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Some tweaks and corrections

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This commit is contained in:
Richard Berger
2018-08-09 16:02:54 -04:00
parent 630a46ad67
commit 4db08f5351
4 changed files with 42 additions and 46 deletions
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3
doc/src/Build.txt
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@ -27,6 +27,9 @@ doc page.
Build_basics
Build_settings
Build_package
.. toctree::
Build_extras
END_RST -->

10
doc/src/Build_basics.txt
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@ -301,15 +301,9 @@ want to copy files to is protected.
[CMake variable]:
cmake CMAKE_INSTALL_PREFIX=path \[options ...\] ~/lammps/cmake
cmake -D CMAKE_INSTALL_PREFIX=path \[options ...\] ~/lammps/cmake
make # perform make after CMake command
make install # perform the installation :pre
Note that The CMAKE_INSTALL_PREFIX=path is not a -D variable like
other LAMMPS settings, but rather an option to the cmake command. The
path is where to install the LAMMPS files.
TODO: is this sub-section correct?
make install # perform the installation into prefix :pre
[Traditional make]:

27
doc/src/Build_cmake.txt
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@ -91,8 +91,8 @@ cmake directory which contains the CMakeLists.txt file.
The argument can be preceeded or followed by various CMake
command-line options. Several useful ones are:
CAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired
CMAKE_BUILD_TYPE=type # type = Release or Debug
-D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired
-D CMAKE_BUILD_TYPE=type # type = Release or Debug
-G output # style of output CMake generates
-DVARIABLE=value # setting for a LAMMPS feature to enable
-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir
@ -103,7 +103,7 @@ All of these variable names are upper-case and their values are
lower-case, e.g. -D LAMMPS_SIZES=smallbig. For boolean values, any of
these forms can be used: yes/no, on/off, 1/0.
By default CMake generates a Makefile to perform the LAMMPS build.
On Unix/Linux CMake generates a Makefile by default to perform the LAMMPS build.
Alternate forms of build info can be generated via the -G switch,
e.g. Visual Studio on a Windows machine. Type "cmake --help" to see
the "Generator" styles of output your system supports.
@ -118,22 +118,22 @@ CMake creates a CMakeCache.txt file when it runs. This stores all the
settings, so that running CMake again from the same directory will
inherit those settings.
TODO: explain how to change settings on a subsequent cmake in the same
build dir. In that case is "." the final arg of cmake?
If you later want to change a setting you can rerun cmake in the build
directory with different setting. Please note that some automatically
detected variables will not change their value. In these cases it is
usually better to start with a fresh build directory.
[Curses version (terminal-style menu) of CMake]:
ccmake ~/lammps/cmake :pre
TODO: give brief explanation of how to find and toggle options, how to
perform the generate, how to use it multiple times.
Please see the "ccmake manual"_https://cmake.org/cmake/help/latest/manual/ccmake.1.html for more information.
[GUI version of CMake]:
cmake-gui ~/lammps/cmake :pre
TODO: give brief explanation of how to find and toggle options, how to
perform the generate, how to use it multiple times.
Please see the "cmake-gui manual"_https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html for more information.
:line
@ -152,8 +152,7 @@ module list # is a cmake module is already loaded
module avail # is a cmake module available?
module load cmake3 # load cmake module with appropriate name :pre
If you do not have CMake or a new enough version, you can install it
as follows:
TODO: give install instructions for Linux, Mac, Windows
If you do not have CMake or a new enough version, you can download the latest
version at "https://cmake.org/download/"_https://cmake.org/download/.
Instructions on how to install it on various platforms can be found
"here"_https://cmake.org/install/.

