fix a bunch more broken, duplicate links and misformatted text

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 libzlib.a (.so) file 

-D ZLIB_LIBRARIES=path      # path to libzlib.a (.so) file :pre

[Traditional make]:

-D OCL_TUNE=value     # hardware choice for GPU_API=opencl

                      # generic (default) or intel (Intel CPU) or phi (Intel Xeon Phi) or fermi (NVIDIA) or kepler (NVIDIA) or cypress (NVIDIA)

-D GPU_ARCH=value     # hardware choice for GPU_API=cuda

                      # value = sm20 (Fermi) or sm30 (Kepler) or sm50 (Maxwell) or sm60 (Pascal) or sm70 (Volta)

                      # value = sm20 (Fermi) or sm30 or sm (Kepler) or sm50 (Maxwell) or sm60 (Pascal) or sm70 (Volta)

                      # default is Cuda-compiler dependent, but typically Fermi

-D CUDPP_OPT=value    # optimization setting for GPU_API=cudea

                      # enables CUDA Performance Primitives Optimizations

                      # on (default) or off

                      # on (default) or off :pre

[Traditional make]:

    sets KOKKOS_ARCH for GPU to appropriate value

  archcpu = SNB or HSW or BGQ or Power7 or Power8 (def = none)

    for CPU = SandyBridge, Haswell, BGQ, Power7, Power8

    sets KOKKOS_ARCH for GPU to appropriate value

    sets KOKKOS_ARCH for GPU to appropriate value :pre

For the KOKKOS package, you have 3 choices when building.  You can

build with either CPU or KNL or GPU support.  Each choice requires

-D LAMMPS_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

-D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it :pre

[Makefile.machine setting]:

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_packages.html doc page.

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

typing "make html" from the the doc directory.

After initial cloning, as bug fixes and new features are added to

LAMMPS, as listed on "this page"_bug.html, you can stay up-to-date by

typing the following Git commands from within the "mylammps"

directory:

LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay

up-to-date by typing the following Git commands from within the

"mylammps" directory:

git checkout unstable      # not needed if you always stay in this branch

git checkout stable        # use one of the 3 checkout commands

git checkout tagID :pre

Stable versions and what tagID to use for a particular stable version

are discussed on "this page"_bug.html.  Note that this command will

print some warnings, because in order to get back to the latest

are discussed on "this page"_Errors_bugs.html.  Note that this command

will print some warnings, because in order to get back to the latest

revision and to be able to update with "git pull" again, you first

will need to first type "git checkout unstable" (or check out any

other desired branch).

Binaries are available for many different versions of Linux:

"Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE"_#rpm

"Pre-built Ubuntu Linux executables"_#unbuntu

"Pre-built Ubuntu Linux executables"_#ubuntu

"Pre-built Gentoo Linux executable"_#gentoo :all(b)

:line