cv] - ref_cv[min_frame_index_1][i_cv];
+            cv[i_cv]->wrap(v3[i_cv]);
+        }
+    }
+}
+
+void colvar::gzpathCV::calc_value() {
+    computeValue();
+    x = z;
+}
+
+void colvar::gzpathCV::calc_gradients() {
+    computeDerivatives();
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // No matter whether the i-th cv uses implicit gradient, compute it first.
+        cv[i_cv]->calc_gradients();
+        // If the gradient is not implicit, then add the gradients to its atom groups
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
+            // Temporary variables storing gradients
+            colvarvalue tmp_cv_grad_v1 = -1.0 * dzdv1[i_cv];
+            colvarvalue tmp_cv_grad_v2 =  1.0 * dzdv2[i_cv];
+            // Compute factors for polynomial combinations
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
+                // Apply the gradients to the atom groups in i-th cv
+                // Loop over all atom groups
+                for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                    // Loop over all atoms in the k-th atom group
+                    for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
+                        // Chain rule
+                        (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = factor_polynomial * ((*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v1[j_elem] + (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad * tmp_cv_grad_v2[j_elem]);
+                    }
+                }
+            }
+        }
+    }
+}
+
+void colvar::gzpathCV::apply_force(colvarvalue const &force) {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        // If this CV us explicit gradients, then atomic gradients is already calculated
+        // We can apply the force to atom groups directly
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
+            for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
+            }
+        }
+        else {
+            colvarvalue tmp_cv_grad_v1 = -1.0 * dzdv1[i_cv];
+            colvarvalue tmp_cv_grad_v2 =  1.0 * dzdv2[i_cv];
+            // Temporary variables storing gradients
+            // Compute factors for polynomial combinations
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            colvarvalue cv_force = force.real_value * factor_polynomial * (tmp_cv_grad_v1 + tmp_cv_grad_v2);
+            cv[i_cv]->apply_force(cv_force);
+        }
+    }
+}
+
+void GeometricPathCV::init_string_cv_map(std::map<std::string, std::function<colvar::cvc* (const std::string& subcv_conf)>>& string_cv_map) {
+    string_cv_map["distance"]              = [](const std::string& conf){return new colvar::distance(conf);};
+    string_cv_map["dihedral"]              = [](const std::string& conf){return new colvar::dihedral(conf);};
+    string_cv_map["angle"]                 = [](const std::string& conf){return new colvar::angle(conf);};
+    string_cv_map["rmsd"]                  = [](const std::string& conf){return new colvar::rmsd(conf);};
+    string_cv_map["gyration"]              = [](const std::string& conf){return new colvar::gyration(conf);};
+    string_cv_map["inertia"]               = [](const std::string& conf){return new colvar::inertia(conf);};
+    string_cv_map["inertiaZ"]              = [](const std::string& conf){return new colvar::inertia_z(conf);};
+    string_cv_map["tilt"]                  = [](const std::string& conf){return new colvar::tilt(conf);};
+    string_cv_map["distanceZ"]             = [](const std::string& conf){return new colvar::distance_z(conf);};
+    string_cv_map["distanceXY"]            = [](const std::string& conf){return new colvar::distance_xy(conf);};
+    string_cv_map["polarTheta"]            = [](const std::string& conf){return new colvar::polar_theta(conf);};
+    string_cv_map["polarPhi"]              = [](const std::string& conf){return new colvar::polar_phi(conf);};
+    string_cv_map["distanceVec"]           = [](const std::string& conf){return new colvar::distance_vec(conf);};
+    string_cv_map["orientationAngle"]      = [](const std::string& conf){return new colvar::orientation_angle(conf);};
+    string_cv_map["distancePairs"]         = [](const std::string& conf){return new colvar::distance_pairs(conf);};
+    string_cv_map["dipoleMagnitude"]       = [](const std::string& conf){return new colvar::dipole_magnitude(conf);};
+    string_cv_map["coordNum"]              = [](const std::string& conf){return new colvar::coordnum(conf);};
+    string_cv_map["selfCoordNum"]          = [](const std::string& conf){return new colvar::selfcoordnum(conf);};
+    string_cv_map["dipoleAngle"]           = [](const std::string& conf){return new colvar::dipole_angle(conf);};
+    string_cv_map["orientation"]           = [](const std::string& conf){return new colvar::orientation(conf);};
+    string_cv_map["orientationProj"]       = [](const std::string& conf){return new colvar::orientation_proj(conf);};
+    string_cv_map["eigenvector"]           = [](const std::string& conf){return new colvar::eigenvector(conf);};
+    string_cv_map["cartesian"]             = [](const std::string& conf){return new colvar::cartesian(conf);};
+    string_cv_map["alpha"]                 = [](const std::string& conf){return new colvar::alpha_angles(conf);};
+    string_cv_map["dihedralPC"]            = [](const std::string& conf){return new colvar::dihedPC(conf);};
+    string_cv_map["linearCombination"]     = [](const std::string& conf){return new colvar::linearCombination(conf);};
+}
+
+#endif

