Merge branch 'sllod' into collected-post-stable-patches

doc/utils/*/*         @rbberger

doc/Makefile          @rbberger

doc/README            @rbberger

# for releases

src/version.h         @sjplimp

endif()

set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit")

set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")

set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)

set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})

validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)

  endif()

endif()

if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE OR PKG_USER-PLUMED)

if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)

  find_package(LAPACK)

  find_package(BLAS)

  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)

    if(PLUMED_MODE STREQUAL "STATIC")

      add_definitions(-D__PLUMED_WRAPPER_CXX=1)

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o

        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS} ${LAPACK_LIBRARIES})

        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})

    elseif(PLUMED_MODE STREQUAL "SHARED")

      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})

    elseif(PLUMED_MODE STREQUAL "RUNTIME")

endif()

if(PKG_USER-ATC)

  if(LAMMPS_SIZES STREQUAL BIGBIG)

    message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")

  endif()

  target_link_libraries(atc ${LAPACK_LIBRARIES})

endif()

# Makefile for LAMMPS documentation

SHELL         = /bin/bash

SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)

SHA1          = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py)

BUILDDIR      = /tmp/lammps-docs-$(SHA1)

RSTDIR        = $(BUILDDIR)/rst

VENV          = $(BUILDDIR)/docenv

[CMake build]:

No additional settings are needed besides "-D PKG_REAX=yes" and "-D

PKG_MANYBODY=yes".

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

and "-D PKG_MANYBODY=yes".

[Traditional make]:

:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)

PLUMED can be linked into MD codes in three different modes: static,

shared, and runtime.  With the "static" mode, all required PLUMED code

is linked statically into the MD code. The MD code is then fully

independent from the PLUMED installation, but also you have to

rebuild/relink the MD code to update the PLUMED code inside it.  With

"shared" linkage mode, the MD code is linked to a shared library

containing the PLUMED code, preferably after it was installed in a

globally accessible location. This way the same installed PLUMED code

can be shared across multiple MD packages and can be updated, for as

long as the shared PLUMED library is ABI-compatible. The third linkage

mode is "runtime" which allows to switch the PLUMED kernel at runtime

between different variants through setting the PLUMED_KERNEL environment

variable, which has to point to the location of the libplumedKernel.so

dynamical shared object, which is then loaded at runtime. This is

particularly convenient for doing PLUMED development and comparing

multiple PLUMED versions without having to recompile the hosting MD

code. All three linkage modes are supported by LAMMPS on selected

operating systems (e.g. Linux) and using either CMake or traditional

make build. The "static" mode should be most portable, the "runtime"

mode support in LAMMPS makes the most assumptions about operating

system and compiler environment. If one mode does not work, try a

different one, or switch to a different build system, or consider

a global PLUMED installation or downloading it during building LAMMPS.

shared, and runtime.  With the "static" mode, all the code that PLUMED

requires is linked statically into LAMMPS. LAMMPS is then fully

independent from the PLUMED installation, but you have to rebuild/relink

it in order to update the PLUMED code inside it.  With the "shared"

linkage mode, LAMMPS is linked to a shared library that contains the

PLUMED code.  This library should preferably be installed in a globally

accessible location. When PLUMED is linked in this way the same library

can be used by multiple MD packages.  Furthermore, the PLUMED library

LAMMPS uses can be updated without the need for a recompile of LAMMPS

for as long as the shared PLUMED library is ABI-compatible.

The third linkage mode is "runtime" which allows the user to specify

which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL

environment variable. This variable should point to the location of the

libplumedKernel.so dynamical shared object, which is then loaded at

runtime. This mode of linking is particularly convenient for doing

PLUMED development and comparing multiple PLUMED versions as these sorts

of comparisons can be done without recompiling the hosting MD code. All

three linkage modes are supported by LAMMPS on selected operating

systems (e.g. Linux) and using either CMake or traditional make

build. The "static" mode should be the most portable, while the

"runtime" mode support in LAMMPS makes the most assumptions about

operating system and compiler environment. If one mode does not work,

try a different one, switch to a different build system, consider a

global PLUMED installation or consider downloading PLUMED during the

LAMMPS build.

