correct some errors and misconceptions about zlib and USER-OMP

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 :pre

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

[Traditional make]:

[CMake build]:

No additional settings are needed besides "-D PKG_USER-OMP=yes".

TODO: Is "-D BUILD_OMP=yes" also needed?  Or is it enabled

if PKG_USER-OMP is set?

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]:

These compile and link flags must be added to your Makefile.machine file.

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

CCFLAGS: -fopenmp               # for GNU Compilers

CCFLAGS: -qopenmp -restrict     # for Intel compilers on Linux

LINKFLAGS: -fopenmp

LINKFLAGS: -fopenmp             # for GNU Compilers

LINKFLAGS: -qopenmp             # for Intel compilers on Linux :pre

For other platforms and compilers, consult the OpenMP documentation

for the compiler.

For other platforms and compilers, please consult the documentation

about OpenMP support for your compiler.

:line

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

keep breaking the interface that the QM/MM code in LAMMPS is using, so

that currently (summer 2018) using this feature requires either

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releases, or using an outdated version of QE.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 in LAMMPS was

version 5.4.1 from 2016.

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.

QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x.  

You must use the traditional make build for this package.

[Traditional 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"_#compress

"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

-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 libzlib.a (.so) 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_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, libzlib.a (.so) files if make cannot find them

JPG_LIB = -ljpeg -lpng -lzlib    # library names :pre

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

:line

Read or write compressed files :h3,link(compress)

Read or write compressed files :h3,link(gzip)

If this option is enabled, large files can be read or written with

gzip compression by several LAMMPS commands, including

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.html enables.

what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables.

:line

USER-OMP package :h3

The USER-OMP package was developed by Axel Kohlmeyer at Temple

University.  It provides multi-threaded versions of most pair styles,

nearly all bonded styles (bond, angle, dihedral, improper), several

Kspace styles, and a few fix styles.  The package currently uses the

OpenMP interface for multi-threading.

University.  It provides optimized and multi-threaded versions

of many pair styles, nearly all bonded styles (bond, angle, dihedral,

improper), several Kspace styles, and a few fix styles.  It uses

the OpenMP interface for multi-threading, but can also be compiled

without OpenMP support, providing optimized serial styles in that case.

Here is a quick overview of how to use the USER-OMP package, assuming

one or more 16-core nodes.  More details follow.

use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine

make yes-user-omp

make mpi                                   # build with USER-OMP package, if settings added to Makefile.mpi

make omp                                   # or Makefile.omp already has settings :pre

make omp                                   # Makefile.omp already has OpenMP settings for GNU compilers

make mpi                                   # or build with USER-OMP package without OpenMP :pre

lmp_mpi -sf omp -pk omp 16 < in.script                         # 1 MPI task, 16 threads

mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task

mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre

env OMP_NUM_THREADS=16 lmp_omp -sf omp -in in.script           # 1 MPI task, 16 threads according to OMP_NUM_THREADS

lmp_mpi -sf omp -in in.script                                  # 1 MPI task, no threads, optimized kernels

mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task

mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre

[Required hardware/software:]

Your compiler must support the OpenMP interface.  You should have one

or more multi-core CPUs so that multiple threads can be launched by

each MPI task running on a CPU.

To enable multi-threading, your compiler must support the OpenMP interface.

You should have one or more multi-core CPUs, as multiple threads can only be

launched by each MPI task on the local node (using shared memory).

[Building LAMMPS with the USER-OMP package:]

details"_Packages_details.html#USER-OMP doc page.

Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must

include "-fopenmp".  Likewise, if you use an Intel compiler, the

CCFLAGS setting must include "-restrict".

include "-fopenmp" for the GNU compilers.  If you use an Intel compiler,

the corresponding flag is "-qopenmp" and the CCFLAGS setting must also

include "-restrict".

[Run with the USER-OMP package from the command line:]