lib/colvars/colvarcomp_protein.cpp

@@ -7,6 +7,8 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
+#include <algorithm>
+
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarparse.h"

lib/colvars/colvargrid.cpp

@@ -109,7 +109,9 @@ cvm::real colvar_grid_scalar::entropy() const
 {
   cvm::real sum = 0.0;
   for (size_t i = 0; i < nt; i++) {
-    sum += -1.0 * data[i] * cvm::logn(data[i]);
+    if (data[i] >0) {
+      sum += -1.0 * data[i] * cvm::logn(data[i]);
+    }
   }
   cvm::real bin_volume = 1.0;
   for (size_t id = 0; id < widths.size(); id++) {

lib/colvars/colvargrid.h

@@ -557,11 +557,11 @@ public:
       data[i] *= a;
   }
 
-  /// \brief Assign all zero elements a scalar constant (fast loop)
-  inline void remove_zeros(cvm::real const &a)
+  /// \brief Assign values that are smaller than scalar constant the latter value (fast loop)
+  inline void remove_small_values(cvm::real const &a)
   {
     for (size_t i = 0; i < nt; i++)
-      if(data[i]==0) data[i] = a;
+      if(data[i]<a) data[i] = a;
   }
 
 

lib/colvars/colvarparse.cpp

@@ -7,7 +7,6 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
-
 #include <sstream>
 #include <iostream>
 #include <algorithm>
@@ -58,6 +57,28 @@ bool colvarparse::get_key_string_value(std::string const &conf,
   return b_found_any;
 }
 
+bool colvarparse::get_key_string_multi_value(std::string const &conf,
+                                             char const *key, std::vector<std::string>& data)
+{
+  bool b_found = false, b_found_any = false;
+  size_t save_pos = 0, found_count = 0;
+
+  data.clear();
+
+  do {
+    std::string data_this = "";
+    b_found = key_lookup(conf, key, &data_this, &save_pos);
+    if (b_found) {
+      if (!b_found_any)
+        b_found_any = true;
+      found_count++;
+      data.push_back(data_this);
+    }
+  } while (b_found);
+
+  return b_found_any;
+}
+
 
 template<typename TYPE>
 void colvarparse::mark_key_set_user(std::string const &key_str,
@@ -843,3 +864,18 @@ int colvarparse::check_braces(std::string const &conf,
   }
   return (brace_count != 0) ? INPUT_ERROR : COLVARS_OK;
 }
+
+void colvarparse::split_string(const std::string& data, const std::string& delim, std::vector<std::string>& dest) {
+    size_t index = 0, new_index = 0;
+    std::string tmpstr;
+    while (index != data.length()) {
+        new_index = data.find(delim, index);
+        if (new_index != std::string::npos) tmpstr = data.substr(index, new_index - index);
+        else tmpstr = data.substr(index, data.length());
+        if (!tmpstr.empty()) {
+            dest.push_back(tmpstr);
+        }
+        if (new_index == std::string::npos) break;
+        index = new_index + 1;
+    }
+}

lib/colvars/colvarparse.h

@@ -212,6 +212,10 @@ protected:
   bool get_key_string_value(std::string const &conf,
                             char const *key, std::string &data);
 
+  /// Get multiple strings from repeated instances of a same keyword
+  bool get_key_string_multi_value(std::string const &conf,
+                                  char const *key, std::vector<std::string>& data);
+
   /// Template for single-value keyword parsers
   template<typename TYPE>
   bool _get_keyval_scalar_(std::string const &conf,
@@ -322,6 +326,12 @@ public:
   /// from this position
   static int check_braces(std::string const &conf, size_t const start_pos);
 
+  /// \brief Split a string with a specified delimiter into a vector
+  /// \param data The string to be splitted
+  /// \param delim A delimiter
+  /// \param dest A destination vector to store the splitted results
+  static void split_string(const std::string& data, const std::string& delim, std::vector<std::string>& dest);
+
 protected:
 
   /// \brief List of legal keywords for this object: this is updated

lib/colvars/colvarproxy.cpp

@@ -7,8 +7,14 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 
+#if !defined(WIN32) || defined(__CYGWIN__)
+#include <unistd.h>
+#endif
+#include <cerrno>
+
 #include <sstream>
 #include <cstring>
+#include <cstdio>
 
 #if defined(_OPENMP)
 #include <omp.h>
@@ -704,6 +710,27 @@ std::ostream * colvarproxy_io::output_stream(std::string const &output_name,
   if (cvm::debug()) {
     cvm::log("Using colvarproxy::output_stream()\n");
   }
+
+  std::ostream *os = get_output_stream(output_name);
+  if (os != NULL) return os;
+
+  if (!(mode & (std::ios_base::app | std::ios_base::ate))) {
+    backup_file(output_name);
+  }
+  std::ofstream *osf = new std::ofstream(output_name.c_str(), mode);
+  if (!osf->is_open()) {
+    cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n",
+               FILE_ERROR);
+    return NULL;
+  }
+  output_stream_names.push_back(output_name);
+  output_files.push_back(osf);
+  return osf;
+}
+
+
+std::ostream *colvarproxy_io::get_output_stream(std::string const &output_name)
+{
   std::list<std::ostream *>::iterator osi  = output_files.begin();
   std::list<std::string>::iterator    osni = output_stream_names.begin();
   for ( ; osi != output_files.end(); osi++, osni++) {
@@ -711,21 +738,11 @@ std::ostream * colvarproxy_io::output_stream(std::string const &output_name,
       return *osi;
     }
   }
-  if (!(mode & (std::ios_base::app | std::ios_base::ate))) {
-    backup_file(output_name);
-  }
-  std::ofstream *os = new std::ofstream(output_name.c_str(), mode);
-  if (!os->is_open()) {
-    cvm::error("Error: cannot write to file/channel \""+output_name+"\".\n",
-               FILE_ERROR);
-    return NULL;
-  }
-  output_stream_names.push_back(output_name);
-  output_files.push_back(os);
-  return os;
+  return NULL;
 }
 
 
+
 int colvarproxy_io::flush_output_stream(std::ostream *os)
 {
   std::list<std::ostream *>::iterator osi  = output_files.begin();
@@ -761,10 +778,45 @@ int colvarproxy_io::close_output_stream(std::string const &output_name)
 
 int colvarproxy_io::backup_file(char const *filename)
 {
+  // TODO implement this using rename_file()
   return COLVARS_NOT_IMPLEMENTED;
 }
 
