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more use of tabs in Build_extras.rst

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Axel Kohlmeyer 2020-09-08 10:11:37 -04:00
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@ -848,27 +848,28 @@ version or a Python 3.x version. Since support for Python 2.x has ended,
using Python 3.x is strongly recommended. See ``lib/python/README`` for
additional details.
CMake build
^^^^^^^^^^^
.. tabs::
.. code-block:: bash
.. tab:: CMake build
-D PYTHON_EXECUTABLE=path # path to Python executable to use
.. code-block:: bash
Without this setting, CMake will guess the default Python version on your
system. To use a different Python version, you can either create a
virtualenv, activate it and then run cmake. Or you can set the
PYTHON_EXECUTABLE variable to specify which Python interpreter should
be used. Note note that you will also need to have the development
headers installed for this version, e.g. python2-devel.
-D PYTHON_EXECUTABLE=path # path to Python executable to use
Traditional make
^^^^^^^^^^^^^^^^
Without this setting, CMake will guess the default Python version
on your system. To use a different Python version, you can either
create a virtualenv, activate it and then run cmake. Or you can
set the PYTHON_EXECUTABLE variable to specify which Python
interpreter should be used. Note note that you will also need to
have the development headers installed for this version,
e.g. python2-devel.
The build uses the ``lib/python/Makefile.lammps`` file in the compile/link
process to find Python. You should only need to create a new
``Makefile.lammps.*`` file (and copy it to ``Makefile.lammps``) if
the LAMMPS build fails.
.. tab:: Traditional make
The build uses the ``lib/python/Makefile.lammps`` file in the
compile/link process to find Python. You should only need to
create a new ``Makefile.lammps.*`` file (and copy it to
``Makefile.lammps``) if the LAMMPS build fails.
----------
@ -877,46 +878,48 @@ the LAMMPS build fails.
VORONOI package
-----------------------------
To build with this package, you must download and build the `Voro++ library <voro-home_>`_.
To build with this package, you must download and build the
`Voro++ library <http://math.lbl.gov/voro++>`_ or install a
binary package provided by your operating system.
.. _voro-home: http://math.lbl.gov/voro++
.. tabs::
CMake build
^^^^^^^^^^^
.. tab:: CMake build
.. code-block:: bash
.. code-block:: bash
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location)
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location)
If ``DOWNLOAD_VORO`` is set, the Voro++ library will be downloaded and
built inside the CMake build directory. If the Voro++ library is
already on your system (in a location CMake cannot find it),
``VORO_LIBRARY`` is the filename (plus path) of the Voro++ library file,
not the directory the library file is in. ``VORO_INCLUDE_DIR`` is the
directory the Voro++ include file is in.
If ``DOWNLOAD_VORO`` is set, the Voro++ library will be downloaded
and built inside the CMake build directory. If the Voro++ library
is already on your system (in a location CMake cannot find it),
``VORO_LIBRARY`` is the filename (plus path) of the Voro++ library
file, not the directory the library file is in.
``VORO_INCLUDE_DIR`` is the directory the Voro++ include file is
in.
Traditional make
^^^^^^^^^^^^^^^^
.. tab:: Traditional make
You can download and build the Voro++ library manually if you prefer;
follow the instructions in ``lib/voronoi/README``. You can also do it in
one step from the ``lammps/src`` dir, using a command like these, which
simply invoke the ``lib/voronoi/Install.py`` script with the specified
args:
You can download and build the Voro++ library manually if you
prefer; follow the instructions in ``lib/voronoi/README``. You
can also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invoke the
``lib/voronoi/Install.py`` script with the specified args:
.. code-block:: bash
.. code-block:: bash
$ make lib-voronoi # print help message
$ make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
$ make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
$ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
$ make lib-voronoi # print help message
$ make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
$ make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
$ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
created in lib/voronoi to point to the Voro++ source dir. When LAMMPS
builds in ``src`` it will use these links. You should not need to edit
the ``lib/voronoi/Makefile.lammps`` file.
Note that 2 symbolic (soft) links, ``includelink`` and
``liblink``, are created in lib/voronoi to point to the Voro++
source dir. When LAMMPS builds in ``src`` it will use these
links. You should not need to edit the
``lib/voronoi/Makefile.lammps`` file.
----------
@ -934,29 +937,30 @@ environment variables have been updated for the local ADIOS installation
and the instructions below are followed for the respective build
systems.
