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

This commit is contained in:
Axel Kohlmeyer 2018-12-29 14:51:21 -05:00
commit 37a597cc0f
4 changed files with 29 additions and 9 deletions

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@ -1325,7 +1325,7 @@ if(BUILD_LIB)
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY) configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY) configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Modules)
else() else()
list(APPEND LMP_SOURCES ${LIB_SOURCES}) list(APPEND LMP_SOURCES ${LIB_SOURCES})
endif() endif()

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@ -24,7 +24,7 @@ tasks, act as a reference and provide examples of typical use cases.
* [Build directory vs. Source Directory](#build-directory-vs-source-directory) * [Build directory vs. Source Directory](#build-directory-vs-source-directory)
* [Defining and using presets](#defining-and-using-presets) * [Defining and using presets](#defining-and-using-presets)
* [Reference](#reference) * [Reference](#reference)
* [Common CMAKE Configuration Options](#common-cmake-configuration-options) * [Common CMake Configuration Options](#common-cmake-configuration-options)
* [LAMMPS Configuration Options](#lammps-configuration-options) * [LAMMPS Configuration Options](#lammps-configuration-options)
* [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages) * [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages)
* [Default Packages](#default-packages) * [Default Packages](#default-packages)
@ -179,7 +179,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
# Reference # Reference
## Common CMAKE Configuration Options ## Common CMake Configuration Options
<table> <table>
@ -208,6 +208,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
</dl> </dl>
</td> </td>
</tr> </tr>
<tr>
<td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
<td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
<td>
<dl>
<dt><code>off</code> (default)</dt>
<dt><code>on</code></dt>
</dl>
</td>
</tr>
</tbody> </tbody>
</table> </table>
@ -1729,6 +1739,13 @@ cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`,
value of `FC` environment variable at first `cmake` run value of `FC` environment variable at first `cmake` run
</td> </td>
</tr> </tr>
<tr>
<td><code>CXX_COMPILER_LAUNCHER</code></td>
<td>CMake will run this tool and pass the compiler and its arguments to the tool. Some example tools are distcc and ccache.</td>
<td>
(empty)
</td>
</tr>
</tbody> </tbody>
</table> </table>

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@ -15,7 +15,7 @@ Binaries are available for different versions of Linux:
"Pre-built Fedora Linux executables"_#fedora "Pre-built Fedora Linux executables"_#fedora
"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel "Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
"Pre-built OpenSuse Linux executables"_#opensuse "Pre-built OpenSuse Linux executables"_#opensuse
"Pre-built Gentoo Linux executable"_#gentoo :all(b) "Gentoo Linux executable"_#gentoo :all(b)
:line :line
@ -87,11 +87,11 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel,
lammps-openmpi-devel), the header for compiling programs using lammps-openmpi-devel), the header for compiling programs using
the C library interface (lammps-headers), and the LAMMPS python the C library interface (lammps-headers), and the LAMMPS python
module for Python 3. All packages can be installed at the same module for Python 3. All packages can be installed at the same
time and the name of the LAMMPS executable is {lmp} in all 3 cases. time and the name of the LAMMPS executable is {lmp} and {lmp_openmpi}
By default, {lmp} will refer to the serial executable, unless or {lmp_mpich} respectively. By default, {lmp} will refer to the
one of the MPI environment modules is loaded serial executable, unless one of the MPI environment modules is loaded
("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64"). ("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
Then the corresponding parallel LAMMPS executable is used. Then the corresponding parallel LAMMPS executable can be used.
The same mechanism applies when loading the LAMMPS python module. The same mechanism applies when loading the LAMMPS python module.
To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do: To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
@ -150,7 +150,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
:line :line
Pre-built Gentoo Linux executable :h4,link(gentoo) Gentoo Linux executable :h4,link(gentoo)
LAMMPS is part of Gentoo's main package tree and can be installed by LAMMPS is part of Gentoo's main package tree and can be installed by
typing: typing:

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@ -566,6 +566,9 @@ double PairLJCutSoft::init_one(int i, int j)
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]); sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
if (lambda[i][i] != lambda[j][j])
error->all(FLERR,"Pair lj/cut/soft different lambda values in mix");
lambda[i][j] = lambda[i][i];
cut[i][j] = mix_distance(cut[i][i],cut[j][j]); cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
} }