 
+int colvarproxy_io::remove_file(char const *filename)
+{
+  if (std::remove(filename)) {
+    if (errno != ENOENT) {
+      return cvm::error("Error: in removing file \""+std::string(filename)+
+                        "\".\n.",
+                        FILE_ERROR);
+    }
+  }
+  return COLVARS_OK;
+}
+
+
+int colvarproxy_io::rename_file(char const *filename, char const *newfilename)
+{
+  int error_code = COLVARS_OK;
+#if defined(WIN32) && !defined(__CYGWIN__)
+  // On straight Windows, must remove the destination before renaming it
+  error_code |= remove_file(newfilename);
+#endif
+  int rename_exit_code = 0;
+  while ((rename_exit_code = std::rename(filename, newfilename)) != 0) {
+    if (errno == EINTR) continue;
+    // Call log() instead of error to allow the next try
+    cvm::log("Error: in renaming file \""+std::string(filename)+"\" to \""+
+             std::string(newfilename)+"\".\n.");
+    error_code |= FILE_ERROR;
+    if (errno == EXDEV) continue;
+    break;
+  }
+  return rename_exit_code ? error_code : COLVARS_OK;
+}
+
+
 
 colvarproxy::colvarproxy()
 {
@@ -826,4 +878,3 @@ int colvarproxy::get_version_from_string(char const *version_string)
   is >> newint;
   return newint;
 }
-

lib/colvars/colvarproxy.h

@@ -571,7 +571,10 @@ public:
   /// if this is not open already, then open it
   virtual std::ostream *output_stream(std::string const &output_name,
                                       std::ios_base::openmode mode =
-                                        std::ios_base::out);
+                                      std::ios_base::out);
+
+  /// Returns a reference to output_name if it exists, NULL otherwise
+  virtual std::ostream *get_output_stream(std::string const &output_name);
 
   /// \brief Flushes the given output channel
   virtual int flush_output_stream(std::ostream *os);
@@ -588,6 +591,25 @@ public:
     return backup_file(filename.c_str());
   }
 
+  /// Remove the given file
+  int remove_file(char const *filename);
+
+  /// Remove the given file
+  inline int remove_file(std::string const &filename)
+  {
+    return remove_file(filename.c_str());
+  }
+
+  /// Rename the given file
+  int rename_file(char const *filename, char const *newfilename);
+
+  /// Rename the given file
+  inline int rename_file(std::string const &filename,
+                         std::string const &newfilename)
+  {
+    return rename_file(filename.c_str(), newfilename.c_str());
+  }
+
   /// \brief Prefix of the input state file
   inline std::string & input_prefix()
   {

lib/colvars/colvars_version.h

@@ -1,5 +1,5 @@
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2019-04-26"
+#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/KOKKOS/kokkos.cpp

@@ -208,6 +208,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   MPI_Comm_size(world,&nmpi);
   if (nmpi > 0) {
 
+#if defined(MPI_VERSION) && (MPI_VERSION > 2)
     // Check for IBM Spectrum MPI
 
     int len;
@@ -226,6 +227,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
         if (me == 0)
           error->warning(FLERR,"The Spectrum MPI '-gpu' flag is not set. Disabling CUDA-aware MPI");
     }
+#endif
 
     if (cuda_aware_flag == 1 && have_cuda_aware == 0) {
       if (me == 0)
@@ -234,10 +236,10 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
       cuda_aware_flag = 0;
     } else if (have_cuda_aware == -1) { // maybe we are dealing with MPICH, MVAPICH2 or some derivative?
     // MVAPICH2
-#if (defined MPICH) && (defined MVAPICH2_VERSION)
+#if defined(MPICH) && defined(MVAPICH2_VERSION)
       char* str;
       cuda_aware_flag = 0;
-      if (str = getenv("MV2_ENABLE_CUDA")
+      if ((str = getenv("MV2_ENABLE_CUDA")))
         if ((strcmp(str,"1") == 0))
           cuda_aware_flag = 1;
 
@@ -245,7 +247,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
         if (me == 0)
           error->warning(FLERR,"MVAPICH2 'MV2_ENABLE_CUDA' environment variable is not set. Disabling CUDA-aware MPI");
     // pure MPICH or some unsupported MPICH derivative
-#elif (defined MPICH) && !(defined MVAPICH2_VERSION)
+#elif defined(MPICH) && !defined(MVAPICH2_VERSION)
       if (me == 0)
         error->warning(FLERR,"Detected MPICH. Disabling CUDA-aware MPI");
       cuda_aware_flag = 0;

src/REPLICA/temper.cpp

@@ -31,6 +31,7 @@
 #include "finish.h"
 #include "timer.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,10 @@ void Temper::command(int narg, char **arg)
   nevery = force->inumeric(FLERR,arg[1]);
   double temp = force->numeric(FLERR,arg[2]);
 
+  // ignore temper command, if walltime limit was already reached
+
+  if (timer->is_timeout()) return;
+
   for (whichfix = 0; whichfix < modify->nfix; whichfix++)
     if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
   if (whichfix == modify->nfix)
@@ -94,39 +99,18 @@ void Temper::command(int narg, char **arg)
   // fix style must be appropriate for temperature control, i.e. it needs
   // to provide a working Fix::reset_target() and must not change the volume.
 
-  if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/asphere") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/asphere/omp") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/body") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/eff") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/intel") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/kk") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/kk/host") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/kk/device") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/omp") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/sphere") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"nvt/sphere/omp") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"langevin") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"langevin/drude") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"langevin/eff") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"gld") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"gle") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"rigid/nvt") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/small") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/omp") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/small/omp") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/berendsen/cuda") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/csvr") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/csld") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/rescale/cuda") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/rescale/eff") != 0))
+  if ((!utils::strmatch(modify->fix[whichfix]->style,"^nvt")) &&
+      (!utils::strmatch(modify->fix[whichfix]->style,"^langevin")) &&
+      (!utils::strmatch(modify->fix[whichfix]->style,"^gl[de]$")) &&
+      (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/nvt")) &&
+      (!utils::strmatch(modify->fix[whichfix]->style,"^temp/")))
     error->universe_all(FLERR,"Tempering temperature fix is not supported");
 
   // setup for long tempering run
 
   update->whichflag = 1;
+  timer->init_timeout();
+
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
@@ -233,7 +217,9 @@ void Temper::command(int narg, char **arg)
 
     // run for nevery timesteps
 
+    timer->init_timeout();
     update->integrate->run(nevery);
+    if (timer->is_timeout()) break;
 
     // compute PE
     // notify compute it will be called at next swap

src/USER-BOCS/fix_bocs.cpp

@@ -59,6 +59,9 @@ enum{NOBIAS,BIAS};
 enum{NONE,XYZ,XY,YZ,XZ};
 enum{ISO,ANISO,TRICLINIC};
 
+// NB: Keep error and warning messages less than 255 chars long.
+const int MAX_MESSAGE_LENGTH = 256;
+
 /* ----------------------------------------------------------------------
    NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
  ---------------------------------------------------------------------- */
@@ -630,24 +633,32 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
   double **data = (double **) calloc(N_columns,sizeof(double *));
   char * line = (char *) calloc(200,sizeof(char));
 
+  bool badInput = false;
+  char badDataMsg[MAX_MESSAGE_LENGTH];
   fpi = fopen(filename,"r");
   if (fpi)
   {
     while (fgets(line,199,fpi)) { ++n_entries; }
-    fclose(fpi);
+
     for (i = 0; i < N_columns; ++i)
     {
       data[i] = (double *) calloc(n_entries,sizeof(double));
     }
-  } else {
-    char errmsg[128];
-    snprintf(errmsg,128,"Unable to open file: %s\n",filename);
-    error->all(FLERR,errmsg);
-  }
 