CMake build
^^^^^^^^^^^
.. tabs::
.. code-block:: bash
.. tab:: CMake build
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
-D PKG_USER-ADIOS=yes
.. code-block:: bash
Traditional make
^^^^^^^^^^^^^^^^
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
-D PKG_USER-ADIOS=yes
Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x
software is installed in PATH, there is nothing else to do:
.. tab:: Traditional make
.. code-block:: bash
Turn on the USER-ADIOS package before building LAMMPS. If the
ADIOS 2.x software is installed in PATH, there is nothing else to
do:
$ make yes-user-adios
.. code-block:: bash
otherwise, set ADIOS2_DIR environment variable when turning on the package:
$ make yes-user-adios
.. code-block:: bash
otherwise, set ADIOS2_DIR environment variable when turning on the package:
$ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed
.. code-block:: bash
$ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed
----------
@ -967,48 +971,50 @@ USER-ATC package
The USER-ATC package requires the MANYBODY package also be installed.
CMake build
^^^^^^^^^^^
.. tabs::
No additional settings are needed besides "-D PKG_USER-ATC=yes"
and "-D PKG_MANYBODY=yes".
.. tab:: CMake build
Traditional make
^^^^^^^^^^^^^^^^
No additional settings are needed besides "-D PKG_USER-ATC=yes"
and "-D PKG_MANYBODY=yes".
Before building LAMMPS, you must build the ATC library in ``lib/atc``.
You can do this manually if you prefer; follow the instructions in
``lib/atc/README``. You can also do it in one step from the
``lammps/src`` dir, using a command like these, which simply invoke the
``lib/atc/Install.py`` script with the specified args:
.. tab:: Traditional make
.. code-block:: bash
Before building LAMMPS, you must build the ATC library in
``lib/atc``. You can do this manually if you prefer; follow the
instructions in ``lib/atc/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/atc/Install.py`` script with the
specified args:
$ make lib-atc # print help message
$ make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-atc args="-m icc" # build with Intel icc compiler
.. code-block:: bash
The build should produce two files: ``lib/atc/libatc.a`` and
``lib/atc/Makefile.lammps``. The latter is copied from an existing
``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
ATC library. If necessary, you can edit/create a new
``lib/atc/Makefile.machine`` file for your system, which should define
an ``EXTRAMAKE`` variable to specify a corresponding
``Makefile.lammps.<machine>`` file.
$ make lib-atc # print help message
$ make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-atc args="-m icc" # build with Intel icc compiler
Note that the Makefile.lammps file has settings for the BLAS and
LAPACK linear algebra libraries. As explained in ``lib/atc/README`` these
can either exist on your system, or you can use the files provided in
``lib/linalg``. In the latter case you also need to build the library in
``lib/linalg`` with a command like these:
The build should produce two files: ``lib/atc/libatc.a`` and
``lib/atc/Makefile.lammps``. The latter is copied from an
existing ``Makefile.lammps.*`` and has settings needed to build
LAMMPS with the ATC library. If necessary, you can edit/create a
new ``lib/atc/Makefile.machine`` file for your system, which
should define an ``EXTRAMAKE`` variable to specify a corresponding
``Makefile.lammps.<machine>`` file.
.. code-block:: bash
Note that the Makefile.lammps file has settings for the BLAS and
LAPACK linear algebra libraries. As explained in
``lib/atc/README`` these can either exist on your system, or you
can use the files provided in ``lib/linalg``. In the latter case
you also need to build the library in ``lib/linalg`` with a
command like these:
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
.. code-block:: bash
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
----------
@ -1017,47 +1023,49 @@ can either exist on your system, or you can use the files provided in
USER-AWPMD package
------------------
CMake build
^^^^^^^^^^^
.. tabs::
No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.
.. tab:: CMake build
Traditional make
^^^^^^^^^^^^^^^^
No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.
Before building LAMMPS, you must build the AWPMD library in ``lib/awpmd``.
You can do this manually if you prefer; follow the instructions in
``lib/awpmd/README``. You can also do it in one step from the ``lammps/src``
dir, using a command like these, which simply invoke the
``lib/awpmd/Install.py`` script with the specified args:
.. tab:: Traditional make
.. code-block:: bash
Before building LAMMPS, you must build the AWPMD library in
``lib/awpmd``. You can do this manually if you prefer; follow the
instructions in ``lib/awpmd/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/awpmd/Install.py`` script with the
specified args:
$ make lib-awpmd # print help message
$ make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-awpmd args="-m icc" # build with Intel icc compiler
.. code-block:: bash
The build should produce two files: ``lib/awpmd/libawpmd.a`` and
``lib/awpmd/Makefile.lammps``. The latter is copied from an existing
``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
AWPMD library. If necessary, you can edit/create a new
``lib/awpmd/Makefile.machine`` file for your system, which should define
an ``EXTRAMAKE`` variable to specify a corresponding
``Makefile.lammps.<machine>`` file.
