patch 22Aug18

Doc updates for release

.github/CODEOWNERS

@@ -9,13 +9,51 @@ lib/kokkos/*          @stanmoore1
 lib/molfile/*         @akohlmey
 lib/qmmm/*            @akohlmey
 lib/vtk/*             @rbberger
+lib/kim/*             @ellio167
 
-# packages
-src/KOKKOS            @stanmoore1
-src/USER-CGSDK        @akohlmey
-src/USER-COLVARS      @giacomofiorin
-src/USER-OMP          @akohlmey
-src/USER-QMMM         @akohlmey
+# whole packages
+src/COMPRESS/*        @akohlmey
+src/GPU/*             @ndtrung81
+src/KOKKOS/*          @stanmoore1
+src/KIM/*             @ellio167
+src/LATTE/*           @cnegre
+src/SPIN/*            @julient31
+src/USER-CGDNA/*      @ohenrich
+src/USER-CGSDK/*      @akohlmey
+src/USER-COLVARS/*    @giacomofiorin
+src/USER-DPD/*        @timattox
+src/USER-INTEL/*      @wmbrownintel
+src/USER-MANIFOLD/*   @Pakketeretet2
+src/USER-MEAMC/*      @martok
+src/USER-MOFFF/*      @hheenen
+src/USER-MOLFILE/*    @akohlmey
+src/USER-NETCDF/*     @pastewka
+src/USER-PHONON/*     @lingtikong
+src/USER-OMP/*        @akohlmey
+src/USER-QMMM/*       @akohlmey
+src/USER-REAXC/*      @hasanmetin
+src/USER-TALLY/*      @akohlmey
+src/USER-UEF/*        @danicholson
+src/USER-VTK/*        @rbberger
+
+# individual files in packages
+src/GPU/pair_vashishta_gpu.*        @andeplane
+src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
+src/MANYBODY/pair_vashishta_table.* @andeplane
+src/USER-MISC/fix_bond_react.*      @jrgissing
+src/USER-MISC/*_grem.*              @dstelter92
 
 # tools
 tools/msi2lmp/*       @akohlmey
+tools/emacs/*         @HaoZeke
+
+# cmake
+cmake/*               @junghans @rbberger
+
+# python
+python/*              @rbberger
+
+# docs
+doc/utils/*/*         @rbberger
+doc/Makefile          @rbberger
+doc/README            @rbberger

README

@@ -25,7 +25,7 @@ The LAMMPS distribution includes the following files and directories:
 README			   this file
 LICENSE			   the GNU General Public License (GPL)
 bench			   benchmark problems
-couple			   code coupling examples using LAMMPS as a library
+cmake			   CMake build system
 doc			   documentation
 examples		   simple test problems
 lib			   libraries LAMMPS can be linked with
@@ -36,7 +36,14 @@ tools			   pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-doc/Manual.html	           the LAMMPS manual
-doc/Section_intro.html	   hi-level introduction to LAMMPS
-doc/Section_start.html	   how to build and use LAMMPS
-doc/Developer.pdf          LAMMPS developer guide
+http://lammps.sandia.gov/doc/Manual.html         the LAMMPS manual
+http://lammps.sandia.gov/doc/Intro.html          hi-level introduction
+http://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
+http://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
+http://lammps.sandia.gov/doc/Developer.pdf       LAMMPS developer guide
+
+You can also create these doc pages locally:
+
+% cd doc
+% make html                # creates HTML pages in doc/html
+% make pdf                 # creates Manual.pdf and Developer.pdf

cmake/Modules/FindFFTW2.cmake

@@ -1,22 +0,0 @@
-# - Find fftw2
-# Find the native FFTW2 headers and libraries.
-#
-#  FFTW2_INCLUDE_DIRS - where to find fftw2.h, etc.
-#  FFTW2_LIBRARIES    - List of libraries when using fftw2.
-#  FFTW2_FOUND        - True if fftw2 found.
-#
-
-find_path(FFTW2_INCLUDE_DIR fftw.h)
-
-find_library(FFTW2_LIBRARY NAMES fftw)
-
-set(FFTW2_LIBRARIES ${FFTW2_LIBRARY})
-set(FFTW2_INCLUDE_DIRS ${FFTW2_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set FFTW2_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(FFTW2 DEFAULT_MSG FFTW2_LIBRARY FFTW2_INCLUDE_DIR)
-
-mark_as_advanced(FFTW2_INCLUDE_DIR FFTW2_LIBRARY )

cmake/Modules/FindFFTW3F.cmake

@@ -0,0 +1,25 @@
+# - Find fftw3f
+# Find the native FFTW3F headers and libraries.
+#
+#  FFTW3F_INCLUDE_DIRS - where to find fftw3f.h, etc.
+#  FFTW3F_LIBRARIES    - List of libraries when using fftw3f.
+#  FFTW3F_FOUND        - True if fftw3f found.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_FFTW3F fftw3f)
+find_path(FFTW3F_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3F_INCLUDE_DIRS})
+
+find_library(FFTW3F_LIBRARY NAMES fftw3f HINTS ${PC_FFTW3F_LIBRARY_DIRS})
+
+set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
+set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set FFTW3F_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(FFTW3F DEFAULT_MSG FFTW3F_LIBRARY FFTW3F_INCLUDE_DIR)
+
+mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY )

cmake/Modules/FindMSCG.cmake

@@ -0,0 +1,22 @@
+# - Find mscg
+# Find the native MSCG headers and libraries.
+#
+#  MSCG_INCLUDE_DIRS - where to find mscg.h, etc.
+#  MSCG_LIBRARIES    - List of libraries when using mscg.
+#  MSCG_FOUND        - True if mscg found.
+#
+
+find_path(MSCG_INCLUDE_DIR mscg.h PATH_SUFFIXES mscg)
+
+find_library(MSCG_LIBRARY NAMES mscg)
+
+set(MSCG_LIBRARIES ${MSCG_LIBRARY})
+set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set MSCG_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(MSCG DEFAULT_MSG MSCG_LIBRARY MSCG_INCLUDE_DIR)
+
+mark_as_advanced(MSCG_INCLUDE_DIR MSCG_LIBRARY )

cmake/Modules/FindQUIP.cmake

@@ -1,8 +1,8 @@
 # - Find quip
 # Find the native QUIP libraries.
 #
-#  QUIP_LIBRARIES    - List of libraries when using fftw3.
-#  QUIP_FOUND        - True if fftw3 found.
+#  QUIP_LIBRARIES    - List of libraries of the QUIP package
+#  QUIP_FOUND        - True if QUIP library was found.
 #
 
 find_library(QUIP_LIBRARY NAMES quip)

cmake/Modules/FindTBB.cmake

@@ -0,0 +1,46 @@
+# - Find parts of TBB
+# Find the native TBB headers and libraries.
+#
+#  TBB_INCLUDE_DIRS - where to find tbb.h, etc.
+#  TBB_LIBRARIES    - List of libraries when using tbb.
+#  TBB_FOUND        - True if tbb found.
+#
+
+########################################################
+# TBB
+
+# TODO use more generic FindTBB
+
+find_path(TBB_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
+find_library(TBB_LIBRARY NAMES tbb PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
+                                         $ENV{TBBROOT}/lib/intel64/gcc4.4
+                                         $ENV{TBBROOT}/lib/intel64/gcc4.1)
+set(TBB_LIBRARIES ${TBB_LIBRARY})
+set(TBB_INCLUDE_DIRS ${TBB_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set TBB_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(TBB DEFAULT_MSG TBB_LIBRARY TBB_INCLUDE_DIR)
+
+mark_as_advanced(TBB_INCLUDE_DIR TBB_LIBRARY )
+
+########################################################
+# TBB Malloc
+
+find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
+find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
+                                                      $ENV{TBBROOT}/lib/intel64/gcc4.4
+                                                      $ENV{TBBROOT}/lib/intel64/gcc4.1)
+
+set(TBB_MALLOC_LIBRARIES ${TBB_MALLOC_LIBRARY})
+set(TBB_MALLOC_INCLUDE_DIRS ${TBB_MALLOC_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set TBB_MALLOC_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(TBB_MALLOC DEFAULT_MSG TBB_MALLOC_LIBRARY TBB_MALLOC_INCLUDE_DIR)
+
+mark_as_advanced(TBB_MALLOC_INCLUDE_DIR TBB_MALLOC_LIBRARY )

cmake/Modules/StyleHeaderUtils.cmake

@@ -45,14 +45,10 @@ function(FindStyleHeadersExt path style_class extension headers sources)
 endfunction(FindStyleHeadersExt)
 
 function(CreateStyleHeader path filename)
-    math(EXPR N "${ARGC}-2")
-
     set(temp "")
-    if(N GREATER 0)
-        math(EXPR ARG_END   "${ARGC}-1")
- 
-        foreach(IDX RANGE 2 ${ARG_END})
-            list(GET ARGV ${IDX} FNAME)
+    if(ARGC GREATER 2)
+        list(REMOVE_AT ARGV 0 1)
+        foreach(FNAME ${ARGV})
             get_filename_component(FNAME ${FNAME} NAME)
             set(temp "${temp}#include \"${FNAME}\"\n")
         endforeach()
@@ -107,35 +103,6 @@ function(RegisterStyles search_path)
     FindStyleHeaders(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
 endfunction(RegisterStyles)
 
-function(RemovePackageHeader headers pkg_header)
-    get_property(hlist GLOBAL PROPERTY ${headers})
-    list(REMOVE_ITEM hlist ${pkg_header})
-    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
-endfunction(RemovePackageHeader)
-
-function(DetectAndRemovePackageHeader fname)
-    RemovePackageHeader(ANGLE     ${fname})
-    RemovePackageHeader(ATOM_VEC  ${fname})
-    RemovePackageHeader(BODY      ${fname})
-    RemovePackageHeader(BOND      ${fname})
-    RemovePackageHeader(COMMAND   ${fname})
-    RemovePackageHeader(COMPUTE   ${fname})
-    RemovePackageHeader(DIHEDRAL  ${fname})
-    RemovePackageHeader(DUMP      ${fname})
-    RemovePackageHeader(FIX       ${fname})
-    RemovePackageHeader(IMPROPER  ${fname})
-    RemovePackageHeader(INTEGRATE ${fname})
-    RemovePackageHeader(KSPACE    ${fname})
-    RemovePackageHeader(MINIMIZE  ${fname})
-    RemovePackageHeader(NBIN      ${fname})
-    RemovePackageHeader(NPAIR     ${fname})
-    RemovePackageHeader(NSTENCIL  ${fname})
-    RemovePackageHeader(NTOPO     ${fname})
-    RemovePackageHeader(PAIR      ${fname})
-    RemovePackageHeader(READER    ${fname})
-    RemovePackageHeader(REGION    ${fname})
-endfunction(DetectAndRemovePackageHeader)
-
 function(RegisterStylesExt search_path extension sources)
     FindStyleHeadersExt(${search_path} ANGLE_CLASS     ${extension}  ANGLE     ${sources})
     FindStyleHeadersExt(${search_path} ATOM_CLASS      ${extension}  ATOM_VEC  ${sources})
@@ -181,3 +148,21 @@ function(GenerateStyleHeaders output_path)
     GenerateStyleHeader(${output_path} READER     reader    ) # read_dump
     GenerateStyleHeader(${output_path} REGION     region    ) # domain
 endfunction(GenerateStyleHeaders)
+
+function(DetectBuildSystemConflict lammps_src_dir)
+  if(ARGC GREATER 1)
+    list(REMOVE_AT ARGV 0)
+    foreach(SRC_FILE ${ARGV})
+        get_filename_component(FILENAME ${SRC_FILE} NAME)
+        if(EXISTS ${lammps_src_dir}/${FILENAME})
+            message(FATAL_ERROR "\n########################################################################\n"
+                                  "Found package(s) installed by the make-based build system\n"
+                                  "\n"
+                                  "Please run\n"
+                                  "make -C ${lammps_src_dir} no-all purge\n"
+                                  "to uninstall\n"
+                                  "########################################################################")
+        endif()
+    endforeach()
+  endif()
+endfunction(DetectBuildSystemConflict)

cmake/etc/profile.d/lammps.csh.in

@@ -0,0 +1,2 @@
+# set environment for LAMMPS executables to find potential files
+if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@

cmake/etc/profile.d/lammps.sh.in

@@ -0,0 +1,2 @@
+# set environment for LAMMPS executables to find potential files
+export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}

cmake/pkgconfig/liblammps.pc.in

@@ -13,6 +13,6 @@ Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
 URL: http://lammps.sandia.gov
 Version:
 Requires:
-Libs: -L${libdir} -llammps@LAMMPS_MACHINE@
+Libs: -L${libdir} -llammps@LIB_SUFFIX@@
 Libs.private: -lm
 Cflags: -I${includedir} @LAMMPS_API_DEFINES@

cmake/presets/all_off.cmake

@@ -0,0 +1,22 @@
+set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+                      MOLECULE MPIIO MSCG OPT PERI POEMS
+                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+
+set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
+                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-UEF USER-VTK)
+
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
+                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
+                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+
+set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} OFF CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/all_on.cmake

@@ -0,0 +1,22 @@
+set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+                      MOLECULE MPIIO MSCG OPT PERI POEMS
+                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+
+set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
+                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-UEF USER-VTK)
+
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
+                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
+                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+
+set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/manual_selection.cmake

@@ -0,0 +1,69 @@
+set(PKG_ASPHERE OFF CACHE BOOL "" FORCE)
+set(PKG_BODY OFF CACHE BOOL "" FORCE)
+set(PKG_CLASS2 OFF CACHE BOOL "" FORCE)
+set(PKG_COLLOID OFF CACHE BOOL "" FORCE)
+set(PKG_COMPRESS OFF CACHE BOOL "" FORCE)
+set(PKG_CORESHELL OFF CACHE BOOL "" FORCE)
+set(PKG_DIPOLE OFF CACHE BOOL "" FORCE)
+set(PKG_GPU OFF CACHE BOOL "" FORCE)
+set(PKG_GRANULAR OFF CACHE BOOL "" FORCE)
+set(PKG_KIM OFF CACHE BOOL "" FORCE)
+set(PKG_KOKKOS OFF CACHE BOOL "" FORCE)
+set(PKG_KSPACE OFF CACHE BOOL "" FORCE)
+set(PKG_LATTE OFF CACHE BOOL "" FORCE)
+set(PKG_LIB OFF CACHE BOOL "" FORCE)
+set(PKG_MANYBODY OFF CACHE BOOL "" FORCE)
+set(PKG_MC OFF CACHE BOOL "" FORCE)
+set(PKG_MEAM OFF CACHE BOOL "" FORCE)
+set(PKG_MISC OFF CACHE BOOL "" FORCE)
+set(PKG_MOLECULE OFF CACHE BOOL "" FORCE)
+set(PKG_MPIIO OFF CACHE BOOL "" FORCE)
+set(PKG_MSCG OFF CACHE BOOL "" FORCE)
+set(PKG_OPT OFF CACHE BOOL "" FORCE)
+set(PKG_PERI OFF CACHE BOOL "" FORCE)
+set(PKG_POEMS OFF CACHE BOOL "" FORCE)
+set(PKG_PYTHOFF OFF CACHE BOOL "" FORCE)
+set(PKG_QEQ OFF CACHE BOOL "" FORCE)
+set(PKG_REAX OFF CACHE BOOL "" FORCE)
+set(PKG_REPLICA OFF CACHE BOOL "" FORCE)
+set(PKG_RIGID OFF CACHE BOOL "" FORCE)
+set(PKG_SHOCK OFF CACHE BOOL "" FORCE)
+set(PKG_SNAP OFF CACHE BOOL "" FORCE)
+set(PKG_SRD OFF CACHE BOOL "" FORCE)
+set(PKG_VOROFFOI OFF CACHE BOOL "" FORCE)
+
+set(PKG_USER OFF CACHE BOOL "" FORCE)
+set(PKG_USER-ATC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-AWPMD OFF CACHE BOOL "" FORCE)
+set(PKG_USER-BOCS OFF CACHE BOOL "" FORCE)
+set(PKG_USER-CGDNA OFF CACHE BOOL "" FORCE)
+set(PKG_USER-CGSDK OFF CACHE BOOL "" FORCE)
+set(PKG_USER-COLVARS OFF CACHE BOOL "" FORCE)
+set(PKG_USER-DIFFRACTIOFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-DPD OFF CACHE BOOL "" FORCE)
+set(PKG_USER-DRUDE OFF CACHE BOOL "" FORCE)
+set(PKG_USER-EFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-FEP OFF CACHE BOOL "" FORCE)
+set(PKG_USER-H5MD OFF CACHE BOOL "" FORCE)
+set(PKG_USER-INTEL OFF CACHE BOOL "" FORCE)
+set(PKG_USER-LB OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MANIFOLD OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MEAMC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MESO OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MGPT OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MISC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
+set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
+set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
+set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
+set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
+set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
+set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
+set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)
+set(PKG_USER-TALLY OFF CACHE BOOL "" FORCE)
+set(PKG_USER-UEF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-VTK OFF CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -0,0 +1,22 @@
+set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+                      MOLECULE MPIIO MSCG OPT PERI POEMS
+                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+
+set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
+                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-UEF USER-VTK)
+
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
+                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
+                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+
+set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
+
+foreach(PKG ${PACKAGES_WITH_LIB})
+  set(PKG_${PKG} OFF CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/std.cmake

@@ -0,0 +1,22 @@
+set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+                      MOLECULE MPIIO MSCG OPT PERI POEMS
+                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+
+set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
+                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-UEF USER-VTK)
+
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
+                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
+                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+
+set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
+
+foreach(PKG ${STANDARD_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/std_nolib.cmake

@@ -0,0 +1,26 @@
+set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+                      MOLECULE MPIIO MSCG OPT PERI POEMS
+                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+
+set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
+                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-UEF USER-VTK)
+
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
+                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
+                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+
+set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
+
+foreach(PKG ${STANDARD_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()
+
+foreach(PKG ${PACKAGES_WITH_LIB})
+  set(PKG_${PKG} OFF CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/user.cmake

@@ -0,0 +1,22 @@
+set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+                      MOLECULE MPIIO MSCG OPT PERI POEMS
+                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+
+set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
+                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-UEF USER-VTK)
+
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
+                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
+                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+
+set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
+
+foreach(PKG ${USER_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()

doc/Makefile

@@ -9,6 +9,7 @@ TXT2RST       = $(VENV)/bin/txt2rst
 ANCHORCHECK   = $(VENV)/bin/doc_anchor_check
 
 PYTHON        = $(shell which python3)
+VIRTUALENV     = virtualenv
 HAS_PYTHON3    = NO
 HAS_VIRTUALENV = NO
 
@@ -16,7 +17,13 @@ ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
 HAS_PYTHON3 = YES
 endif
 
+ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0)
+VIRTUALENV     = virtualenv-3
+HAS_VIRTUALENV = YES
+endif
+
 ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
+VIRTUALENV     = virtualenv
 HAS_VIRTUALENV = YES
 endif
 
@@ -42,11 +49,11 @@ help:
 
 # ------------------------------------------
 
-clean-all:
+clean-all: clean
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
 
 clean:
-	rm -rf $(RSTDIR) html
+	rm -rf $(RSTDIR) html old epub
 	rm -rf spelling
 
 clean-spelling:
@@ -150,7 +157,7 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
 	@(\
 		mkdir -p $(RSTDIR) ; \
 		. $(VENV)/bin/activate ;\
-		txt2rst $< > $@ ;\
+		txt2rst -v $< > $@ ;\
 		deactivate ;\
 	)
 
@@ -158,7 +165,7 @@ $(VENV):
 	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@( \
-		virtualenv -p $(PYTHON) $(VENV); \
+		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install Sphinx; \
 		pip install sphinxcontrib-images; \

doc/src/Build.txt

@@ -0,0 +1,49 @@
+"Previous Section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run_head.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Build LAMMPS :h2
+
+LAMMPS can be built as an executable or library from source code via
+either traditional makefiles (which may require manual editing)
+for use with GNU make or gmake, or a build environment generated by CMake
+(Unix Makefiles, Xcode, Visual Studio, KDevelop or more).  As an
+alternative you can download a package with pre-built executables
+as described on the "Install"_Install.html doc page.
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   Build_cmake
+   Build_make
+   Build_link
+   Build_basics
+   Build_settings
+   Build_package
+   Build_extras
+   Build_windows
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Build LAMMPS with CMake"_Build_cmake.html
+"Build LAMMPS with make"_Build_make.html
+"Link LAMMPS as a library to another code"_Build_link.html
+"Basic build options"_Build_basics.html
+"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)
+
+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
+help.  If you're still stuck, send an email to the "LAMMPS mail
+list"_http://lammps.sandia.gov/mail.html.

doc/src/Build_basics.txt

@@ -0,0 +1,315 @@
+"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
+
+Basic build options :h3
+
+The following topics are covered on this page, for building both with
+CMake and make:
+
+"Serial vs parallel build"_#serial
+"Choice of compiler and compile/link options"_#compile
+"Build LAMMPS as an executable or a library"_#exe
+"Build the LAMMPS documentation"_#doc
+"Install LAMMPS after a build"_#install :ul
+
+:line
+
+Serial vs parallel build :h4,link(serial)
+
+LAMMPS can be built to run in parallel using the ubiquitous "MPI
+(message-passing
+interface)"_https://en.wikipedia.org/wiki/Message_Passing_Interface
+library.  Or it can built to run on a single processor (serial)
+without MPI.  It can also be built with support for OpenMP threading
+(see more discussion below).
+
+[CMake variables]:
+
+-D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
+-D BUILD_OMP=value        # yes or no (default)
+-D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
+                          # no default value :pre
+
+The executable created by CMake (after running make) is lmp_name.  If
+the LAMMPS_MACHINE variable is not specified, the executable is just
+lmp.  Using BUILD_MPI=no will produce a serial executable.
+
+[Traditional make]:
+
+cd lammps/src
+make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
+make serial             # serial build, produces lmp_serial using Makefile/serial
+make mybox :pre         # uses Makefile.mybox to produce lmp_mybox :pre
+
+Serial build (see src/MAKE/Makefile.serial):
+
+MPI_INC =       -I../STUBS 
+MPI_PATH =      -L../STUBS
+MPI_LIB =	-lmpi_stubs :pre
+
+For a parallel build, if MPI is installed on your system in the usual
+place (e.g. under /usr/local), you do not need to specify the 3
+variables MPI_INC, MPI_PATH, MPI_LIB.  The MPI wrapper on the compiler
+(e.g. mpicxx, mpiCC) knows where to find the needed include and
+library files.  Failing this, these 3 variables can be used to specify
+where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH)
+are found, and the name of the library files (MPI_LIB).
+
+For a serial build, you need to specify the 3 varaibles, as shown
+above.
+
+For a serial LAMMPS build, use the dummy MPI library provided in
+src/STUBS.  You also need to build the STUBS library for your platform
+before making LAMMPS itself.  A "make serial" build does this for.
+Otherwise, type "make mpi-stubs" from the src directory, or "make"
+from the src/STUBS dir.  If the build fails, you will need to edit the
+STUBS/Makefile for your platform.
+
+The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
+that calls gettimeofday() .  If your system doesn't support
+gettimeofday() , you'll need to insert code to call another timer.
+Note that the ANSI-standard function clock() rolls over after an hour
+or so, and is therefore insufficient for timing long LAMMPS
+simulations.
+
+[CMake and make info]:
+
+If you are installing MPI yourself, we recommend MPICH2 from Argonne
+National Laboratory or OpenMPI.  MPICH can be downloaded from the
+"Argonne MPI site"_http://www.mcs.anl.gov/research/projects/mpich2/.
+OpenMPI can be downloaded from the "OpenMPI
+site"_http://www.open-mpi.org.  Other MPI packages should also work.
+If you are running on a large parallel machine, your system admins or
+the vendor should have already installed a version of MPI, which is
+likely to be faster than a self-installed MPICH or OpenMPI, so find
+out how to build and link with it.
+
+The majority of OpenMP (threading) support in LAMMPS is provided by
+the USER-OMP package; see the "Speed omp"_Speed_omp.html doc page for
+details. The USER-INTEL package also provides OpenMP support (it is
+compatible with USER-OMP) and adds vectorization support when compiled
+with the Intel compilers on top of that. Also, the KOKKOS package can
+be compiled for using OpenMP threading.
+
+However, there are a few commands in LAMMPS that have native OpenMP
+support.  These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
+USER-DPD packages.  In addition some packages support OpenMP threading
+indirectly through the libraries they interface to: e.g. LATTE and
+USER-COLVARS.  See the "Packages details"_Packages_details.html doc
+page for more info on these packages and the doc pages for their
+respective commands for OpenMP threading info.
+
+For CMake, if you use BUILD_OMP=yes, you can use these packages and
+turn on their native OpenMP support and turn on their native OpenMP
+support at run time, by setting the OMP_NUM_THREADS environment
+variable before you launch LAMMPS.
+
+For building via conventional make, the CCFLAGS and LINKFLAGS
+variables in Makefile.machine need to include the compiler flag that
+enables OpenMP. For GNU compilers it is -fopenmp.  For (recent) Intel
+compilers it is -qopenmp.  If you are using a different compiler,
+please refer to its documentation.
+
+:line
+
+Choice of compiler and compile/link options :h4,link(compile)
+
+The choice of compiler and compiler flags can be important for
+performance.  Vendor compilers can produce faster code than
+open-source compilers like GNU.  On boxes with Intel CPUs, we suggest
+trying the "Intel C++ compiler"_intel.
+
+:link(intel,https://software.intel.com/en-us/intel-compilers)
+
+On parallel clusters or supercomputers which use "modules" for their
+compile/link environments, you can often access different compilers by
+simply loading the appropriate module before building LAMMPS.
+
+[CMake variables]:
+
+-D CMAKE_CXX_COMPILER=name            # name of C++ compiler
+-D CMAKE_C_COMPILER=name              # name of C compiler
+-D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler :pre
+
+-D CMAKE_CXX_FlAGS=string             # flags to use with C++ compiler
+-D CMAKE_C_FlAGS=string               # flags to use with C compiler
+-D CMAKE_Fortran_FlAGS=string         # flags to use with Fortran compiler :pre
+
+By default CMake will use a compiler it finds and it will add
+optimization flags appropriate to that compiler and any "accelerator
+packages"_Speed_packages.html you have included in the build.
+
+You can tell CMake to look for a specific compiler with these varaible
+settings.  Likewise you can specify the FLAGS variables if you want to
+experiment with alternate optimization flags.  You should specify all
+3 compilers, so that the small number of LAMMPS source files written
+in C or Fortran are built with a compiler consistent with the one used
+for all the C++ files:
+
+Building with GNU Compilers:
+cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
+Building with Intel Compilers:
+cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+Building with LLVM/Clang Compilers:
+cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang :pre
+
+NOTE: When the cmake command completes, it prints info to the screen
+as to which compilers it is using, and what flags will be used in the
+compilation.  Note that if the top-level compiler is mpicxx, it is
+simply a wrapper on a real compiler.  The underlying compiler info is
+what will be listed in the CMake output.  You should check to insure
+you are using the compiler and optimization flags are the ones you
+want.
+
+[Makefile.machine settings]:
+
+Parallel build (see src/MAKE/Makefile.mpi):
+
+CC =		mpicxx
+CCFLAGS =	-g -O3 
+LINK =		mpicxx
+LINKFLAGS =	-g -O :pre
+
+Serial build (see src/MAKE/Makefile.serial):
+
+CC =		g++
+CCFLAGS =	-g -O3
+LINK =		g++
+LINKFLAGS =	-g -O :pre
+
+The "compiler/linker settings" section of a Makefile.machine lists
+compiler and linker settings for your C++ compiler, including
+optimization flags.  You should always use mpicxx or mpiCC for
+a parallel build, since these compiler wrappers will include
+a variety of settings appropriate for your MPI installation.
+
+NOTE: If you build LAMMPS with any "accelerator
+packages"_Speed_packages.html included, they have specific
+optimization flags that are either required or recommended for optimal
+performance.  You need to include these in the CCFLAGS and LINKFLAGS
+settings above.  For details, see the individual package doc pages
+listed on the "Speed packages"_Speed_packages.html doc page.  Or
+examine these files in the src/MAKE/OPTIONS directory.  They
+correspond to each of the 5 accelerator packages and their hardware
+variants:
+
+Makefile.opt                   # OPT package
+Makefile.omp                   # USER-OMP package
+Makefile.intel_cpu             # USER-INTEL package for CPUs
+Makefile.intel_coprocessor     # USER-INTEL package for KNLs
+Makefile.gpu                   # GPU package
+Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
+Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
+Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP) :pre
+
+:line
+
+Build LAMMPS as an executable or a library :h4,link(exe)
+
+LAMMPS can be built as either an executable or as a static or shared
+library.  The LAMMPS library can be called from another application or
+a scripting language.  See the "Howto couple"_Howto_couple.html doc
+page for more info on coupling LAMMPS to other codes.  See the
+"Python"_Python doc page for more info on wrapping and running LAMMPS
+from Python via its library interface.
+
+[CMake variables]:
+
+-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
+
+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.
+
+[Traditional make]:
+
+cd lammps/src
+make machine               # build LAMMPS executable lmp_machine
+make mode=lib machine      # build LAMMPS static lib liblammps_machine.a
+make mode=shlib machine    # build LAMMPS shared lib liblammps_machine.so :pre
+
+The two library builds also create generic soft links, named
+liblammps.a and liblammps.so, which point to the liblammps_machine
+files.
+
+[CMake and make info]:
+
+Note that for a shared library to be usable by a calling program, all
+the auxiliary libraries it depends on must also exist as shared
+libraries.  This will be the case for libraries included with LAMMPS,
+such as the dummy MPI library in src/STUBS or any package libraries in
+the lib/packages directroy, since they are always built as shared
+libraries using the -fPIC switch.  However, if a library like MPI or
+FFTW does not exist as a shared library, the shared library build will
+generate an error.  This means you will need to install a shared
+library version of the auxiliary library.  The build instructions for
+the library should tell you how to do this.
+
+As an example, here is how to build and install the "MPICH
+library"_mpich, a popular open-source version of MPI, distributed by
+Argonne National Lab, as a shared library in the default
+/usr/local/lib location:
+
+:link(mpich,http://www-unix.mcs.anl.gov/mpi)
+
+./configure --enable-shared
+make
+make install :pre
+
+You may need to use "sudo make install" in place of the last line if
+you do not have write privileges for /usr/local/lib.  The end result
+should be the file /usr/local/lib/libmpich.so.
+
+:line
+
+Build the LAMMPS documentation :h4,link(doc)
+
+[CMake variable]:
+
+-D BUILD_DOC=value       # yes or no (default) :pre
+
+This will create the HTML doc pages within the CMake build directory.
+The reason to do this is if you want to "install" LAMMPS on a system
+after the CMake build via "make install", and include the doc pages in
+the install.
+
+[Traditional make]:
+
+cd lammps/doc
+make html       # html doc pages
+make pdf        # single Manual.pdf file :pre
+
+This will create a lammps/doc/html dir with the HTML doc pages so that
+you can browse them locally on your system.  Type "make" from the
+lammps/doc dir to see other options.
+
+:line
+
+Install LAMMPS after a build :h4,link(install)
+
+After building LAMMPS, you may wish to copy the LAMMPS executable of
+library, along with other LAMMPS files (library header, doc files) to
+a globally visible place on your system, for others to access.  Note
+that you may need super-user priveleges (e.g. sudo) if the directory
+you want to copy files to is protected.
+
+[CMake variable]:
+
+cmake -D CMAKE_INSTALL_PREFIX=path \[options ...\] ../cmake
+make                        # perform make after CMake command
+make install                # perform the installation into prefix :pre
+
+[Traditional make]:
+
+There is no "install" option in the src/Makefile for LAMMPS.  If you
+wish to do this you will need to first build LAMMPS, then manually
+copy the desired LAMMPS files to the appropriate system directories.