-  n_entries = 0;
-  fpi = fopen(filename,"r");
-  if (fpi) {
+    // Don't need to re-open the file to make a second pass through it
+    // simply rewind to beginning
+    rewind(fpi);
+
+    double stdVolumeInterval = 0.0;
+    double currVolumeInterval = 0.0;
+    // When comparing doubles/floats, we need an Epsilon.
+    // The literature indicates getting this value right in the
+    // general case can be pretty complicated. I don't think it
+    // needs to be complicated here, though. At least based on the
+    // sample data I've seen where the volume values are fairly
+    // large.
+    const double volumeIntervalTolerance = 0.001;
+    n_entries = 0;
     while( fgets(line,199,fpi)) {
       ++n_entries;
       test_sscanf = sscanf(line," %f , %f ",&f1, &f2);
@@ -655,19 +666,47 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
       {
         data[0][n_entries-1] = (double) f1;
         data[1][n_entries-1] = (double) f2;
+        if (n_entries == 2) {
+          stdVolumeInterval = data[0][n_entries-1] - data[0][n_entries-2];
+        }
+        else if (n_entries > 2) {
+          currVolumeInterval = data[0][n_entries-1] - data[0][n_entries-2];
+          if (fabs(currVolumeInterval - stdVolumeInterval) > volumeIntervalTolerance) {
+            snprintf(badDataMsg,MAX_MESSAGE_LENGTH,
+                     "BAD VOLUME INTERVAL: spline analysis requires uniform"
+                     " volume distribution, found inconsistent volume"
+                     " differential, line %d of file %s\n\tline: %s",
+                     n_entries,filename,line);
+            error->message(FLERR,badDataMsg);
+            badInput = true;
+          }
+        }
+        // no else -- first entry is simply ignored
       }
       else
       {
-        fprintf(stderr,"WARNING: did not find 2 comma separated values in "
-                 "line %d of file %s\n\tline: %s",n_entries,filename,line);
+        snprintf(badDataMsg,MAX_MESSAGE_LENGTH,
+                 "BAD INPUT FORMAT: did not find 2 comma separated numeric"
+                 " values in line %d of file %s\n\tline: %s",
+                 n_entries,filename,line);
+        error->message(FLERR,badDataMsg);
+        badInput = true;
       }
     }
-  } else {
-    char errmsg[128];
-    snprintf(errmsg,128,"Unable to open file: %s\n",filename);
+    fclose(fpi);
+  }
+  else {
+    char errmsg[MAX_MESSAGE_LENGTH];
+    snprintf(errmsg,MAX_MESSAGE_LENGTH,"Unable to open file: %s\n",filename);
+    error->all(FLERR,errmsg);
+  }
+
+  if (badInput) {
+    char errmsg[MAX_MESSAGE_LENGTH];
+    snprintf(errmsg,MAX_MESSAGE_LENGTH,
+             "Bad volume / pressure-correction data: %s\nSee details above",filename);
     error->all(FLERR,errmsg);
   }
-  fclose(fpi);
 
   if (p_basis_type == 1)
   {
@@ -691,9 +730,10 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
   }
   else
   {
-    char * errmsg = (char *) calloc(70,sizeof(char));
-    sprintf(errmsg,"ERROR: invalid p_basis_type value "
-                                    "of %d in read_F_table",p_basis_type);
+    char errmsg[MAX_MESSAGE_LENGTH];
+    snprintf(errmsg, MAX_MESSAGE_LENGTH,
+             "ERROR: invalid p_basis_type value of %d in read_F_table",
+             p_basis_type);
     error->all(FLERR,errmsg);
   }
   // cleanup

src/USER-COLVARS/colvarproxy_lammps_version.h

@@ -1,5 +1,5 @@
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2019-04-09"
+#define COLVARPROXY_VERSION "2019-08-01"
 // 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

src/USER-INTEL/fix_intel.cpp

@@ -352,15 +352,15 @@ void FixIntel::init()
   if (_offload_balance != 0.0) off_mode = 1;
   if (_precision_mode == PREC_MODE_SINGLE) {
     _single_buffers->zero_ev();
-    _single_buffers->grow_ncache(off_mode,_nthreads);
+    _single_buffers->grow_ncache(off_mode, comm->nthreads);
     _single_buffers->free_list_ptrs();
   } else if (_precision_mode == PREC_MODE_MIXED) {
     _mixed_buffers->zero_ev();
-    _mixed_buffers->grow_ncache(off_mode,_nthreads);
+    _mixed_buffers->grow_ncache(off_mode, comm->nthreads);
     _mixed_buffers->free_list_ptrs();
   } else {
     _double_buffers->zero_ev();
-    _double_buffers->grow_ncache(off_mode,_nthreads);
+    _double_buffers->grow_ncache(off_mode, comm->nthreads);
     _double_buffers->free_list_ptrs();
   }
 

src/USER-INTEL/intel_intrinsics_airebo.h

@@ -2223,7 +2223,9 @@ public:
   }
 
   VEC_INLINE static ivec unpackloepi32(const fvec &a) {
-    return reinterpret_cast<const int*>(&a.val_)[0];
+    union { int i; flt_t f; } atype;
+    atype.f = a.val_;
+    return ivec(atype.i);
   }
 
   VEC_INLINE static fvec mask_sincos(

src/USER-INTEL/pair_eam_intel.cpp

@@ -451,7 +451,6 @@ void PairEAMIntel::eval(const int offload, const int vflag,
 
       if (tid == 0)
         comm->forward_comm_pair(this);
-      if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T));
 
       #if defined(_OPENMP)
       #pragma omp barrier

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/USER-MISC/pair_ilp_graphene_hbn.h

@@ -34,9 +34,10 @@ class PairILPGrapheneHBN : public Pair {
   void coeff(int, char **);
   double init_one(int, int);
   void init_style();
+  void ILP_neigh();
   void calc_normal();
-  int pack_forward_comm(int, int *, double *, int, int *);
-  void unpack_forward_comm(int, int, double *);
+  void calc_FRep(int, int);
+  void calc_FvdW(int, int);
   double single(int, int, int, int, double, double, double, double &);
 
  protected:
@@ -74,7 +75,6 @@ class PairILPGrapheneHBN : public Pair {
 
   void read_file( char * );
   void allocate();
-  void ILP_neigh();
 
   /* ----Calculate the long-range cutoff term */
   inline double calc_Tap(double r_ij, double Rcut) {

src/USER-MISC/pair_kolmogorov_crespi_full.h

@@ -34,9 +34,10 @@ class PairKolmogorovCrespiFull : public Pair {
   void coeff(int, char **);
   double init_one(int, int);
   void init_style();
+  void KC_neigh();
   void calc_normal();
-  int pack_forward_comm(int, int *, double *, int, int *);
-  void unpack_forward_comm(int, int, double *);
+  void calc_FRep(int, int);
+  void calc_FvdW(int, int);
   double single(int, int, int, int, double, double, double, double &);
 
  protected:
@@ -75,7 +76,6 @@ class PairKolmogorovCrespiFull : public Pair {
 
   void read_file( char * );
   void allocate();
-  void KC_neigh();
 
 
   /* ----Calculate the long-range cutoff term */

src/USER-MISC/temper_grem.cpp

@@ -71,6 +71,9 @@ void TemperGrem::command(int narg, char **arg)
   nevery = force->inumeric(FLERR,arg[1]);
   double lambda = force->numeric(FLERR,arg[2]);
 
+  // ignore temper command, if walltime limit was already reached
+  if (timer->is_timeout()) return;
+
   // Get and check if gREM fix exists
   for (whichfix = 0; whichfix < modify->nfix; whichfix++)
     if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
@@ -127,6 +130,8 @@ void TemperGrem::command(int narg, char **arg)
   // setup for long tempering run
 
   update->whichflag = 1;
+  timer->init_timeout();
+
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
@@ -234,7 +239,9 @@ void TemperGrem::command(int narg, char **arg)
 
     // run for nevery timesteps
 
+    timer->init_timeout();
     update->integrate->run(nevery);
+    if (timer->is_timeout()) break;
 
     // compute PE
     // notify compute it will be called at next swap
@@ -242,7 +249,6 @@ void TemperGrem::command(int narg, char **arg)
     pe = pe_compute->compute_scalar();
     pe_compute->addstep(update->ntimestep + nevery);
 
-
     // which = which of 2 kinds of swaps to do (0,1)
 
     if (!ranswap) which = iswap % 2;

src/USER-MISC/temper_npt.cpp

@@ -33,6 +33,7 @@
 #include "finish.h"
 #include "timer.h"
 #include "error.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 
@@ -73,6 +74,10 @@ void TemperNPT::command(int narg, char **arg)
   double temp = force->numeric(FLERR,arg[2]);
   double press_set = force->numeric(FLERR,arg[6]);
 
+  // ignore temper command, if walltime limit was already reached
+
+  if (timer->is_timeout()) return;
+
   for (whichfix = 0; whichfix < modify->nfix; whichfix++)
     if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break;
   if (whichfix == modify->nfix)
@@ -97,13 +102,15 @@ void TemperNPT::command(int narg, char **arg)
   // change the volume. This currently only applies to fix npt and
   // fix rigid/npt variants
 
-  if ((strncmp(modify->fix[whichfix]->style,"npt",3) != 0)
-      && (strncmp(modify->fix[whichfix]->style,"rigid/npt",9) != 0))
+  if ( (!utils::strmatch(modify->fix[whichfix]->style,"^npt")) &&
+       (!utils::strmatch(modify->fix[whichfix]->style,"^rigid/npt")) )
     error->universe_all(FLERR,"Tempering temperature and pressure fix is not supported");
 
   // setup for long tempering run
 
   update->whichflag = 1;
+  timer->init_timeout();
+
   update->nsteps = nsteps;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + nsteps;
@@ -211,7 +218,9 @@ void TemperNPT::command(int narg, char **arg)
 
     // run for nevery timesteps
 
+    timer->init_timeout();
     update->integrate->run(nevery);
+    if (timer->is_timeout()) break;
 
     // compute PE
     // notify compute it will be called at next swap

src/USER-OMP/thr_data.h

@@ -31,7 +31,7 @@ class ThrData {
 
  public:
   ThrData(int tid, class Timer *t);
-  ~ThrData() { delete _timer; _timer = nullptr; };
+  ~ThrData() { delete _timer; _timer = NULL; };
 
   void check_tid(int);    // thread id consistency check
   int get_tid() const { return _tid; }; // our thread id.
@@ -136,7 +136,7 @@ class ThrData {
 
  // disabled default methods
  private:
-  ThrData() : _tid(-1), _timer(nullptr) {};
+  ThrData() : _tid(-1), _timer(NULL) {};
 };
 
 ////////////////////////////////////////////////////////////////////////

src/USER-PHONON/Install.sh

@@ -42,5 +42,3 @@ action fix_phonon.cpp fft3d_wrap.h
 action fix_phonon.h fft3d_wrap.h
 action dynamical_matrix.cpp
 action dynamical_matrix.h
-action third_order.cpp
-action third_order.h

src/USER-PTM/ptm_initialize_data.h

@@ -15,6 +15,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #include "ptm_deformation_gradient.h"
 #include "ptm_fundamental_mappings.h"
 #include "ptm_alt_templates.h"
+#include <cstddef>
 
 
 namespace ptm {

src/error.cpp

@@ -19,6 +19,10 @@
 #include "output.h"
 #include "input.h"
 
+#if defined(LAMMPS_EXCEPTIONS)
+#include "update.h"
+#endif
+
 using namespace LAMMPS_NS;
 
 // helper function to truncate a string to a segment starting with "src/";