$ make lib-awpmd # print help message
$ make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-awpmd args="-m icc" # build with Intel icc compiler
Note that the ``Makefile.lammps`` file has settings for the BLAS and
LAPACK linear algebra libraries. As explained in ``lib/awpmd/README``
these can either exist on your system, or you can use the files
provided in ``lib/linalg``. In the latter case you also need to build the
library in ``lib/linalg`` with a command like these:
The build should produce two files: ``lib/awpmd/libawpmd.a`` and
``lib/awpmd/Makefile.lammps``. The latter is copied from an
existing ``Makefile.lammps.*`` and has settings needed to build
LAMMPS with the AWPMD library. If necessary, you can edit/create
a new ``lib/awpmd/Makefile.machine`` file for your system, which
should define an ``EXTRAMAKE`` variable to specify a corresponding
``Makefile.lammps.<machine>`` file.
.. code-block:: bash
Note that the ``Makefile.lammps`` file has settings for the BLAS
and LAPACK linear algebra libraries. As explained in
``lib/awpmd/README`` these can either exist on your system, or you
can use the files provided in ``lib/linalg``. In the latter case
you also need to build the library in ``lib/linalg`` with a
command like these:
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
.. code-block:: bash
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
----------
@ -1066,54 +1074,56 @@ library in ``lib/linalg`` with a command like these:
USER-COLVARS package
---------------------------------------
This package includes into the LAMMPS distribution the Colvars library, which
can be built for the most part with all major versions of the C++ language.
This package includes the `Colvars library
<https://colvars.github.io/>`_ into the LAMMPS distribution, which can
be built for the most part with all major versions of the C++ language.
CMake build
^^^^^^^^^^^
.. tabs::
This is the recommended build recipe: no additional settings are normally
needed besides ``-D PKG_USER-COLVARS=yes``.
.. tab:: CMake build
Traditional make
^^^^^^^^^^^^^^^^
This is the recommended build recipe: no additional settings are normally
needed besides ``-D PKG_USER-COLVARS=yes``.
Before building LAMMPS, one must build the Colvars library in lib/colvars.
.. tab:: Traditional make
This can be done manually in the same folder by using or adapting one of
the provided Makefiles: for example, ``Makefile.g++`` for the GNU C++
compiler. C++11 compatibility may need to be enabled for some older
compilers (as is done in the example makefile).
Before building LAMMPS, one must build the Colvars library in lib/colvars.
In general, it is safer to use build setting consistent with the rest of
LAMMPS. This is best carried out from the LAMMPS src directory using a
command like these, which simply invoke the ``lib/colvars/Install.py`` script with
the specified args:
This can be done manually in the same folder by using or adapting
one of the provided Makefiles: for example, ``Makefile.g++`` for
the GNU C++ compiler. C++11 compatibility may need to be enabled
for some older compilers (as is done in the example makefile).
.. code-block:: bash
In general, it is safer to use build setting consistent with the
rest of LAMMPS. This is best carried out from the LAMMPS src
directory using a command like these, which simply invoke the
``lib/colvars/Install.py`` script with the specified args:
$ make lib-colvars # print help message
$ make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
$ make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
.. code-block:: bash
The "machine" argument of the "-m" flag is used to find a Makefile.machine to
use as build recipe. If it does not already exist in ``lib/colvars``, it will be
auto-generated by using compiler flags consistent with those parsed from the
core LAMMPS makefiles.
$ make lib-colvars # print help message
$ make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
$ make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
Optional flags may be specified as environment variables:
The "machine" argument of the "-m" flag is used to find a
Makefile.machine to use as build recipe. If it does not already
exist in ``lib/colvars``, it will be auto-generated by using
compiler flags consistent with those parsed from the core LAMMPS
makefiles.
.. code-block:: bash
Optional flags may be specified as environment variables:
$ COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
$ COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
.. code-block:: bash
The build should produce two files: the library ``lib/colvars/libcolvars.a``
(which also includes Lepton objects if enabled) and the specification file
``lib/colvars/Makefile.lammps``. The latter is auto-generated, and normally does
not need to be edited.
$ COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
$ COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
The build should produce two files: the library ``lib/colvars/libcolvars.a``
(which also includes Lepton objects if enabled) and the specification file
``lib/colvars/Makefile.lammps``. The latter is auto-generated, and normally does
not need to be edited.
----------
@ -1159,84 +1169,91 @@ 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
^^^^^^^^^^^
.. tabs::
When the ``-D PKG_USER-PLUMED=yes`` 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 variables
that control the manner in which PLUMED is obtained and linked into
LAMMPS.
.. tab:: CMake build
.. code-block:: bash
When the ``-D PKG_USER-PLUMED=yes`` 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
variables 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
.. code-block:: bash
If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
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.
-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
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.