48
doc/src/Build_extras.txt
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@ -68,7 +68,7 @@ name.
:line
GPU package :h3,link(gpu)
GPU package :h4,link(gpu)
To build with this package, you need to choose options for precision
and which GPU hardware to build for. To build with make you also need
@ -134,7 +134,7 @@ GPU library.
:line
KIM package :h3,link(kim)
KIM package :h4,link(kim)
To build with this package, the KIM library must be downloaded and
built on your system. It must include the KIM models that you want to
@ -178,7 +178,7 @@ make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_14162719659
:line
KOKKOS package :h3,link(kokkos)
KOKKOS package :h4,link(kokkos)
To build with this package, you have to choose a Kokkos setting for
either CPU (multi-threading via OpenMP) or KNL (OpenMP) or GPU (Cuda)
@ -241,7 +241,7 @@ do not recommend building with other acceleration packages installed
:line
LATTE package :h3,link(latte)
LATTE package :h4,link(latte)
To build with this package, you must download and build the LATTE
library.
@ -272,7 +272,7 @@ the compiler you use on your system to build LATTE.
:line
MEAM package :h3,link(meam)
MEAM package :h4,link(meam)
NOTE: You should test building the MEAM library with both the Intel
and GNU compilers to see if a simulation runs faster with one versus
@ -307,7 +307,7 @@ file.
:line
MSCG package :h3,link(mscg)
MSCG package :h4,link(mscg)
Before building LAMMPS with this package, you must first download and
build the MS-CG library.
@ -342,7 +342,7 @@ You should not need to edit the lib/mscg/Makefile.lammps file.
:line
OPT package :h3,link(opt)
OPT package :h4,link(opt)
[CMake build]:
@ -359,7 +359,7 @@ CCFLAGS: add -restrict for Intel compilers :ul
:line
POEMS package :h3,link(poems)
POEMS package :h4,link(poems)
[CMake build]:
@ -388,7 +388,7 @@ a corresponding Makefile.lammps.machine file.
:line
PYTHON package :h3,link(python)
PYTHON package :h4,link(python)
Building with the PYTHON package assumes you have a Python shared
library available on your system, which needs to be a Python 2
@ -407,7 +407,7 @@ process. You should only need to create a new Makefile.lammps.* file
:line
REAX package :h3,link(reax)
REAX package :h4,link(reax)
[CMake build]:
@ -438,7 +438,7 @@ file.
:line
VORONOI package :h3,link(voronoi)
VORONOI package :h4,link(voronoi)
[CMake build]:
@ -466,7 +466,7 @@ the lib/voronoi/Makefile.lammps file.
:line
:line
USER-ATC package :h3,link(user-atc)
USER-ATC package :h4,link(user-atc)
[CMake build]:
@ -507,7 +507,7 @@ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
:line
USER-AWPMD package :h3,link(user-awpmd)
USER-AWPMD package :h4,link(user-awpmd)
[CMake build]:
@ -547,7 +547,7 @@ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
:line
USER-COLVARS package :h3,link(user-colvars)
USER-COLVARS package :h4,link(user-colvars)
[CMake build]:
@ -577,7 +577,7 @@ a corresponding Makefile.lammps.machine file.
:line
USER-H5MD package :h3,link(user-h5md)
USER-H5MD package :h4,link(user-h5md)
[CMake build]:
@ -608,7 +608,7 @@ file.
:line
USER-INTEL package :h3,link(user-intel)
USER-INTEL package :h4,link(user-intel)
[CMake build]:
@ -651,7 +651,7 @@ explained on the "Speed intel"_Speed_intel.html doc page.
:line
USER-MOLFILE package :h3,link(user-molfile)
USER-MOLFILE package :h4,link(user-molfile)
[CMake build]:
@ -668,7 +668,7 @@ lib/molfile/Makefile.lammps for details.
:line
USER-NETCDF package :h3,link(user-netcdf)
USER-NETCDF package :h4,link(user-netcdf)
[CMake build]:
@ -685,7 +685,7 @@ lib/netcdf/README for details.
:line
USER-OMP package :h3,link(user-omp)
USER-OMP package :h4,link(user-omp)
[CMake build]:
@ -698,7 +698,7 @@ LINKFLAGS: add -fopenmp :ul
:line
USER-QMMM package :h3,link(user-qmmm)
USER-QMMM package :h4,link(user-qmmm)
The LAMMPS executable these steps produce is not yet functional for a
QM/MM simulation. You must also build Quantum ESPRESSO and create a
@ -736,7 +736,7 @@ usual manner:
:line
USER-QUIP package :h3,link(user-quip)
USER-QUIP package :h4,link(user-quip)
[CMake build]:
@ -756,11 +756,11 @@ settings to successfully build on your system.
:line
USER-SMD package :h3,link(user-smd)
USER-SMD package :h4,link(user-smd)
[CMake build]:
-D EIGEN3_INCLUDE_DIR
-D EIGEN3_INCLUDE_DIR=path
[Traditional make]:
@ -784,7 +784,7 @@ usual manner:
:line
USER-VTK package :h3,link(user-vtk)
USER-VTK package :h4,link(user-vtk)
[CMake build]: