replace more "parsed-literal" with "code-block" in build docs

**CMake variables**\ :

.. parsed-literal::

.. code-block:: bash

   -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no

   -D BUILD_OMP=value        # yes or no (default)

**Traditional make**\ :

.. parsed-literal::

.. code-block:: bash

   cd lammps/src

   make mpi                # parallel build, produces lmp_mpi using Makefile.mpi

Serial build (see src/MAKE/Makefile.serial):

.. parsed-literal::

.. code-block:: make

   MPI_INC =       -I../STUBS

   MPI_PATH =      -L../STUBS

**CMake variables**\ :

.. parsed-literal::

.. code-block:: bash

   -D CMAKE_CXX_COMPILER=name            # name of C++ compiler

   -D CMAKE_C_COMPILER=name              # name of C compiler

for all the C++ files:

.. parsed-literal::

.. code-block:: bash

   Building with GNU Compilers:

   # Building with GNU Compilers:

   cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran

   Building with Intel Compilers:

   # Building with Intel Compilers:

   cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort

   Building with LLVM/Clang Compilers:

   # Building with LLVM/Clang Compilers:

   cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang

.. 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.

   When the cmake command completes, it prints a summary to the screen

   which compilers it is using and what flags and settings will be used

   for 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 CMake will try to determine and report.  You should check

   to confirm you are using the compiler and optimization flags you want.

**Makefile.machine settings**\ :

Parallel build (see src/MAKE/Makefile.mpi):

.. parsed-literal::

.. code-block:: bash

   CC =            mpicxx

   CCFLAGS =       -g -O3

Serial build (see src/MAKE/Makefile.serial):

.. parsed-literal::

.. code-block:: make

   CC =            g++

   CCFLAGS =       -g -O3

   variants:

.. parsed-literal::

.. code-block:: bash

   Makefile.opt                   # OPT package

   Makefile.omp                   # USER-OMP package

**CMake variables**\ :

.. parsed-literal::

.. code-block:: bash

   -D BUILD_EXE=value           # yes (default) or no

   -D BUILD_LIB=value           # yes or no (default)

**Traditional make**\ :

.. parsed-literal::

.. code-block:: bash

   cd lammps/src

   make machine               # build LAMMPS executable lmp_machine

.. parsed-literal::

.. code-block:: bash

   ./configure --enable-shared

   make

**CMake variable**\ :

.. parsed-literal::

.. code-block:: bash

   -D BUILD_DOC=value       # yes or no (default)

**Traditional make**\ :

.. parsed-literal::

.. code-block:: bash

   cd lammps/doc

   make html       # html doc pages

**CMake variable**\ :

.. parsed-literal::

.. code-block:: bash

   -D BUILD_TOOLS=value       # yes or no (default)

**Traditional make**\ :

.. parsed-literal::

.. code-block:: bash

   cd lammps/tools

   make all              # build all binaries of tools

**CMake variable**\ :

.. parsed-literal::

.. code-block:: bash

   cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake

   make                        # perform make after CMake command

Makefile(s). Example:

.. parsed-literal::

.. code-block:: bash

   cd lammps                        # change to the LAMMPS distribution directory

   mkdir build; cd build            # create a new directory (folder) for build

your system with:

.. parsed-literal::

.. code-block:: bash

   make install    # optional, copy LAMMPS executable & library elsewhere

**Command-line version of CMake**\ :

.. parsed-literal::

.. code-block:: bash

   cmake [options ...] /path/to/lammps/cmake  # build from any dir

   cmake [options ...] ../cmake               # build from lammps/build

command-line options.  Several useful ones are:

.. parsed-literal::

.. code-block:: bash

   -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired

   -D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug

**Curses version (terminal-style menu) of CMake**\ :

.. parsed-literal::

.. code-block:: bash

   ccmake ../cmake

**GUI version of CMake**\ :

.. parsed-literal::

.. code-block:: bash

   cmake-gui ../cmake

Check if your machine already has CMake installed:

.. parsed-literal::

.. code-block:: bash

   which cmake             # do you have it?

   which cmake3            # version 3 may have this name

software packages, do this:

.. parsed-literal::

.. code-block:: bash

   module list            # is a cmake module already loaded?

   module avail           # is a cmake module available?

   module list            # is a module for cmake already loaded?

   module avail           # is a module for cmake available?

   module load cmake3     # load cmake module with appropriate name

Most Linux distributions offer pre-compiled cmake packages through

compilation you can use the following option.

.. parsed-literal::

.. code-block:: bash

   -D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes

Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:

.. parsed-literal::

.. code-block:: bash

   make VERBOSE=1

usually faster than using tools like Valgrind.

.. parsed-literal::

.. code-block:: bash

   -D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes

   -D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes

   this is incomplete and only represents a small subset of tests that we run

.. parsed-literal::

.. code-block:: bash

   -D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes

   -D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)

If you enable testing in the CMake build it will create an additional target called "test". You can run them with:

.. parsed-literal::

.. code-block:: bash

   make test

coverage support during building.

.. parsed-literal::

.. code-block:: bash

   -D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes

This will also add the following targets to generate coverage reports after running the LAMMPS executable:

.. parsed-literal::

.. code-block:: bash

   make test               # run tests first!

   make gen_coverage_html  # generate coverage report in HTML format

These reports require GCOVR to be installed. The easiest way to do this to install it via pip:

.. parsed-literal::

.. code-block:: bash

   pip install git+https://github.com/gcovr/gcovr.git

in addition to:

.. parsed-literal::

.. code-block:: bash

   -D PKG_NAME=yes    # CMake

   make yes-name      # make

If CMake cannot find the library, you can set these variables:

.. parsed-literal::

.. code-block:: bash

   -D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file

   -D ZLIB_LIBRARIES=path      # path to libz.a (.so) file

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -D GPU_API=value          # value = opencl (default) or cuda

   -D GPU_PREC=value         # precision setting

script with the specified args:

.. parsed-literal::

.. code-block:: bash

   make lib-gpu               # print help message

   make lib-gpu args="-b"     # build GPU library with default Makefile.linux

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes

   -D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off, value = off (default) or on

invoke the lib/kim/Install.py script with the specified args.

.. parsed-literal::

.. code-block:: bash

   make lib-kim              # print help message

   make lib-kim args="-b "   # (re-)install KIM API lib with only example models

For multicore CPUs using OpenMP, set these 2 variables.

.. parsed-literal::

.. code-block:: bash

   -D KOKKOS_ARCH=archCPU         # archCPU = CPU from list above

   -D KOKKOS_ENABLE_OPENMP=yes

For Intel KNLs using OpenMP, set these 2 variables:

.. parsed-literal::

.. code-block:: bash

   -D KOKKOS_ARCH=KNL

   -D KOKKOS_ENABLE_OPENMP=yes

For NVIDIA GPUs using CUDA, set these 4 variables:

.. parsed-literal::

.. code-block:: bash

   -D KOKKOS_ARCH="archCPU;archGPU"   # archCPU = CPU from list above that is hosting the GPU

                                      # archGPU = GPU from list above

include the full path name to the wrapper, e.g.

.. parsed-literal::

.. code-block:: bash

   -D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper

For multicore CPUs using OpenMP:

.. parsed-literal::

.. code-block:: make

   KOKKOS_DEVICES = OpenMP

   KOKKOS_ARCH = archCPU      # archCPU = CPU from list above

For Intel KNLs using OpenMP:

.. parsed-literal::

.. code-block:: make

   KOKKOS_DEVICES = OpenMP

   KOKKOS_ARCH = KNL

For NVIDIA GPUs using CUDA:

.. parsed-literal::

.. code-block:: make

   KOKKOS_DEVICES = Cuda

   KOKKOS_ARCH = archCPU,archGPU    # archCPU = CPU from list above that is hosting the GPU

files.

.. parsed-literal::

.. code-block:: make

   KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)

   export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -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)

args:

.. parsed-literal::

.. code-block:: bash

   make lib-latte                          # print help message

   make lib-latte args="-b"                # download and build in lib/latte/LATTE-master

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -D MESSAGE_ZMQ=value    # build with ZeroMQ support, value = no (default) or yes

   -D ZMQ_LIBRARY=path     # ZMQ library file (only needed if a custom location)

simply invoke the lib/message/Install.py script with the specified args:

.. parsed-literal::

.. code-block:: bash

   make lib-message               # print help message

   make lib-message args="-m -z"  # build with MPI and socket (ZMQ) support

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -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)

invoke the lib/mscg/Install.py script with the specified args:

.. parsed-literal::

.. code-block:: bash

   make lib-mscg             # print help message

   make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master

lib/poems/Install.py script with the specified args:

.. parsed-literal::

.. code-block:: bash

   make lib-poems                   # print help message

   make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -D PYTHON_EXECUTABLE=path   # path to Python executable to use

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -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)

args:

.. parsed-literal::

.. code-block:: bash

   make lib-voronoi                          # print help message

   make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed

   -D PKG_USER-ADIOS=yes

Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:

.. parsed-literal::

.. code-block:: bash

   make yes-user-adios

otherwise, set ADIOS2\_DIR environment variable when turning on the package:

.. parsed-literal::

.. code-block:: bash

   ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed

lib/atc/Install.py script with the specified args:

.. parsed-literal::

.. code-block:: bash

   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")

lib/linalg with a command like these:

.. parsed-literal::

.. code-block:: bash

   make lib-linalg                     # print help message

   make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")

lib/awpmd/Install.py script with the specified args:

.. parsed-literal::

.. code-block:: bash

   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")

library in lib/linalg with a command like these:

.. parsed-literal::

.. code-block:: bash

   make lib-linalg                     # print help message

   make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")

the specified args:

.. parsed-literal::

.. code-block:: bash

   make lib-colvars                      # print help message

   make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")

the manner in which PLUMED is obtained and linked into LAMMPS.

.. parsed-literal::

.. code-block:: bash

   -D DOWNLOAD_PLUMED=value   # download PLUMED for build, value = no (default) or yes

   -D PLUMED_MODE=value       # Linkage mode for PLUMED, value = static (default), shared, or runtime

from the src folder through the following make args:

.. parsed-literal::

.. code-block:: bash

   make lib-plumed                         # print help message

   make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2

package and compile LAMMPS in the usual manner:

.. parsed-literal::

.. code-block:: bash

   make yes-user-plumed

   make machine

lib/h5md/Install.py script with the specified args:

.. parsed-literal::

.. code-block:: bash

   make lib-h5md                     # print help message

   make lib-h5md args="-m h5cc"      # build with h5cc compiler

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -D INTEL_ARCH=value     # value = cpu (default) or knl

   -D INTEL_LRT_MODE=value # value = threads, none, or c++11

For CPUs:

.. parsed-literal::

.. code-block:: make

   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)

For KNLs:

.. parsed-literal::

.. code-block:: make

   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)

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -D MOLFILE_INCLUDE_DIRS=path   # (optional) path where VMD molfile plugin headers are installed

   -D PKG_USER-MOLFILE=yes

lib/qmmm/Install.py script with the specified args:

.. parsed-literal::

.. code-block:: bash

   make lib-qmmm                      # print help message

   make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -D DOWNLOAD_SCAFACOS=value    # download ScaFaCoS for build, value = no (default) or yes

   -D SCAFACOS_LIBRARY=path      # ScaFaCos library file (only needed if at custom location)

**CMake build**\ :

.. parsed-literal::

.. code-block:: bash

   -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)

the lib/smd/Install.py script with the specified args:

.. parsed-literal::

.. code-block:: bash

   make lib-smd                         # print help message

   make lib-smd args="-b"               # download to lib/smd/eigen3

executable lmp\_serial or lmp\_mpi in lammps/src:

.. parsed-literal::

.. code-block:: bash

   cd lammps/src

   make serial     # build a serial LAMMPS executable

settings may become outdated:

.. parsed-literal::

.. code-block:: bash

   make mac             # build serial LAMMPS on a Mac

   make mac_mpi         # build parallel LAMMPS on a Mac