Merge pull request #600 from akohlmey/install-and-docs-reviewed

use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu

:tb(c=2,s=|)

Note that the first 4 steps can be done as a single command, using the

src/Make.py tool.  This tool is discussed in "Section

Note that the first 4 steps can be done as a single command with

suitable make command invocations. This is discussed in "Section

4"_Section_packages.html of the manual, and its use is

illustrated in the individual accelerator sections.  Typically these

steps only need to be done once, to create an executable that uses one

Lowercase directories :h4

accelerate: run with various acceleration options (OpenMP, GPU, Phi)

airebo:   polyethylene with AIREBO potential

balance:  dynamic load balancing, 2d system

body:     body particles, 2d system

cmap:     CMAP 5-body contributions to CHARMM force field

"DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -

"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, WWW bench, int

"GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -

"KIM"_#KIM, openKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext

"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext

"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, WWW bench, -

"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -

"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -

in lib/linalg with a command like these:

make lib-linalg                      # print help message

make lib-atc args="-m gfortran"      # build with GNU Fortran compiler

make lib-linalg args="-m gfortran"   # build with GNU Fortran compiler

You can then install/un-install the package and build LAMMPS in the

usual manner:

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

make lib-smd                            # print help message

make lib-smd args="-g -l"               # download in default lib/smd/eigen-eigen-*

make lib-smd args="-h . eigen -g -l"    # download in lib/smd/eigen

make lib-smd args="-g -l"               # download and build in default lib/smd/eigen-eigen-*

make lib-smd args="-h . eigen -g -l"    # download and build in lib/smd/eigen

make lib-smd args="-h ~ eigen -g -l"    # download and build in ~/eigen :pre

Note that the final -l switch is to create a symbolic (soft) link

This requires two steps (a,b): build the GPU library, then build

LAMMPS with the GPU package.

You can do both these steps in one line, using the src/Make.py script,

described in "Section 4"_Section_packages.html of the manual.

Type "Make.py -h" for help.  If run from the src directory, this

command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the

starting Makefile.machine:

Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi :pre

You can do both these steps in one line as described in

"Section 4"_Section_packages.html of the manual.

Or you can follow these two (a,b) steps:

# or psxevars.csh for C-shell

make intel_cpu_intelmpi :pre

Alternatively, the build can be accomplished with the src/Make.py

script, described in "Section 4"_Section_packages.html of the

manual. Type "Make.py -h" for help. For an example:

Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre

Alternatively this can be done as a single command with

suitable make command invocations. This is discussed in "Section

4"_Section_packages.html of the manual.

Note that if you build with support for a Phi coprocessor, the same

binary can be used on nodes with or without coprocessors installed.

is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.

Other recommended CCFLAG options for best performance are

"-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2

-no-prec-div". The Make.py command will add all of these

automatically.

-no-prec-div".

NOTE: The vectorization and math capabilities can differ depending on

the CPU. For Intel compilers, the "-x" flag specifies the type of