[CMake build]:

When the "-D PKG_USER-PLUMED" flag is included in the cmake command you

must ensure that GSL is installed in locations that are specified in

your environment.  There are then two additional commands that control

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

-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 :pre

If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be

downloaded (the version of that is hard-coded to a vetted version of

PLUMED, usually a recent stable release version) and built inside the

CMake build directory.  If DOWNLOAD_PLUMED is set to "no" (the default),

CMake will try to detect an installed version of PLUMED and link to

that. For this to work, the PLUMED library has to be installed into a

location where the pkg-config tool can find it or the PKG_CONFIG_PATH

environment variable has to be set up accordingly.

The PLUMED_MODE setting determines the linkage mode of the PLUMED

library.  Allowed values are "static" (default), "shared", or "runtime".

For a discussion of PLUMED linkage modes, please see above.  When

enabling DOWNLOAD_PLUMED, the static linkage mode is recommended.

downloaded (the version of PLUMED that will be downloaded is hard-coded

to a vetted version of PLUMED, usually a recent stable release version)

and built inside the CMake build directory.  If DOWNLOAD_PLUMED is set

to "no" (the default), CMake will try to detect and link to an installed

version of PLUMED.  For this to work, the PLUMED library has to be

installed into a location where the pkg-config tool can find it or the

PKG_CONFIG_PATH environment variable has to be set up accordingly.

PLUMED should be installed in such a location if you compile it using

the default make; make install commands.

The PLUMED_MODE setting determines the linkage mode for the PLUMED

library.  The allowed values for this flag are "static" (default),

"shared", or "runtime".  For a discussion of PLUMED linkage modes,

please see above.  When DOWNLOAD_PLUMED is enabled the static linkage

mode is recommended.

[Traditional make]:

Before installing the USER-PLUMED package, first the PLUMED library

needs to be configured so that LAMMPS can find the right settings when

compiling and linking the LAMMPS executable itself. You can either

download and build PLUMED inside the LAMMPS plumed library folder or use

a previously installed PLUMED library and point LAMMPS to its

location. You also have to choose the linkage mode: "static" (default),

"shared" or "runtime".  For a discussion of PLUMED linkage modes, please

see above.

PLUMED needs to be installed before the USER-PLUMED package is installed

so that LAMMPS can find the right settings when compiling and linking

the LAMMPS executable.  You can either download and build PLUMED inside

the LAMMPS plumed library folder or use a previously installed PLUMED

library and point LAMMPS to its location. You also have to choose the

linkage mode: "static" (default), "shared" or "runtime".  For a

discussion of PLUMED linkage modes, please see above.

Download/compilation/configuration of the plumed library can be done

from the src folder through the following make args:

:pre

Note that 2 symbolic (soft) links, "includelink" and "liblink" are

created in lib/plumed to point into the location of the PLUMED build to

use and also a new file lib/plumed/Makefile.lammps is created with

settings suitable for LAMMPS to compile and link PLUMED in the desired

linkage mode. After this step is completed, you can install the

USER-PLUMED package and compile LAMMPS in the usual manner:

created in lib/plumed that point to the location of the PLUMED build to

use. A new file lib/plumed/Makefile.lammps is also created with settings

suitable for LAMMPS to compile and link PLUMED using the desired linkage

mode. After this step is completed, you can install the USER-PLUMED

package and compile LAMMPS in the usual manner:

make yes-user-plumed

make machine :pre

<!-- HTML_ONLY -->

<HEAD>

<TITLE>LAMMPS Users Manual</TITLE>

<META NAME="docnumber" CONTENT="27 Nov 2018 version">

<META NAME="docnumber" CONTENT="12 Dec 2018 version">

<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">

<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">

</HEAD>

:line

LAMMPS Documentation :c,h1

27 Nov 2018 version :c,h2

12 Dec 2018 version :c,h2

"What is a LAMMPS version?"_Manual_version.html