doc/src/Build_cmake.txt

@@ -0,0 +1,196 @@
+"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
+
+Build LAMMPS with CMake :h3
+
+This page is a short summary of how to use CMake to build LAMMPS.
+Details on CMake variables that enable specific LAMMPS build options
+are given on the pages linked to from the "Build"_Build.html doc page.
+
+Richard Berger (Temple U) has also written a "more comprehensive
+guide"_https://github.com/lammps/lammps/blob/master/cmake/README.md
+for how to use CMake to build LAMMPS.  If you are new to CMake it is a
+good place to start.
+
+:line
+
+Building LAMMPS with CMake is a two-step process.  First you use CMake
+to create a build environment in a new directory.  On Linux systems,
+this will be based on makefiles for use with make.  Then you use the
+make command to build LAMMPS, which uses the created
+Makefile(s). Example:
+
+cd lammps                        # change to the LAMMPS distribution directory
+mkdir build; cd build            # create a new directory (folder) for build       
+cmake ../cmake \[options ...\]   # configuration with (command-line) cmake
+make                             # compilation :pre
+
+The cmake command will detect available features, enable selected
+packages and options, and will generate the build environment.  The make
+command will then compile and link LAMMPS, producing (by default) an
+executable called "lmp" and a library called "liblammps.a" in the
+"build" folder.
+
+If your machine has multiple CPU cores (most do these days), using a
+command like "make -jN" (with N being the number of available local
+CPU cores) can be much faster.  If you plan to do development on
+LAMMPS or need to recompile LAMMPS repeatedly, installation of the
+ccache (= Compiler Cache) software may speed up compilation even more.
+
+After compilation, you can optionally copy the LAMMPS executable and
+library into your system folders (by default under /usr/local) with:
+
+make install    # optional, copy LAMMPS executable & library elsewhere :pre
+
+:line
+
+There are 3 variants of CMake: a command-line verison (cmake), a text mode
+UI version (ccmake), and a graphical GUI version (cmake-GUI).  You can use
+any of them interchangeably to configure and create the LAMMPS build
+environment.  On Linux all the versions produce a Makefile as their
+output.  See more details on each below.
+
+You can specify a variety of options with any of the 3 versions, which
+affect how the build is performed and what is included in the LAMMPS
+executable.  Links to pages explaining all the options are listed on
+the "Build"_Build.html doc page.
+
+You must perform the CMake build system generation and compilation in
+a new directory you create.  It can be anywhere on your local machine.
+In these Build pages we assume that you are building in a directory
+called "lammps/build".  You can perform separate builds independently
+with different options, so long as you perform each of them in a
+separate directory you create.  All the auxiliary files created by one
+build process (executable, object files, log files, etc) are stored in
+this directory or sub-directories within it that CMake creates.
+
+NOTE: To perform a CMake build, no packages can be installed or a
+build been previously attempted in the LAMMPS src directory by using
+"make" commands to "perform a conventional LAMMPS
+build"_Build_make.html.  CMake detects if this is the case and
+generates an error, telling you to type "make no-all purge" in the src
+directory to un-install all packages.  The purge removes all the *.h
+files auto-generated by make.
+
+You must have CMake version 2.8 or later on your system to build
+LAMMPS.  A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
+later version.  CMake will print a message telling you if a later
+version is required.  Installation instructions for CMake are below.
+
+After the initial build, if you edit LAMMPS source files, or add your
+own new files to the source directory, you can just re-type make from
+your build directory and it will re-compile only the files that have
+changed.  If you want to change CMake options you can run cmake (or
+ccmake or cmake-gui) again from the same build directory and alter
+various options; see details below.  Or you can remove the entire build
+folder, recreate the directory and start over.
+
+:line
+
+[Command-line version of CMake]:
+
+cmake \[options ...\] /path/to/lammps/cmake  # build from any dir
+cmake \[options ...\] ../cmake               # build from lammps/build :pre
+
+The cmake command takes one required argument, which is the LAMMPS
+cmake directory which contains the CMakeLists.txt file.
+
+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
+-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 :pre
+
+All the LAMMPS-specific -D variables that a LAMMPS build supports are
+described on the pages linked to from the "Build"_Build.html doc page.
+All of these variable names are upper-case and their values are
+lower-case, e.g. -D LAMMPS_SIZES=smallbig.  For boolean values, any of
+these forms can be used: yes/no, on/off, 1/0.
+
+On Unix/Linux machines, CMake generates a Makefile by default to
+perform the LAMMPS build.  Alternate forms of build info can be
+generated via the -G switch, e.g. Visual Studio on a Windows machine,
+Xcode on MacOS, or KDevelop on Linux.  Type "cmake --help" to see the
+"Generator" styles of output your system supports.
+
+NOTE: When CMake runs, it prints configuration info to the screen.
+You should review this to verify all the features you requested were
+enabled, including packages.  You can also see what compilers and
+compile options will be used for the build.  Any errors in CMake
+variable syntax will also be flagged, e.g. mis-typed variable names or
+variable values.
+
+CMake creates a CMakeCache.txt file when it runs.  This stores all the
+settings, so that when running CMake again you can use the current
+folder '.' instead of the path to the LAMMPS cmake folder as the
+required argument to the CMake command. Either way the existing
+settings will be inherited unless the CMakeCache.txt file is removed.
+
+If you later want to change a setting you can rerun cmake in the build
+directory with different setting. Please note that some automatically
+detected variables will not change their value when you rerun cmake.
+In these cases it is usually better to first remove all the
+files/directories in the build directory, or start with a fresh build
+directory.
+
+:line
+
+[Curses version (terminal-style menu) of CMake]:
+
+ccmake ../cmake :pre
+
+You initiate the configuration and build environment generation steps
+separately. For the first you have to type [c], for the second you
+have to type [g]. You may need to type [c] multiple times, and may be
+required to edit some of the entries of CMake configuration variables
+in between.  Please see the "ccmake
+manual"_https://cmake.org/cmake/help/latest/manual/ccmake.1.html for
+more information.
+
+:line
+
+[GUI version of CMake]:
+
+cmake-gui ../cmake :pre
+
+You initiate the configuration and build environment generation steps
+separately. For the first you have to click on the [Configure] button,
+for the second you have to click on the [Generate] button.  You may
+need to click on [Configure] multiple times, and may be required to
+edit some of the entries of CMake configuration variables in between.
+Please see the "cmake-gui
+manual"_https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html
+for more information.
+
+:line
+
+[Installing CMake]
+
+Check if your machine already has CMake installed:
+
+which cmake             # do you have it?
+which cmake3            # version 3 may have this name
+cmake --version         # what specific version you have :pre
+
+On clusters or supercomputers which use environment modules to manage
+software packages, do this:
+
+module list            # is a cmake module already loaded?
+module avail           # is a cmake module available?
+module load cmake3     # load cmake module with appropriate name :pre
+
+Most Linux distributions offer precompiled cmake packages through
+their package management system. If you do not have CMake or a new
+enough version, you can download the latest version at
+"https://cmake.org/download/"_https://cmake.org/download/.
+Instructions on how to install it on various platforms can be found
+"on this page"_https://cmake.org/install/.

doc/src/Build_extras.txt

@@ -0,0 +1,952 @@
+"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
+
+Packages with extra build options :h3
+
+When building with some packages, additional steps may be required,
+in addition to:
+
+-D PKG_NAME=yes    # CMake
+make yes-name      # make :pre
+
+as described on the "Build_package"_Build_package.html doc page.
+
+For a CMake build there may be additional optional or required
+variables to set.  For a build with make, a provided library under the
+lammps/lib directory may need to be built first.  Or an external
+library may need to exist on your system or be downloaded and built.
+You may need to tell LAMMPS where it is found on your system.
+
+This is the list of packages that may require additional steps.
+
+"COMPRESS"_#compress,
+"GPU"_#gpu,
+"KIM"_#kim,
+"KOKKOS"_#kokkos,
+"LATTE"_#latte,
+"MEAM"_#meam,
+"MSCG"_#mscg,
+"OPT"_#opt,
+"POEMS"_#poems,
+"PYTHON"_#python,
+"REAX"_#reax,
+"VORONOI"_#voronoi,
+"USER-ATC"_#user-atc,
+"USER-AWPMD"_#user-awpmd,
+"USER-COLVARS"_#user-colvars,
+"USER-H5MD"_#user-h5md,
+"USER-INTEL"_#user-intel,
+"USER-MOLFILE"_#user-molfile,
+"USER-NETCDF"_#user-netcdf,
+"USER-OMP"_#user-omp,
+"USER-QMMM"_#user-qmmm,
+"USER-QUIP"_#user-quip,
+"USER-SMD"_#user-smd,
+"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l)
+
+:line
+
+COMPRESS package :h4,link(compress)
+
+To build with this package you must have the zlib compression library
+available on your system.
+
+[CMake build]:
+
+If CMake cannot find the library, you can set these variables:
+
+-D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file 
+-D ZLIB_LIBRARIES=path      # path to libz.a (.so) file :pre
+
+[Traditional make]:
+
+If make cannot find the library, you can edit the
+lib/compress/Makefile.lammps file to specify the paths and library
+name.
+
+:line
+
+GPU package :h4,link(gpu)
+
+To build with this package, you must choose options for precision and
+which GPU hardware to build for.
+
+[CMake build]:
+
+-D GPU_API=value      # value = opencl (default) or cuda
+-D GPU_PREC=value     # precision setting
+                      # value = double or mixed (default) or single
+-D OCL_TUNE=value     # hardware choice for GPU_API=opencl
+                      # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
+-D GPU_ARCH=value     # hardware choice for GPU_API=cuda
+                      # value = sm_XX, see below
+                      # default is Cuda-compiler dependent, but typically sm_20
+-D CUDPP_OPT=value    # optimization setting for GPU_API=cudea
+                      # enables CUDA Performance Primitives Optimizations
+                      # yes (default) or no :pre
+
+GPU_ARCH settings for different GPU hardware is as follows:
+
+sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0) or GeForce GTX 580 or similar
+sm_30 for Kepler (K10)
+sm_35 for Kepler (K40) or GeForce GTX Titan or similar
+sm_37 for Kepler (dual K80)
+sm_50 for Maxwell
+sm_60 for Pascal (P100)
+sm_70 for Volta :ul
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the GPU library in lib/gpu.
+You can do this manually if you prefer; follow the instructions in
+lib/gpu/README.  Note that the GPU library uses MPI calls, so you must
+use the same MPI library (or the STUBS library) settings as the main
+LAMMPS code.  This also applies to the -DLAMMPS_BIGBIG,
+-DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL settings in whichever
+Makefile you use.
+
+You can also build the library in one step from the lammps/src dir,
+using a command like these, which simply invoke the lib/gpu/Install.py
+script with the specified args:
+
+make lib-gpu               # print help message
+make lib-gpu args="-b"     # build GPU library with default Makefile.linux
+make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
+make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi :pre
+
+Note that this procedure starts with a Makefile.machine in lib/gpu, as
+specified by the "-m" switch.  For your convenience, machine makefiles
+for "mpi" and "serial" are provided, which have the same settings as
+the corresponding machine makefiles in the main LAMMPS source
+folder. In addition you can alter 4 important settings in the
+Makefile.machine you start from via the corresponding -h, -a, -p, -e
+switches (as in the examples above), and also save a copy of the new
+Makefile if desired:
+
+CUDA_HOME = where NVIDIA CUDA software is installed on your system
+CUDA_ARCH = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above
+CUDA_PRECISION = precision (double, mixed, single)
+EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
+
+If the library build is successful, 3 files should be created:
+lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and
+lib/gpu/Makefile.lammps.  The latter has settings that enable LAMMPS
+to link with CUDA libraries.  If the settings in Makefile.lammps for
+your machine are not correct, the LAMMPS build will fail, and
+lib/gpu/Makefile.lammps may need to be edited.
+
+NOTE: If you re-build the GPU library in lib/gpu, you should always
+un-install the GPU package in lammps/src, then re-install it and
+re-build LAMMPS.  This is because the compilation of files in the GPU
+package uses the library settings from the lib/gpu/Makefile.machine
+used to build the GPU library.
+
+:line
+ 
+KIM package :h4,link(kim)
+
+To build with this package, the KIM library must be downloaded and
+built on your system.  It must include the KIM models that you want to
+use with LAMMPS.
+
+Note that in LAMMPS lingo, a KIM model driver is a pair style
+(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
+element or alloy and set of parameters, e.g. EAM for Cu with a
+specific EAM potential file.  Also note that installing the KIM API
+library with all its models, may take around 30 min to build.  Of
+course you only need to do that once.
+
+See the list of KIM model drivers here:
+https://openkim.org/kim-items/model-drivers/alphabetical
+
+See the list of all KIM models here:
+https://openkim.org/kim-items/models/by-model-drivers
+
+See the list of example KIM models included by default here:
+https://openkim.org/kim-api on the "What is in the KIM API source
+package?" page.
+
+[CMake build]:
+
+-D DOWNLOAD_KIM=value    # download OpenKIM API v1 for build, value = no (default) or yes
+-D KIM_LIBRARY=path      # KIM library file (only needed if a custom location) 
+-D KIM_INCLUDE_DIR=path  # KIM include directory (only needed if a custom location) :pre
+
+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), KIM_LIBRARY is the
+filename (plus path) of the KIM library file, not the directory the
+library file is in.  KIM_INCLUDE_DIR is the directory the KIM include
+file is in.
+
+[Traditional make]:
+
+You can download and build the KIM library manually if you prefer;
+follow the instructions in lib/kim/README.  You can also do it in one
+step from the lammps/src dir, using a command like these, which simply
+invoke the lib/kim/Install.py script with the specified args.
+
+make lib-kim              # print help message
+make lib-kim args="-b "   # (re-)install KIM API lib with only example models
+make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+make lib-kim args="-b -a everything"     # install KIM API lib with all models
+make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
+make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
+make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
+
+:line
+
+KOKKOS package :h4,link(kokkos)
+
+To build with this package, you must choose which hardware you want to
+build for, either CPUs (multi-threading via OpenMP) or KNLs (OpenMP)
+or GPUs (NVIDIA Cuda).
+
+For a CMake or make build, these are the possible choices for the
+KOKKOS_ARCH settings described below.  Note that for CMake, these are
+really Kokkos variables, not LAMMPS variables.  Hence you must use
+case-sensitive values, e.g. BDW, not bdw.
+
+ARMv80 = ARMv8.0 Compatible CPU
+ARMv81 = ARMv8.1 Compatible CPU
+ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
+BGQ = IBM Blue Gene/Q CPUs
+Power8 = IBM POWER8 CPUs
+Power9 = IBM POWER9 CPUs
+SNB = Intel Sandy/Ivy Bridge CPUs
+HSW = Intel Haswell CPUs
+BDW = Intel Broadwell Xeon E-class CPUs
+SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
+KNC = Intel Knights Corner Xeon Phi
+KNL = Intel Knights Landing Xeon Phi
+Kepler30 = NVIDIA Kepler generation CC 3.0
+Kepler32 = NVIDIA Kepler generation CC 3.2
+Kepler35 = NVIDIA Kepler generation CC 3.5
+Kepler37 = NVIDIA Kepler generation CC 3.7
+Maxwell50 = NVIDIA Maxwell generation CC 5.0
+Maxwell52 = NVIDIA Maxwell generation CC 5.2
+Maxwell53 = NVIDIA Maxwell generation CC 5.3
+Pascal60 = NVIDIA Pascal generation CC 6.0
+Pascal61 = NVIDIA Pascal generation CC 6.1 :ul
+
+[CMake build]:
+
+For multicore CPUs using OpenMP, set these 2 variables.
+
+-D KOKKOS_ARCH=archCPU         # archCPU = CPU from list above
+-D KOKKOS_ENABLE_OPENMP=yes :pre
+
+For Intel KNLs using OpenMP, set these 2 variables:
+
+-D KOKKOS_ARCH=KNL
+-D KOKKOS_ENABLE_OPENMP=yes :pre
+
+For NVIDIA GPUs using CUDA, set these 4 variables:
+
+-D KOKKOS_ARCH="archCPU;archGPU"   # archCPU = CPU from list above that is hosting the GPU
+                                   # archGPU = GPU from list above
+-D KOKKOS_ENABLE_CUDA=yes
+-D KOKKOS_ENABLE_OPENMP=yes 
+-D CMAKE_CXX_COMPILER=wrapper      # wrapper = full path to Cuda nvcc wrapper :pre
+
+The wrapper value is the Cuda nvcc compiler wrapper provided in the
+Kokkos library: lib/kokkos/bin/nvcc_wrapper.  The setting should
+include the full path name to the wrapper, e.g.
+
+-D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper :pre
+
+[Traditional make]:
+
+Choose which hardware to support in Makefile.machine via
+KOKKOS_DEVICES and KOKKOS_ARCH settings.  See the
+src/MAKE/OPTIONS/Makefile.kokkos* files for examples.
+
+For multicore CPUs using OpenMP:
+
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = archCPU      # archCPU = CPU from list above :pre
+
+For Intel KNLs using OpenMP:
+
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = KNL :pre
+
+For NVIDIA GPUs using CUDA:
+
+KOKKOS_DEVICES = Cuda
+KOKKOS_ARCH = archCPU,archGPU    # archCPU = CPU from list above that is hosting the GPU
+                                 # archGPU = GPU from list above :pre
+
+For GPUs, you also need these 2 lines in your Makefile.machine before
+the CC line is defined, in this case for use with OpenMPI mpicxx.  The
+2 lines define a nvcc wrapper compiler, which will use nvcc for
+compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA
+files.
+
+KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
+export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
+CC =		mpicxx :pre
+
+:line
+ 
+LATTE package :h4,link(latte)
+
+To build with this package, you must download and build the LATTE
+library.
+
+[CMake build]:
+
+-D DOWNLOAD_LATTE=value    # download LATTE for build, value = no (default) or yes
+-D LATTE_LIBRARY=path      # LATTE library file (only needed if a custom location) :pre
+
+If DOWNLOAD_LATTE is set, the LATTE library will be downloaded and
+built inside the CMake build directory.  If the LATTE library is
+already on your system (in a location CMake cannot find it),
+LATTE_LIBRARY is the filename (plus path) of the LATTE library file,
+not the directory the library file is in.
+
+[Traditional make]:
+
+You can download and build the LATTE library manually if you prefer;
+follow the instructions in lib/latte/README.  You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invokes the lib/latte/Install.py script with the specified
+args:
+
+make lib-latte                          # print help message
+make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
+make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
+make lib-latte args="-b -m gfortran"    # download and build in lib/latte and 
+                                        #   copy Makefile.lammps.gfortran to Makefile.lammps
+:pre
+
+Note that 3 symbolic (soft) links, "includelink" and "liblink" and
+"filelink.o", are created in lib/latte to point into the LATTE home
+dir.  When LAMMPS itself is built it will use these links.  You should
+also check that the Makefile.lammps file you create is appropriate for
+the compiler you use on your system to build LATTE.
+
+:line
+ 
+MEAM package :h4,link(meam)
+
+NOTE: the use of the MEAM package is discouraged, as it has been
+superseded by the USER-MEAMC package, which is a direct translation of
+the Fortran code in the MEAM library to C++. The code in USER-MEAMC
+should be functionally equivalent to the MEAM package, fully supports
+use of "pair_style hybrid"_pair_hybrid.html (the MEAM packaged doesn
+not), and has optimizations that make it significantly faster than the
+MEAM package.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_MEAM=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the MEAM library in lib/meam.
+You can build the MEAM library manually if you prefer; follow the
+instructions in lib/meam/README.  You can also do it in one step from
+the lammps/src dir, using a command like these, which simply invoke
+the lib/meam/Install.py script with the specified args:
+
+make lib-meam                  # print help message
+make lib-meam args="-m mpi"    # build with default Fortran compiler compatible with your MPI library
+make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
+make lib-meam args="-m ifort"  # build with Intel Fortran compiler using Makefile.ifort :pre
+
+The build should produce two files: lib/meam/libmeam.a and
+lib/meam/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
+Fortran (MEAM library).  Typically the two compilers used for LAMMPS
+and the MEAM library need to be consistent (e.g. both Intel or both
+GNU compilers).  If necessary, you can edit/create a new
+lib/meam/Makefile.machine file for your system, which should define an
+EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
+file.
+
+:line
+ 
+MSCG package :h4,link(mscg)
+
+To build with this package, you must download and build the MS-CG
+library.  Building the MS-CG library and using it from LAMMPS requires
+a C++11 compatible compiler and that the GSL (GNU Scientific Library)
+headers and libraries are installed on your machine.  See the
+lib/mscg/README and MSCG/Install files for more details.
+
+[CMake build]:
+
+-D DOWNLOAD_MSCG=value    # download MSCG for build, value = no (default) or yes
+-D MSCG_LIBRARY=path      # MSCG library file (only needed if a custom location) 
+-D MSCG_INCLUDE_DIR=path  # MSCG include directory (only needed if a custom location) :pre
+
+If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built
+inside the CMake build directory.  If the MSCG library is already on
+your system (in a location CMake cannot find it), MSCG_LIBRARY is the
+filename (plus path) of the MSCG library file, not the directory the
+library file is in.  MSCG_INCLUDE_DIR is the directory the MSCG
+include file is in.
+
+[Traditional make]:
+
+You can download and build the MS-CG library manually if you prefer;
+follow the instructions in lib/mscg/README.  You can also do it in one
+step from the lammps/src dir, using a command like these, which simply
+invoke the lib/mscg/Install.py script with the specified args:
+
+make lib-mscg             # print help message
+make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
+                                    # with the settings compatible with "make serial"
+make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
+                                    # with the settings compatible with "make mpi"
+make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink", will
+be created in lib/mscg to point to the MS-CG src/installation dir.
+When LAMMPS is built in src it will use these links.  You should not
+need to edit the lib/mscg/Makefile.lammps file.
+
+:line
+
+OPT package :h4,link(opt)
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_OPT=yes".
+
+[Traditional make]:
+
+The compile flag "-restrict" must be used to build LAMMPS with the OPT
+package when using Intel compilers.  It should be added to the CCFLAGS
+line of your Makefile.machine.  See src/MAKE/OPTIONS/Makefile.opt for
+an example.
+
+:line
+ 
+POEMS package :h4,link(poems)
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_OPT=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the POEMS library in lib/poems.
+You can do this manually if you prefer; follow the instructions in
+lib/poems/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/poems/Install.py script with the specified args:
+
+make lib-poems                   # print help message
+make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
+make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+make lib-poems args="-m icc"     # build with Intel icc compiler :pre
+
+The build should produce two files: lib/poems/libpoems.a and
+lib/poems/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the
+POEMS library (though typically the settings are just blank).  If
+necessary, you can edit/create a new lib/poems/Makefile.machine file
+for your system, which should define an EXTRAMAKE variable to specify
+a corresponding Makefile.lammps.machine file.
+
+:line
+ 
+PYTHON package :h4,link(python)
+
+Building with the PYTHON package requires you have a Python shared
+library available on your system, which needs to be a Python 2
+version, 2.6 or later.  Python 3 is not yet supported.  See
+lib/python/README for more details.
+
+[CMake build]:
+
+-D PYTHON_EXECUTABLE=path   # path to Python executable to use :pre
+
+Without this setting, CMake will ues the default Python on your
+system.  To use a different Python version, you can either create a
+virtualenv, activate it and then run cmake.  Or you can set the
+PYTHON_EXECUTABLE variable to specify which Python interpreter should
+be used.  Note note that you will also need to have the development
+headers installed for this version, e.g. python2-devel.
+
+[Traditional make]:
+
+The build uses the lib/python/Makefile.lammps file in the compile/link
+process to find Python.  You should only need to create a new
+Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS
+build fails.
+
+:line
+ 
+REAX package :h4,link(reax)
+
+NOTE: the use of the REAX package and its "pair_style
+reax"_pair_reax.html command is discouraged, as it is no longer
+maintained.  Please use the USER-REAXC package and its "pair_style
+reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
+enabled variant (pair_style reax/c/kk), which has a more robust memory
+management.  See the "pair_style reax/c"_pair_reaxc.html doc page for
+details.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_REAX=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the REAX library in lib/reax.
+You can do this manually if you prefer; follow the instructions in
+lib/reax/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/reax/Install.py script with the specified args:
+
+make lib-reax                    # print help message
+make lib-reax args="-m serial"   # build with GNU Fortran compiler (settings as with "make serial")
+make lib-reax args="-m mpi"      # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-reax args="-m ifort"    # build with Intel ifort compiler :pre
+
+The build should produce two files: lib/reax/libreax.a and
+lib/reax/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
+Fortran (REAX library).  Typically the two compilers used for LAMMPS
+and the REAX library need to be consistent (e.g. both Intel or both
+GNU compilers).  If necessary, you can edit/create a new
+lib/reax/Makefile.machine file for your system, which should define an
+EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
+file.
+
+:line
+
+VORONOI package :h4,link(voronoi)
+
+To build with this package, you must download and build the "Voro++
+library"_voro_home.
+
+:link(voro_home,http://math.lbl.gov/voro++)
+
+[CMake build]:
+
+-D DOWNLOAD_VORO=value    # download Voro++ for build, value = no (default) or yes
+-D VORO_LIBRARY=path      # Voro++ library file (only needed if at custom location) 
+-D VORO_INCLUDE_DIR=path  # Voro++ include directory (only needed if at custom location) :pre
+
+If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and
+built inside the CMake build directory.  If the Voro++ library is
+already on your system (in a location CMake cannot find it),
+VORO_LIBRARY is the filename (plus path) of the Voro++ library file,
+not the directory the library file is in.  VORO_INCLUDE_DIR is the
+directory the Voro++ include file is in.
+
+[Traditional make]:
+
+You can download and build the Voro++ library manually if you prefer;
+follow the instructions in lib/voronoi/README.  You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invoke the lib/voronoi/Install.py script with the specified
+args:
+
+make lib-voronoi                          # print help message
+make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
+make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
+make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre
+
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
+created in lib/voronoi to point to the Voro++ src dir.  When LAMMPS
+builds in src it will use these links.  You should not need to edit
+the lib/voronoi/Makefile.lammps file.
+
+:line
+
+USER-ATC package :h4,link(user-atc)
+
+The USER-ATC package requires the MANYBODY package also be installed.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_REAX=yes" and "-D
+PKG_MANYBODY=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the ATC library in lib/atc.
+You can do this manually if you prefer; follow the instructions in
+lib/atc/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/atc/Install.py script with the specified args:
+
+make lib-atc                      # print help message
+make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+make lib-atc args="-m icc"        # build with Intel icc compiler :pre
+
+The build should produce two files: lib/atc/libatc.a and
+lib/atc/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the ATC
+library.  If necessary, you can edit/create a new
+lib/atc/Makefile.machine file for your system, which should define an
+EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
+file.
+
+Note that the Makefile.lammps file has settings for the BLAS and
+LAPACK linear algebra libraries.  As explained in lib/atc/README these
+can either exist on your system, or you can use the files provided in
+lib/linalg.  In the latter case you also need to build the library in
+lib/linalg with a command like these:
+
+make lib-linalg                     # print help message
+make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
+
+:line
+
+USER-AWPMD package :h4,link(user-awpmd)
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-AQPMD=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the AWPMD library in lib/awpmd.
+You can do this manually if you prefer; follow the instructions in
+lib/awpmd/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/awpmd/Install.py script with the specified args:
+
+make lib-awpmd                   # print help message
+make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+make lib-awpmd args="-m icc"     # build with Intel icc compiler :pre
+
+The build should produce two files: lib/awpmd/libawpmd.a and
+lib/awpmd/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the
+AWPMD library.  If necessary, you can edit/create a new
+lib/awpmd/Makefile.machine file for your system, which should define
+an EXTRAMAKE variable to specify a corresponding
+Makefile.lammps.machine file.
+
+Note that the Makefile.lammps file has settings for the BLAS and
+LAPACK linear algebra libraries.  As explained in lib/awpmd/README
+these can either exist on your system, or you can use the files
+provided in lib/linalg.  In the latter case you also need to build the
+library in lib/linalg with a command like these:
+
+make lib-linalg                     # print help message
+make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
+
+:line
+
+USER-COLVARS package :h4,link(user-colvars)
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-COLVARS=yes".
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the COLVARS library in
+lib/colvars.  You can do this manually if you prefer; follow the
+instructions in lib/colvars/README.  You can also do it in one step
+from the lammps/src dir, using a command like these, which simply
+invoke the lib/colvars/Install.py script with the specified args:
+
+make lib-colvars                      # print help message
+make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled :pre
+
+The build should produce two files: lib/colvars/libcolvars.a and
+lib/colvars/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the
+COLVARS library (though typically the settings are just blank).  If
+necessary, you can edit/create a new lib/colvars/Makefile.machine file
+for your system, which should define an EXTRAMAKE variable to specify
+a corresponding Makefile.lammps.machine file.
+
+:line
+
+USER-H5MD package :h4,link(user-h5md)
+
+To build with this package you must have the HDF5 software package
+installed on your system, which should include the h5cc compiler and
+the HDF5 library.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-H5MD=yes".
+
+This should autodetect the H5MD library on your system.  Several
+advanced CMake H5MD options exist if you need to specify where it is
+installed.  Use the ccmake (terminal window) or cmake-gui (graphical)
+tools to see these options and set them interactively from their user
+interfaces.
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the CH5MD library in lib/h5md.
+You can do this manually if you prefer; follow the instructions in
+lib/h5md/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/h5md/Install.py script with the specified args:
+
+make lib-h5md                     # print help message
+make lib-hm5d args="-m h5cc"      # build with h5cc compiler :pre
+
+The build should produce two files: lib/h5md/libch5md.a and
+lib/h5md/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the
+system HDF5 library.  If necessary, you can edit/create a new
+lib/h5md/Makefile.machine file for your system, which should define an
+EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
+file.
+
+:line
+
+USER-INTEL package :h4,link(user-intel)
+
+To build with this package, you must choose which hardware you want to
+build for, either Intel CPUs or Intel KNLs.  You should also typically
+"install the USER-OMP package"_#user-omp, as it can be used in tandem
+with the USER-INTEL package to good effect, as explained on the "Speed
+intel"_Speed_intel.html doc page.
+
+[CMake build]:
+
+-D INTEL_ARCH=value     # value = cpu (default) or knl
+-D BUILD_OMP=yes        # also required to build with the USER-INTEl package :pre
+
+Requires an Intel compiler as well as the Intel TBB and MKL libraries.
+
+[Traditional make]:
+
+Choose which hardware to compile for in Makefile.machine via the
+following settings.  See src/MAKE/OPTIONS/Makefile.intel_cpu* and
+Makefile.knl files for examples.
+
+For CPUs:
+
+OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
+CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
+LIB =           -ltbbmalloc :pre
+
+For KNLs:
+
+OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
+CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
+LIB =           -ltbbmalloc :pre
+
+:line
+
+USER-MOLFILE package :h4,link(user-molfile)
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".
+
+[Traditional make]:
+
+The lib/molfile/Makefile.lammps file has a setting for a dynamic
+loading library libdl.a that is typically present on all systems.  It
+is required for LAMMPS to link with this package.  If the setting is
+not valid for your system, you will need to edit the Makefile.lammps
+file.  See lib/molfile/README and lib/molfile/Makefile.lammps for
+details.
+
+:line
+
+USER-NETCDF package :h4,link(user-netcdf)
+
+To build with this package you must have the NetCDF library installed
+on your system.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-NETCDF=yes".
+
+This should autodetect the NETCDF library if it is installed on your
+system at standard locations.  Several advanced CMake NETCDF options
+exist if you need to specify where it was installed.  Use the ccmake
+(terminal window) or cmake-gui (graphical) tools to see these options
+and set them interactively from their user interfaces.
+
+[Traditional make]:
+
+The lib/netcdf/Makefile.lammps file has settings for NetCDF include
+and library files which LAMMPS needs to build with this package.  If
+the settings are not valid for your system, you will need to edit the
+Makefile.lammps file.  See lib/netcdf/README for details.
+
+:line
+
+USER-OMP package :h4,link(user-omp)
+
+[CMake build]:
+
+No additional settings are required besides "-D PKG_USER-OMP=yes".  If
+CMake detects OpenMP support, the USER-OMP code will be compiled with
+multi-threading support enabled, otherwise as optimized serial code.
+
+[Traditional make]:
+
+To enable multi-threading support in the USER-OMP package (and other
+styles supporting OpenMP) the following compile and link flags must
+be added to your Makefile.machine file.
+See src/MAKE/OPTIONS/Makefile.omp for an example.
+
+CCFLAGS: -fopenmp               # for GNU Compilers
+CCFLAGS: -qopenmp -restrict     # for Intel compilers on Linux
+LINKFLAGS: -fopenmp             # for GNU Compilers
+LINKFLAGS: -qopenmp             # for Intel compilers on Linux :pre
+
+For other platforms and compilers, please consult the documentation
+about OpenMP support for your compiler.
+
+:line
+
+USER-QMMM package :h4,link(user-qmmm)
+
+NOTE: The LAMMPS executable these steps produce is not yet functional
+for a QM/MM simulation.  You must also build Quantum ESPRESSO and
+create a new executable (pwqmmm.x) which links LAMMPS and Quantum
+ESPRESSO together.  These are steps 3 and 4 described in the
+lib/qmmm/README file.  Unfortunately, the Quantum ESPRESSO developers
+have been breaking the interface that the QM/MM code in LAMMPS is using,
+so that currently (Summer 2018) using this feature requires either
+correcting the library interface feature in recent Quantum ESPRESSO
+releases, or using an outdated version of QE. The last version of
+Quantum ESPRESSO known to work with this QM/MM interface was version
+5.4.1 from 2016.
+
+[CMake build]:
+
+The CMake build system currently does not support building the full
+QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.  
+You must use the traditional make build for this package.
+
+[Traditional make]:
+
+Before building LAMMPS, you must build the QMMM library in lib/qmmm.
+You can do this manually if you prefer; follow the first two steps
+explained in lib/qmmm/README.  You can also do it in one step from the
+lammps/src dir, using a command like these, which simply invoke the
+lib/qmmm/Install.py script with the specified args:
+
+make lib-qmmm                      # print help message
+make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
+make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
+make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler :pre
+
+The build should produce two files: lib/qmmm/libqmmm.a and
+lib/qmmm/Makefile.lammps.  The latter is copied from an existing
+Makefile.lammps.* and has settings needed to build LAMMPS with the
+QMMM library (though typically the settings are just blank).  If
+necessary, you can edit/create a new lib/qmmm/Makefile.machine file
+for your system, which should define an EXTRAMAKE variable to specify
+a corresponding Makefile.lammps.machine file.
+
+You can then install QMMM package and build LAMMPS in the usual
+manner.  After completing the LAMMPS build and compiling Quantum
+ESPRESSO with external library support, go back to the lib/qmmm folder
+and follow the instructions on the README file to build the combined
+LAMMPS/QE QM/MM executable (pwqmmm.x) in the lib/qmmm folder.
+
+:line
+
+USER-QUIP package :h4,link(user-quip)
+
+To build with this package, you must download and build the QUIP
+library.  It can be obtained from GitHub.  For support of GAP
+potentials, additional files with specific licensing conditions need
+to be downloaded and configured.  See step 1 and step 1.1 in the
+lib/quip/README file for details on how to do this.
+
+[CMake build]:
+
+-D QUIP_LIBRARIES=path     # path to libquip.a (only needed if a custom location) :pre
+
+CMake will not download and build the QUIP library.  But once you have
+done that, a CMake build of LAMMPS with "-D PKG_USER-QUIP=yes" should
+work.  Set QUIP_LIBRARIES if CMake cannot find the QUIP library.
+
+[Traditional make]:
+
+The download/build procedure for the QUIP library, described in
+lib/quip/README file requires setting two environment variables,
+QUIP_ROOT and QUIP_ARCH.  These are accessed by the
+lib/quip/Makefile.lammps file which is used when you compile and link
+LAMMPS with this package.  You should only need to edit
+Makefile.lammps if the LAMMPS build can not use its settings to
+successfully build on your system.
+
+:line
+
+USER-SMD package :h4,link(user-smd)
+
+To build with this package, you must download the Eigen3 library.
+Eigen3 is a template library, so you do not need to build it.
+
+[CMake build]:
+
+-D DOWNLOAD_EIGEN3            # download Eigen3, value = no (default) or yes
+-D EIGEN3_INCLUDE_DIR=path    # path to Eigen library (only needed if a custom location) :pre
+
+If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and
+inside the CMake build directory.  If the Eig3n3 library is already on
+your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR
+is the directory the Eigen3++ include file is in.
+
+[Traditional make]:
+
+You can download the Eigen3 library manually if you prefer; follow the
+instructions in lib/smd/README.  You can also do it in one step from
+the lammps/src dir, using a command like these, which simply invoke
+the lib/smd/Install.py script with the specified args:
+
+make lib-smd                         # print help message
+make lib-smd args="-b"               # download to lib/smd/eigen3
+make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3 :pre
+
+Note that a symbolic (soft) link named "includelink" is created in
+lib/smd to point to the Eigen dir.  When LAMMPS builds it will use
+this link.  You should not need to edit the lib/smd/Makefile.lammps
+file.
+
+:line
+
+USER-VTK package :h4,link(user-vtk)
+
+To build with this package you must have the VTK library installed on
+your system.
+
+[CMake build]:
+
+No additional settings are needed besides "-D PKG_USER-VTK=yes".
+
+This should autodetect the VTK library if it is installed on your
+system at standard locations.  Several advanced VTK options exist if
+you need to specify where it was installed.  Use the ccmake (terminal
+window) or cmake-gui (graphical) tools to see these options and set
+them interactively from their user interfaces.
+
+[Traditional make]:
+
+The lib/vtk/Makefile.lammps file has settings for accessing VTK files
+and its library, which LAMMPS needs to build with this package.  If
+the settings are not valid for your system, check if one of the other
+lib/vtk/Makefile.lammps.* files is compatible and copy it to
+Makefile.lammps.  If none of the provided files work, you will need to
+edit the Makefile.lammps file.  See lib/vtk/README for details.

doc/src/Build_link.txt

@@ -0,0 +1,85 @@
+"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
+
+Link LAMMPS as a library to another code :h3
+
+LAMMPS can be used as a library by another application, including
+Python scripts.  The files src/library.cpp and library.h define the
+C-style API for using LAMMPS as a library.  See the "Howto
+library"_Howto_library.html doc page for a description of the
+interface and how to extend it for your needs.
+
+The "Build basics"_Build_basics.html doc page explains how to build
+LAMMPS as either a shared or static library.  This results in one of
+these 2 files:
+
+liblammps.so      # shared library
+liblammps.a       # static library
+
+:line
+
+[Link with LAMMPS as a static library]:
+
+The calling application can link to LAMMPS as a static library with a
+link command like this:
+
+g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller
+
+The -L argument is the path to where the liblammps.a file is.  The
+-llammps argument is shorthand for the file liblammps.a.
+
+:line
+
+[Link with LAMMPS as a shared library]:
+
+If you wish to link to liblammps.so, the operating system finds shared
+libraries to load at run-time using the environment variable
+LD_LIBRARY_PATH.  To enable this you can do one of two things:
+
+(1) Copy the liblammps.so file to a location the system can find it,
+such as /usr/local/lib.  I.e. a directory already listed in your
+LD_LIBRARY_PATH variable.  You can type
+
+printenv LD_LIBRARY_PATH :pre
+
+to see what directories are in that list.
+
+(2) Add the LAMMPS src directory (or the directory you perform CMake
+build in) to your LD_LIBRARY_PATH, so that the current version of the
+shared library is always available to programs that use it.
+
+For the csh or tcsh shells, you would add something like this to your
+~/.cshrc file:
+
+setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
+
+:line
+
+[Calling the LAMMPS library]:
+
+Either flavor of library (static or shared) allows one or more LAMMPS
+objects to be instantiated from the calling program.
+
+When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
+namespace; you can safely use any of its classes and methods from
+within the calling code, as needed.
+
+When used from a C or Fortran program, the library has a simple
+C-style interface, provided in src/library.cpp and src/library.h.
+
+See the "Python library"_Python_library.html doc page for a
+description of the Python interface to LAMMPS, which wraps the C-style
+interface.
+
+See the sample codes in examples/COUPLE/simple for examples of C++ and
+C and Fortran codes that invoke LAMMPS thru its library interface.
+Other examples in the COUPLE directory use coupling ideas discussed on
+the "Howto couple"_Howto_couple.html doc page.
+
+

doc/src/Build_make.txt

@@ -0,0 +1,85 @@
+"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
+
+Build LAMMPS with make :h3
+
+Building LAMMPS with traditional makefiles requires that you have a
+Makefile."machine" file appropriate for your system in the src/MAKE,
+src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see
+below).  It can include various options for customizing your LAMMPS
+build with a number of global compilation options and features.
+
+To include LAMMPS packages (i.e. optional commands and styles) you
+must install them first, as discussed on the "Build
+package"_Build_package.html doc page.  If the packages require
+provided or external libraries, you must build those libraries before
+building LAMMPS.  Building "LAMMPS with CMake"_Build_cmake.html can
+automate all of this for many types of machines, especially
+workstations, desktops and laptops, so we suggest you try it first.
+
+These commands perform a default LAMMPS build, producing the LAMMPS
+executable lmp_serial or lmp_mpi in lammps/src:
+
+cd lammps/src
+make serial     # build a serial LAMMPS executable
+make mpi        # build a parallel LAMMPS executable with MPI
+make            # see a variety of make options :pre
+
+This initial compilation can take a long time, since LAMMPS is a large
+project with many features. If your machine has multiple CPU cores
+(most do these days), using a command like "make -jN mpi" (with N =
+the number of available CPU cores) can be much faster.  If you plan to
+do development on LAMMPS or need to recompile LAMMPS repeatedly, the
+installation of the ccache (= Compiler Cache) software may speed up
+compilation even more.
+
+After the initial build, whenever you edit LAMMPS source files, or add
+or remove new files to the source directory (e.g. by installing or
+uninstalling packages), you must recompile and relink the LAMMPS
+executable with the same "make" command.  This makefiles dependencies
+should insure that only the subset of files that need to be are
+recompiled.
+
+NOTE: When you build LAMMPS for the first time, a long list of *.d
+files will be printed out rapidly.  This is not an error; it is the
+Makefile doing its normal creation of dependencies.
+
+:line
+
+The lammps/src/MAKE tree contains all the Makefile.machine files
+included in the LAMMPS distribution.  Typing "make machine" uses
+Makefile.machine.  Thus the "make serial" or "make mpi" lines above
+use Makefile.serial and Makefile.mpi.  Others are in these dirs:
+
+OPTIONS      # Makefiles which enable specific options
+MACHINES     # Makefiles for specific machines
+MINE         # customized Makefiles you create (you may need to create this folder) :pre
+
+Typing "make" lists all the available Makefile.machine files.  A file
+with the same name can appear in multiple folders (not a good idea).
+The order the dirs are searched is as follows: src/MAKE/MINE,
+src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.  This gives preference
+to a customized file you put in src/MAKE/MINE.
+
+Makefiles you may wish to try include these (some require a package
+first be installed).  Many of these include specific compiler flags
+for optimized performance.  Please note, however, that some of these
+customized machine Makefile are contributed by users.  Since both
+compilers, OS configs, and LAMMPS itself keep changing, their settings
+may become outdated:
+
+make mac             # build serial LAMMPS on a Mac
+make mac_mpi         # build parallel LAMMPS on a Mac
+make intel_cpu       # build with the USER-INTEL package optimized for CPUs
+make knl             # build with the USER-INTEL package optimized for KNLs
+make opt             # build with the OPT package optimized for CPUs
+make omp             # build with the USER-OMP package optimized for OpenMP
+make kokkos_omp      # build with the KOKKOS package for OpenMP
+make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
+make kokkos_phi      # build with the KOKKOS package for KNLs :pre

doc/src/Build_package.txt

@@ -0,0 +1,223 @@
+"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
+
+Include packages in build :h3
+
+In LAMMPS, a package is a group of files that enable a specific set of
+features.  For example, force fields for molecular systems or
+rigid-body constraints are in packages.  In the src directory, each
+package is a sub-directory with the package name in capital letters.
+
+An overview of packages is given on the "Packages"_Packages.html doc
+page.  Brief overviews of each package are on the "Packages
+details"_Packages_details.html doc page.
+
+When building LAMMPS, you can choose to include or exclude each
+package.  In general there is no need to include a package if you
+never plan to use its features.
+
+If you get a run-time error that a LAMMPS command or style is
+"Unknown", it is often because the command is contained in a package,
+and your build did not include that package.  Running LAMMPS with the
+"-h command-line switch"_Run_options.html will print all the included
+packages and commands for that executable.
+
+For the majority of packages, if you follow the single step below to
+include it, you can then build LAMMPS exactly the same as you would
+without any packages installed.  A few packages may require additional
+steps, as explained on the "Build extras"_Build_extras.html doc page.
+
+These links take you to the extra instructions for those select
+packages:
+
+"COMPRESS"_Build_extras.html#compress,
+"GPU"_Build_extras.html#gpu,
+"KIM"_Build_extras.html#kim,
+"KOKKOS"_Build_extras.html#kokkos,
+"LATTE"_Build_extras.html#latte,
+"MEAM"_Build_extras.html#meam,
+"MSCG"_Build_extras.html#mscg,
+"OPT"_Build_extras.html#opt,
+"POEMS"_Build_extras.html#poems,
+"PYTHON"_Build_extras.html#python,
+"REAX"_Build_extras.html#reax,
+"VORONOI"_Build_extras.html#voronoi,
+"USER-ATC"_Build_extras.html#user-atc,
+"USER-AWPMD"_Build_extras.html#user-awpmd,
+"USER-COLVARS"_Build_extras.html#user-colvars,
+"USER-H5MD"_Build_extras.html#user-h5md,
+"USER-INTEL"_Build_extras.html#user-intel,
+"USER-MOLFILE"_Build_extras.html#user-molfile,
+"USER-NETCDF"_Build_extras.html#user-netcdf,
+"USER-OMP"_Build_extras.html#user-omp,
+"USER-QMMM"_Build_extras.html#user-qmmm,
+"USER-QUIP"_Build_extras.html#user-quip,
+"USER-SMD"_Build_extras.html#user-smd,
+"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
+
+The mechanism for including packages is simple but different for CMake
+versus make.
+
+[CMake variables]:
+
+-D PKG_NAME=value          # yes or no (default) :pre
+
+Examples:
+
+-D PKG_MANYBODY=yes
+-D PKG_USER-INTEL=yes :pre
+
+All standard and user packages are included the same way.  Note that
+USER packages have a hyphen between USER and the rest of the package
+name, not an underscore.
+
+See the shortcut section below for how to install many packages at
+once with CMake.
+
+NOTE: If you toggle back and forth between building with CMake vs
+make, no packages in the src directory can be installed when you
+invoke cmake.  CMake will give an error if that is not the case,
+indicating how you can un-install all packages in the src dir.
+
+[Traditional make]:
+
+cd lammps/src
+make ps                    # check which packages are currently installed
+make yes-name              # install a package with name
+make no-name               # un-install a package with name
+make mpi                   # build LAMMPS with whatever packages are now installed :pre
+
+Examples:
+
+make no-rigid
+make yes-user-intel :pre
+
+All standard and user packages are included the same way.
+
+See the shortcut section below for how to install many packages at
+once with make.
+
+NOTE: You must always re-build LAMMPS (via make) after installing or
+un-installing a package, for the action to take effect.
+
+NOTE: You cannot install or un-install packages and build LAMMPS in a
+single make command with multiple targets, e.g. make yes-colloid mpi.
+This is because the make procedure creates a list of source files that
+will be out-of-date for the build if the package configuration changes
+within the same command.  You can include or exclude multiple packages
+in a single make command, e.g. make yes-colloid no-manybody.
+
+[CMake and make info]:
+
+Any package can be included or excluded in a LAMMPS build, independent
+of all other packages.  However, some packages include files derived
+from files in other packages.  LAMMPS checks for this and does the
+right thing.  Individual files are only included if their dependencies
+are already included.  Likewise, if a package is excluded, other files
+dependent on that package are also excluded.
+
+When you download a LAMMPS tarball or download LAMMPS source files
+from the Git or SVN repositories, no packages are pre-installed in the
+src directory.
+
+NOTE: Prior to Aug 2018, if you downloaded a tarball, 3 packages
+(KSPACE, MANYBODY, MOLECULE) were pre-installed in the src directory.
+That is no longer the case, so that CMake will build as-is without the
+need to un-install those packages.
+
+:line
+
+[CMake shortcuts for installing many packages]:
+
+Instead of specifying all the CMake options via the command-line,
+CMake allows initializing the variable cache using script files. These
+are regular CMake files which can manipulate and set variables, and
+can also contain control flow constructs.
+
+LAMMPS includes several of these files to define configuration
+"presets", similar to the options that exist for the Make based
+system. Using these files you can enable/disable portions of the
+available packages in LAMMPS. If you need a custom preset you can take
+one of them as a starting point and customize it to your needs.
+
+cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake | enable all packages
+cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake | disable all packages
+cmake -C ../cmake/presets/std.cmake \[OPTIONS\] ../cmake | enable standard packages
+cmake -C ../cmake/presets/user.cmake \[OPTIONS\] ../cmake | enable user packages
+cmake -C ../cmake/presets/std_nolib.cmake \[OPTIONS\] ../cmake | enable standard packages that do not require extra libraries
+cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | disable all packages that do not require extra libraries
+cmake -C ../cmake/presets/manual_selection.cmake \[OPTIONS\] ../cmake | example of how to create a manual selection of packages :tb(s=|,a=l)
+
+NOTE: Running cmake this way manipulates the variable cache in your
+current build directory. You can combine presets and options with
+multiple cmake runs.
+
+[Example:]
+
+# build LAMMPS with all "standard" packages which don't
+# use libraries and enable GPU package
+mkdir build
+cd build
+cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake :pre
+
+:line
+
+[Make shortcuts for installing many packages]:
+
+The following commands are useful for managing package source files
+and their installation when building LAMMPS via traditional make.
+Just type "make" in lammps/src to see a one-line summary.
+
+These commands install/un-install sets of packages:
+
+make yes-all | install all packages
+make no-all | un-install all packages
+make yes-standard or make yes-std | install standard packages
+make no-standard or make no-std| un-install standard packages
+make yes-user | install user packages
+make no-user | un-install user packages
+make yes-lib | install packages that require extra libraries
+make no-lib | un-install packages that require extra libraries
+make yes-ext | install packages that require external libraries
+make no-ext | un-install packages that require external libraries :tb(s=|,a=l)
+
+which install/un-install various sets of packages.  Typing "make
+package" will list all the these commands.
+
+NOTE: Installing or un-installing a package works by simply copying
+files back and forth between the main src directory and
+sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
+so that the files are included or excluded when LAMMPS is built.
+
+The following make commands help manage files that exist in both the
+src directory and in package sub-directories.  You do not normally
+need to use these commands unless you are editing LAMMPS files or are
+"installing a patch"_Install_patch.html downloaded from the LAMMPS web
+site.
+
+Type "make package-status" or "make ps" to show which packages are
+currently installed.  For those that are installed, it will list any
+files that are different in the src directory and package
+sub-directory.
+
+Type "make package-installed" or "make pi" to show which packages are
+currently installed, without listing the status of packages that are
+not installed.
+
+Type "make package-update" or "make pu" to overwrite src files with
+files from the package sub-directories if the package is installed.
+It should be used after a "patch has been applied"_Install_patch.html,
+since patches only update the files in the package sub-directory, but
+not the src files.
+
+Type "make package-overwrite" to overwrite files in the package
+sub-directories with src files.
+
+Type "make package-diff" to list all differences between pairs of
+files in both the src dir and a package dir.

doc/src/Build_settings.txt

@@ -0,0 +1,341 @@
+"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
+
+Optional build settings :h3
+
+LAMMPS can be built with several optional settings.  Each sub-section
+explain how to do this for building both with CMake and make.
+
+"FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command
+"Size of LAMMPS data types"_#size
+"Read or write compressed files"_#gzip
+"Output of JPG and PNG files"_#graphics via the "dump image"_dump_image.html command
+"Output of movie files"_#graphics via the "dump_movie"_dump_image.html command
+"Memory allocation alignment"_#align
+"Workaround for long long integers"_#longlong
+"Error handling exceptions"_#exceptions when using LAMMPS as a library :all(b)
+
+:line
+ 
+FFT library :h4,link(fft)
+
+When the KSPACE package is included in a LAMMPS build, the
+"kspace_style pppm"_kspace_style.html command performs 3d FFTs which
+require use of an FFT library to compute 1d FFTs.  The KISS FFT
+library is included with LAMMPS but other libraries can be faster.
+LAMMPS can use them if they are available on your system.
+
+[CMake variables]:
+
+-D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
+-D FFT_SINGLE=value       # yes or no (default), no = double precision
+-D FFT_PACK=value         # array (default) or pointer or memcpy :pre
+
+NOTE: The values for the FFT variable must be in upper-case.  This is
+an exception to the rule that all CMake variables can be specified
+with lower-case values.
+
+Usually these settings are all that is needed.  If CMake cannot find
+the FFT library, you can set these variables:
+
+-D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
+-D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
+-D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
+-D MKL_LIBRARIES=path :pre
+
+[Makefile.machine settings]:
+
+FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
+                              # default is KISS if not specified
+FFT_INC = -DFFT_SINGLE        # do not specify for double precision
+FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY :pre
+                              # default is FFT_PACK_ARRAY if not specified
+
+FFT_INC =    	-I/usr/local/include
+FFT_PATH =      -L/usr/local/lib
+FFT_LIB =	-lfftw3             # FFTW3 double precision
+FFT_LIB =	-lfftw3 -lfftw3f    # FFTW3 single precision
+FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  # MKL with Intel compiler
+FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core     # MKL with GNU compier :pre
+
+As with CMake, you do not need to set paths in FFT_INC or FFT_PATH, if
+make can find the FFT header and library files.  You must specify
+FFT_LIB with the appropriate FFT libraries to include in the link.
+
+[CMake and make info]:
+
+The "KISS FFT library"_http://kissfft.sf.net is included in the LAMMPS
+distribution.  It is portable across all platforms.  Depending on the
+size of the FFTs and the number of processors used, the other
+libraries listed here can be faster.  
+
+However, note that long-range Coulombics are only a portion of the
+per-timestep CPU cost, FFTs are only a portion of long-range
+Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
+communication can be costly).  A breakdown of these timings is printed
+to the screen at the end of a run using the "kspace_style
+pppm"_kspace_style.html command.  The "Run output"_doc page gives more
+details.
+
+FFTW is a fast, portable FFT library that should also work on any
+platform and can be faster than the KISS FFT library.  You can
+download it from "www.fftw.org"_http://www.fftw.org.  LAMMPS requires
+version 3.X; the legacy version 2.1.X is no longer supported.
+
+Building FFTW for your box should be as simple as ./configure; make;
+make install.  The install command typically requires root privileges
+(e.g. invoke it via sudo), unless you specify a local directory with
+the "--prefix" option of configure.  Type "./configure --help" to see
+various options. 
+
+The Intel MKL math library is part of the Intel compiler suite.  It
+can be used with the Intel or GNU compiler (see FFT_LIB setting above).
+
+Performing 3d FFTs in parallel can be time consuming due to data
+access and required communication.  This cost can be reduced by
+performing single-precision FFTs instead of double precision.  Single
+precision means the real and imaginary parts of a complex datum are
+4-byte floats.  Double precesion means they are 8-byte doubles.  Note
+that Fourier transform and related PPPM operations are somewhat less
+sensitive to floating point truncation errors and thus the resulting
+error is less than the difference in precision. Using the -DFFT_SINGLE
+setting trades off a little accuracy for reduced memory use and
+parallel communication costs for transposing 3d FFT data.
+
+When using -DFFT_SINGLE with FFTW3 you may need to build the FFTW
+library a second time with support for single-precision.
+
+For FFTW3, do the following, which should produce the additional
+library libfftw3f.a
+
+make clean
+./configure --enable-single; make; make install :pre
+
+Performing 3d FFTs requires communication to transpose the 3d FFT
+grid.  The data packing/unpacking for this can be done in one of 3
+modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
+Depending on the machine, the size of the FFT grid, the number of
+processors used, one option may be slightly faster.  The default is
+ARRAY mode.
+
+:line
+
+Size of LAMMPS data types :h4,link(size)
+
+LAMMPS has a few integer data types which can be defined as 4-byte or
+8-byte integers.  The default setting of "smallbig" is almost always
+adequate.
+
+[CMake variable]:
+
+-D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre
+                               # default is LAMMMPS_SMALLBIG if not specified
+[CMake and make info]:
+
+The default "smallbig" setting allows for simulations with:
+ 
+total atom count = 2^63 atoms (about 9e18)
+total timesteps = 2^63 (about 9e18)
+atom IDs = 2^31 (about 2 billion)
+image flags = roll over at 512 :ul
+  
+The "bigbig" setting increases the latter two limits.  It allows for:
+
+total atom count = 2^63 atoms (about 9e18)
+total timesteps = 2^63 (about 9e18)
+atom IDs = 2^63 (about 9e18)
+image flags = roll over at about 1 million (2^20) :ul
+
+The "smallsmall" setting is only needed if your machine does not
+support 8-byte integers.  It allows for:
+
+total atom count = 2^31 atoms (about 2 billion)
+total timesteps = 2^31 (about 2 billion)
+atom IDs = 2^31 (about 2 billion)
+image flags = roll over at 512 (2^9) :ul
+
+Atom IDs are not required for atomic systems which do not store bond
+topology information, though IDs are enabled by default.  The
+"atom_modify id no"_atom_modify.html command will turn them off.  Atom
+IDs are required for molecular systems with bond topology (bonds,
+angles, dihedrals, etc).  Thus if you model a molecular system with
+more than 2 billion atoms, you need the "bigbig" setting.
+
+Image flags store 3 values per atom which count the number of times an
+atom has moved through the periodic box in each dimension.  See the
+"dump"_dump.html doc page for a discussion.  If an atom moves through
+the periodic box more than this limit, the value will "roll over",
+e.g. from 511 to -512, which can cause diagnostics like the
+mean-squared displacement, as calculated by the "compute
+msd"_compute_msd.html command, to be faulty.
+
+Note that the USER-ATC package is not currently compatible with the
+"bigbig" setting.
+
+Also note that the GPU package requires its lib/gpu library to be
+compiled with the same size setting, or the link will fail.  A CMake
+build does this automatically.  When building with make, the setting
+in whichever lib/gpu/Makefile is used must be the same as above.
+
+:line
+
+Output of JPG, PNG, and movie files :h4,link(graphics)
+
+The "dump image"_dump_image.html command has options to output JPEG or
+PNG image files.  Likewise the "dump movie"_dump_image.html command
+ouputs movie files in MPEG format.  Using these options requires the
+following settings:
+
+[CMake variables]:
+
+-D WITH_JPEG=value      # yes or no
+                          # default = yes if CMake finds JPEG files, else no
+-D WITH_PNG=value       # yes or no
+                          # default = yes if CMake finds PNG and ZLIB files, else no
+-D WITH_FFMPEG=value    # yes or no
+                          # default = yes if CMake can find ffmpeg, else no :pre
+
+Usually these settings are all that is needed.  If CMake cannot find
+the graphics header, library, executuable files, you can set these
+variables:
+
+-D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file 
+-D JPEG_LIBRARIES=path      # path to libjpeg.a (.so) file 
+-D PNG_INCLUDE_DIR=path     # path to png.h header file 
+-D PNG_LIBRARIES=path       # path to libpng.a (.so) file 
+-D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file 
+-D ZLIB_LIBRARIES=path      # path to libz.a (.so) file 
+-D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable :pre
+
+[Makefile.machine settings]:
+
+LMP_INC = -DLAMMPS_JPEG
+LMP_INC = -DLAMMPS_PNG
+LMP_INC = -DLAMMPS_FFMPEG :pre
+
+JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
+JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
+JPG_LIB = -ljpeg -lpng -lz       # library names :pre
+
+As with CMake, you do not need to set JPG_INC or JPG_PATH, if make can
+find the graphics header and library files.  You must specify JPG_LIB
+with a list of graphics libraries to include in the link.  You must
+insure ffmpeg is in a directory where LAMMPS can find it at runtime,
+i.e. a dir in your PATH environment variable.
+
+[CMake and make info]:
+
+Using ffmpeg to output movie files requires that your machine
+supports the "popen" function in the standard runtime library.
+
+NOTE: On some clusters with high-speed networks, using the fork()
+library calls (required by popen()) can interfere with the fast
+communication library and lead to simulations using ffmpeg to hang or
+crash.
+
+:line
+
+Read or write compressed files :h4,link(gzip)
+
+If this option is enabled, large files can be read or written with
+gzip compression by several LAMMPS commands, including
+"read_data"_read_data.html, "rerun"_rerun.html, and "dump"_dump.html.
+
+[CMake variables]:
+
+-D WITH_GZIP=value       # yes or no
+                         # default is yes if CMake can find gzip, else no
+-D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_GZIP :pre
+
+[CMake and make info]:
+
+This option requires that your machine supports the "popen()" function
+in the standard runtime library and that a gzip executable can be
+found by LAMMPS during a run.
+
+NOTE: On some clusters with high-speed networks, using the fork()
+library calls (required by popen()) can interfere with the fast
+communication library and lead to simulations using compressed output
+or input to hang or crash. For selected operations, compressed file
+I/O is also available using a compression library instead, which is
+what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables.
+
+:line
+
+Memory allocation alignment :h4,link(align)
+
+This setting enables the use of the posix_memalign() call instead of
+malloc() when LAMMPS allocates large chunks or memory.  This can make
+vector instructions on CPUs more efficient, if dynamically allocated
+memory is aligned on larger-than-default byte boundaries.
+On most current systems, the malloc() implementation returns
+pointers that are aligned to 16-byte boundaries. Using SSE vector
+instructions efficiently, however, requires memory blocks being
+aligned on 64-byte boundaries.
+
+[CMake variable]:
+
+-D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default) :pre
+
+Use a LAMMPS_MEMALIGN value of 0 to disable using posix_memalign()
+and revert to using the malloc() C-library function instead.  When
+compiling LAMMPS for Windows systems, malloc() will always be used
+and this setting ignored.
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64 :pre
+
+Do not set -DLAMMPS_MEMALIGN, if you want to have memory allocated
+with the malloc() function call instead. -DLAMMPS_MEMALIGN [cannot]
+be used on Windows, as it does use different function calls for
+allocating aligned memory, that are not compatible with how LAMMPS
+manages its dynamical memory.
+
+:line
+
+Workaround for long long integers :h4,link(longlong)
+
+If your system or MPI version does not recognize "long long" data
+types, the following setting will be needed.  It converts "long long"
+to a "long" data type, which should be the desired 8-byte integer on
+those systems:
+
+[CMake variable]:
+
+-D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default) :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_LONGLONG_TO_LONG :pre
+
+:line
+
+Exception handling when using LAMMPS as a library :h4,link(exceptions)
+
+This setting is useful when external codes drive LAMMPS as a library.
+With this option enabled LAMMPS errors do not kill the caller.
+Instead, the call stack is unwound and control returns to the caller,
+e.g. to Python.
+
+[CMake variable]:
+
+-D LAMMPS_EXCEPTIONS=value        # yes or no (default) :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_EXCEPTIONS :pre

doc/src/Build_windows.txt

@@ -0,0 +1,97 @@
+"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
+
+Notes for building LAMMPS on Windows :h3
+
+"General remarks"_#generic
+"Running Linux on Windows"_#linux
+"Using GNU GCC ported to Windows"_#gnu
+"Using a cross-compiler"_#cross :ul
+
+:line
+
+General remarks :h4,link(generic)
+
+LAMMPS is developed and tested primarily on Linux machines.  The vast
+majority of HPC clusters and supercomputers today runs on Linux as well.
+Thus portability to other platforms is desired, but not always achieved.
+The LAMMPS developers strongly rely on LAMMPS users giving feedback and
+providing assistance in resolving portability issues. This particularly
+true for compiling LAMMPS on Windows, since this platform has significant
+differences with some low-level functionality.
+
+
+Running Linux on Windows :h4,link(linux)
+
+So before trying to build LAMMPS on Windows, please consider if using
+the pre-compiled Windows binary packages are sufficient for your needs
+(as an aside, those packages themselves are build on a Linux machine
+using cross-compilers).  If it is necessary for your to compile LAMMPS
+on a Windows machine (e.g. because it is your main desktop), please also
+consider using a virtual machine software and run a Linux virtual machine,
+or - if have a recently updated Windows 10 installation - consider using
+the Windows subsystem for Linux, which allows to run a bash shell from
+Ubuntu and from there on, you can pretty much use that shell like you
+are running on an Ubuntu Linux machine (e.g. installing software via
+apt-get). For more details on that, please see "this tutorial"_Howto_bash.html
+
+
+Using GNU GCC ported to Windows :h4,link(gnu)
+
+One option for compiling LAMMPS on Windows natively, that has been known
+to work in the past is to install a bash shell, unix shell utilities,
+perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
+provides a unix/linux interface to low-level Windows functions, so LAMMPS
+can be compiled on Windows. The necessary (minor) modifications to LAMMPS
+are included, but may not always up-to-date for recently added functionality
+and the corresponding new code. A machine makefile for using cygwin for
+the old build system is provided. The CMake build system is untested
+for this; you will have to request that makefiles are generated and
+manually set the compiler.  
+
+When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
+in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
+flags in LIB makefile variable. Try adding -static-libgcc or -static or 
+both to the linker flags when your resulting LAMMPS Windows executable
+complains about missing .dll files. The CMake configuration should set
+this up automatically, but is untested. 
+
+In case of problems, you are recommended to contact somebody with
+experience in using cygwin.  If you do come across portability problems
+requiring changes to the LAMMPS source code, or figure out corrections
+yourself, please report them on the lammps-users mailing list, or file
+them as an issue or pull request on the LAMMPS github project.
+
+
+Using a cross-compiler :h4,link(cross)
+
+If you need to provide custom LAMMPS binaries for Windows, but do not
+need to do the compilation on Windows, please consider using a Linux
+to Windows cross-compiler. This is how currently the Windows binary
+packages are created by the LAMMPS developers. Because of that, this is
+probably the currently best tested and supported way to build LAMMPS
+executables for Windows.  There are makefiles provided for the
+traditional build system, but CMake has also been successfully tested
+using the mingw32-cmake and mingw64-cmake wrappers that are bundled
+with the cross-compiler environment on Fedora machines.
+
+Please keep in mind, though, that this only applies to compiling LAMMPS.
+Whether the resulting binaries do work correctly is no tested by the
+LAMMPS developers.  We instead rely on the feedback of the users
+of these precompiled LAMMPS packages for Windows.  We will try to resolve
+issues to the best of our abilities if we become aware of them. However
+this is subject to time constraints and focus on HPC platforms.
+
+
+Native Visual C++ support :h4,link(native)
+
+Support for the Visual C++ compilers is currently not available. The
+CMake build system is capable of creating suitable a Visual Studio
+style build environment, but the LAMMPS code itself is not fully ported
+to support Visual C++. Volunteers to take on this task are welcome.

doc/src/Commands.txt

@@ -0,0 +1,53 @@
+"Previous Section"_Run_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Packages.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html#comm)
+
+:line
+
+Commands :h2
+
+These pages describe how a LAMMPS input script is formatted and the
+commands in it are used to define a LAMMPS simulation.
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   Commands_input
+   Commands_parse
+   Commands_structure
+   Commands_category
+
+.. toctree::
+   :maxdepth: 1
+
+   Commands_all
+   Commands_fix
+   Commands_compute
+   Commands_pair
+   Commands_bond
+   Commands_kspace
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"LAMMPS input scripts"_Commands_input.html
+"Parsing rules for input scripts"_Commands_parse.html
+"Input script structure"_Commands_structure.html
+"Commands by category"_Commands_category.html :all(b)
+
+"All commands"_Commands_all.html 
+"Fix commands"_Commands_fix.html 
+"Compute commands"_Commands_compute.html 
+"Pair commands"_Commands_pair.html 
+"Bond, angle, dihedral, improper commands"_Commands_bond.html
+"KSpace solvers"_Commands_kspace.html  :all(b)
+
+<!-- END_HTML_ONLY -->
+

doc/src/Commands_all.txt

@@ -0,0 +1,128 @@
+"Higher level section"_Commands.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
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+All commands :h3
+
+An alphabetic list of all LAMMPS commmands.
+
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"clear"_clear.html,
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"create_box"_create_box.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"dimension"_dimension.html,
+"displace_atoms"_displace_atoms.html,
+"dump"_dump.html,
+"dump image"_dump_image.html,
+"dump_modify"_dump_modify.html,
+"dump movie"_dump_image.html,
+"dump netcdf"_dump_netcdf.html,
+"dump netcdf/mpiio"_dump_netcdf.html,
+"dump vtk"_dump_vtk.html,
+"echo"_echo.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"group"_group.html,
+"group2ndx"_group2ndx.html,
+"if"_if.html,
+"info"_info.html,
+"improper_coeff"_improper_coeff.html,
+"improper_style"_improper_style.html,
+"include"_include.html,
+"jump"_jump.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"label"_label.html,
+"lattice"_lattice.html,
+"log"_log.html,
+"mass"_mass.html,
+"minimize"_minimize.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"molecule"_molecule.html,
+"ndx2group"_group2ndx.html,
+"neb"_neb.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"newton"_newton.html,
+"next"_next.html,
+"package"_package.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
+"partition"_partition.html,
+"prd"_prd.html,
+"print"_print.html,
+"processors"_processors.html,
+"python"_python.html,
+"quit"_quit.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"region"_region.html,
+"replicate"_replicate.html,
+"rerun"_rerun.html,
+"reset_ids"_reset_ids.html,
+"reset_timestep"_reset_timestep.html,
+"restart"_restart.html,
+"run"_run.html,
+"run_style"_run_style.html,
+"set"_set.html,
+"shell"_shell.html,
+"special_bonds"_special_bonds.html,
+"suffix"_suffix.html,
+"tad"_tad.html,
+"temper"_temper.html,
+"temper/grem"_temper_grem.html,
+"temper/npt"_temper_npt.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html,
+"uncompute"_uncompute.html,
+"undump"_undump.html,
+"unfix"_unfix.html,
+"units"_units.html,
+"variable"_variable.html,
+"velocity"_velocity.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html :tb(c=6,ea=c)

doc/src/Commands_bond.txt

@@ -0,0 +1,124 @@
+"Higher level section"_Commands.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)
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html#bond,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Bond, angle, dihedral, and improper commands :h3
+
+:line
+
+Bond_style potentials :h3,link(bond)
+
+All LAMMPS "bond_style"_bond_style.html commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_bond_none.html,
+"zero"_bond_zero.html,
+"hybrid"_bond_hybrid.html :tb(c=3,ea=c)
+
+"class2 (ko)"_bond_class2.html,
+"fene (iko)"_bond_fene.html,
+"fene/expand (o)"_bond_fene_expand.html,
+"gromos (o)"_bond_gromos.html,
+"harmonic (ko)"_bond_harmonic.html,
+"harmonic/shift (o)"_bond_harmonic_shift.html,
+"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"morse (o)"_bond_morse.html,
+"nonlinear (o)"_bond_nonlinear.html,
+"oxdna/fene"_bond_oxdna.html,
+"oxdna2/fene"_bond_oxdna.html,
+"quartic (o)"_bond_quartic.html,
+"table (o)"_bond_table.html :tb(c=4,ea=c)
+
+:line
+
+Angle_style potentials :h3,link(angle)
+
+All LAMMPS "angle_style"_angle_style.html commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_angle_none.html,
+"zero"_angle_zero.html,
+"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
+
+"charmm (ko)"_angle_charmm.html,
+"class2 (ko)"_angle_class2.html,
+"cosine (o)"_angle_cosine.html,
+"cosine/delta (o)"_angle_cosine_delta.html,
+"cosine/periodic (o)"_angle_cosine_periodic.html,
+"cosine/shift (o)"_angle_cosine_shift.html,
+"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
+"cosine/squared (o)"_angle_cosine_squared.html,
+"dipole (o)"_angle_dipole.html,
+"fourier (o)"_angle_fourier.html,
+"fourier/simple (o)"_angle_fourier_simple.html,
+"harmonic (iko)"_angle_harmonic.html,
+"quartic (o)"_angle_quartic.html,
+"sdk"_angle_sdk.html,
+"table (o)"_angle_table.html :tb(c=4,ea=c)
+
+:line
+
+Dihedral_style potentials :h3,link(dihedral)
+
+All LAMMPS "dihedral_style"_dihedral_style.html commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_dihedral_none.html,
+"zero"_dihedral_zero.html,
+"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)
+
+"charmm (iko)"_dihedral_charmm.html,
+"charmmfsw"_dihedral_charmm.html,
+"class2 (ko)"_dihedral_class2.html,
+"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
+"fourier (io)"_dihedral_fourier.html,
+"harmonic (io)"_dihedral_harmonic.html,
+"helix (o)"_dihedral_helix.html,
+"multi/harmonic (o)"_dihedral_multi_harmonic.html,
+"nharmonic (o)"_dihedral_nharmonic.html,
+"opls (iko)"_dihedral_opls.htm;,
+"quadratic (o)"_dihedral_quadratic.html,
+"spherical (o)"_dihedral_spherical.html,
+"table (o)"_dihedral_table.html,
+"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
+
+:line
+
+Improper_style potentials :h3,link(improper)
+
+All LAMMPS "improper_style"_improper_style.html commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_improper_none.html,
+"zero"_improper_zero.html,
+"hybrid"_improper_hybrid.html  :tb(c=3,ea=c)
+
+"class2 (ko)"_improper_class2.html,
+"cossq (o)"_improper_cossq.html,
+"cvff (io)"_improper_cvff.html,
+"distance"_improper_distance.html,
+"fourier (o)"_improper_fourier.html,
+"harmonic (iko)"_improper_harmonic.html,
+"ring (o)"_improper_ring.html,
+"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

doc/src/Commands_category.txt

@@ -0,0 +1,141 @@
+"Higher level section"_Commands.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
+
+Commands by category :h3
+
+This page lists most of the LAMMPS commands, grouped by category.  The
+"Commands all"_Commands_all.html doc page lists all commands
+alphabetically.  It also includes long lists of style options for
+entries that appear in the following categories as a single command
+(fix, compute, pair, etc).
+
+Initialization:
+
+"newton"_newton.html,
+"package"_package.html,
+"processors"_processors.html,
+"suffix"_suffix.html,
+"units"_units.html :ul
+
+Setup simulation box:
+
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"create_box"_create_box.html,
+"dimension"_dimension.html,
+"lattice"_lattice.html,
+"region"_region.html :ul
+
+Setup atoms:
+
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"displace_atoms"_displace_atoms.html,
+"group"_group.html,
+"mass"_mass.html,
+"molecule"_molecule.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"replicate"_replicate.html,
+"set"_set.html,
+"velocity"_velocity.html :ul
+
+Force fields:
+
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"improper_coeff"_improper_coeff.html,
+"improper_style"_improper_style.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
+"special_bonds"_special_bonds.html :ul
+
+Settings:
+
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"info"_info.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"partition"_partition.html,
+"reset_timestep"_reset_timestep.html,
+"run_style"_run_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html :ul
+
+Operations within timestepping (fixes) and diagnostics (computes):
+
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"uncompute"_uncompute.html,
+"unfix"_unfix.html :ul
+
+Output:
+
+"dump image"_dump_image.html,
+"dump movie"_dump_image.html,
+"dump"_dump.html,
+"dump_modify"_dump_modify.html,
+"restart"_restart.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"undump"_undump.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html :ul
+
+Actions:
+
+"minimize"_minimize.html,
+"neb"_neb.html,
+"prd"_prd.html,
+"rerun"_rerun.html,
+"run"_run.html,
+"tad"_tad.html,
+"temper"_temper.html :ul
+
+Input script control:
+
+"clear"_clear.html,
+"echo"_echo.html,
+"if"_if.html,
+"include"_include.html,
+"jump"_jump.html,
+"label"_label.html,
+"log"_log.html,
+"next"_next.html,
+"print"_print.html,
+"python"_python.html,
+"quit"_quit.html,
+"shell"_shell.html,
+"variable"_variable.html :ul
+

doc/src/Commands_compute.txt

@@ -0,0 +1,153 @@
+"Higher level section"_Commands.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
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Compute commands :h3
+
+An alphabetic list of all LAMMPS "compute"_compute.html commands.
+Some styles have accelerated versions.  This is indicated by
+additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+
+"ackland/atom"_compute_ackland_atom.html,
+"aggregate/atom"_compute_cluster_atom.html,
+"angle"_compute_angle.html,
+"angle/local"_compute_angle_local.html,
+"angmom/chunk"_compute_angmom_chunk.html,
+"basal/atom"_compute_basal_atom.html,
+"body/local"_compute_body_local.html,
+"bond"_compute_bond.html,
+"bond/local"_compute_bond_local.html,
+"centro/atom"_compute_centro_atom.html,
+"chunk/atom"_compute_chunk_atom.html,
+"cluster/atom"_compute_cluster_atom.html,
+"cna/atom"_compute_cna_atom.html,
+"cnp/atom"_compute_cnp_atom.html,
+"com"_compute_com.html,
+"com/chunk"_compute_com_chunk.html,
+"contact/atom"_compute_contact_atom.html,
+"coord/atom"_compute_coord_atom.html,
+"damage/atom"_compute_damage_atom.html,
+"dihedral"_compute_dihedral.html,
+"dihedral/local"_compute_dihedral_local.html,
+"dilatation/atom"_compute_dilatation_atom.html,
+"dipole/chunk"_compute_dipole_chunk.html,
+"displace/atom"_compute_displace_atom.html,
+"dpd"_compute_dpd.html,
+"dpd/atom"_compute_dpd_atom.html,
+"edpd/temp/atom"_compute_edpd_temp_atom.html,
+"entropy/atom"_compute_entropy_atom.html,
+"erotate/asphere"_compute_erotate_asphere.html,
+"erotate/rigid"_compute_erotate_rigid.html,
+"erotate/sphere"_compute_erotate_sphere.html,
+"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
+"event/displace"_compute_event_displace.html,
+"fep"_compute_fep.html,
+"force/tally"_compute_tally.html,
+"fragment/atom"_compute_cluster_atom.html,
+"global/atom"_compute_global_atom.html,
+"group/group"_compute_group_group.html,
+"gyration"_compute_gyration.html,
+"gyration/chunk"_compute_gyration_chunk.html,
+"heat/flux"_compute_heat_flux.html,
+"heat/flux/tally"_compute_tally.html,
+"hexorder/atom"_compute_hexorder_atom.html,
+"improper"_compute_improper.html,
+"improper/local"_compute_improper_local.html,
+"inertia/chunk"_compute_inertia_chunk.html,
+"ke"_compute_ke.html,
+"ke/atom"_compute_ke_atom.html,
+"ke/atom/eff"_compute_ke_atom_eff.html,
+"ke/eff"_compute_ke_eff.html,
+"ke/rigid"_compute_ke_rigid.html,
+"meso/e/atom"_compute_meso_e_atom.html,
+"meso/rho/atom"_compute_meso_rho_atom.html,
+"meso/t/atom"_compute_meso_t_atom.html,
+"msd"_compute_msd.html,
+"msd/chunk"_compute_msd_chunk.html,
+"msd/nongauss"_compute_msd_nongauss.html,
+"omega/chunk"_compute_omega_chunk.html,
+"orientorder/atom"_compute_orientorder_atom.html,
+"pair"_compute_pair.html,
+"pair/local"_compute_pair_local.html,
+"pe"_compute_pe.html,
+"pe/atom"_compute_pe_atom.html,
+"pe/mol/tally"_compute_tally.html,
+"pe/tally"_compute_tally.html,
+"plasticity/atom"_compute_plasticity_atom.html,
+"pressure"_compute_pressure.html,
+"pressure/uef"_compute_pressure_uef.html,
+"property/atom"_compute_property_atom.html,
+"property/chunk"_compute_property_chunk.html,
+"property/local"_compute_property_local.html,
+"rdf"_compute_rdf.html,
+"reduce"_compute_reduce.html,
+"reduce/region"_compute_reduce.html,
+"rigid/local"_compute_rigid_local.html,
+"saed"_compute_saed.html,
+"slice"_compute_slice.html,
+"smd/contact/radius"_compute_smd_contact_radius.html,
+"smd/damage"_compute_smd_damage.html,
+"smd/hourglass/error"_compute_smd_hourglass_error.html,
+"smd/internal/energy"_compute_smd_internal_energy.html,
+"smd/plastic/strain"_compute_smd_plastic_strain.html,
+"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
+"smd/rho"_compute_smd_rho.html,
+"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
+"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
+"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
+"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
+"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
+"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
+"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
+"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
+"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
+"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
+"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
+"smd/vol"_compute_smd_vol.html,
+"sna/atom"_compute_sna_atom.html,
+"snad/atom"_compute_sna_atom.html,
+"snav/atom"_compute_sna_atom.html,
+"spin"_compute_spin.html,
+"stress/atom"_compute_stress_atom.html,
+"stress/tally"_compute_tally.html,
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
+"temp (k)"_compute_temp.html,
+"temp/asphere"_compute_temp_asphere.html,
+"temp/body"_compute_temp_body.html,
+"temp/chunk"_compute_temp_chunk.html,
+"temp/com"_compute_temp_com.html,
+"temp/deform"_compute_temp_deform.html,
+"temp/deform/eff"_compute_temp_deform_eff.html,
+"temp/drude"_compute_temp_drude.html,
+"temp/eff"_compute_temp_eff.html,
+"temp/partial"_compute_temp_partial.html,
+"temp/profile"_compute_temp_profile.html,
+"temp/ramp"_compute_temp_ramp.html,
+"temp/region"_compute_temp_region.html,
+"temp/region/eff"_compute_temp_region_eff.html,
+"temp/rotate"_compute_temp_rotate.html,
+"temp/sphere"_compute_temp_sphere.html,
+"temp/uef"_compute_temp_uef.html,
+"ti"_compute_ti.html,
+"torque/chunk"_compute_torque_chunk.html,
+"vacf"_compute_vacf.html,
+"vcm/chunk"_compute_vcm_chunk.html,
+"voronoi/atom"_compute_voronoi_atom.html,
+"xrd"_compute_xrd.html :tb(c=6,ea=c)

doc/src/Commands_fix.txt

@@ -0,0 +1,229 @@
+"Higher level section"_Commands.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
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Fix commands :h3
+
+An alphabetic list of all LAMMPS "fix"_fix.html commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"adapt"_fix_adapt.html,
+"adapt/fep"_fix_adapt_fep.html,
+"addforce"_fix_addforce.html,
+"addtorque"_fix_addtorque.html,
+"append/atoms"_fix_append_atoms.html,
+"atc"_fix_atc.html,
+"atom/swap"_fix_atom_swap.html,
+"ave/atom"_fix_ave_atom.html,
+"ave/chunk"_fix_ave_chunk.html,
+"ave/correlate"_fix_ave_correlate.html,
+"ave/correlate/long"_fix_ave_correlate_long.html,
+"ave/histo"_fix_ave_histo.html,
+"ave/histo/weight"_fix_ave_histo.html,
+"ave/time"_fix_ave_time.html,
+"aveforce"_fix_aveforce.html,
+"balance"_fix_balance.html,
+"bond/break"_fix_bond_break.html,
+"bond/create"_fix_bond_create.html,
+"bond/react"_fix_bond_react.html,
+"bond/swap"_fix_bond_swap.html,
+"box/relax"_fix_box_relax.html,
+"cmap"_fix_cmap.html,
+"colvars"_fix_colvars.html,
+"controller"_fix_controller.html,
+"deform (k)"_fix_deform.html,
+"deposit"_fix_deposit.html,
+"dpd/energy (k)"_fix_dpd_energy.html,
+"drag"_fix_drag.html,
+"drude"_fix_drude.html,
+"drude/transform/direct"_fix_drude_transform.html,
+"drude/transform/reverse"_fix_drude_transform.html,
+"dt/reset"_fix_dt_reset.html,
+"edpd/source"_fix_dpd_source.html,
+"efield"_fix_efield.html,
+"ehex"_fix_ehex.html,
+"enforce2d (k)"_fix_enforce2d.html,
+"eos/cv"_fix_eos_cv.html,
+"eos/table"_fix_eos_table.html,
+"eos/table/rx (k)"_fix_eos_table_rx.html,
+"evaporate"_fix_evaporate.html,
+"external"_fix_external.html,
+"filter/corotate"_fix_filter_corotate.html,
+"flow/gauss"_fix_flow_gauss.html,
+"freeze"_fix_freeze.html,
+"gcmc"_fix_gcmc.html,
+"gld"_fix_gld.html,
+"gle"_fix_gle.html,
+"gravity (o)"_fix_gravity.html,
+"grem"_fix_grem.html,
+"halt"_fix_halt.html,
+"heat"_fix_heat.html,
+"imd"_fix_imd.html,
+"indent"_fix_indent.html,
+"ipi"_fix_ipi.html,
+"langevin (k)"_fix_langevin.html,
+"langevin/drude"_fix_langevin_drude.html,
+"langevin/eff"_fix_langevin_eff.html,
+"langevin/spin"_fix_langevin_spin.html,
+"latte"_fix_latte.html,
+"lb/fluid"_fix_lb_fluid.html,
+"lb/momentum"_fix_lb_momentum.html,
+"lb/pc"_fix_lb_pc.html,
+"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
+"lb/viscous"_fix_lb_viscous.html,
+"lineforce"_fix_lineforce.html,
+"manifoldforce"_fix_manifoldforce.html,
+"meso"_fix_meso.html,
+"meso/stationary"_fix_meso_stationary.html,
+"momentum (k)"_fix_momentum.html,
+"move"_fix_move.html,
+"mscg"_fix_mscg.html,
+"msst"_fix_msst.html,
+"mvv/dpd"_fix_mvv_dpd.html,
+"mvv/edpd"_fix_mvv_dpd.html,
+"mvv/tdpd"_fix_mvv_dpd.html,
+"neb"_fix_neb.html,
+"nph (ko)"_fix_nh.html,
+"nph/asphere (o)"_fix_nph_asphere.html,
+"nph/body"_fix_nph_body.html,
+"nph/eff"_fix_nh_eff.html,
+"nph/sphere (o)"_fix_nph_sphere.html,
+"nphug (o)"_fix_nphug.html,
+"npt (kio)"_fix_nh.html,
+"npt/asphere (o)"_fix_npt_asphere.html,
+"npt/body"_fix_npt_body.html,
+"npt/eff"_fix_nh_eff.html,
+"npt/sphere (o)"_fix_npt_sphere.html,
+"npt/uef"_fix_nh_uef.html,
+"nve (kio)"_fix_nve.html,
+"nve/asphere (i)"_fix_nve_asphere.html,
+"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
+"nve/body"_fix_nve_body.html,
+"nve/dot"_fix_nve_dot.html,
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
+"nve/eff"_fix_nve_eff.html,
+"nve/limit"_fix_nve_limit.html,
+"nve/line"_fix_nve_line.html,
+"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
+"nve/noforce"_fix_nve_noforce.html,
+"nve/sphere (o)"_fix_nve_sphere.html,
+"nve/spin"_fix_nve_spin.html,
+"nve/tri"_fix_nve_tri.html,
+"nvk"_fix_nvk.html,
+"nvt (iko)"_fix_nh.html,
+"nvt/asphere (o)"_fix_nvt_asphere.html,
+"nvt/body"_fix_nvt_body.html,
+"nvt/eff"_fix_nh_eff.html,
+"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
+"nvt/sllod (io)"_fix_nvt_sllod.html,
+"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
+"nvt/sphere (o)"_fix_nvt_sphere.html,
+"nvt/uef"_fix_nh_uef.html,
+"oneway"_fix_oneway.html,
+"orient/bcc"_fix_orient.html,
+"orient/fcc"_fix_orient.html,
+"phonon"_fix_phonon.html,
+"pimd"_fix_pimd.html,
+"planeforce"_fix_planeforce.html,
+"poems"_fix_poems.html,
+"pour"_fix_pour.html,
+"precession/spin"_fix_precession_spin.html,
+"press/berendsen"_fix_press_berendsen.html,
+"print"_fix_print.html,
+"property/atom (k)"_fix_property_atom.html,
+"python/invoke"_fix_python_invoke.html,
+"python/move"_fix_python_move.html,
+"qbmsst"_fix_qbmsst.html,
+"qeq/comb (o)"_fix_qeq_comb.html,
+"qeq/dynamic"_fix_qeq.html,
+"qeq/fire"_fix_qeq.html,
+"qeq/point"_fix_qeq.html,
+"qeq/reax (ko)"_fix_qeq_reax.html,
+"qeq/shielded"_fix_qeq.html,
+"qeq/slater"_fix_qeq.html,
+"qmmm"_fix_qmmm.html,
+"qtb"_fix_qtb.html,
+"rattle"_fix_shake.html,
+"reax/bonds"_fix_reax_bonds.html,
+"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/species (k)"_fix_reaxc_species.html,
+"recenter"_fix_recenter.html,
+"restrain"_fix_restrain.html,
+"rhok"_fix_rhok.html,
+"rigid (o)"_fix_rigid.html,
+"rigid/nph (o)"_fix_rigid.html,
+"rigid/npt (o)"_fix_rigid.html,
+"rigid/nve (o)"_fix_rigid.html,
+"rigid/nvt (o)"_fix_rigid.html,
+"rigid/small (o)"_fix_rigid.html,
+"rigid/small/nph"_fix_rigid.html,
+"rigid/small/npt"_fix_rigid.html,
+"rigid/small/nve"_fix_rigid.html,
+"rigid/small/nvt"_fix_rigid.html,
+"rx (k)"_fix_rx.html,
+"saed/vtk"_fix_saed_vtk.html,
+"setforce (k)"_fix_setforce.html,
+"shake"_fix_shake.html,
+"shardlow (k)"_fix_shardlow.html,
+"smd"_fix_smd.html,
+"smd/adjust/dt"_fix_smd_adjust_dt.html,
+"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
+"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
+"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
+"smd/setvel"_fix_smd_setvel.html,
+"smd/wall/surface"_fix_smd_wall_surface.html,
+"spring"_fix_spring.html,
+"spring/chunk"_fix_spring_chunk.html,
+"spring/rg"_fix_spring_rg.html,
+"spring/self"_fix_spring_self.html,
+"srd"_fix_srd.html,
+"store/force"_fix_store_force.html,
+"store/state"_fix_store_state.html,
+"tdpd/source"_fix_dpd_source.html,
+"temp/berendsen"_fix_temp_berendsen.html,
+"temp/csld"_fix_temp_csvr.html,
+"temp/csvr"_fix_temp_csvr.html,
+"temp/rescale"_fix_temp_rescale.html,
+"temp/rescale/eff"_fix_temp_rescale_eff.html,
+"tfmc"_fix_tfmc.html,
+"thermal/conductivity"_fix_thermal_conductivity.html,
+"ti/spring"_fix_ti_spring.html,
+"tmd"_fix_tmd.html,
+"ttm"_fix_ttm.html,
+"ttm/mod"_fix_ttm.html,
+"tune/kspace"_fix_tune_kspace.html,
+"vector"_fix_vector.html,
+"viscosity"_fix_viscosity.html,
+"viscous"_fix_viscous.html,
+"wall/body/polygon"_fix_wall_body_polygon.html,
+"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
+"wall/colloid"_fix_wall.html,
+"wall/ees"_fix_wall_ees.html,
+"wall/gran"_fix_wall_gran.html,
+"wall/gran/region"_fix_wall_gran_region.html,
+"wall/harmonic"_fix_wall.html,
+"wall/lj1043"_fix_wall.html,
+"wall/lj126"_fix_wall.html,
+"wall/lj93 (k)"_fix_wall.html,
+"wall/piston"_fix_wall_piston.html,
+"wall/reflect (k)"_fix_wall_reflect.html,
+"wall/region"_fix_wall_region.html,
+"wall/region/ees"_fix_wall_ees.html,
+"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)

doc/src/Commands_input.txt

@@ -0,0 +1,60 @@
+"Higher level section"_Commands.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
+
+LAMMPS input scripts :h3
+
+LAMMPS executes by reading commands from a input script (text file),
+one line at a time.  When the input script ends, LAMMPS exits.  Each
+command causes LAMMPS to take some action.  It may set an internal
+variable, read in a file, or run a simulation.  Most commands have
+default settings, which means you only need to use the command if you
+wish to change the default.
+
+In many cases, the ordering of commands in an input script is not
+important.  However the following rules apply:
+
+(1) LAMMPS does not read your entire input script and then perform a
+simulation with all the settings.  Rather, the input script is read
+one line at a time and each command takes effect when it is read.
+Thus this sequence of commands:
+
+timestep 0.5
+run      100
+run      100 :pre
+
+does something different than this sequence:
+
+run      100
+timestep 0.5
+run      100 :pre
+
+In the first case, the specified timestep (0.5 fs) is used for two
+simulations of 100 timesteps each.  In the 2nd case, the default
+timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
+timestep is used for the 2nd one.
+
+(2) Some commands are only valid when they follow other commands.  For
+example you cannot set the temperature of a group of atoms until atoms
+have been defined and a group command is used to define which atoms
+belong to the group.
+
+(3) Sometimes command B will use values that can be set by command A.
+This means command A must precede command B in the input script if it
+is to have the desired effect.  For example, the
+"read_data"_read_data.html command initializes the system by setting
+up the simulation box and assigning atoms to processors.  If default
+values are not desired, the "processors"_processors.html and
+"boundary"_boundary.html commands need to be used before read_data to
+tell LAMMPS how to map processors to the simulation box.
+
+Many input script errors are detected by LAMMPS and an ERROR or
+WARNING message is printed.  The "Errors"_Errors.html doc page gives
+more information on what errors mean.  The documentation for each
+command lists restrictions on how the command can be used.
+

doc/src/Commands_kspace.txt

@@ -0,0 +1,36 @@
+"Higher level section"_Commands.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.html)
+
+:line
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+KSpace solvers :h3
+
+All LAMMPS "kspace_style"_kspace_style.html solvers.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"ewald (o)"_kspace_style.html,
+"ewald/disp"_kspace_style.html,
+"msm (o)"_kspace_style.html,
+"msm/cg (o)"_kspace_style.html,
+"pppm (gok)"_kspace_style.html,
+"pppm/cg (o)"_kspace_style.html,
+"pppm/disp (i)"_kspace_style.html,
+"pppm/disp/tip4p"_kspace_style.html,
+"pppm/stagger"_kspace_style.html,
+"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)

doc/src/Commands_pair.txt

@@ -0,0 +1,231 @@
+"Higher level section"_Commands.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
+
+"All commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Pair_style potentials :h3
+
+All LAMMPS "pair_style"_pair_style.html commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_pair_none.html,
+"zero"_pair_zero.html,
+"hybrid"_pair_hybrid.html,
+"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
+
+"adp (o)"_pair_adp.html,
+"agni (o)"_pair_agni.html,
+"airebo (oi)"_pair_airebo.html,
+"airebo/morse (oi)"_pair_airebo.html,
+"awpmd/cut"_pair_awpmd.html,
+"beck (go)"_pair_beck.html,
+"body/nparticle"_pair_body_nparticle.html,
+"body/rounded/polygon"_pair_body_rounded_polygon.html,
+"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html,
+"bop"_pair_bop.html,
+"born (go)"_pair_born.html,
+"born/coul/dsf"_pair_born.html,
+"born/coul/dsf/cs"_pair_born.html,
+"born/coul/long (go)"_pair_born.html,
+"born/coul/long/cs"_pair_born.html,
+"born/coul/msm (o)"_pair_born.html,
+"born/coul/wolf (go)"_pair_born.html,
+"born/coul/wolf/cs"_pair_born.html,
+"brownian (o)"_pair_brownian.html,
+"brownian/poly (o)"_pair_brownian.html,
+"buck (giko)"_pair_buck.html,
+"buck/coul/cut (giko)"_pair_buck.html,
+"buck/coul/long (giko)"_pair_buck.html,
+"buck/coul/long/cs"_pair_buck.html,
+"buck/coul/msm (o)"_pair_buck.html,
+"buck/long/coul/long (o)"_pair_buck_long.html,
+"buck/mdf"_pair_mdf.html,
+"colloid (go)"_pair_colloid.html,
+"comb (o)"_pair_comb.html,
+"comb3"_pair_comb.html,
+"coul/cut (gko)"_pair_coul.html,
+"coul/cut/soft (o)"_pair_lj_soft.html,
+"coul/debye (gko)"_pair_coul.html,
+"coul/diel (o)"_pair_coul_diel.html,
+"coul/dsf (gko)"_pair_coul.html,
+"coul/long (gko)"_pair_coul.html,
+"coul/long/cs"_pair_coul.html,
+"coul/long/soft (o)"_pair_lj_soft.html,
+"coul/msm"_pair_coul.html,
+"coul/shield"_pair_coul_shield.html,
+"coul/streitz"_pair_coul.html,
+"coul/wolf (ko)"_pair_coul.html,
+"coul/wolf/cs"_pair_coul.html,
+"dpd (gio)"_pair_dpd.html,
+"dpd/fdt"_pair_dpd_fdt.html,
+"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
+"dpd/tstat (go)"_pair_dpd.html,
+"dsmc"_pair_dsmc.html,
+"eam (gikot)"_pair_eam.html,
+"eam/alloy (gikot)"_pair_eam.html,
+"eam/cd (o)"_pair_eam.html,
+"eam/fs (gikot)"_pair_eam.html,
+"edip (o)"_pair_edip.html,
+"edip/multi"_pair_edip.html,
+"edpd"_pair_meso.html,
+"eff/cut"_pair_eff.html,
+"eim (o)"_pair_eim.html,
+"exp6/rx (k)"_pair_exp6_rx.html,
+"extep"_pair_extep.html,
+"gauss (go)"_pair_gauss.html,
+"gauss/cut"_pair_gauss.html,
+"gayberne (gio)"_pair_gayberne.html,
+"gran/hertz/history (o)"_pair_gran.html,
+"gran/hooke (o)"_pair_gran.html,
+"gran/hooke/history (o)"_pair_gran.html,
+"gw"_pair_gw.html,
+"gw/zbl"_pair_gw.html,
+"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
+"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
+"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
+"kim"_pair_kim.html,
+"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
+"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
+"lcbop"_pair_lcbop.html,
+"lennard/mdf"_pair_mdf.html,
+"line/lj"_pair_line_lj.html,
+"list"_pair_list.html,
+"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
+"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
+"lj/charmm/coul/long (giko)"_pair_charmm.html,
+"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
+"lj/charmm/coul/msm"_pair_charmm.html,
+"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
+"lj/charmmfsw/coul/long"_pair_charmm.html,
+"lj/class2 (gko)"_pair_class2.html,
+"lj/class2/coul/cut (ko)"_pair_class2.html,
+"lj/class2/coul/long (gko)"_pair_class2.html,
+"lj/cubic (go)"_pair_lj_cubic.html,
+"lj/cut (gikot)"_pair_lj.html,
+"lj/cut/coul/cut (gko)"_pair_lj.html,
+"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/debye (gko)"_pair_lj.html,
+"lj/cut/coul/dsf (gko)"_pair_lj.html,
+"lj/cut/coul/long (gikot)"_pair_lj.html,
+"lj/cut/coul/long/cs"_pair_lj.html,
+"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/msm (go)"_pair_lj.html,
+"lj/cut/coul/wolf (o)"_pair_lj.html,
+"lj/cut/dipole/cut (go)"_pair_dipole.html,
+"lj/cut/dipole/long"_pair_dipole.html,
+"lj/cut/dipole/sf (go)"_pair_dipole.html,
+"lj/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/thole/long (o)"_pair_thole.html,
+"lj/cut/tip4p/cut (o)"_pair_lj.html,
+"lj/cut/tip4p/long (ot)"_pair_lj.html,
+"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
+"lj/expand (gko)"_pair_lj_expand.html,
+"lj/gromacs (gko)"_pair_gromacs.html,
+"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
+"lj/long/coul/long (io)"_pair_lj_long.html,
+"lj/long/dipole/long"_pair_dipole.html,
+"lj/long/tip4p/long"_pair_lj_long.html,
+"lj/mdf"_pair_mdf.html,
+"lj/sdk (gko)"_pair_sdk.html,
+"lj/sdk/coul/long (go)"_pair_sdk.html,
+"lj/sdk/coul/msm (o)"_pair_sdk.html,
+"lj/smooth (o)"_pair_lj_smooth.html,
+"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
+"lj96/cut (go)"_pair_lj96.html,
+"lubricate (o)"_pair_lubricate.html,
+"lubricate/poly (o)"_pair_lubricate.html,
+"lubricateU"_pair_lubricateU.html,
+"lubricateU/poly"_pair_lubricateU.html,
+"mdpd"_pair_meso.html,
+"mdpd/rhosum"_pair_meso.html,
+"meam"_pair_meam.html,
+"meam/c"_pair_meam.html,
+"meam/spline (o)"_pair_meam_spline.html,
+"meam/sw/spline"_pair_meam_sw_spline.html,
+"mgpt"_pair_mgpt.html,
+"mie/cut (o)"_pair_mie.html,
+"momb"_pair_momb.html,
+"morse (gkot)"_pair_morse.html,
+"morse/smooth/linear"_pair_morse.html,
+"morse/soft"_pair_morse.html,
+"multi/lucy"_pair_multi_lucy.html,
+"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
+"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
+"nm/cut (o)"_pair_nm.html,
+"nm/cut/coul/cut (o)"_pair_nm.html,
+"nm/cut/coul/long (o)"_pair_nm.html,
+"oxdna/coaxstk"_pair_oxdna.html,
+"oxdna/excv"_pair_oxdna.html,
+"oxdna/hbond"_pair_oxdna.html,
+"oxdna/stk"_pair_oxdna.html,
+"oxdna/xstk"_pair_oxdna.html,
+"oxdna2/coaxstk"_pair_oxdna2.html,
+"oxdna2/dh"_pair_oxdna2.html,
+"oxdna2/excv"_pair_oxdna2.html,
+"oxdna2/stk"_pair_oxdna2.html,
+"peri/eps"_pair_peri.html,
+"peri/lps (o)"_pair_peri.html,
+"peri/pmb (o)"_pair_peri.html,
+"peri/ves"_pair_peri.html,
+"polymorphic"_pair_polymorphic.html,
+"python"_pair_python.html,
+"quip"_pair_quip.html,
+"reax"_pair_reax.html,
+"reax/c (ko)"_pair_reaxc.html,
+"rebo (oi)"_pair_airebo.html,
+"resquared (go)"_pair_resquared.html,
+"smd/hertz"_pair_smd_hertz.html,
+"smd/tlsph"_pair_smd_tlsph.html,
+"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
+"smd/ulsph"_pair_smd_ulsph.html,
+"smtbq"_pair_smtbq.html,
+"snap (k)"_pair_snap.html,
+"snap (k)"_pair_snap.html,
+"soft (go)"_pair_soft.html,
+"sph/heatconduction"_pair_sph_heatconduction.html,
+"sph/idealgas"_pair_sph_idealgas.html,
+"sph/lj"_pair_sph_lj.html,
+"sph/rhosum"_pair_sph_rhosum.html,
+"sph/taitwater"_pair_sph_taitwater.html,
+"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
+"spin/dmi"_pair_spin_dmi.html,
+"spin/exchange"_pair_spin_exchange.html,
+"spin/magelec"_pair_spin_magelec.html,
+"spin/neel"_pair_spin_neel.html,
+"srp"_pair_srp.html,
+"sw (giko)"_pair_sw.html,
+"table (gko)"_pair_table.html,
+"table/rx (k)"_pair_table_rx.html,
+"tdpd"_pair_meso.html,
+"tersoff (giko)"_pair_tersoff.html,
+"tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/mod/c (o)"_pair_tersoff_mod.html,
+"tersoff/table (o)"_pair_tersoff.html,
+"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
+"thole"_pair_thole.html,
+"tip4p/cut (o)"_pair_coul.html,
+"tip4p/long (o)"_pair_coul.html,
+"tip4p/long/soft (o)"_pair_lj_soft.html,
+"tri/lj"_pair_tri_lj.html,
+"ufm (got)"_pair_ufm.html,
+"vashishta (ko)"_pair_vashishta.html,
+"vashishta/table (o)"_pair_vashishta.html,
+"yukawa (gok)"_pair_yukawa.html,
+"yukawa/colloid (go)"_pair_yukawa_colloid.html,
+"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)

doc/src/Commands_parse.txt

@@ -0,0 +1,136 @@
+"Higher level section"_Commands.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
+
+Parsing rules for input scripts :h3
+
+Each non-blank line in the input script is treated as a command.
+LAMMPS commands are case sensitive.  Command names are lower-case, as
+are specified command arguments.  Upper case letters may be used in
+file names or user-chosen ID strings.
+
+Here are 6 rulse for how each line in the input script is parsed by
+LAMMPS:
+
+(1) If the last printable character on the line is a "&" character,
+the command is assumed to continue on the next line.  The next line is
+concatenated to the previous line by removing the "&" character and
+line break.  This allows long commands to be continued across two or
+more lines.  See the discussion of triple quotes in (6) for how to
+continue a command across multiple line without using "&" characters.
+
+(2) All characters from the first "#" character onward are treated as
+comment and discarded.  See an exception in (6).  Note that a
+comment after a trailing "&" character will prevent the command from
+continuing on the next line.  Also note that for multi-line commands a
+single leading "#" will comment out the entire command.
+
+(3) The line is searched repeatedly for $ characters, which indicate
+variables that are replaced with a text string.  See an exception in
+(6).
+
+If the $ is followed by curly brackets, then the variable name is the
+text inside the curly brackets.  If no curly brackets follow the $,
+then the variable name is the single character immediately following
+the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
+"x".
+
+How the variable is converted to a text string depends on what style
+of variable it is; see the "variable"_variable.html doc page for details.
+It can be a variable that stores multiple text strings, and return one
+of them.  The returned text string can be multiple "words" (space
+separated) which will then be interpreted as multiple arguments in the
+input command.  The variable can also store a numeric formula which
+will be evaluated and its numeric result returned as a string.
+
+As a special case, if the $ is followed by parenthesis, then the text
+inside the parenthesis is treated as an "immediate" variable and
+evaluated as an "equal-style variable"_variable.html.  This is a way
+to use numeric formulas in an input script without having to assign
+them to variable names.  For example, these 3 input script lines:
+
+variable X equal (xlo+xhi)/2+sqrt(v_area)
+region 1 block $X 2 INF INF EDGE EDGE
+variable X delete :pre
+
+can be replaced by
+
+region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
+
+so that you do not have to define (or discard) a temporary variable X.
+
+Additionally, the "immediate" variable expression may be followed by a
+colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
+The format string must be appropriate for a double-precision
+floating-point value.  The format string is used to output the result
+of the variable expression evaluation.  If a format string is not
+specified a high-precision "%.20g" is used as the default.
+
+This can be useful for formatting print output to a desired precion:
+
+print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
+
+Note that neither the curly-bracket or immediate form of variables can
+contain nested $ characters for other variables to substitute for.
+Thus you cannot do this:
+
+variable        a equal 2
+variable        b2 equal 4
+print           "B2 = $\{b$a\}" :pre
+
+Nor can you specify this $($x-1.0) for an immediate variable, but
+you could use $(v_x-1.0), since the latter is valid syntax for an
+"equal-style variable"_variable.html.
+
+See the "variable"_variable.html command for more details of how
+strings are assigned to variables and evaluated, and how they can be
+used in input script commands.
+
+(4) The line is broken into "words" separated by whitespace (tabs,
+spaces).  Note that words can thus contain letters, digits,
+underscores, or punctuation characters.
+
+(5) The first word is the command name.  All successive words in the
+line are arguments.
+
+(6) If you want text with spaces to be treated as a single argument,
+it can be enclosed in either single or double or triple quotes.  A
+long single argument enclosed in single or double quotes can span
+multiple lines if the "&" character is used, as described above.  When
+the lines are concatenated together (and the "&" characters and line
+breaks removed), the text will become a single line.  If you want
+multiple lines of an argument to retain their line breaks, the text
+can be enclosed in triple quotes, in which case "&" characters are not
+needed.  For example:
+
+print "Volume = $v"
+print 'Volume = $v'
+if "$\{steps\} > 1000" then quit
+variable a string "red green blue &
+                   purple orange cyan"
+print """
+System volume = $v
+System temperature = $t
+""" :pre
+
+In each case, the single, double, or triple quotes are removed when
+the single argument they enclose is stored internally.
+
+See the "dump modify format"_dump_modify.html, "print"_print.html,
+"if"_if.html, and "python"_python.html commands for examples.
+
+A "#" or "$" character that is between quotes will not be treated as a
+comment indicator in (2) or substituted for as a variable in (3).
+
+NOTE: If the argument is itself a command that requires a quoted
+argument (e.g. using a "print"_print.html command as part of an
+"if"_if.html or "run every"_run.html command), then single, double, or
+triple quotes can be nested in the usual manner.  See the doc pages
+for those commands for examples.  Only one of level of nesting is
+allowed, but that should be sufficient for most use cases.
+

doc/src/Commands_structure.txt

@@ -0,0 +1,95 @@
+"Higher level section"_Commands.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
+
+Input script structure :h3
+
+This page describes the structure of a typical LAMMPS input script.
+The examples directory in the LAMMPS distribution contains many sample
+input scripts; it is discussed on the "Examples"_Examples.html doc
+page.
+
+A LAMMPS input script typically has 4 parts:
+
+Initialization
+Atom definition
+Settings
+Run a simulation :ol
+
+The last 2 parts can be repeated as many times as desired.  I.e. run a
+simulation, change some settings, run some more, etc.  Each of the 4
+parts is now described in more detail.  Remember that almost all
+commands need only be used if a non-default value is desired.
+
+(1) Initialization
+
+Set parameters that need to be defined before atoms are created or
+read-in from a file.
+
+The relevant commands are "units"_units.html,
+"dimension"_dimension.html, "newton"_newton.html,
+"processors"_processors.html, "boundary"_boundary.html,
+"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
+
+If force-field parameters appear in the files that will be read, these
+commands tell LAMMPS what kinds of force fields are being used:
+"pair_style"_pair_style.html, "bond_style"_bond_style.html,
+"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
+"improper_style"_improper_style.html.
+
+(2) Atom definition
+
+There are 3 ways to define atoms in LAMMPS.  Read them in from a data
+or restart file via the "read_data"_read_data.html or
+"read_restart"_read_restart.html commands.  These files can contain
+molecular topology information.  Or create atoms on a lattice (with no
+molecular topology), using these commands: "lattice"_lattice.html,
+"region"_region.html, "create_box"_create_box.html,
+"create_atoms"_create_atoms.html.  The entire set of atoms can be
+duplicated to make a larger simulation using the
+"replicate"_replicate.html command.
+
+(3) Settings
+
+Once atoms and molecular topology are defined, a variety of settings
+can be specified: force field coefficients, simulation parameters,
+output options, etc.
+
+Force field coefficients are set by these commands (they can also be
+set in the read-in files): "pair_coeff"_pair_coeff.html,
+"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"improper_coeff"_improper_coeff.html,
+"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
+"special_bonds"_special_bonds.html.
+
+Various simulation parameters are set by these commands:
+"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
+"group"_group.html, "timestep"_timestep.html,
+"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
+"min_style"_min_style.html, "min_modify"_min_modify.html.
+
+Fixes impose a variety of boundary conditions, time integration, and
+diagnostic options.  The "fix"_fix.html command comes in many flavors.
+
+Various computations can be specified for execution during a
+simulation using the "compute"_compute.html,
+"compute_modify"_compute_modify.html, and "variable"_variable.html
+commands.
+
+Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
+and "restart"_restart.html commands.
+
+(4) Run a simulation
+
+A molecular dynamics simulation is run using the "run"_run.html
+command.  Energy minimization (molecular statics) is performed using
+the "minimize"_minimize.html command.  A parallel tempering
+(replica-exchange) simulation can be run using the
+"temper"_temper.html command.
+

doc/src/Developer/developer.tex

@@ -449,15 +449,15 @@ Writing fixes is a flexible way of extending LAMMPS.  Users can
 implement many things using fixes:
 
 \begin{itemize}
-\item changing particles attributes (positions, velocities, forces, etc.). 
+\item changing particles attributes (positions, velocities, forces, etc.).
 Example: FixFreeze.
 \item reading/writing data. Example: FixRestart.
 \item implementing boundary conditions. Example: FixWall.
-\item saving information about particles for future use (previous positions, 
+\item saving information about particles for future use (previous positions,
 for instance). Example: FixStoreState.
 \end{itemize}
 
-All fixes are derived from class Fix and must have constructor with the 
+All fixes are derived from class Fix and must have constructor with the
 signature: FixMine(class LAMMPS *, int, char **).
 
 Every fix must be registered in LAMMPS by writing the following lines
@@ -476,9 +476,9 @@ is the name of the class. This code allows LAMMPS to find your fix
 when it parses input script. In addition, your fix header must be
 included in the file "style\_fix.h". In case if you use LAMMPS make,
 this file is generated automatically - all files starting with prefix
-fix\_ are included, so call your header the same way. Otherwise, don<EFBFBD>t
+fix\_ are included, so call your header the same way. Otherwise, don't
 forget to add your include into "style\_fix.h".
- 
+
 Let's write a simple fix which will print average velocity at the end
 of each timestep. First of all, implement a constructor:
 
@@ -487,11 +487,11 @@ of each timestep. First of all, implement a constructor:
 FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
 : Fix(lmp, narg, arg)
 {
-  if (narg < 4) 
+  if (narg < 4)
       error->all(FLERR,"Illegal fix print command");
- 
+
   nevery = atoi(arg[3]);
-  if (nevery <= 0) 
+  if (nevery <= 0)
       error->all(FLERR,"Illegal fix print command");
 }
   \end{verbatim}
@@ -545,7 +545,7 @@ void FixPrintVel::end_of_step()
 {
   // for add3, scale3
   using namespace MathExtra;
-  
+
   double** v = atom->v;
   int nlocal = atom->nlocal;
   double localAvgVel[4]; // 4th element for particles count
@@ -559,7 +559,7 @@ void FixPrintVel::end_of_step()
   MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
   scale3(1.0 / globalAvgVel[3], globalAvgVel);
   if (comm->me == 0) {
-    printf("\%e, \%e, \%e\n", 
+    printf("\%e, \%e, \%e\n",
       globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
   }
 }
@@ -607,14 +607,15 @@ this situation there are several methods which should be implemented:
 
 \begin{itemize}
 \item \verb|double memory_usage| - return how much memory fix uses
-\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays 
+\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays
   in your fix
-\item \verb|void copy_arrays(int i, int j)| - copy i-th per-particle information 
-  to j-th. Used when atoms sorting is performed
+\item \verb|void copy_arrays(int i, int j, int delflag)| - copy i-th per-particle
+  information to j-th. Used when atoms sorting is performed. if delflag is set
+  and atom j owns a body, move the body information to atom i.
 \item \verb|void set_arrays(int i)| - sets i-th particle related information to zero
 \end{itemize}
 
-Note, that if your class implements these methods, it must call add calls of 
+Note, that if your class implements these methods, it must call add calls of
 add\_callback and delete\_callback to constructor and destructor:
 
 \begin{center}
@@ -654,7 +655,7 @@ void FixSavePos::grow_arrays(int nmax)
     memory->grow(this->x, nmax, 3, "FixSavePos:x");
 }
 
-void FixSavePos::copy_arrays(int i, int j)
+void FixSavePos::copy_arrays(int i, int j, int delflag)
 {
     memcpy(this->x[j], this->x[i], sizeof(double) * 3);
 }
@@ -670,7 +671,7 @@ int FixSavePos::pack_exchange(int i, double *buf)
   buf[m++] = x[i][0];
   buf[m++] = x[i][1];
   buf[m++] = x[i][2];
-  
+
   return m;
 }
 

doc/src/Eqs/dihedral_table_cut.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+        f(\theta) & = & K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
+        f(\theta) & = & K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
+\end{eqnarray*}
+
+\end{document}
+

doc/src/Eqs/fix_integration_spin_stdecomposition.tex

@@ -0,0 +1,40 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm,tikz}
+\usetikzlibrary{automata,arrows,shapes,snakes}
+\begin{document}
+\begin{varwidth}{50in}
+\begin{tikzpicture}
+
+%Global
+\node (v1) at (0,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ };
+\node (s1) at (0,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ };
+\node (r)  at (0,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{r} \leftarrow \bm{r}+L_r.\Delta t$ };
+\node (s2) at (0,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ };
+\node (v2) at (0,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ };
+
+\draw[line width=2pt, ->] (v1) -- (s1);
+\draw[line width=2pt, ->] (s1) -- (r);
+\draw[line width=2pt, ->] (r) -- (s2);
+\draw[line width=2pt, ->] (s2) -- (v2);
+
+%Spin
+\node (s01) at (6,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ };
+\node (sN1) at (6,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$};
+\node (sN)  at (6,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N} \leftarrow \bm{s}_{\rm N}+L_{s_{\rm N}}.\Delta t/2$ };
+\node (sN2) at (6,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$};
+\node (s02) at (6,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ };
+
+\draw[line width=2pt,dashed, ->] (s01) -- (sN1);
+\draw[line width=2pt, ->] (sN1) -- (sN);
+\draw[line width=2pt, ->] (sN) -- (sN2);
+\draw[line width=2pt,dashed, ->] (sN2) -- (s02);
+
+%from Global to Spin
+\draw[line width=2pt, dashed, ->] (s1) -- (s01.west);
+\draw[line width=2pt, dashed, ->] (s1) -- (s02.west);
+
+\end{tikzpicture}
+\end{varwidth}
+\end{document}

doc/src/Eqs/fix_langevin_spin_sLLG.tex

@@ -0,0 +1,14 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \frac{d \vec{s}_{i}}{dt} = \frac{1}{\left(1+\lambda^2 \right)} \left( \left(
+    \vec{\omega}_{i} +\vec{\eta} \right) \times \vec{s}_{i} + \lambda\, \vec{s}_{i}
+  \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) \right), \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/force_spin_aniso.tex

@@ -0,0 +1,11 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{aniso}  = -\sum_{{ i}=1}^{N} K_{an}(\bm{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2, \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/force_spin_zeeman.tex

@@ -0,0 +1,11 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{zeeman} = -\mu_{B}\mu_0\sum_{i=0}^{N}g_{i} \vec{s}_{i} \cdot \vec{H}_{ext} \nonumber 
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_body_rounded.tex

@@ -0,0 +1,13 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ F_n &=& k_n \delta_n - c_n v_n, \qquad \delta_n \le 0 \\
+     &=& -k_{na} \delta_n - c_n v_n, \qquad 0 < \delta_n \le r_c \\
+     &=& 0 \qquad \qquad \qquad \qquad \delta_n > r_c \\
+ F_t &=& \mu k_n \delta_n - c_t v_t, \qquad \delta_n \le 0 \\
+     &=& 0 \qquad \qquad \qquad \qquad \delta_n > 0
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_entropy.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+
+$$
+   s_S^i=-2\pi\rho k_B \int\limits_0^{r_m} \left [ g(r) \ln g(r) - g(r) + 1 \right ] r^2 dr ,
+$$
+
+\end{document}

doc/src/Eqs/pair_entropy2.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+
+$$
+   g_m^i(r) = \frac{1}{4 \pi \rho r^2} \sum\limits_{j} \frac{1}{\sqrt{2 \pi \sigma^2}} e^{-(r-r_{ij})^2/(2\sigma^2)} ,
+$$
+
+\end{document}

doc/src/Eqs/pair_entropy3.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+
+$$
+  \bar{s}_S^i  = \frac{\sum_j s_S^j + s_S^i}{N + 1} ,
+$$
+
+\end{document}

doc/src/Eqs/pair_spin_dmi_forces.tex

@@ -0,0 +1,14 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right) 
+    ~~{\rm and}~~
+    \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right) 
+    , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_dmi_interaction.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{dm} = \sum_{{ i,j}=1,i\neq j}^{N} 
+    \left( \vec{e}_{ij} \times \vec{D} \right)
+    \cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right), 
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}
+    \vec{D}\left(r_{ij}\right) 
+    {\rm ~and~}  \vec{D}\left(r_{ij}\right) = \vec{e}_{ij} \times \vec{D}  

doc/src/Eqs/pair_spin_exchange_forces.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} 
+    \left(r_{ij} \right)\,\vec{s}_{j} 
+    ~~{\rm and}~~ 
+    \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
+    \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}  
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_exchange_function.tex

@@ -0,0 +1,13 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d}  \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d}  \right)^2 \right) e^{-\left( \frac{r_{ij}}{d}  
+    \right)^2 }\Theta (R_c - r_{ij}) \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_exchange_interaction.tex

@@ -0,0 +1,11 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{ex} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_me_forces.tex

@@ -0,0 +1,13 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{F}^{i} = -\sum_{j}^{Neighbor} \left( \vec{s}_{i}\times \vec{s}_{j} \right)
+    \times \vec{E} ~~{\rm and}~~ \vec{\omega}^{i} = -\frac{1}{\hbar} 
+    \sum_{j}^{Neighbor} \vec{s}_j \times \left(\vec{E}\times r_{ij} \right),\nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_me_interaction.tex

@@ -0,0 +1,12 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times\vec{D}(r_{ij}) ~~{\rm and}~~
+    \vec{F}_i = -\sum_{j}^{Neighb} \frac{\partial D(r_{ij})}{\partial r_{ij}} \left(\vec{s}_{i}\times \vec{s}_{j} \right) \cdot \vec{r}_{ij}, \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_neel_functions.tex

@@ -0,0 +1,13 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{eqnarray}
+    g_1(r_{ij}) &=& g(r_{ij}) + \frac{12}{35} q(r_{ij}) \nonumber \\
+    q_1(r_{ij}) &=& \frac{9}{5} q(r_{ij}) \nonumber \\
+    q_2(r_{ij}) &=& - \frac{2}{5} q(r_{ij}) \nonumber
+  \end{eqnarray}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_neel_interaction.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\bm e}_{ij}\cdot {\bm s}_{i})({\bm e}_{ij}
+    \cdot {\bm s}_{j})-\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
+    +q_1(r_{ij})\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3}\right)
+    \left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right)
+    + q_2(r_{ij}) \Big( ({\bm e}_{ij}\cdot {\bm s}_{i}) ({\bm e}_{ij}\cdot {\bm s}_{j})^3 + ({\bm e}_{ij}\cdot
+    {\bm s}_{j}) ({\bm e}_{ij}\cdot {\bm s}_{i})^3\Big) \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Errors.txt

@@ -0,0 +1,38 @@
+"Previous Section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Manual.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Errors :h2
+
+These doc pages describe the errors you can encounter when using
+LAMMPS.  The common problems include conceptual issues.  The messages
+and warnings doc pages give complete lists of all the messages the
+code may generate (except those generated by USER packages), with
+additional details for many of them.
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   Errors_common
+   Errors_bugs
+   Errors_messages
+   Errors_warnings
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Common problems"_Errors_common.html
+"Reporting bugs"_Errors_bugs.html
+"Error messages"_Errors_messages.html 
+"Warning messages"_Errors_warnings.html :all(b)
+
+<!-- END_HTML_ONLY -->

doc/src/Errors_bugs.txt

@@ -0,0 +1,35 @@
+"Higher level section"_Errors.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
+
+Reporting bugs :h3
+
+If you are confident that you have found a bug in LAMMPS, follow these
+steps.
+
+Check the "New features and bug
+fixes"_http://lammps.sandia.gov/bug.html section of the "LAMMPS WWW
+site"_lws to see if the bug has already been reported or fixed or the
+"Unfixed bug"_http://lammps.sandia.gov/unbug.html to see if a fix is
+pending.
+
+Check the "mailing list"_http://lammps.sandia.gov/mail.html to see if
+it has been discussed before.
+
+If not, send an email to the mailing list describing the problem with
+any ideas you have as to what is causing it or where in the code the
+problem might be.  The developers will ask for more info if needed,
+such as an input script or data files.
+
+The most useful thing you can do to help us fix the bug is to isolate
+the problem.  Run it on the smallest number of atoms and fewest number
+of processors and with the simplest input script that reproduces the
+bug and try to identify what command or combination of commands is
+causing the problem.
+
+NOTE: this page needs to have GitHub issues info added

doc/src/Errors_common.txt

@@ -0,0 +1,123 @@
+"Higher level section"_Errors.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
+
+Common problems :h3
+
+If two LAMMPS runs do not produce the exact same answer on different
+machines or different numbers of processors, this is typically not a
+bug.  In theory you should get identical answers on any number of
+processors and on any machine.  In practice, numerical round-off can
+cause slight differences and eventual divergence of molecular dynamics
+phase space trajectories within a few 100s or few 1000s of timesteps.
+However, the statistical properties of the two runs (e.g. average
+energy or temperature) should still be the same.
+
+If the "velocity"_velocity.html command is used to set initial atom
+velocities, a particular atom can be assigned a different velocity
+when the problem is run on a different number of processors or on
+different machines.  If this happens, the phase space trajectories of
+the two simulations will rapidly diverge.  See the discussion of the
+{loop} option in the "velocity"_velocity.html command for details and
+options that avoid this issue.
+
+Similarly, the "create_atoms"_create_atoms.html command generates a
+lattice of atoms.  For the same physical system, the ordering and
+numbering of atoms by atom ID may be different depending on the number
+of processors.
+
+Some commands use random number generators which may be setup to
+produce different random number streams on each processor and hence
+will produce different effects when run on different numbers of
+processors.  A commonly-used example is the "fix
+langevin"_fix_langevin.html command for thermostatting.
+
+A LAMMPS simulation typically has two stages, setup and run.  Most
+LAMMPS errors are detected at setup time; others like a bond
+stretching too far may not occur until the middle of a run.
+
+LAMMPS tries to flag errors and print informative error messages so
+you can fix the problem.  For most errors it will also print the last
+input script command that it was processing.  Of course, LAMMPS cannot
+figure out your physics or numerical mistakes, like choosing too big a
+timestep, specifying erroneous force field coefficients, or putting 2
+atoms on top of each other!  If you run into errors that LAMMPS
+doesn't catch that you think it should flag, please send an email to
+the "developers"_http://lammps.sandia.gov/authors.html.
+
+If you get an error message about an invalid command in your input
+script, you can determine what command is causing the problem by
+looking in the log.lammps file or using the "echo command"_echo.html
+to see it on the screen.  If you get an error like "Invalid ...
+style", with ... being fix, compute, pair, etc, it means that you
+mistyped the style name or that the command is part of an optional
+package which was not compiled into your executable.  The list of
+available styles in your executable can be listed by using "the -h
+command-line swith"_Run_options.html.  The installation and
+compilation of optional packages is explained on the "Build
+packages"_Build_package.html doc page.
+
+For a given command, LAMMPS expects certain arguments in a specified
+order.  If you mess this up, LAMMPS will often flag the error, but it
+may also simply read a bogus argument and assign a value that is
+valid, but not what you wanted.  E.g. trying to read the string "abc"
+as an integer value of 0.  Careful reading of the associated doc page
+for the command should allow you to fix these problems. In most cases,
+where LAMMPS expects to read a number, either integer or floating point,
+it performs a stringent test on whether the provided input actually
+is an integer or floating-point number, respectively, and reject the
+input with an error message (for instance, when an integer is required,
+but a floating-point number 1.0 is provided):
+
+ERROR: Expected integer parameter in input script or data file :pre
+
+Some commands allow for using variable references in place of numeric
+constants so that the value can be evaluated and may change over the
+course of a run.  This is typically done with the syntax {v_name} for a
+parameter, where name is the name of the variable. On the other hand,
+immediate variable expansion with the syntax ${name} is performed while
+reading the input and before parsing commands,
+
+NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
+the documentation of the corresponding command explicitly says it is.
+
+Generally, LAMMPS will print a message to the screen and logfile and
+exit gracefully when it encounters a fatal error.  Sometimes it will
+print a WARNING to the screen and logfile and continue on; you can
+decide if the WARNING is important or not.  A WARNING message that is
+generated in the middle of a run is only printed to the screen, not to
+the logfile, to avoid cluttering up thermodynamic output.  If LAMMPS
+crashes or hangs without spitting out an error message first then it
+could be a bug (see "this section"_Errors_bugs.html) or one of the following
+cases:
+
+LAMMPS runs in the available memory a processor allows to be
+allocated.  Most reasonable MD runs are compute limited, not memory
+limited, so this shouldn't be a bottleneck on most platforms.  Almost
+all large memory allocations in the code are done via C-style malloc's
+which will generate an error message if you run out of memory.
+Smaller chunks of memory are allocated via C++ "new" statements.  If
+you are unlucky you could run out of memory just when one of these
+small requests is made, in which case the code will crash or hang (in
+parallel), since LAMMPS doesn't trap on those errors.
+
+Illegal arithmetic can cause LAMMPS to run slow or crash.  This is
+typically due to invalid physics and numerics that your simulation is
+computing.  If you see wild thermodynamic values or NaN values in your
+LAMMPS output, something is wrong with your simulation.  If you
+suspect this is happening, it is a good idea to print out
+thermodynamic info frequently (e.g. every timestep) via the
+"thermo"_thermo.html so you can monitor what is happening.
+Visualizing the atom movement is also a good idea to insure your model
+is behaving as you expect.
+
+In parallel, one way LAMMPS can hang is due to how different MPI
+implementations handle buffering of messages.  If the code hangs
+without an error message, it may be that you need to specify an MPI
+setting or two (usually via an environment variable) to enable
+buffering or boost the sizes of messages that can be buffered.

doc/src/Errors_warnings.txt

@@ -0,0 +1,934 @@
+"Higher level section"_Errors.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
+
+Warning messages :h3
+
+This is an alphabetic list of the WARNING messages LAMMPS prints out
+and the reason why.  If the explanation here is not sufficient, the
+documentation for the offending command may help.  Warning messages
+also list the source file and line number where the warning was
+generated.  For example, a message lile this:
+
+WARNING: Bond atom missing in box size check (domain.cpp:187) :pre
+
+means that line #187 in the file src/domain.cpp generated the error.
+Looking in the source code may help you figure out what went wrong.
+
+Note that warning messages from "user-contributed
+packages"_Packages_user.html are not listed here.  If such a warning
+occurs and is not self-explanatory, you'll need to look in the source
+code or contact the author of the package.
+
+Doc page with "ERROR messages"_Errors_messages.html
+
+:line
+
+:dlb
+
+{Adjusting Coulombic cutoff for MSM, new cutoff = %g} :dt
+
+The adjust/cutoff command is turned on and the Coulombic cutoff has been
+adjusted to match the user-specified accuracy. :dd
+
+{Angle atoms missing at step %ld} :dt
+
+One or more of 3 atoms needed to compute a particular angle are
+missing on this processor.  Typically this is because the pairwise
+cutoff is set too short or the angle has blown apart and an atom is
+too far away. :dd
+
+{Angle style in data file differs from currently defined angle style} :dt
+
+Self-explanatory. :dd
+
+{Atom style in data file differs from currently defined atom style} :dt
+
+Self-explanatory. :dd
+
+{Bond atom missing in box size check} :dt
+
+The 2nd atoms needed to compute a particular bond is missing on this
+processor.  Typically this is because the pairwise cutoff is set too
+short or the bond has blown apart and an atom is too far away. :dd
+
+{Bond atom missing in image check} :dt
+
+The 2nd atom in a particular bond is missing on this processor.
+Typically this is because the pairwise cutoff is set too short or the
+bond has blown apart and an atom is too far away. :dd
+
+{Bond atoms missing at step %ld} :dt
+
+The 2nd atom needed to compute a particular bond is missing on this
+processor.  Typically this is because the pairwise cutoff is set too
+short or the bond has blown apart and an atom is too far away. :dd
+
+{Bond style in data file differs from currently defined bond style} :dt
+
+Self-explanatory. :dd
+
+{Bond/angle/dihedral extent > half of periodic box length} :dt
+
+This is a restriction because LAMMPS can be confused about which image
+of an atom in the bonded interaction is the correct one to use.
+"Extent" in this context means the maximum end-to-end length of the
+bond/angle/dihedral.  LAMMPS computes this by taking the maximum bond
+length, multiplying by the number of bonds in the interaction (e.g. 3
+for a dihedral) and adding a small amount of stretch. :dd
+
+{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt
+
+Self-explanatory. :dd
+
+{Calling write_dump before a full system init.} :dt
+
+The write_dump command is used before the system has been fully
+initialized as part of a 'run' or 'minimize' command. Not all dump
+styles and features are fully supported at this point and thus the
+command may fail or produce incomplete or incorrect output. Insert
+a "run 0" command, if a full system init is required. :dd
+
+{Cannot count rigid body degrees-of-freedom before bodies are fully initialized} :dt
+
+This means the temperature associated with the rigid bodies may be
+incorrect on this timestep. :dd
+
+{Cannot count rigid body degrees-of-freedom before bodies are initialized} :dt
+
+This means the temperature associated with the rigid bodies may be
+incorrect on this timestep. :dd
+
+{Cannot include log terms without 1/r terms; setting flagHI to 1} :dt
+
+Self-explanatory. :dd
+
+{Cannot include log terms without 1/r terms; setting flagHI to 1.} :dt
+
+Self-explanatory. :dd
+
+{Charges are set, but coulombic solver is not used} :dt
+
+Self-explanatory. :dd
+
+{Charges did not converge at step %ld: %lg} :dt
+
+Self-explanatory. :dd
+
+{Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt
+
+Self-explanatory. :dd
+
+{Compute cna/atom cutoff may be too large to find ghost atom neighbors} :dt
+
+The neighbor cutoff used may not encompass enough ghost atoms
+to perform this operation correctly. :dd
+
+{Computing temperature of portions of rigid bodies} :dt
+
+The group defined by the temperature compute does not encompass all
+the atoms in one or more rigid bodies, so the change in
+degrees-of-freedom for the atoms in those partial rigid bodies will
+not be accounted for. :dd
+
+{Create_bonds max distance > minimum neighbor cutoff} :dt
+
+This means atom pairs for some atom types may not be in the neighbor
+list and thus no bond can be created between them. :dd
+
+{Delete_atoms cutoff > minimum neighbor cutoff} :dt
+
+This means atom pairs for some atom types may not be in the neighbor
+list and thus an atom in that pair cannot be deleted. :dd
+
+{Dihedral atoms missing at step %ld} :dt
+
+One or more of 4 atoms needed to compute a particular dihedral are
+missing on this processor.  Typically this is because the pairwise
+cutoff is set too short or the dihedral has blown apart and an atom is
+too far away. :dd
+
+{Dihedral problem} :dt
+
+Conformation of the 4 listed dihedral atoms is extreme; you may want
+to check your simulation geometry. :dd
+
+{Dihedral problem: %d %ld %d %d %d %d} :dt
+
+Conformation of the 4 listed dihedral atoms is extreme; you may want
+to check your simulation geometry. :dd
+
+{Dihedral style in data file differs from currently defined dihedral style} :dt
+
+Self-explanatory. :dd
+
+{Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt
+
+If the fix changes the timestep, the dump dcd file will not
+reflect the change. :dd
+
+{Energy due to X extra global DOFs will be included in minimizer energies} :dt
+
+When using fixes like box/relax, the potential energy used by the minimizer
+is augmented by an additional energy provided by the fix. Thus the printed
+converged energy may be different from the total potential energy. :dd
+
+{Energy tally does not account for 'zero yes'} :dt
+
+The energy removed by using the 'zero yes' flag is not accounted
+for in the energy tally and thus energy conservation cannot be
+monitored in this case. :dd
+
+{Estimated error in splitting of dispersion coeffs is %g} :dt
+
+Error is greater than 0.0001 percent. :dd
+
+{Ewald/disp Newton solver failed, using old method to estimate g_ewald} :dt
+
+Self-explanatory. Choosing a different cutoff value may help. :dd
+
+{FENE bond too long} :dt
+
+A FENE bond has stretched dangerously far.  It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up. :dd
+
+{FENE bond too long: %ld %d %d %g} :dt
+
+A FENE bond has stretched dangerously far.  It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up. :dd
+
+{FENE bond too long: %ld %g} :dt
+
+A FENE bond has stretched dangerously far.  It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up. :dd
+
+{Fix SRD walls overlap but fix srd overlap not set} :dt
+
+You likely want to set this in your input script. :dd
+
+{Fix bond/swap will ignore defined angles} :dt
+
+See the doc page for fix bond/swap for more info on this
+restriction. :dd
+
+{Fix deposit near setting < possible overlap separation %g} :dt
+
+This test is performed for finite size particles with a diameter, not
+for point particles.  The near setting is smaller than the particle
+diameter which can lead to overlaps. :dd
+
+{Fix evaporate may delete atom with non-zero molecule ID} :dt
+
+This is probably an error, since you should not delete only one atom
+of a molecule. :dd
+
+{Fix gcmc using full_energy option} :dt
+
+Fix gcmc has automatically turned on the full_energy option since it
+is required for systems like the one specified by the user. User input
+included one or more of the following: kspace, triclinic, a hybrid
+pair style, an eam pair style, or no "single" function for the pair
+style. :dd
+
+{Fix property/atom mol or charge w/out ghost communication} :dt
+
+A model typically needs these properties defined for ghost atoms. :dd
+
+{Fix qeq CG convergence failed (%g) after %d iterations at %ld step} :dt
+
+Self-explanatory. :dd
+
+{Fix qeq has non-zero lower Taper radius cutoff} :dt
+
+Absolute value must be <= 0.01. :dd
+
+{Fix qeq has very low Taper radius cutoff} :dt
+
+Value should typically be >= 5.0. :dd
+
+{Fix qeq/dynamic tolerance may be too small for damped dynamics} :dt
+
+Self-explanatory. :dd
+
+{Fix qeq/fire tolerance may be too small for damped fires} :dt
+
+Self-explanatory. :dd
+
+{Fix rattle should come after all other integration fixes} :dt
+
+This fix is designed to work after all other integration fixes change
+atom positions.  Thus it should be the last integration fix specified.
+If not, it will not satisfy the desired constraints as well as it
+otherwise would. :dd
+
+{Fix recenter should come after all other integration fixes} :dt
+
+Other fixes may change the position of the center-of-mass, so
+fix recenter should come last. :dd
+
+{Fix srd SRD moves may trigger frequent reneighboring} :dt
+
+This is because the SRD particles may move long distances. :dd
+
+{Fix srd grid size > 1/4 of big particle diameter} :dt
+
+This may cause accuracy problems. :dd
+
+{Fix srd particle moved outside valid domain} :dt
+
+This may indicate a problem with your simulation parameters. :dd
+
+{Fix srd particles may move > big particle diameter} :dt
+
+This may cause accuracy problems. :dd
+
+{Fix srd viscosity < 0.0 due to low SRD density} :dt
+
+This may cause accuracy problems. :dd
+
+{Fix thermal/conductivity comes before fix ave/spatial} :dt
+
+The order of these 2 fixes in your input script is such that fix
+thermal/conductivity comes first.  If you are using fix ave/spatial to
+measure the temperature profile induced by fix viscosity, then this
+may cause a glitch in the profile since you are averaging immediately
+after swaps have occurred.  Flipping the order of the 2 fixes
+typically helps. :dd
+
+{Fix viscosity comes before fix ave/spatial} :dt
+
+The order of these 2 fixes in your input script is such that
+fix viscosity comes first.  If you are using fix ave/spatial
+to measure the velocity profile induced by fix viscosity, then
+this may cause a glitch in the profile since you are averaging
+immediately after swaps have occurred.  Flipping the order
+of the 2 fixes typically helps. :dd
+
+{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt
+
+This is current restriction with Kokkos. :dd
+
+{For better accuracy use 'pair_modify table 0'} :dt
+
+The user-specified force accuracy cannot be achieved unless the table
+feature is disabled by using 'pair_modify table 0'. :dd
+
+{Geometric mixing assumed for 1/r^6 coefficients} :dt
+
+Self-explanatory. :dd
+
+{Group for fix_modify temp != fix group} :dt
+
+The fix_modify command is specifying a temperature computation that
+computes a temperature on a different group of atoms than the fix
+itself operates on.  This is probably not what you want to do. :dd
+
+{H matrix size has been exceeded: m_fill=%d H.m=%d\n} :dt
+
+This is the size of the matrix. :dd
+
+{Ignoring unknown or incorrect info command flag} :dt
+
+Self-explanatory.  An unknown argument was given to the info command.
+Compare your input with the documentation. :dd
+
+{Improper atoms missing at step %ld} :dt
+
+One or more of 4 atoms needed to compute a particular improper are
+missing on this processor.  Typically this is because the pairwise
+cutoff is set too short or the improper has blown apart and an atom is
+too far away. :dd
+
+{Improper problem: %d %ld %d %d %d %d} :dt
+
+Conformation of the 4 listed improper atoms is extreme; you may want
+to check your simulation geometry. :dd
+
+{Improper style in data file differs from currently defined improper style} :dt
+
+Self-explanatory. :dd
+
+{Inconsistent image flags} :dt
+
+The image flags for a pair on bonded atoms appear to be inconsistent.
+Inconsistent means that when the coordinates of the two atoms are
+unwrapped using the image flags, the two atoms are far apart.
+Specifically they are further apart than half a periodic box length.
+Or they are more than a box length apart in a non-periodic dimension.
+This is usually due to the initial data file not having correct image
+flags for the 2 atoms in a bond that straddles a periodic boundary.
+They should be different by 1 in that case.  This is a warning because
+inconsistent image flags will not cause problems for dynamics or most
+LAMMPS simulations.  However they can cause problems when such atoms
+are used with the fix rigid or replicate commands.  Note that if you
+have an infinite periodic crystal with bonds then it is impossible to
+have fully consistent image flags, since some bonds will cross
+periodic boundaries and connect two atoms with the same image
+flag. :dd
+
+{KIM Model does not provide 'energy'; Potential energy will be zero} :dt
+
+Self-explanatory. :dd
+
+{KIM Model does not provide 'forces'; Forces will be zero} :dt
+
+Self-explanatory. :dd
+
+{KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt
+
+Self-explanatory. :dd
+
+{KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt
+
+Self-explanatory. :dd
+
+{Kspace_modify slab param < 2.0 may cause unphysical behavior} :dt
+
+The kspace_modify slab parameter should be larger to insure periodic
+grids padded with empty space do not overlap. :dd
+
+{Less insertions than requested} :dt
+
+The fix pour command was unsuccessful at finding open space
+for as many particles as it tried to insert. :dd
+
+{Library error in lammps_gather_atoms} :dt
+
+This library function cannot be used if atom IDs are not defined
+or are not consecutively numbered. :dd
+
+{Library error in lammps_scatter_atoms} :dt
+
+This library function cannot be used if atom IDs are not defined or
+are not consecutively numbered, or if no atom map is defined.  See the
+atom_modify command for details about atom maps. :dd
+
+{Lost atoms via change_box: original %ld current %ld} :dt
+
+The command options you have used caused atoms to be lost. :dd
+
+{Lost atoms via displace_atoms: original %ld current %ld} :dt
+
+The command options you have used caused atoms to be lost. :dd
+
+{Lost atoms: original %ld current %ld} :dt
+
+Lost atoms are checked for each time thermo output is done.  See the
+thermo_modify lost command for options.  Lost atoms usually indicate
+bad dynamics, e.g. atoms have been blown far out of the simulation
+box, or moved further than one processor's sub-domain away before
+reneighboring. :dd
+
+{MSM mesh too small, increasing to 2 points in each direction} :dt
+
+Self-explanatory. :dd
+
+{Mismatch between velocity and compute groups} :dt
+
+The temperature computation used by the velocity command will not be
+on the same group of atoms that velocities are being set for. :dd
+
+{Mixing forced for lj coefficients} :dt
+
+Self-explanatory. :dd
+
+{Molecule attributes do not match system attributes} :dt
+
+An attribute is specified (e.g. diameter, charge) that is
+not defined for the specified atom style. :dd
+
+{Molecule has bond topology but no special bond settings} :dt
+
+This means the bonded atoms will not be excluded in pair-wise
+interactions. :dd
+
+{Molecule template for create_atoms has multiple molecules} :dt
+
+The create_atoms command will only create molecules of a single type,
+i.e. the first molecule in the template. :dd
+
+{Molecule template for fix gcmc has multiple molecules} :dt
+
+The fix gcmc command will only create molecules of a single type,
+i.e. the first molecule in the template. :dd
+
+{Molecule template for fix shake has multiple molecules} :dt
+
+The fix shake command will only recognize molecules of a single
+type, i.e. the first molecule in the template. :dd
+
+{More than one compute centro/atom} :dt
+
+It is not efficient to use compute centro/atom more than once. :dd
+
+{More than one compute cluster/atom} :dt
+
+It is not efficient to use compute cluster/atom  more than once. :dd
+
+{More than one compute cna/atom defined} :dt
+
+It is not efficient to use compute cna/atom  more than once. :dd
+
+{More than one compute contact/atom} :dt
+
+It is not efficient to use compute contact/atom more than once. :dd
+
+{More than one compute coord/atom} :dt
+
+It is not efficient to use compute coord/atom more than once. :dd
+
+{More than one compute damage/atom} :dt
+
+It is not efficient to use compute ke/atom more than once. :dd
+
+{More than one compute dilatation/atom} :dt
+
+Self-explanatory. :dd
+
+{More than one compute erotate/sphere/atom} :dt
+
+It is not efficient to use compute erorate/sphere/atom more than once. :dd
+
+{More than one compute hexorder/atom} :dt
+
+It is not efficient to use compute hexorder/atom more than once. :dd
+
+{More than one compute ke/atom} :dt
+
+It is not efficient to use compute ke/atom more than once. :dd
+
+{More than one compute orientorder/atom} :dt
+
+It is not efficient to use compute orientorder/atom more than once. :dd
+
+{More than one compute plasticity/atom} :dt
+
+Self-explanatory. :dd
+
+{More than one compute sna/atom} :dt
+
+Self-explanatory. :dd
+
+{More than one compute snad/atom} :dt
+
+Self-explanatory. :dd
+
+{More than one compute snav/atom} :dt
+
+Self-explanatory. :dd
+
+{More than one fix poems} :dt
+
+It is not efficient to use fix poems more than once. :dd
+
+{More than one fix rigid} :dt
+
+It is not efficient to use fix rigid more than once. :dd
+
+{Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies} :dt
+
+This is because excluding specific pair interactions also excludes
+them from long-range interactions which may not be the desired effect.
+The special_bonds command handles this consistently by insuring
+excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
+consistently by both the short-range pair style and the long-range
+solver.  This is not done for exclusions of charged atom pairs via the
+neigh_modify exclude command. :dd
+
+{New thermo_style command, previous thermo_modify settings will be lost} :dt
+
+If a thermo_style command is used after a thermo_modify command, the
+settings changed by the thermo_modify command will be reset to their
+default values.  This is because the thermo_modify command acts on
+the currently defined thermo style, and a thermo_style command creates
+a new style. :dd
+
+{No Kspace calculation with verlet/split} :dt
+
+The 2nd partition performs a kspace calculation so the kspace_style
+command must be used. :dd
+
+{No automatic unit conversion to XTC file format conventions possible for units lj} :dt
+
+This means no scaling will be performed. :dd
+
+{No fixes defined, atoms won't move} :dt
+
+If you are not using a fix like nve, nvt, npt then atom velocities and
+coordinates will not be updated during timestepping. :dd
+
+{No joints between rigid bodies, use fix rigid instead} :dt
+
+The bodies defined by fix poems are not connected by joints.  POEMS
+will integrate the body motion, but it would be more efficient to use
+fix rigid. :dd
+
+{Not using real units with pair reax} :dt
+
+This is most likely an error, unless you have created your own ReaxFF
+parameter file in a different set of units. :dd
+
+{Number of MSM mesh points changed to be a multiple of 2} :dt
+
+MSM requires that the number of grid points in each direction be a multiple
+of two and the number of grid points in one or more directions have been
+adjusted to meet this requirement. :dd
+
+{OMP_NUM_THREADS environment is not set.} :dt
+
+This environment variable must be set appropriately to use the
+USER-OMP package. :dd
+
+{One or more atoms are time integrated more than once} :dt
+
+This is probably an error since you typically do not want to
+advance the positions or velocities of an atom more than once
+per timestep. :dd
+
+{One or more chunks do not contain all atoms in molecule} :dt
+
+This may not be what you intended. :dd
+
+{One or more dynamic groups may not be updated at correct point in timestep} :dt
+
+If there are other fixes that act immediately after the initial stage
+of time integration within a timestep (i.e. after atoms move), then
+the command that sets up the dynamic group should appear after those
+fixes.  This will insure that dynamic group assignments are made
+after all atoms have moved. :dd
+
+{One or more respa levels compute no forces} :dt
+
+This is computationally inefficient. :dd
+
+{Pair COMB charge %.10f with force %.10f hit max barrier} :dt
+
+Something is possibly wrong with your model. :dd
+
+{Pair COMB charge %.10f with force %.10f hit min barrier} :dt
+
+Something is possibly wrong with your model. :dd
+
+{Pair brownian needs newton pair on for momentum conservation} :dt
+
+Self-explanatory. :dd
+
+{Pair dpd needs newton pair on for momentum conservation} :dt
+
+Self-explanatory. :dd
+
+{Pair dsmc: num_of_collisions > number_of_A} :dt
+
+Collision model in DSMC is breaking down. :dd
+
+{Pair dsmc: num_of_collisions > number_of_B} :dt
+
+Collision model in DSMC is breaking down. :dd
+
+{Pair style in data file differs from currently defined pair style} :dt
+
+Self-explanatory. :dd
+
+{Pair style restartinfo set but has no restart support} :dt
+
+This pair style has a bug, where it does not support reading and
+writing information to a restart file, but does not set the member
+variable "restartinfo" to 0 as required in that case. :dd
+
+{Particle deposition was unsuccessful} :dt
+
+The fix deposit command was not able to insert as many atoms as
+needed.  The requested volume fraction may be too high, or other atoms
+may be in the insertion region. :dd
+
+{Proc sub-domain size < neighbor skin, could lead to lost atoms} :dt
+
+The decomposition of the physical domain (likely due to load
+balancing) has led to a processor's sub-domain being smaller than the
+neighbor skin in one or more dimensions.  Since reneighboring is
+triggered by atoms moving the skin distance, this may lead to lost
+atoms, if an atom moves all the way across a neighboring processor's
+sub-domain before reneighboring is triggered. :dd
+
+{Reducing PPPM order b/c stencil extends beyond nearest neighbor processor} :dt
+
+This may lead to a larger grid than desired.  See the kspace_modify overlap
+command to prevent changing of the PPPM order. :dd
+
+{Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor} :dt
+
+This may lead to a larger grid than desired.  See the kspace_modify overlap
+command to prevent changing of the PPPM order. :dd
+
+{Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor} :dt
+
+This may lead to a larger grid than desired.  See the kspace_modify overlap
+command to prevent changing of the PPPM order. :dd
+
+{Replacing a fix, but new group != old group} :dt
+
+The ID and style of a fix match for a fix you are changing with a fix
+command, but the new group you are specifying does not match the old
+group. :dd
+
+{Replicating in a non-periodic dimension} :dt
+
+The parameters for a replicate command will cause a non-periodic
+dimension to be replicated; this may cause unwanted behavior. :dd
+
+{Resetting reneighboring criteria during PRD} :dt
+
+A PRD simulation requires that neigh_modify settings be delay = 0,
+every = 1, check = yes.  Since these settings were not in place,
+LAMMPS changed them and will restore them to their original values
+after the PRD simulation. :dd
+
+{Resetting reneighboring criteria during TAD} :dt
+
+A TAD simulation requires that neigh_modify settings be delay = 0,
+every = 1, check = yes.  Since these settings were not in place,
+LAMMPS changed them and will restore them to their original values
+after the PRD simulation. :dd
+
+{Resetting reneighboring criteria during minimization} :dt
+
+Minimization requires that neigh_modify settings be delay = 0, every =
+1, check = yes.  Since these settings were not in place, LAMMPS
+changed them and will restore them to their original values after the
+minimization. :dd
+
+{Restart file used different # of processors} :dt
+
+The restart file was written out by a LAMMPS simulation running on a
+different number of processors.  Due to round-off, the trajectories of
+your restarted simulation may diverge a little more quickly than if
+you ran on the same # of processors. :dd
+
+{Restart file used different 3d processor grid} :dt
+
+The restart file was written out by a LAMMPS simulation running on a
+different 3d grid of processors.  Due to round-off, the trajectories
+of your restarted simulation may diverge a little more quickly than if
+you ran on the same # of processors. :dd
+
+{Restart file used different boundary settings, using restart file values} :dt
+
+Your input script cannot change these restart file settings. :dd
+
+{Restart file used different newton bond setting, using restart file value} :dt
+
+The restart file value will override the setting in the input script. :dd
+
+{Restart file used different newton pair setting, using input script value} :dt
+
+The input script value will override the setting in the restart file. :dd
+
+{Restrain problem: %d %ld %d %d %d %d} :dt
+
+Conformation of the 4 listed dihedral atoms is extreme; you may want
+to check your simulation geometry. :dd
+
+{Running PRD with only one replica} :dt
+
+This is allowed, but you will get no parallel speed-up. :dd
+
+{SRD bin shifting turned on due to small lamda} :dt
+
+This is done to try to preserve accuracy. :dd
+
+{SRD bin size for fix srd differs from user request} :dt
+
+Fix SRD had to adjust the bin size to fit the simulation box.  See the
+cubic keyword if you want this message to be an error vs warning. :dd
+
+{SRD bins for fix srd are not cubic enough} :dt
+
+The bin shape is not within tolerance of cubic.  See the cubic
+keyword if you want this message to be an error vs warning. :dd
+
+{SRD particle %d started inside big particle %d on step %ld bounce %d} :dt
+
+See the inside keyword if you want this message to be an error vs
+warning. :dd
+
+{SRD particle %d started inside wall %d on step %ld bounce %d} :dt
+
+See the inside keyword if you want this message to be an error vs
+warning. :dd
+
+{Shake determinant < 0.0} :dt
+
+The determinant of the quadratic equation being solved for a single
+cluster specified by the fix shake command is numerically suspect.  LAMMPS
+will set it to 0.0 and continue. :dd
+
+{Shell command '%s' failed with error '%s'} :dt
+
+Self-explanatory. :dd
+
+{Shell command returned with non-zero status} :dt
+
+This may indicate the shell command did not operate as expected. :dd
+
+{Should not allow rigid bodies to bounce off relecting walls} :dt
+
+LAMMPS allows this, but their dynamics are not computed correctly. :dd
+
+{Should not use fix nve/limit with fix shake or fix rattle} :dt
+
+This will lead to invalid constraint forces in the SHAKE/RATTLE
+computation. :dd
+
+{Simulations might be very slow because of large number of structure factors} :dt
+
+Self-explanatory. :dd
+
+{Slab correction not needed for MSM} :dt
+
+Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM. :dd
+
+{System is not charge neutral, net charge = %g} :dt
+
+The total charge on all atoms on the system is not 0.0.
+For some KSpace solvers this is only a warning. :dd
+
+{Table inner cutoff >= outer cutoff} :dt
+
+You specified an inner cutoff for a Coulombic table that is longer
+than the global cutoff.  Probably not what you wanted. :dd
+
+{Temperature for MSST is not for group all} :dt
+
+User-assigned temperature to MSST fix does not compute temperature for
+all atoms.  Since MSST computes a global pressure, the kinetic energy
+contribution from the temperature is assumed to also be for all atoms.
+Thus the pressure used by MSST could be inaccurate. :dd
+
+{Temperature for NPT is not for group all} :dt
+
+User-assigned temperature to NPT fix does not compute temperature for
+all atoms.  Since NPT computes a global pressure, the kinetic energy
+contribution from the temperature is assumed to also be for all atoms.
+Thus the pressure used by NPT could be inaccurate. :dd
+
+{Temperature for fix modify is not for group all} :dt
+
+The temperature compute is being used with a pressure calculation
+which does operate on group all, so this may be inconsistent. :dd
+
+{Temperature for thermo pressure is not for group all} :dt
+
+User-assigned temperature to thermo via the thermo_modify command does
+not compute temperature for all atoms.  Since thermo computes a global
+pressure, the kinetic energy contribution from the temperature is
+assumed to also be for all atoms.  Thus the pressure printed by thermo
+could be inaccurate. :dd
+
+{The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015} :dt
+
+Self-explanatory. :dd
+
+{The minimizer does not re-orient dipoles when using fix efield} :dt
+
+This means that only the atom coordinates will be minimized,
+not the orientation of the dipoles. :dd
+
+{Too many common neighbors in CNA %d times} :dt
+
+More than the maximum # of neighbors was found multiple times.  This
+was unexpected. :dd
+
+{Too many inner timesteps in fix ttm} :dt
+
+Self-explanatory. :dd
+
+{Too many neighbors in CNA for %d atoms} :dt
+
+More than the maximum # of neighbors was found multiple times.  This
+was unexpected. :dd
+
+{Triclinic box skew is large} :dt
+
+The displacement in a skewed direction is normally required to be less
+than half the box length in that dimension.  E.g. the xy tilt must be
+between -half and +half of the x box length.  You have relaxed the
+constraint using the box tilt command, but the warning means that a
+LAMMPS simulation may be inefficient as a result. :dd
+
+{Use special bonds = 0,1,1 with bond style fene} :dt
+
+Most FENE models need this setting for the special_bonds command. :dd
+
+{Use special bonds = 0,1,1 with bond style fene/expand} :dt
+
+Most FENE models need this setting for the special_bonds command. :dd
+
+{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt
+
+This is likely not what you want to do.  The exclusion settings will
+eliminate neighbors in the neighbor list, which the manybody potential
+needs to calculated its terms correctly. :dd
+
+{Using compute temp/deform with inconsistent fix deform remap option} :dt
+
+Fix nvt/sllod assumes deforming atoms have a velocity profile provided
+by "remap v" or "remap none" as a fix deform option. :dd
+
+{Using compute temp/deform with no fix deform defined} :dt
+
+This is probably an error, since it makes little sense to use
+compute temp/deform in this case. :dd
+
+{Using fix srd with box deformation but no SRD thermostat} :dt
+
+The deformation will heat the SRD particles so this can
+be dangerous. :dd
+
+{Using kspace solver on system with no charge} :dt
+
+Self-explanatory. :dd
+
+{Using largest cut-off for lj/long/dipole/long long long} :dt
+
+Self-explanatory. :dd
+
+{Using largest cutoff for buck/long/coul/long} :dt
+
+Self-explanatory. :dd
+
+{Using largest cutoff for lj/long/coul/long} :dt
+
+Self-explanatory. :dd
+
+{Using largest cutoff for pair_style lj/long/tip4p/long} :dt
+
+Self-explanatory. :dd
+
+{Using package gpu without any pair style defined} :dt
+
+Self-explanatory. :dd
+
+{Using pair potential shift with pair_modify compute no} :dt
+
+The shift effects will thus not be computed. :dd
+
+{Using pair tail corrections with nonperiodic system} :dt
+
+This is probably a bogus thing to do, since tail corrections are
+computed by integrating the density of a periodic system out to
+infinity. :dd
+
+{Using pair tail corrections with pair_modify compute no} :dt
+
+The tail corrections will thus not be computed. :dd
+
+{pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c} :dt
+
+Self-explanatory. :dd
+
+:dle

doc/src/Examples.txt

@@ -1,12 +1,14 @@
-"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_perf.html :c
+"Previous Section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Tools.html :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
-7. Example problems :h2
+Example scripts :h3
 
 The LAMMPS distribution includes an examples sub-directory with many
 sample problems.  Many are 2d models that run quickly are are
@@ -46,7 +48,7 @@ Lists of both kinds of directories are given below.
 
 :line
 
-Lowercase directories :h3
+Lowercase directories :h4
 
 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
 airebo:   polyethylene with AIREBO potential
@@ -110,10 +112,10 @@ web site.
 
 If you uncomment the "dump image"_dump_image.html line(s) in the input
 script a series of JPG images will be produced by the run (assuming
-you built LAMMPS with JPG support; see "Section
-2.2"_Section_start.html#start_2 for details).  These can be viewed
-individually or turned into a movie or animated by tools like
-ImageMagick or QuickTime or various Windows-based tools.  See the
+you built LAMMPS with JPG support; see the
+"Build_settings"_Build_settings.html doc page for details).  These can
+be viewed individually or turned into a movie or animated by tools
+like ImageMagick or QuickTime or various Windows-based tools.  See the
 "dump image"_dump_image.html doc page for more details.  E.g. this
 Imagemagick command would create a GIF file suitable for viewing in a
 browser.
@@ -122,7 +124,7 @@ browser.
 
 :line
 
-Uppercase directories :h3
+Uppercase directories :h4
 
 ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc
 COUPLE: examples of how to use LAMMPS as a library
@@ -141,5 +143,5 @@ The USER directory has a large number of sub-directories which
 correspond by name to a USER package.  They contain scripts that
 illustrate how to use the command(s) provided in that package.  Many
 of the sub-directories have their own README files which give further
-instructions.  See the "Section 4"_Section_packages.html doc
+instructions.  See the "Packages_details"_Packages_details.html doc
 page for more info on specific USER packages.

doc/src/Howto.txt

@@ -0,0 +1,189 @@
+"Previous Section"_Performance.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Examples.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html#comm)
+
+:line
+
+Howto discussions :h2
+
+These doc pages describe how to perform various tasks with LAMMPS,
+both for users and developers.  The
+"glossary"_http://lammps.sandia.gov website page also lists MD
+terminology with links to corresponding LAMMPS manual pages.  The
+example input scripts included in the examples dir of the LAMMPS
+distribution and highlighted on the "Examples"_Examples.html doc page
+also show how to setup and run various kinds of simulations.
+
+Tutorials howto :h3
+
+<!-- RST
+
+.. toctree::
+   :name: tutorials
+   :maxdepth: 1
+
+   Howto_github
+   Howto_pylammps
+   Howto_bash
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Using GitHub with LAMMPS"_Howto_github.html
+"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
+"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+General howto :h3
+
+<!-- RST
+
+.. toctree::
+   :name: general
+   :maxdepth: 1
+
+   Howto_restart
+   Howto_viz
+   Howto_multiple
+   Howto_replica
+   Howto_library
+   Howto_couple
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Restart a simulation"_Howto_restart.html
+"Visualize LAMMPS snapshots"_Howto_viz.html
+"Run multiple simulations from one input script"_Howto_multiple.html
+"Multi-replica simulations"_Howto_replica.html
+"Library interface to LAMMPS"_Howto_library.html
+"Couple LAMMPS to other codes"_Howto_couple.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Settings howto :h3
+
+<!-- RST
+
+.. toctree::
+   :name: settings
+   :maxdepth: 1
+
+   Howto_2d
+   Howto_triclinic
+   Howto_thermostat
+   Howto_barostat
+   Howto_walls
+   Howto_nemd
+   Howto_dispersion
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"2d simulations"_Howto_2d.html
+"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html
+"Thermostats"_Howto_thermostat.html
+"Barostats"_Howto_barostat.html
+"Walls"_Howto_walls.html
+"NEMD simulations"_Howto_nemd.html
+"Long-range dispersion settings"_Howto_dispersion.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+
+Analysis howto :h3
+
+<!-- RST
+
+.. toctree::
+   :name: analysis
+   :maxdepth: 1
+
+   Howto_output
+   Howto_chunk
+   Howto_temperature
+   Howto_elastic
+   Howto_kappa
+   Howto_viscosity
+   Howto_diffusion
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html
+"Use chunks to calculate system properties"_Howto_chunk.html :all(b)
+"Calculate temperature"_Howto_temperature.html
+"Calculate elastic constants"_Howto_elastic.html
+"Calculate thermal conductivity"_Howto_kappa.html
+"Calculate viscosity"_Howto_viscosity.html
+"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Force fields howto :h3
+
+<!-- RST
+
+.. toctree::
+   :name: force
+   :maxdepth: 1
+
+   Howto_bioFF
+   Howto_tip3p
+   Howto_tip4p
+   Howto_spc
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
+"TIP3P water model"_Howto_tip3p.html
+"TIP4P water model"_Howto_tip4p.html
+"SPC water model"_Howto_spc.html :all(b)
+
+<!-- END_HTML_ONLY -->
+
+Packages howto :h3
+
+<!-- RST
+
+.. toctree::
+   :name: packages
+   :maxdepth: 1
+
+   Howto_spherical
+   Howto_granular
+   Howto_body
+   Howto_polarizable
+   Howto_coreshell
+   Howto_drude
+   Howto_drude2
+   Howto_manifold
+   Howto_spins
+
+END_RST -->
+
+
+<!-- HTML_ONLY -->
+
+"Finite-size spherical and aspherical particles"_Howto_spherical.html
+"Granular models"_Howto_granular.html
+"Body style particles"_Howto_body.html
+"Polarizable models"_Howto_polarizable.html
+"Adiabatic core/shell model"_Howto_coreshell.html
+"Drude induced dipoles"_Howto_drude.html
+"Drude induced dipoles (extended)"_Howto_drude2.html
+"Manifolds (surfaces)"_Howto_manifold.html
+"Magnetic spins"_Howto_spins.html :all(b)
+
+<!-- END_HTML_ONLY -->

doc/src/Howto_2d.txt

@@ -0,0 +1,48 @@
+"Higher level section"_Howto.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
+
+2d simulations :h3
+
+Use the "dimension"_dimension.html command to specify a 2d simulation.
+
+Make the simulation box periodic in z via the "boundary"_boundary.html
+command.  This is the default.
+
+If using the "create box"_create_box.html command to define a
+simulation box, set the z dimensions narrow, but finite, so that the
+create_atoms command will tile the 3d simulation box with a single z
+plane of atoms - e.g.
+
+"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre
+
+If using the "read data"_read_data.html command to read in a file of
+atom coordinates, set the "zlo zhi" values to be finite but narrow,
+similar to the create_box command settings just described.  For each
+atom in the file, assign a z coordinate so it falls inside the
+z-boundaries of the box - e.g. 0.0.
+
+Use the "fix enforce2d"_fix_enforce2d.html command as the last
+defined fix to insure that the z-components of velocities and forces
+are zeroed out every timestep.  The reason to make it the last fix is
+so that any forces induced by other fixes will be zeroed out.
+
+Many of the example input scripts included in the LAMMPS distribution
+are for 2d models.
+
+NOTE: Some models in LAMMPS treat particles as finite-size spheres, as
+opposed to point particles.  See the "atom_style
+sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html
+commands for details.  By default, for 2d simulations, such particles
+will still be modeled as 3d spheres, not 2d discs (circles), meaning
+their moment of inertia will be that of a sphere.  If you wish to
+model them as 2d discs, see the "set density/disc"_set.html command
+and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html,
+"fix nvt/sphere"_fix_nvt_sphere.html, "fix
+nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html
+commands.

doc/src/Howto_barostat.txt

@@ -0,0 +1,75 @@
+"Higher level section"_Howto.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
+
+Barostats :h3
+
+Barostatting means controlling the pressure in an MD simulation.
+"Thermostatting"_Howto_thermostat.html means controlling the
+temperature of the particles.  Since the pressure includes a kinetic
+component due to particle velocities, both these operations require
+calculation of the temperature.  Typically a target temperature (T)
+and/or pressure (P) is specified by the user, and the thermostat or
+barostat attempts to equilibrate the system to the requested T and/or
+P.
+
+Barostatting in LAMMPS is performed by "fixes"_fix.html.  Two
+barosttating methods are currently available: Nose-Hoover (npt and
+nph) and Berendsen:
+
+"fix npt"_fix_nh.html
+"fix npt/sphere"_fix_npt_sphere.html
+"fix npt/asphere"_fix_npt_asphere.html
+"fix nph"_fix_nh.html
+"fix press/berendsen"_fix_press_berendsen.html :ul
+
+The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
+and barostat.  "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
+it does no thermostatting.  Both "fix nph"_fix_nh.html and "fix
+press/berendsen"_fix_press_berendsen.html can be used in conjunction
+with any of the thermostatting fixes.
+
+As with the "thermostats"_Howto_thermostat.html, "fix npt"_fix_nh.html
+and "fix nph"_fix_nh.html only use translational motion of the
+particles in computing T and P and performing thermo/barostatting.
+"Fix npt/sphere"_fix_npt_sphere.html and "fix
+npt/asphere"_fix_npt_asphere.html thermo/barostat using not only
+translation velocities but also rotational velocities for spherical
+and aspherical particles.
+
+All of the barostatting fixes use the "compute
+pressure"_compute_pressure.html compute to calculate a current
+pressure.  By default, this compute is created with a simple "compute
+temp"_compute_temp.html (see the last argument of the "compute
+pressure"_compute_pressure.html command), which is used to calculated
+the kinetic component of the pressure.  The barostatting fixes can
+also use temperature computes that remove bias for the purpose of
+computing the kinetic component which contributes to the current
+pressure.  See the doc pages for the individual fixes and for the
+"fix_modify"_fix_modify.html command for instructions on how to assign
+a temperature or pressure compute to a barostatting fix.
+
+NOTE: As with the thermostats, the Nose/Hoover methods ("fix
+npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration.
+"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should
+be used with one of the constant NVE fixes or with one of the NVT
+fixes.
+
+Thermodynamic output, which can be setup via the
+"thermo_style"_thermo_style.html command, often includes pressure
+values.  As explained on the doc page for the
+"thermo_style"_thermo_style.html command, the default pressure is
+setup by the thermo command itself.  It is NOT the presure associated
+with any barostatting fix you have defined or with any compute you
+have defined that calculates a presure.  The doc pages for the
+barostatting fixes explain the ID of the pressure compute they create.
+Thus if you want to view these pressurse, you need to specify them
+explicitly via the "thermo_style custom"_thermo_style.html command.
+Or you can use the "thermo_modify"_thermo_modify.html command to
+re-define what pressure compute is used for default thermodynamic
+output.

doc/src/Howto_bash.txt

@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -10,6 +10,7 @@ Using LAMMPS with Bash on Windows :h3
 [written by Richard Berger]
 
 :line
+
 Starting with Windows 10 you can install Linux tools directly in Windows. This
 allows you to compile LAMMPS following the same procedure as on a real Ubuntu
 Linux installation. Software can be easily installed using the package manager

doc/src/Howto_bioFF.txt

@@ -0,0 +1,105 @@
+"Higher level section"_Howto.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
+
+CHARMM, AMBER, and DREIDING force fields :h3
+
+A force field has 2 parts: the formulas that define it and the
+coefficients used for a particular system.  Here we only discuss
+formulas implemented in LAMMPS that correspond to formulas commonly
+used in the CHARMM, AMBER, and DREIDING force fields.  Setting
+coefficients is done in the input data file via the
+"read_data"_read_data.html command or in the input script with
+commands like "pair_coeff"_pair_coeff.html or
+"bond_coeff"_bond_coeff.html.  See the "Tools"_Tools.html doc page for
+additional tools that can use CHARMM or AMBER to assign force field
+coefficients and convert their output into LAMMPS input.
+
+See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
+field.  See "(Cornell)"_#howto-Cornell for a description of the AMBER force
+field.
+
+:link(charmm,http://www.scripps.edu/brooks)
+:link(amber,http://amber.scripps.edu)
+
+These style choices compute force field formulas that are consistent
+with common options in CHARMM or AMBER.  See each command's
+documentation for the formula it computes.
+
+"bond_style"_bond_harmonic.html harmonic
+"angle_style"_angle_charmm.html charmm
+"dihedral_style"_dihedral_charmm.html charmmfsh
+"dihedral_style"_dihedral_charmm.html charmm
+"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh
+"pair_style"_pair_charmm.html lj/charmmfsw/coul/long
+"pair_style"_pair_charmm.html lj/charmm/coul/charmm
+"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
+"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
+
+"special_bonds"_special_bonds.html charmm
+"special_bonds"_special_bonds.html amber :ul
+
+NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
+released in March 2017.  We recommend they be used instead of the
+older {charmm} styles.  See discussion of the differences on the "pair
+charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
+doc pages.
+
+DREIDING is a generic force field developed by the "Goddard
+group"_http://www.wag.caltech.edu at Caltech and is useful for
+predicting structures and dynamics of organic, biological and
+main-group inorganic molecules. The philosophy in DREIDING is to use
+general force constants and geometry parameters based on simple
+hybridization considerations, rather than individual force constants
+and geometric parameters that depend on the particular combinations of
+atoms involved in the bond, angle, or torsion terms. DREIDING has an
+"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
+interactions involving a hydrogen atom on very electronegative atoms
+(N, O, F).
+
+See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
+
+These style choices compute force field formulas that are consistent
+with the DREIDING force field.  See each command's
+documentation for the formula it computes.
+
+"bond_style"_bond_harmonic.html harmonic
+"bond_style"_bond_morse.html morse :ul
+
+"angle_style"_angle_harmonic.html harmonic
+"angle_style"_angle_cosine.html cosine
+"angle_style"_angle_cosine_periodic.html cosine/periodic :ul
+
+"dihedral_style"_dihedral_charmm.html charmm
+"improper_style"_improper_umbrella.html umbrella :ul
+
+"pair_style"_pair_buck.html buck
+"pair_style"_pair_buck.html buck/coul/cut
+"pair_style"_pair_buck.html buck/coul/long
+"pair_style"_pair_lj.html lj/cut
+"pair_style"_pair_lj.html lj/cut/coul/cut
+"pair_style"_pair_lj.html lj/cut/coul/long :ul
+
+"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj
+"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul
+
+"special_bonds"_special_bonds.html dreiding :ul
+
+:line
+
+:link(howto-MacKerell)
+[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
+:link(howto-Cornell)
+[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+
+:link(howto-Mayo)
+[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).

doc/src/Howto_body.txt

@@ -1,24 +1,24 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
-Body particles :h2
+Body particles :h3
 
 [Overview:]
 
-This doc page is not about a LAMMPS input script command, but about
-body particles, which are generalized finite-size particles.
+In LAMMPS, body particles are generalized finite-size particles.
 Individual body particles can represent complex entities, such as
 surface meshes of discrete points, collections of sub-particles,
 deformable objects, etc.  Note that other kinds of finite-size
 spherical and aspherical particles are also supported by LAMMPS, such
 as spheres, ellipsoids, line segments, and triangles, but they are
-simpler entities that body particles.  See "Section
-6.14"_Section_howto.html#howto_14 for a general overview of all
+simpler entities that body particles.  See the "Howto
+spherical"_Howto_spherical.html doc page for a general overview of all
 these particle types.
 
 Body particles are used via the "atom_style body"_atom_style.html
@@ -27,19 +27,17 @@ styles supported by LAMMPS are as follows.  The name in the first
 column is used as the {bstyle} argument for the "atom_style
 body"_atom_style.html command.
 
-{nparticle} | rigid body with N sub-particles |
-{rounded/polygon} | 2d convex polygon with N vertices :tb(c=2,s=|)
+{nparticle} : rigid body with N sub-particles
+{rounded/polygon} : 2d polygons with N vertices
+{rounded/polyhedron} : 3d polyhedra with N vertices, E edges and F faces :tb(s=:)
 
 The body style determines what attributes are stored for each body and
 thus how they can be used to compute pairwise body/body or
 bond/non-body (point particle) interactions.  More details of each
 style are described below.
 
-NOTE: The rounded/polygon style listed in the table above and
-described below has not yet been relesed in LAMMPS.  It will be soon.
-
-We hope to add more styles in the future.  See "Section
-10.12"_Section_modify.html#mod_12 for details on how to add a new body
+More styles may be added in the future.  See the "Modify
+body"_Modify_body.html doc page for details on how to add a new body
 style to the code.
 
 :line
@@ -61,7 +59,7 @@ the simple particles.
 By contrast, when body particles are used, LAMMPS treats an entire
 body as a single particle for purposes of computing pairwise
 interactions, building neighbor lists, migrating particles between
-processors, outputting particles to a dump file, etc.  This means that
+processors, output of particles to a dump file, etc.  This means that
 interactions between pairs of bodies or between a body and non-body
 (point) particle need to be encoded in an appropriate pair style.  If
 such a pair style were to mimic the "fix rigid"_fix_rigid.html model,
@@ -72,17 +70,20 @@ single body/body interaction was computed.
 Thus it only makes sense to use body particles and develop such a pair
 style, when particle/particle interactions are more complex than what
 the "fix rigid"_fix_rigid.html command can already calculate.  For
-example, if particles have one or more of the following attributes:
+example, consider particles with one or more of the following
+attributes:
 
 represented by a surface mesh
 represented by a collection of geometric entities (e.g. planes + spheres)
 deformable
 internal stress that induces fragmentation :ul
 
-then the interaction between pairs of particles is likely to be more
-complex than the summation of simple sub-particle interactions.  An
-example is contact or frictional forces between particles with planar
-surfaces that inter-penetrate.
+For these models, the interaction between pairs of particles is likely
+to be more complex than the summation of simple pairwise interactions.
+An example is contact or frictional forces between particles with
+planar surfaces that inter-penetrate.  Likewise, the body particle may
+store internal state, such as a stress tensor used to compute a
+fracture criterion.
 
 These are additional LAMMPS commands that can be used with body
 particles of different styles
@@ -130,7 +131,9 @@ x1 y1 z1
 ...
 xN yN zN :pre
 
-N is the number of sub-particles in the body particle.  M = 6 + 3*N.
+where M = 6 + 3*N, and N is the number of sub-particles in the body
+particle.  
+
 The integer line has a single value N.  The floating point line(s)
 list 6 moments of inertia followed by the coordinates of the N
 sub-particles (x1 to zN) as 3N values.  These values can be listed on
@@ -148,8 +151,8 @@ center-of-mass position of the particle is specified by the x,y,z
 values in the {Atoms} section of the data file, as is the total mass
 of the body particle.
 
-The "pair_style body"_pair_body.html command can be used with this
-body style to compute body/body and body/non-body interactions.
+The "pair_style body/nparticle"_pair_body_nparticle.html command can be used
+with this body style to compute body/body and body/non-body interactions.
 
 For output purposes via the "compute
 body/local"_compute_body_local.html and "dump local"_dump.html
@@ -175,15 +178,18 @@ The {bflag2} argument is ignored.
 
 [Specifics of body style rounded/polygon:]
 
-NOTE: Aug 2016 - This body style has not yet been added to LAMMPS.
-The info below is a placeholder.
+The {rounded/polygon} body style represents body particles as a 2d
+polygon with a variable number of N vertices.  This style can only be
+used for 2d models; see the "boundary"_boundary.html command.  See the
+"pair_style body/rounded/polygon" doc page for a diagram of two
+squares with rounded circles at the vertices.  Special cases for N = 1
+(circle) and N = 2 (rod with rounded ends) can also be specified.
 
-The {rounded/polygon} body style represents body particles as a convex
-polygon with a variable number N > 2 of vertices, which can only be
-used for 2d models.  One example use of this body style is for 2d
-discrete element models, as described in "Fraige"_#Fraige.  Similar to
-body style {nparticle}, the atom_style body command for this body
-style takes two additional arguments:
+One use of this body style is for 2d discrete element models, as
+described in "Fraige"_#body-Fraige.
+
+Similar to body style {nparticle}, the atom_style body command for
+this body style takes two additional arguments:
 
 atom_style body rounded/polygon Nmin Nmax
 Nmin = minimum # of vertices in any body in the system
@@ -203,17 +209,20 @@ x1 y1 z1
 ...
 xN yN zN
 i j j k k ...
-radius :pre
+diameter :pre
 
-N is the number of vertices in the body particle.  M = 6 + 3*N + 2*N +
-1.  The integer line has a single value N.  The floating point line(s)
+where M = 6 + 3*N + 2*N + 1, and N is the number of vertices in the
+body particle.
+
+The integer line has a single value N.  The floating point line(s)
 list 6 moments of inertia followed by the coordinates of the N
-vertices (x1 to zN) as 3N values, followed by 2N vertex indices
-corresponding to the end points of the N edges, followed by a single
-radius value = the smallest circle encompassing the polygon.  That
-last value is used to facilitate the body/body contact detection.
-These floating-point values can be listed on as many lines as you
-wish; see the "read_data"_read_data.html command for more details.
+vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by
+2N vertex indices corresponding to the end points of the N edges,
+followed by a single diameter value = the rounded diameter of the
+circle that surrounds each vertex. The diameter value can be different
+for each body particle. These floating-point values can be listed on
+as many lines as you wish; see the "read_data"_read_data.html command
+for more details.
 
 The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
 values consistent with the current orientation of the rigid body
@@ -225,8 +234,11 @@ from the center-of-mass of the body particle.  The center-of-mass
 position of the particle is specified by the x,y,z values in the
 {Atoms} section of the data file.
 
-For example, the following information would specify a square
-particles whose edge length is sqrt(2):
+For example, the following information would specify a square particle
+whose edge length is sqrt(2) and rounded diameter is 1.0.  The
+orientation of the square is aligned with the xy coordinate axes which
+is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
+1 1 4 0 0 0. Note that only Izz matters in 2D simulations.
 
 3 1 27
 4
@@ -235,12 +247,178 @@ particles whose edge length is sqrt(2):
 -0.7071 0.7071 0
 0.7071 0.7071 0
 0.7071 -0.7071 0
-0 1 1 2 2 3 3 0
+0 1
+1 2
+2 3
+3 0
 1.0 :pre
 
+A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends
+by circles of diameter 0.5, is specified as follows:
+
+1 1 13
+2
+1 1 1.33333 0 0 0
+-2 0 0
+2 0 0
+0.5 :pre
+
+A disk, whose diameter is 3.0, mass 1.0, is specified as follows:
+
+1 1 10
+1
+1 1 4.5 0 0 0
+0 0 0
+3.0 :pre
+
 The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html
 command can be used with this body style to compute body/body
-interactions.
+interactions.  The "fix wall/body/polygon"_fix_wall_body_polygon.html
+command can be used with this body style to compute the interaction of
+body particles with a wall.
+
+:line
+
+[Specifics of body style rounded/polyhedron:]
+
+The {rounded/polyhedron} body style represents body particles as a 3d
+polyhedron with a variable number of N vertices, E edges and F faces.
+This style can only be used for 3d models; see the
+"boundary"_boundary.html command.  See the "pair_style
+body/rounded/polygon" doc page for a diagram of a two 2d squares with
+rounded circles at the vertices.  A 3d cube with rounded spheres at
+the 8 vertices and 12 rounded edges would be similar.  Special cases
+for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be
+specified.
+
+This body style is for 3d discrete element models, as described in
+"Wang"_#body-Wang.
+
+Similar to body style {rounded/polygon}, the atom_style body command
+for this body style takes two additional arguments:
+
+atom_style body rounded/polyhedron Nmin Nmax
+Nmin = minimum # of vertices in any body in the system
+Nmax = maximum # of vertices in any body in the system :pre
+
+The Nmin and Nmax arguments are used to bound the size of data
+structures used internally by each particle.
+
+When the "read_data"_read_data.html command reads a data file for this
+body style, the following information must be provided for each entry
+in the {Bodies} section of the data file:
+
+atom-ID 3 M
+N E F
+ixx iyy izz ixy ixz iyz
+x1 y1 z1
+...
+xN yN zN
+0 1
+1 2 
+2 3
+...
+0 1 2 -1
+0 2 3 -1
+...
+1 2 3 4
+diameter :pre
+
+where M = 6 + 3*N + 2*E + 4*F + 1, and N is the number of vertices in
+the body particle, E = number of edges, F = number of faces.
+
+The integer line has three values: number of vertices (N), number of
+edges (E) and number of faces (F). The floating point line(s) list 6
+moments of inertia followed by the coordinates of the N vertices (x1
+to zN) as 3N values, followed by 2N vertex indices corresponding to
+the end points of the E edges, then 4*F vertex indices defining F
+faces.  The last value is the diameter value = the rounded diameter of
+the sphere that surrounds each vertex. The diameter value can be
+different for each body particle. These floating-point values can be
+listed on as many lines as you wish; see the
+"read_data"_read_data.html command for more details.  Because the
+maxmimum vertices per face is hard-coded to be 4
+(i.e. quadrilaterals), faces with more than 4 vertices need to be
+split into triangles or quadrilaterals.  For triangular faces, the
+last vertex index should be set to -1.
+
+The ordering of the 4 vertices within a face should follow
+the right-hand rule so that the normal vector of the face points
+outwards from the center of mass.
+
+The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
+values consistent with the current orientation of the rigid body
+around its center of mass.  The values are with respect to the
+simulation box XYZ axes, not with respect to the principal axes of the
+rigid body itself.  LAMMPS performs the latter calculation internally.
+The coordinates of each vertex are specified as its x,y,z displacement
+from the center-of-mass of the body particle.  The center-of-mass
+position of the particle is specified by the x,y,z values in the
+{Atoms} section of the data file.
+
+For example, the following information would specify a cubic particle
+whose edge length is 2.0 and rounded diameter is 0.5.
+The orientation of the cube is aligned with the xyz coordinate axes
+which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz
+iyz = 0.667 0.667 0.667 0 0 0.
+
+1 3 79
+8 12 6
+0.667 0.667 0.667 0 0 0
+1 1 1
+1 -1 1
+-1 -1 1
+-1 1 1
+1 1 -1
+1 -1 -1
+-1 -1 -1
+-1 1 -1
+0 1
+1 2
+2 3
+3 0
+4 5
+5 6
+6 7
+7 4
+0 4
+1 5
+2 6
+3 7
+0 1 2 3
+4 5 6 7
+0 1 5 4
+1 2 6 5
+2 3 7 6
+3 0 4 7
+0.5 :pre
+
+A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends
+by circles of diameter 0.5, is specified as follows:
+
+1 1 13
+2
+0 1.33333 1.33333 0 0 0
+-2 0 0
+2 0 0
+0.5 :pre
+
+A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
+
+1 1 10
+1
+0.9 0.9 0.9 0 0 0
+0 0 0
+3.0 :pre
+
+The "pair_style
+body/rounded/polhedron"_pair_body_rounded_polyhedron.html command can
+be used with this body style to compute body/body interactions.  The
+"fix wall/body/polyhedron"_fix_wall_body_polygon.html command can be
+used with this body style to compute the interaction of body particles
+with a wall.
+
+:line
 
 For output purposes via the "compute
 body/local"_compute_body_local.html and "dump local"_dump.html
@@ -257,10 +435,10 @@ the body particle itself.  These values are calculated using the
 current COM and orientation of the body particle.
 
 For images created by the "dump image"_dump_image.html command, if the
-{body} keyword is set, then each body particle is drawn as a convex
-polygon consisting of N line segments.  Note that the line segments
-are drawn between the N vertices, which does not correspond exactly to
-the physical extent of the body (because the "pair_style
+{body} keyword is set, then each body particle is drawn as a polygon
+consisting of N line segments.  Note that the line segments are drawn
+between the N vertices, which does not correspond exactly to the
+physical extent of the body (because the "pair_style
 rounded/polygon"_pair_body_rounded_polygon.html defines finite-size
 spheres at those point and the line segments between the spheres are
 tangent to the spheres).  The drawn diameter of each line segment is
@@ -269,6 +447,10 @@ determined by the {bflag1} parameter for the {body} keyword.  The
 
 :line
 
-:link(Fraige)
+:link(body-Fraige)
 [(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
 Particuology, 6, 455 (2008).
+
+:link(body-Wang)
+[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
+Matter, 13, 1 (2011).

doc/src/Howto_chunk.txt

@@ -0,0 +1,166 @@
+"Higher level section"_Howto.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
+
+Use chunks to calculate system properties :h3
+
+In LAMMS, "chunks" are collections of atoms, as defined by the
+"compute chunk/atom"_compute_chunk_atom.html command, which assigns
+each atom to a chunk ID (or to no chunk at all).  The number of chunks
+and the assignment of chunk IDs to atoms can be static or change over
+time.  Examples of "chunks" are molecules or spatial bins or atoms
+with similar values (e.g. coordination number or potential energy).
+
+The per-atom chunk IDs can be used as input to two other kinds of
+commands, to calculate various properties of a system:
+
+"fix ave/chunk"_fix_ave_chunk.html
+any of the "compute */chunk"_compute.html commands :ul
+
+Here, each of the 3 kinds of chunk-related commands is briefly
+overviewed.  Then some examples are given of how to compute different
+properties with chunk commands.
+
+Compute chunk/atom command: :h4
+
+This compute can assign atoms to chunks of various styles.  Only atoms
+in the specified group and optional specified region are assigned to a
+chunk.  Here are some possible chunk definitions:
+
+atoms in same molecule | chunk ID = molecule ID |
+atoms of same atom type | chunk ID = atom type |
+all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom |
+atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command |
+atoms in same spatial bin | chunk ID = bin ID |
+atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies |
+atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html |
+atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2)
+
+Note that chunk IDs are integer values, so for atom properties or
+computes that produce a floating point value, they will be truncated
+to an integer.  You could also use the compute in a variable that
+scales the floating point value to spread it across multiple integers.
+
+Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
+pencils, 3d bins = boxes, spherical bins, cylindrical bins.
+
+This compute also calculates the number of chunks {Nchunk}, which is
+used by other commands to tally per-chunk data.  {Nchunk} can be a
+static value or change over time (e.g. the number of clusters).  The
+chunk ID for an individual atom can also be static (e.g. a molecule
+ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
+
+Note that this compute allows the per-atom output of other
+"computes"_compute.html, "fixes"_fix.html, and
+"variables"_variable.html to be used to define chunk IDs for each
+atom.  This means you can write your own compute or fix to output a
+per-atom quantity to use as chunk ID.  See the "Modify"_Modify.html
+doc pages for info on how to do this.  You can also define a "per-atom
+variable"_variable.html in the input script that uses a formula to
+generate a chunk ID for each atom.
+
+Fix ave/chunk command: :h4
+
+This fix takes the ID of a "compute
+chunk/atom"_compute_chunk_atom.html command as input.  For each chunk,
+it then sums one or more specified per-atom values over the atoms in
+each chunk.  The per-atom values can be any atom property, such as
+velocity, force, charge, potential energy, kinetic energy, stress,
+etc.  Additional keywords are defined for per-chunk properties like
+density and temperature.  More generally any per-atom value generated
+by other "computes"_compute.html, "fixes"_fix.html, and "per-atom
+variables"_variable.html, can be summed over atoms in each chunk.
+
+Similar to other averaging fixes, this fix allows the summed per-chunk
+values to be time-averaged in various ways, and output to a file.  The
+fix produces a global array as output with one row of values per
+chunk.
+
+Compute */chunk commands: :h4
+
+Currently the following computes operate on chunks of atoms to produce
+per-chunk values.
+
+"compute com/chunk"_compute_com_chunk.html
+"compute gyration/chunk"_compute_gyration_chunk.html
+"compute inertia/chunk"_compute_inertia_chunk.html
+"compute msd/chunk"_compute_msd_chunk.html
+"compute property/chunk"_compute_property_chunk.html
+"compute temp/chunk"_compute_temp_chunk.html
+"compute torque/chunk"_compute_vcm_chunk.html
+"compute vcm/chunk"_compute_vcm_chunk.html :ul
+
+They each take the ID of a "compute
+chunk/atom"_compute_chunk_atom.html command as input.  As their names
+indicate, they calculate the center-of-mass, radius of gyration,
+moments of inertia, mean-squared displacement, temperature, torque,
+and velocity of center-of-mass for each chunk of atoms.  The "compute
+property/chunk"_compute_property_chunk.html command can tally the
+count of atoms in each chunk and extract other per-chunk properties.
+
+The reason these various calculations are not part of the "fix
+ave/chunk command"_fix_ave_chunk.html, is that each requires a more
+complicated operation than simply summing and averaging over per-atom
+values in each chunk.  For example, many of them require calculation
+of a center of mass, which requires summing mass*position over the
+atoms and then dividing by summed mass.
+
+All of these computes produce a global vector or global array as
+output, wih one or more values per chunk.  They can be used
+in various ways:
+
+As input to the "fix ave/time"_fix_ave_time.html command, which can
+write the values to a file and optionally time average them. :ulb,l
+
+As input to the "fix ave/histo"_fix_ave_histo.html command to
+histogram values across chunks.  E.g. a histogram of cluster sizes or
+molecule diffusion rates. :l
+
+As input to special functions of "equal-style
+variables"_variable.html, like sum() and max().  E.g. to find the
+largest cluster or fastest diffusing molecule. :l
+:ule
+
+Example calculations with chunks :h4
+
+Here are examples using chunk commands to calculate various
+properties:
+
+(1) Average velocity in each of 1000 2d spatial bins:
+
+compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
+fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre
+
+(2) Temperature in each spatial bin, after subtracting a flow
+velocity:
+
+compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
+compute vbias all temp/profile 1 0 0 y 10
+fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre
+
+(3) Center of mass of each molecule:
+
+compute cc1 all chunk/atom molecule
+compute myChunk all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre
+
+(4) Total force on each molecule and ave/max across all molecules:
+
+compute cc1 all chunk/atom molecule
+fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
+variable xave equal ave(f_1\[2\])
+variable xmax equal max(f_1\[2\])
+thermo 1000
+thermo_style custom step temp v_xave v_xmax :pre
+
+(5) Histogram of cluster sizes:
+
+compute cluster all cluster/atom 1.0
+compute cc1 all chunk/atom c_cluster compress yes
+compute size all property/chunk cc1 count
+fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre

doc/src/Howto_coreshell.txt

@@ -0,0 +1,253 @@
+"Higher level section"_Howto.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
+
+Adiabatic core/shell model :h3
+
+The adiabatic core-shell model by "Mitchell and
+Fincham"_#MitchellFincham is a simple method for adding polarizability
+to a system.  In order to mimic the electron shell of an ion, a
+satellite particle is attached to it. This way the ions are split into
+a core and a shell where the latter is meant to react to the
+electrostatic environment inducing polarizability.  See the "Howto
+polarizable"_Howto_polarizable.html doc page for a discussion of all
+the polarizable models available in LAMMPS.
+
+Technically, shells are attached to the cores by a spring force f =
+k*r where k is a parametrized spring constant and r is the distance
+between the core and the shell. The charges of the core and the shell
+add up to the ion charge, thus q(ion) = q(core) + q(shell). This
+setup introduces the ion polarizability (alpha) given by
+alpha = q(shell)^2 / k. In a
+similar fashion the mass of the ion is distributed on the core and the
+shell with the core having the larger mass.
+
+To run this model in LAMMPS, "atom_style"_atom_style.html {full} can
+be used since atom charge and bonds are needed.  Each kind of
+core/shell pair requires two atom types and a bond type.  The core and
+shell of a core/shell pair should be bonded to each other with a
+harmonic bond that provides the spring force. For example, a data file
+for NaCl, as found in examples/coreshell, has this format:
+
+432   atoms  # core and shell atoms
+216   bonds  # number of core/shell springs :pre
+
+4     atom types  # 2 cores and 2 shells for Na and Cl
+2     bond types :pre
+
+0.0 24.09597 xlo xhi
+0.0 24.09597 ylo yhi
+0.0 24.09597 zlo zhi :pre
+
+Masses       # core/shell mass ratio = 0.1 :pre
+
+1 20.690784  # Na core
+2 31.90500   # Cl core
+3 2.298976   # Na shell
+4 3.54500    # Cl shell :pre
+
+Atoms :pre
+
+1    1    2   1.5005    0.00000000   0.00000000   0.00000000 # core of core/shell pair 1
+2    1    4  -2.5005    0.00000000   0.00000000   0.00000000 # shell of core/shell pair 1
+3    2    1   1.5056    4.01599500   4.01599500   4.01599500 # core of core/shell pair 2
+4    2    3  -0.5056    4.01599500   4.01599500   4.01599500 # shell of core/shell pair 2
+(...) :pre
+
+Bonds   # Bond topology for spring forces :pre
+
+1     2     1     2   # spring for core/shell pair 1
+2     2     3     4   # spring for core/shell pair 2
+(...) :pre
+
+Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
+defined between the shells.  Coulombic interactions are defined
+between all cores and shells.  If desired, additional bonds can be
+specified between cores.
+
+The "special_bonds"_special_bonds.html command should be used to
+turn-off the Coulombic interaction within core/shell pairs, since that
+interaction is set by the bond spring.  This is done using the
+"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0,
+which is the default value.  It needs to be considered whether one has
+to adjust the "special_bonds"_special_bonds.html weighting according
+to the molecular topology since the interactions of the shells are
+bypassed over an extra bond.
+
+Note that this core/shell implementation does not require all ions to
+be polarized.  One can mix core/shell pairs and ions without a
+satellite particle if desired.
+
+Since the core/shell model permits distances of r = 0.0 between the
+core and shell, a pair style with a "cs" suffix needs to be used to
+implement a valid long-range Coulombic correction.  Several such pair
+styles are provided in the CORESHELL package.  See "this doc
+page"_pair_cs.html for details.  All of the core/shell enabled pair
+styles require the use of a long-range Coulombic solver, as specified
+by the "kspace_style"_kspace_style.html command.  Either the PPPM or
+Ewald solvers can be used.
+
+For the NaCL example problem, these pair style and bond style settings
+are used:
+
+pair_style      born/coul/long/cs 20.0 20.0
+pair_coeff      * *      0.0 1.000   0.00  0.00   0.00
+pair_coeff      3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+pair_coeff      3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+pair_coeff      4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre
+
+bond_style      harmonic
+bond_coeff      1 63.014 0.0
+bond_coeff      2 25.724 0.0 :pre
+
+When running dynamics with the adiabatic core/shell model, the
+following issues should be considered.  The relative motion of
+the core and shell particles corresponds to the polarization,
+hereby an instantaneous relaxation of the shells is approximated
+and a fast core/shell spring frequency ensures a nearly constant
+internal kinetic energy during the simulation.
+Thermostats can alter this polarization behaviour, by scaling the
+internal kinetic energy, meaning the shell will not react freely to
+its electrostatic environment.
+Therefore it is typically desirable to decouple the relative motion of
+the core/shell pair, which is an imaginary degree of freedom, from the
+real physical system.  To do that, the "compute
+temp/cs"_compute_temp_cs.html command can be used, in conjunction with
+any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
+langevin"_fix_langevin.html.  This compute uses the center-of-mass velocity
+of the core/shell pairs to calculate a temperature, and insures that
+velocity is what is rescaled for thermostatting purposes.  This
+compute also works for a system with both core/shell pairs and
+non-polarized ions (ions without an attached satellite particle).  The
+"compute temp/cs"_compute_temp_cs.html command requires input of two
+groups, one for the core atoms, another for the shell atoms.
+Non-polarized ions which might also be included in the treated system
+should not be included into either of these groups, they are taken
+into account by the {group-ID} (2nd argument) of the compute.  The
+groups can be defined using the "group {type}"_group.html command.
+Note that to perform thermostatting using this definition of
+temperature, the "fix modify temp"_fix_modify.html command should be
+used to assign the compute to the thermostat fix.  Likewise the
+"thermo_modify temp"_thermo_modify.html command can be used to make
+this temperature be output for the overall system.
+
+For the NaCl example, this can be done as follows:
+
+group cores type 1 2
+group shells type 3 4
+compute CSequ all temp/cs cores shells
+fix thermoberendsen all temp/berendsen 1427 1427 0.4    # thermostat for the true physical system
+fix thermostatequ all nve                               # integrator as needed for the berendsen thermostat
+fix_modify thermoberendsen temp CSequ
+thermo_modify temp CSequ                                # output of center-of-mass derived temperature :pre
+
+The pressure for the core/shell system is computed via the regular
+LAMMPS convention by "treating the cores and shells as individual
+particles"_#MitchellFincham2. For the thermo output of the pressure
+as well as for the application of a barostat, it is necessary to
+use an additional "pressure"_compute_pressure.html compute based on
+the default "temperature"_compute_temp.html and specifying it as a
+second argument in "fix modify"_fix_modify.html and
+"thermo_modify"_thermo_modify.html resulting in:
+
+(...)
+compute CSequ all temp/cs cores shells
+compute thermo_press_lmp all pressure thermo_temp       # pressure for individual particles
+thermo_modify temp CSequ press thermo_press_lmp         # modify thermo to regular pressure
+fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
+fix_modify press_bar temp CSequ press thermo_press_lmp  # pressure modification for correct kinetic scalar :pre
+
+If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
+relative motion of the core and the shell should in theory be
+stable.  However numerical fluctuation can introduce a small
+momentum to the system, which is noticable over long trajectories.
+Therefore it is recommendable to use the "fix
+momentum"_fix_momentum.html command in combination with "compute
+temp/cs"_compute_temp_cs.html when equilibrating the system to
+prevent any drift.
+
+When initializing the velocities of a system with core/shell pairs, it
+is also desirable to not introduce energy into the relative motion of
+the core/shell particles, but only assign a center-of-mass velocity to
+the pairs.  This can be done by using the {bias} keyword of the
+"velocity create"_velocity.html command and assigning the "compute
+temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
+"velocity"_velocity.html command, e.g.
+
+velocity all create 1427 134 bias yes temp CSequ
+velocity all scale 1427 temp CSequ :pre
+
+To maintain the correct polarizability of the core/shell pairs, the
+kinetic energy of the internal motion shall remain nearly constant.
+Therefore the choice of spring force and mass ratio need to ensure
+much faster relative motion of the 2 atoms within the core/shell pair
+than their center-of-mass velocity. This allows the shells to
+effectively react instantaneously to the electrostatic environment and
+limits energy transfer to or from the core/shell oscillators.
+This fast movement also dictates the timestep that can be used.
+
+The primary literature of the adiabatic core/shell model suggests that
+the fast relative motion of the core/shell pairs only allows negligible
+energy transfer to the environment.
+The mentioned energy transfer will typically lead to a small drift
+in total energy over time.  This internal energy can be monitored
+using the "compute chunk/atom"_compute_chunk_atom.html and "compute
+temp/chunk"_compute_temp_chunk.html commands.  The internal kinetic
+energies of each core/shell pair can then be summed using the sum()
+special function of the "variable"_variable.html command.  Or they can
+be time/averaged and output using the "fix ave/time"_fix_ave_time.html
+command.  To use these commands, each core/shell pair must be defined
+as a "chunk".  If each core/shell pair is defined as its own molecule,
+the molecule ID can be used to define the chunks.  If cores are bonded
+to each other to form larger molecules, the chunks can be identified
+by the "fix property/atom"_fix_property_atom.html via assigning a
+core/shell ID to each atom using a special field in the data file read
+by the "read_data"_read_data.html command.  This field can then be
+accessed by the "compute property/atom"_compute_property_atom.html
+command, to use as input to the "compute
+chunk/atom"_compute_chunk_atom.html command to define the core/shell
+pairs as chunks.
+
+For example if core/shell pairs are the only molecules:
+
+read_data NaCl_CS_x0.1_prop.data
+compute prop all property/atom molecule
+compute cs_chunk all chunk/atom c_prop
+compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
+fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
+
+For example if core/shell pairs and other molecules are present:
+
+fix csinfo all property/atom i_CSID                       # property/atom command
+read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info  # atom property added in the data-file
+compute prop all property/atom i_CSID
+(...) :pre
+
+The additional section in the date file would be formatted like this:
+
+CS-Info         # header of additional section :pre
+
+1   1           # column 1 = atom ID, column 2 = core/shell ID
+2   1
+3   2
+4   2
+5   3
+6   3
+7   4
+8   4
+(...) :pre
+
+:line
+
+:link(MitchellFincham)
+[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter,
+5, 1031-1038 (1993).
+
+:link(MitchellFincham2)
+[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
+6, 393-404 (1994).

doc/src/Howto_couple.txt

@@ -0,0 +1,104 @@
+"Higher level section"_Howto.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
+
+Coupling LAMMPS to other codes :h3
+
+LAMMPS is designed to allow it to be coupled to other codes.  For
+example, a quantum mechanics code might compute forces on a subset of
+atoms and pass those forces to LAMMPS.  Or a continuum finite element
+(FE) simulation might use atom positions as boundary conditions on FE
+nodal points, compute a FE solution, and return interpolated forces on
+MD atoms.
+
+LAMMPS can be coupled to other codes in at least 3 ways.  Each has
+advantages and disadvantages, which you'll have to think about in the
+context of your application.
+
+(1) Define a new "fix"_fix.html command that calls the other code.  In
+this scenario, LAMMPS is the driver code.  During its timestepping,
+the fix is invoked, and can make library calls to the other code,
+which has been linked to LAMMPS as a library.  This is the way the
+"POEMS"_poems package that performs constrained rigid-body motion on
+groups of atoms is hooked to LAMMPS.  See the "fix
+poems"_fix_poems.html command for more details.  See the
+"Modify"_Modify.html doc pages for info on how to add a new fix to
+LAMMPS.
+
+:link(poems,http://www.rpi.edu/~anderk5/lab)
+
+(2) Define a new LAMMPS command that calls the other code.  This is
+conceptually similar to method (1), but in this case LAMMPS and the
+other code are on a more equal footing.  Note that now the other code
+is not called during the timestepping of a LAMMPS run, but between
+runs.  The LAMMPS input script can be used to alternate LAMMPS runs
+with calls to the other code, invoked via the new command.  The
+"run"_run.html command facilitates this with its {every} option, which
+makes it easy to run a few steps, invoke the command, run a few steps,
+invoke the command, etc.
+
+In this scenario, the other code can be called as a library, as in
+(1), or it could be a stand-alone code, invoked by a system() call
+made by the command (assuming your parallel machine allows one or more
+processors to start up another program).  In the latter case the
+stand-alone code could communicate with LAMMPS thru files that the
+command writes and reads.
+
+See the "Modify command"_Modify_command.html doc page for info on how
+to add a new command to LAMMPS.
+
+(3) Use LAMMPS as a library called by another code.  In this case the
+other code is the driver and calls LAMMPS as needed.  Or a wrapper
+code could link and call both LAMMPS and another code as libraries.
+Again, the "run"_run.html command has options that allow it to be
+invoked with minimal overhead (no setup or clean-up) if you wish to do
+multiple short runs, driven by another program.
+
+Examples of driver codes that call LAMMPS as a library are included in
+the examples/COUPLE directory of the LAMMPS distribution; see
+examples/COUPLE/README for more details:
+
+simple: simple driver programs in C++ and C which invoke LAMMPS as a
+library :ulb,l
+
+lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical
+MD with quantum forces calculated by a density functional code :l
+
+lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple
+a kinetic Monte Carlo model for grain growth using MD to calculate
+strain induced across grain boundaries :l
+:ule
+
+:link(quest,http://dft.sandia.gov/Quest)
+:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
+
+The "Build basics"_Build_basics.html doc page describes how to build
+LAMMPS as a library.  Once this is done, you can interface with LAMMPS
+either via C++, C, Fortran, or Python (or any other language that
+supports a vanilla C-like interface).  For example, from C++ you could
+create one (or more) "instances" of LAMMPS, pass it an input script to
+process, or execute individual commands, all by invoking the correct
+class methods in LAMMPS.  From C or Fortran you can make function
+calls to do the same things.  See the "Python"_Python_head.html doc
+pages for a description of the Python wrapper provided with LAMMPS
+that operates through the LAMMPS library interface.
+
+The files src/library.cpp and library.h contain the C-style interface
+to LAMMPS.  See the "Howto library"_Howto_library.html doc page for a
+description of the interface and how to extend it for your needs.
+
+Note that the lammps_open() function that creates an instance of
+LAMMPS takes an MPI communicator as an argument.  This means that
+instance of LAMMPS will run on the set of processors in the
+communicator.  Thus the calling code can run LAMMPS on all or a subset
+of processors.  For example, a wrapper script might decide to
+alternate between LAMMPS and another code, allowing them both to run
+on all the processors.  Or it might allocate half the processors to
+LAMMPS and half to the other code and run both codes simultaneously
+before syncing them up periodically.  Or it might instantiate multiple
+instances of LAMMPS to perform different calculations.

doc/src/Howto_diffusion.txt

@@ -0,0 +1,31 @@
+"Higher level section"_Howto.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
+
+Calculate diffusion coefficients :h3
+
+The diffusion coefficient D of a material can be measured in at least
+2 ways using various options in LAMMPS.  See the examples/DIFFUSE
+directory for scripts that implement the 2 methods discussed here for
+a simple Lennard-Jones fluid model.
+
+The first method is to measure the mean-squared displacement (MSD) of
+the system, via the "compute msd"_compute_msd.html command.  The slope
+of the MSD versus time is proportional to the diffusion coefficient.
+The instantaneous MSD values can be accumulated in a vector via the
+"fix vector"_fix_vector.html command, and a line fit to the vector to
+compute its slope via the "variable slope"_variable.html function, and
+thus extract D.
+
+The second method is to measure the velocity auto-correlation function
+(VACF) of the system, via the "compute vacf"_compute_vacf.html
+command.  The time-integral of the VACF is proportional to the
+diffusion coefficient.  The instantaneous VACF values can be
+accumulated in a vector via the "fix vector"_fix_vector.html command,
+and time integrated via the "variable trap"_variable.html function,
+and thus extract D.

doc/src/Howto_dispersion.txt

@@ -0,0 +1,108 @@
+"Higher level section"_Howto.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
+
+Long-range dispersion settings :h3
+
+The PPPM method computes interactions by splitting the pair potential
+into two parts, one of which is computed in a normal pairwise fashion,
+the so-called real-space part, and one of which is computed using the
+Fourier transform, the so called reciprocal-space or kspace part.  For
+both parts, the potential is not computed exactly but is approximated.
+Thus, there is an error in both parts of the computation, the
+real-space and the kspace error. The just mentioned facts are true
+both for the PPPM for Coulomb as well as dispersion interactions. The
+deciding difference - and also the reason why the parameters for
+pppm/disp have to be selected with more care - is the impact of the
+errors on the results: The kspace error of the PPPM for Coulomb and
+dispersion interaction and the real-space error of the PPPM for
+Coulomb interaction have the character of noise. In contrast, the
+real-space error of the PPPM for dispersion has a clear physical
+interpretation: the underprediction of cohesion. As a consequence, the
+real-space error has a much stronger effect than the kspace error on
+simulation results for pppm/disp.  Parameters must thus be chosen in a
+way that this error is much smaller than the kspace error.
+
+When using pppm/disp and not making any specifications on the PPPM
+parameters via the kspace modify command, parameters will be tuned
+such that the real-space error and the kspace error are equal.  This
+will result in simulations that are either inaccurate or slow, both of
+which is not desirable. For selecting parameters for the pppm/disp
+that provide fast and accurate simulations, there are two approaches,
+which both have their up- and downsides.
+
+The first approach is to set desired real-space an kspace accuracies
+via the {kspace_modify force/disp/real} and {kspace_modify
+force/disp/kspace} commands. Note that the accuracies have to be
+specified in force units and are thus dependent on the chosen unit
+settings. For real units, 0.0001 and 0.002 seem to provide reasonable
+accurate and efficient computations for the real-space and kspace
+accuracies.  0.002 and 0.05 work well for most systems using lj
+units. PPPM parameters will be generated based on the desired
+accuracies. The upside of this approach is that it usually provides a
+good set of parameters and will work for both the {kspace_modify diff
+ad} and {kspace_modify diff ik} options.  The downside of the method
+is that setting the PPPM parameters will take some time during the
+initialization of the simulation.
+
+The second approach is to set the parameters for the pppm/disp
+explicitly using the {kspace_modify mesh/disp}, {kspace_modify
+order/disp}, and {kspace_modify gewald/disp} commands. This approach
+requires a more experienced user who understands well the impact of
+the choice of parameters on the simulation accuracy and
+performance. This approach provides a fast initialization of the
+simulation. However, it is sensitive to errors: A combination of
+parameters that will perform well for one system might result in
+far-from-optimal conditions for other simulations. For example,
+parameters that provide accurate and fast computations for
+all-atomistic force fields can provide insufficient accuracy or
+united-atomistic force fields (which is related to that the latter
+typically have larger dispersion coefficients).
+
+To avoid inaccurate or inefficient simulations, the pppm/disp stops
+simulations with an error message if no action is taken to control the
+PPPM parameters. If the automatic parameter generation is desired and
+real-space and kspace accuracies are desired to be equal, this error
+message can be suppressed using the {kspace_modify disp/auto yes}
+command.
+
+A reasonable approach that combines the upsides of both methods is to
+make the first run using the {kspace_modify force/disp/real} and
+{kspace_modify force/disp/kspace} commands, write down the PPPM
+parameters from the outut, and specify these parameters using the
+second approach in subsequent runs (which have the same composition,
+force field, and approximately the same volume).
+
+Concerning the performance of the pppm/disp there are two more things
+to consider. The first is that when using the pppm/disp, the cutoff
+parameter does no longer affect the accuracy of the simulation
+(subject to that gewald/disp is adjusted when changing the cutoff).
+The performance can thus be increased by examining different values
+for the cutoff parameter. A lower bound for the cutoff is only set by
+the truncation error of the repulsive term of pair potentials.
+
+The second is that the mixing rule of the pair style has an impact on
+the computation time when using the pppm/disp. Fastest computations
+are achieved when using the geometric mixing rule. Using the
+arithmetic mixing rule substantially increases the computational cost.
+The computational overhead can be reduced using the {kspace_modify
+mix/disp geom} and {kspace_modify splittol} commands. The first
+command simply enforces geometric mixing of the dispersion
+coefficients in kspace computations.  This introduces some error in
+the computations but will also significantly speed-up the
+simulations. The second keyword sets the accuracy with which the
+dispersion coefficients are approximated using a matrix factorization
+approach.  This may result in better accuracy then using the first
+command, but will usually also not provide an equally good increase of
+efficiency.
+
+Finally, pppm/disp can also be used when no mixing rules apply.
+This can be achieved using the {kspace_modify mix/disp none} command.
+Note that the code does not check automatically whether any mixing
+rule is fulfilled. If mixing rules do not apply, the user will have
+to specify this command explicitly.

doc/src/Howto_drude.txt

@@ -0,0 +1,77 @@
+"Higher level section"_Howto.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
+
+Drude induced dipoles :h3
+
+The thermalized Drude model represents induced dipoles by a pair of
+charges (the core atom and the Drude particle) connected by a harmonic
+spring.  See the "Howto polarizable"_Howto_polarizable.html doc page
+for a discussion of all the polarizable models available in LAMMPS.
+
+The Drude model has a number of features aimed at its use in
+molecular systems ("Lamoureux and Roux"_#howto-Lamoureux):
+
+Thermostating of the additional degrees of freedom associated with the
+induced dipoles at very low temperature, in terms of the reduced
+coordinates of the Drude particles with respect to their cores. This
+makes the trajectory close to that of relaxed induced dipoles. :ulb,l
+
+Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle
+pair represents a single (polarizable) atom, so the special screening
+factors in a covalent structure should be the same for the core and
+the Drude particle.  Drude particles have to inherit the 1-2, 1-3, 1-4
+special neighbor relations from their respective cores. :l
+
+Stabilization of the interactions between induced dipoles. Drude
+dipoles on covalently bonded atoms interact too strongly due to the
+short distances, so an atom may capture the Drude particle of a
+neighbor, or the induced dipoles within the same molecule may align
+too much. To avoid this, damping at short range can be done by Thole
+functions (for which there are physical grounds). This Thole damping
+is applied to the point charges composing the induced dipole (the
+charge of the Drude particle and the opposite charge on the core, not
+to the total charge of the core atom). :l,ule
+
+A detailed tutorial covering the usage of Drude induced dipoles in
+LAMMPS is on the "Howto drude2e"_Howto_drude2.html doc page.
+
+As with the core-shell model, the cores and Drude particles should
+appear in the data file as standard atoms. The same holds for the
+springs between them, which are described by standard harmonic bonds.
+The nature of the atoms (core, Drude particle or non-polarizable) is
+specified via the "fix drude"_fix_drude.html command.  The special
+list of neighbors is automatically refactored to account for the
+equivalence of core and Drude particles as regards special 1-2 to 1-4
+screening. It may be necessary to use the {extra/special/per/atom}
+keyword of the "read_data"_read_data.html command. If using "fix
+shake"_fix_shake.html, make sure no Drude particle is in this fix
+group.
+
+There are two ways to thermostat the Drude particles at a low
+temperature: use either "fix langevin/drude"_fix_langevin_drude.html
+for a Langevin thermostat, or "fix
+drude/transform/*"_fix_drude_transform.html for a Nose-Hoover
+thermostat. The former requires use of the command "comm_modify vel
+yes"_comm_modify.html. The latter requires two separate integration
+fixes like {nvt} or {npt}. The correct temperatures of the reduced
+degrees of freedom can be calculated using the "compute
+temp/drude"_compute_temp_drude.html. This requires also to use the
+command {comm_modify vel yes}.
+
+Short-range damping of the induced dipole interactions can be achieved
+using Thole functions through the "pair style
+thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
+with a Coulomb pair style. It may be useful to use {coul/long/cs} or
+similar from the CORESHELL package if the core and Drude particle come
+too close, which can cause numerical issues.
+
+:line
+
+:link(howto-Lamoureux)
+[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)

doc/src/Howto_drude2.txt

@@ -9,7 +9,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 

doc/src/Howto_elastic.txt

@@ -0,0 +1,47 @@
+"Higher level section"_Howto.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
+
+Calculate elastic constants :h3
+
+Elastic constants characterize the stiffness of a material. The formal
+definition is provided by the linear relation that holds between the
+stress and strain tensors in the limit of infinitesimal deformation.
+In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
+the repeated indices imply summation. s_ij are the elements of the
+symmetric stress tensor. e_kl are the elements of the symmetric strain
+tensor. C_ijkl are the elements of the fourth rank tensor of elastic
+constants. In three dimensions, this tensor has 3^4=81 elements. Using
+Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
+is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
+derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
+most 7*6/2 = 21 distinct elements.
+
+At zero temperature, it is easy to estimate these derivatives by
+deforming the simulation box in one of the six directions using the
+"change_box"_change_box.html command and measuring the change in the
+stress tensor. A general-purpose script that does this is given in the
+examples/elastic directory described on the "Examples"_Examples.html
+doc page.
+
+Calculating elastic constants at finite temperature is more
+challenging, because it is necessary to run a simulation that perfoms
+time averages of differential properties. One way to do this is to
+measure the change in average stress tensor in an NVT simulations when
+the cell volume undergoes a finite deformation. In order to balance
+the systematic and statistical errors in this method, the magnitude of
+the deformation must be chosen judiciously, and care must be taken to
+fully equilibrate the deformed cell before sampling the stress
+tensor. Another approach is to sample the triclinic cell fluctuations
+that occur in an NPT simulation. This method can also be slow to
+converge and requires careful post-processing "(Shinoda)"_#Shinoda1
+
+:line
+
+:link(Shinoda1)
+[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

doc/src/Howto_github.txt

@@ -2,7 +2,7 @@
 
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
+:link(lc,Commands_all.html)
 
 :line
 
@@ -26,7 +26,7 @@ work required by the LAMMPS developers. Consequently, creating a pull
 request will increase your chances to have your contribution included
 and will reduce the time until the integration is complete. For more
 information on the requirements to have your code included into LAMMPS
-please see "Section 10.15"_Section_modify.html#mod_15
+please see the "Modify contribute"_Modify_contribute.html doc page.
 
 :line
 
@@ -124,7 +124,7 @@ unrelated feature, you should switch branches!
 
 After everything is done, add the files to the branch and commit them:
 
- $ git add doc/src/tutorial_github.txt
+ $ git add doc/src/Howto_github.txt
  $ git add doc/src/JPG/tutorial*.png :pre
 
 IMPORTANT NOTE: Do not use {git commit -a} (or {git add -A}).  The -a
@@ -318,7 +318,7 @@ Because the changes are OK with us, we are going to merge by clicking on
 Now, since in the meantime our local text for the tutorial also changed,
 we need to pull Axel's change back into our branch, and merge them:
 
- $ git add tutorial_github.txt
+ $ git add Howto_github.txt
  $ git add JPG/tutorial_reverse_pull_request*.png
  $ git commit -m "Updated text and images on reverse pull requests"
  $ git pull :pre
@@ -331,7 +331,7 @@ With Axel's changes merged in and some final text updates, our feature
 branch is now perfect as far as we are concerned, so we are going to
 commit and push again:
 
- $ git add tutorial_github.txt
+ $ git add Howto_github.txt
  $ git add JPG/tutorial_reverse_pull_request6.png
  $ git commit -m "Merged Axel's suggestions and updated text"
  $ git push git@github.com:Pakketeretet2/lammps :pre

doc/src/Howto_granular.txt

@@ -0,0 +1,57 @@
+"Higher level section"_Howto.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
+
+Granular models :h3
+
+Granular system are composed of spherical particles with a diameter,
+as opposed to point particles.  This means they have an angular
+velocity and torque can be imparted to them to cause them to rotate.
+
+To run a simulation of a granular model, you will want to use
+the following commands:
+
+"atom_style sphere"_atom_style.html
+"fix nve/sphere"_fix_nve_sphere.html
+"fix gravity"_fix_gravity.html :ul
+
+This compute
+
+"compute erotate/sphere"_compute_erotate_sphere.html :ul
+
+calculates rotational kinetic energy which can be "output with
+thermodynamic info"_Howto_output.html.
+
+Use one of these 3 pair potentials, which compute forces and torques
+between interacting pairs of particles:
+
+"pair_style"_pair_style.html gran/history
+"pair_style"_pair_style.html gran/no_history
+"pair_style"_pair_style.html gran/hertzian :ul
+
+These commands implement fix options specific to granular systems:
+
+"fix freeze"_fix_freeze.html
+"fix pour"_fix_pour.html
+"fix viscous"_fix_viscous.html
+"fix wall/gran"_fix_wall_gran.html :ul
+
+The fix style {freeze} zeroes both the force and torque of frozen
+atoms, and should be used for granular system instead of the fix style
+{setforce}.
+
+For computational efficiency, you can eliminate needless pairwise
+computations between frozen atoms by using this command:
+
+"neigh_modify"_neigh_modify.html exclude :ul
+
+NOTE: By default, for 2d systems, granular particles are still modeled
+as 3d spheres, not 2d discs (circles), meaning their moment of inertia
+will be the same as in 3d.  If you wish to model granular particles in
+2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d.html
+doc page, where 2d simulations are discussed.