If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
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.
Traditional make
^^^^^^^^^^^^^^^^
The ``PLUMED_MODE`` setting determines the linkage mode for the
PLUMED library. The allowed values for this flag are "static"
(default), "shared", or "runtime". If you want to switch the
linkage mode, just re-run CMake with a different setting. For a
discussion of PLUMED linkage modes, please see above. When
``DOWNLOAD_PLUMED`` is enabled the static linkage mode is
recommended.
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.
.. tab:: Traditional make
Download/compilation/configuration of the plumed library can be done
from the src folder through the following make args:
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.
.. code-block:: bash
Download/compilation/configuration of the plumed library can be done
from the src folder through the following make args:
$ make lib-plumed # print help message
$ make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2
$ make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local
$ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
# /usr/local and use shared linkage mode
.. code-block:: bash
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink`` are
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 lib-plumed # print help message
$ make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2
$ make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local
$ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
# /usr/local and use shared linkage mode
.. code-block:: bash
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``
are 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
.. code-block:: bash
Once this compilation completes you should be able to run LAMMPS in the
usual way. For shared linkage mode, libplumed.so must be found by the
LAMMPS executable, which on many operating systems means, you have to
set the LD_LIBRARY_PATH environment variable accordingly.
$ make yes-user-plumed
$ make machine
Support for the different linkage modes in LAMMPS varies for different
operating systems, using the static linkage is expected to be the most
portable, and thus set to be the default.
Once this compilation completes you should be able to run LAMMPS
in the usual way. For shared linkage mode, libplumed.so must be
found by the LAMMPS executable, which on many operating systems
means, you have to set the LD_LIBRARY_PATH environment variable
accordingly.
If you want to change the linkage mode, you have to re-run "make
lib-plumed" with the desired settings **and** do a re-install if the
USER-PLUMED package with "make yes-user-plumed" to update the required
makefile settings with the changes in the lib/plumed folder.
Support for the different linkage modes in LAMMPS varies for
different operating systems, using the static linkage is expected
to be the most portable, and thus set to be the default.
If you want to change the linkage mode, you have to re-run "make
lib-plumed" with the desired settings **and** do a re-install if
the USER-PLUMED package with "make yes-user-plumed" to update the
required makefile settings with the changes in the lib/plumed
folder.
----------
@ -1249,38 +1266,39 @@ To build with this package you must have the HDF5 software package
installed on your system, which should include the h5cc compiler and
the HDF5 library.
CMake build
^^^^^^^^^^^
.. tabs::
No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.
.. tab:: CMake build
This should auto-detect the H5MD library on your system. Several
advanced CMake H5MD options exist if you need to specify where it is
installed. Use the ccmake (terminal window) or cmake-gui (graphical)
tools to see these options and set them interactively from their user
interfaces.
No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.
Traditional make
^^^^^^^^^^^^^^^^
This should auto-detect the H5MD library on your system. Several
advanced CMake H5MD options exist if you need to specify where it
is installed. Use the ccmake (terminal window) or cmake-gui
(graphical) tools to see these options and set them interactively
from their user interfaces.
Before building LAMMPS, you must build the CH5MD library in
``lib/h5md``. You can do this manually if you prefer; follow the
instructions in ``lib/h5md/README``. You can also do it in one step
from the ``lammps/src`` dir, using a command like these, which simply
invoke the ``lib/h5md/Install.py`` script with the specified args:
.. tab:: Traditional make
.. code-block:: bash
Before building LAMMPS, you must build the CH5MD library in
``lib/h5md``. You can do this manually if you prefer; follow the
instructions in ``lib/h5md/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/h5md/Install.py`` script with the
specified args:
$ make lib-h5md # print help message
$ make lib-h5md args="-m h5cc" # build with h5cc compiler
.. code-block:: bash
The build should produce two files: ``lib/h5md/libch5md.a`` and
``lib/h5md/Makefile.lammps``. The latter is copied from an existing
``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
system HDF5 library. If necessary, you can edit/create a new
``lib/h5md/Makefile.machine`` file for your system, which should define
an EXTRAMAKE variable to specify a corresponding
``Makefile.lammps.<machine>`` file.
$ make lib-h5md # print help message
$ make lib-h5md args="-m h5cc" # build with h5cc compiler
The build should produce two files: ``lib/h5md/libch5md.a`` and
``lib/h5md/Makefile.lammps``. The latter is copied from an
existing ``Makefile.lammps.*`` and has settings needed to build
LAMMPS with the system HDF5 library. If necessary, you can
edit/create a new ``lib/h5md/Makefile.machine`` file for your
system, which should define an EXTRAMAKE variable to specify a
corresponding ``Makefile.lammps.<machine>`` file.
----------