Some tweaks and corrections

doc/src/Build.txt

@@ -27,6 +27,9 @@ doc page.
    Build_basics
    Build_settings
    Build_package
+
+.. toctree::
+
    Build_extras
 
 END_RST -->

doc/src/Build_basics.txt

@@ -301,15 +301,9 @@ want to copy files to is protected.
 
 [CMake variable]:
 
-cmake CMAKE_INSTALL_PREFIX=path \[options ...\] ~/lammps/cmake
+cmake -D CMAKE_INSTALL_PREFIX=path \[options ...\] ~/lammps/cmake
 make                        # perform make after CMake command
-make install                # perform the installation :pre
-
-Note that The CMAKE_INSTALL_PREFIX=path is not a -D variable like
-other LAMMPS settings, but rather an option to the cmake command.  The
-path is where to install the LAMMPS files.
-
-TODO: is this sub-section correct?
+make install                # perform the installation into prefix :pre
 
 [Traditional make]:
 

doc/src/Build_cmake.txt

@@ -91,8 +91,8 @@ 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:
 
-CAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
-CMAKE_BUILD_TYPE=type     # type = Release or Debug
+-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
@@ -103,7 +103,7 @@ 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.
 
-By default CMake generates a Makefile to perform the LAMMPS build.
+On Unix/Linux 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.  Type "cmake --help" to see
 the "Generator" styles of output your system supports.
@@ -118,22 +118,22 @@ CMake creates a CMakeCache.txt file when it runs.  This stores all the
 settings, so that running CMake again from the same directory will
 inherit those settings.
 
-TODO: explain how to change settings on a subsequent cmake in the same
-build dir.  In that case is "." the final arg of cmake?
+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. In these cases it is
+usually better to start with a fresh build directory.
 
 [Curses version (terminal-style menu) of CMake]:
 
 ccmake ~/lammps/cmake :pre
 
-TODO: give brief explanation of how to find and toggle options, how to
-perform the generate, how to use it multiple times.
+Please see the "ccmake manual"_https://cmake.org/cmake/help/latest/manual/ccmake.1.html for more information.
 
 [GUI version of CMake]:
 
 cmake-gui ~/lammps/cmake :pre
 
-TODO: give brief explanation of how to find and toggle options, how to
-perform the generate, how to use it multiple times.
+Please see the "cmake-gui manual"_https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html for more information.
 
 :line
 
@@ -152,8 +152,7 @@ module list            # is a cmake module is already loaded
 module avail           # is a cmake module available?
 module load cmake3     # load cmake module with appropriate name :pre
 
-If you do not have CMake or a new enough version, you can install it
-as follows:
-
-TODO: give install instructions for Linux, Mac, Windows
-
+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
+"here"_https://cmake.org/install/.

doc/src/Build_extras.txt

@@ -68,7 +68,7 @@ name.
 
 :line
 
-GPU package :h3,link(gpu)
+GPU package :h4,link(gpu)
 
 To build with this package, you need to choose options for precision
 and which GPU hardware to build for.  To build with make you also need
@@ -134,7 +134,7 @@ GPU library.
 
 :line
  
-KIM package :h3,link(kim)
+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
@@ -178,7 +178,7 @@ make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_14162719659
 
 :line
  
-KOKKOS package :h3,link(kokkos)
+KOKKOS package :h4,link(kokkos)
 
 To build with this package, you have to choose a Kokkos setting for
 either CPU (multi-threading via OpenMP) or KNL (OpenMP) or GPU (Cuda)
@@ -241,7 +241,7 @@ do not recommend building with other acceleration packages installed
 
 :line
  
-LATTE package :h3,link(latte)
+LATTE package :h4,link(latte)
 
 To build with this package, you must download and build the LATTE
 library.
@@ -272,7 +272,7 @@ the compiler you use on your system to build LATTE.
 
 :line
  
-MEAM package :h3,link(meam)
+MEAM package :h4,link(meam)
 
 NOTE: You should test building the MEAM library with both the Intel
 and GNU compilers to see if a simulation runs faster with one versus
@@ -307,7 +307,7 @@ file.
 
 :line
  
-MSCG package :h3,link(mscg)
+MSCG package :h4,link(mscg)
 
 Before building LAMMPS with this package, you must first download and
 build the MS-CG library.  
@@ -342,7 +342,7 @@ You should not need to edit the lib/mscg/Makefile.lammps file.
 
 :line
 
-OPT package :h3,link(opt)
+OPT package :h4,link(opt)
 
 [CMake build]:
 
@@ -359,7 +359,7 @@ CCFLAGS: add -restrict for Intel compilers :ul
 
 :line
  
-POEMS package :h3,link(poems)
+POEMS package :h4,link(poems)
 
 [CMake build]:
 
@@ -388,7 +388,7 @@ a corresponding Makefile.lammps.machine file.
 
 :line
  
-PYTHON package :h3,link(python)
+PYTHON package :h4,link(python)
 
 Building with the PYTHON package assumes you have a Python shared
 library available on your system, which needs to be a Python 2
@@ -407,7 +407,7 @@ process.  You should only need to create a new Makefile.lammps.* file
 
 :line
  
-REAX package :h3,link(reax)
+REAX package :h4,link(reax)
 
 [CMake build]:
 
@@ -438,7 +438,7 @@ file.
 
 :line
 
-VORONOI package :h3,link(voronoi)
+VORONOI package :h4,link(voronoi)
 
 [CMake build]:
 
@@ -466,7 +466,7 @@ the lib/voronoi/Makefile.lammps file.
 :line
 :line
 
-USER-ATC package :h3,link(user-atc)
+USER-ATC package :h4,link(user-atc)
 
 [CMake build]:
 
@@ -507,7 +507,7 @@ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
 
 :line
 
-USER-AWPMD package :h3,link(user-awpmd)
+USER-AWPMD package :h4,link(user-awpmd)
 
 [CMake build]:
 
@@ -547,7 +547,7 @@ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
 
 :line
 
-USER-COLVARS package :h3,link(user-colvars)
+USER-COLVARS package :h4,link(user-colvars)
 
 [CMake build]:
 
@@ -577,7 +577,7 @@ a corresponding Makefile.lammps.machine file.
 
 :line
 
-USER-H5MD package :h3,link(user-h5md)
+USER-H5MD package :h4,link(user-h5md)
 
 [CMake build]:
 
@@ -608,7 +608,7 @@ file.
 
 :line
 
-USER-INTEL package :h3,link(user-intel)
+USER-INTEL package :h4,link(user-intel)
 
 [CMake build]:
 
@@ -651,7 +651,7 @@ explained on the "Speed intel"_Speed_intel.html doc page.
 
 :line
 
-USER-MOLFILE package :h3,link(user-molfile)
+USER-MOLFILE package :h4,link(user-molfile)
 
 [CMake build]:
 
@@ -668,7 +668,7 @@ lib/molfile/Makefile.lammps for details.
 
 :line
 
-USER-NETCDF package :h3,link(user-netcdf)
+USER-NETCDF package :h4,link(user-netcdf)
 
 [CMake build]:
 
@@ -685,7 +685,7 @@ lib/netcdf/README for details.
 
 :line
 
-USER-OMP package :h3,link(user-omp)
+USER-OMP package :h4,link(user-omp)
 
 [CMake build]:
 
@@ -698,7 +698,7 @@ LINKFLAGS: add -fopenmp :ul
 
 :line
 
-USER-QMMM package :h3,link(user-qmmm)
+USER-QMMM package :h4,link(user-qmmm)
 
 The LAMMPS executable these steps produce is not yet functional for a
 QM/MM simulation.  You must also build Quantum ESPRESSO and create a
@@ -736,7 +736,7 @@ usual manner:
 
 :line
 
-USER-QUIP package :h3,link(user-quip)
+USER-QUIP package :h4,link(user-quip)
 
 [CMake build]:
 
@@ -756,11 +756,11 @@ settings to successfully build on your system.
 
 :line
 
-USER-SMD package :h3,link(user-smd)
+USER-SMD package :h4,link(user-smd)
 
 [CMake build]:
 
--D EIGEN3_INCLUDE_DIR 	
+-D EIGEN3_INCLUDE_DIR=path
 
 [Traditional make]:
 
@@ -784,7 +784,7 @@ usual manner:
 
 :line
 
-USER-VTK package :h3,link(user-vtk)
+USER-VTK package :h4,link(user-vtk)
 
 [CMake build]: