make subheaders and typesetting more consistent
This commit is contained in:
Axel Kohlmeyer
@ -372,7 +372,8 @@ it. The build step will also create generic soft links, named
|
||||
``liblammps.a`` and ``liblammps.so``\ , which point to the specific
|
||||
``liblammps_machine.a/so`` files.
|
||||
|
||||
**CMake and make info**\ :
|
||||
CMake and make info
|
||||
^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
Note that for creating a shared library, all the libraries it depends on
|
||||
must be compiled to be compatible with shared libraries. This should be
|
||||
@ -462,7 +463,8 @@ tool. The actual translation is then done via make commands.
|
||||
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
|
||||
.. _sphinx: https://sphinx-doc.org
|
||||
|
||||
**Documentation make option**\ :
|
||||
Documentation make option
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
The following make commands can be issued in the doc folder of the
|
||||
LAMMPS source distribution.
|
||||
@ -489,7 +491,8 @@ your system.
|
||||
current LAMMPS version (HTML and PDF files), from the website
|
||||
`download page <https://lammps.sandia.gov/download.html>`_.
|
||||
|
||||
**CMake build option**\ :
|
||||
CMake build option
|
||||
^^^^^^^^^^^^^^^^^^
|
||||
|
||||
It is also possible to create the HTML version of the manual within
|
||||
the :doc:`CMake build directory <Build_cmake>`. The reason for this
|
||||
@ -512,7 +515,8 @@ Build LAMMPS tools
|
||||
Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
|
||||
using CMake or Make.
|
||||
|
||||
**CMake build3**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -521,7 +525,8 @@ using CMake or Make.
|
||||
The generated binaries will also become part of the LAMMPS installation
|
||||
(see below).
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -545,7 +550,8 @@ a globally visible place on your system, for others to access. Note
|
||||
that you may need super-user privileges (e.g. sudo) if the directory
|
||||
you want to copy files to is protected.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -553,7 +559,8 @@ you want to copy files to is protected.
|
||||
make # perform make after CMake command
|
||||
make install # perform the installation into prefix
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
There is no "install" option in the ``src/Makefile`` for LAMMPS. If
|
||||
you wish to do this you will need to first build LAMMPS, then manually
|
||||
|
||||
@ -59,12 +59,13 @@ This is the list of packages that may require additional steps.
|
||||
.. _compress:
|
||||
|
||||
COMPRESS package
|
||||
-------------------------------
|
||||
----------------
|
||||
|
||||
To build with this package you must have the zlib compression library
|
||||
available on your system.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
If CMake cannot find the library, you can set these variables:
|
||||
|
||||
@ -73,10 +74,11 @@ 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 libz.a (.so) file
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
If make cannot find the library, you can edit the file
|
||||
lib/compress/Makefile.lammps to specify the paths and library
|
||||
``lib/compress/Makefile.lammps`` to specify the paths and library
|
||||
name.
|
||||
|
||||
----------
|
||||
@ -90,7 +92,8 @@ To build with this package, you must choose options for precision and
|
||||
which GPU hardware to build for. The GPU package currently supports
|
||||
three different types of backends: OpenCL, CUDA and HIP.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -158,7 +161,8 @@ and the linker to work correctly.
|
||||
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
|
||||
make -j 4
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ .
|
||||
You can do this manually if you prefer; follow the instructions in
|
||||
@ -207,10 +211,10 @@ your machine are not correct, the LAMMPS build will fail, and
|
||||
|
||||
.. note::
|
||||
|
||||
If you re-build the GPU library in lib/gpu, you should always
|
||||
un-install the GPU package in lammps/src, then re-install it and
|
||||
If you re-build the GPU library in ``lib/gpu``, you should always
|
||||
un-install the GPU package in ``lammps/src``, then re-install it and
|
||||
re-build LAMMPS. This is because the compilation of files in the GPU
|
||||
package uses the library settings from the lib/gpu/Makefile.machine
|
||||
package uses the library settings from the ``lib/gpu/Makefile.machine``
|
||||
used to build the GPU library.
|
||||
|
||||
----------
|
||||
@ -249,7 +253,8 @@ See the list of all KIM models here: https://openkim.org/browse/models
|
||||
the KIM API library with all its models, may take a long time (tens of
|
||||
minutes to hours) to build. Of course you only need to do that once.)
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -281,7 +286,8 @@ As an alternative, you can specify your own CA cert path by setting the
|
||||
environment variable ``CURL_CA_BUNDLE`` to the path of your choice. A call
|
||||
to the KIM web query would get this value from the environmental variable.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
You can download and build the KIM library manually if you prefer;
|
||||
follow the instructions in ``lib/kim/README``\ . You can also do it in one
|
||||
@ -299,7 +305,7 @@ invoke the ``lib/kim/Install.py`` script with the specified args.
|
||||
$ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
|
||||
|
||||
Settings for OpenKIM web queries discussed above need to be applied by adding
|
||||
them to the ``LMP_INC`` variable through editing the Makefile.machine you are
|
||||
them to the ``LMP_INC`` variable through editing the ``Makefile.machine`` you are
|
||||
using. For example:
|
||||
|
||||
.. code-block:: make
|
||||
@ -604,7 +610,8 @@ LATTE package
|
||||
To build with this package, you must download and build the LATTE
|
||||
library.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -617,7 +624,8 @@ already on your system (in a location CMake cannot find it),
|
||||
``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library file,
|
||||
not the directory the library file is in.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
You can download and build the LATTE library manually if you prefer;
|
||||
follow the instructions in ``lib/latte/README``\ . You can also do it in
|
||||
@ -633,11 +641,12 @@ args:
|
||||
$ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
|
||||
# copy Makefile.lammps.gfortran to Makefile.lammps
|
||||
|
||||
Note that 3 symbolic (soft) links, "includelink" and "liblink" and
|
||||
"filelink.o", are created in lib/latte to point into the LATTE home
|
||||
dir. When LAMMPS itself is built it will use these links. You should
|
||||
also check that the Makefile.lammps file you create is appropriate for
|
||||
the compiler you use on your system to build LATTE.
|
||||
Note that 3 symbolic (soft) links, ``includelink`` and ``liblink`` and
|
||||
``filelink.o``, are created in ``lib/latte`` to point to required
|
||||
folders and files in the LATTE home directory. When LAMMPS itself is
|
||||
built it will use these links. You should also check that the
|
||||
``Makefile.lammps`` file you create is appropriate for the compiler you
|
||||
use on your system to build LATTE.
|
||||
|
||||
----------
|
||||
|
||||
@ -650,7 +659,8 @@ This package can optionally include support for messaging via sockets,
|
||||
using the open-source `ZeroMQ library <http://zeromq.org>`_, which must
|
||||
be installed on your system.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -658,7 +668,8 @@ be installed on your system.
|
||||
-D ZMQ_LIBRARY=path # ZMQ library file (only needed if a custom location)
|
||||
-D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
Before building LAMMPS, you must build the CSlib library in
|
||||
``lib/message``\ . You can build the CSlib library manually if you prefer;
|
||||
@ -673,8 +684,8 @@ simply invoke the ``lib/message/Install.py`` script with the specified args:
|
||||
$ make lib-message args="-s" # build as serial lib with no ZMQ support
|
||||
|
||||
The build should produce two files: ``lib/message/cslib/src/libmessage.a``
|
||||
and ``lib/message/Makefile.lammps``\ . The latter is copied from an
|
||||
existing ``Makefile.lammps.\*`` and has settings to link with the ZeroMQ
|
||||
and ``lib/message/Makefile.lammps``. The latter is copied from an
|
||||
existing ``Makefile.lammps.*`` and has settings to link with the ZeroMQ
|
||||
library if requested in the build.
|
||||
|
||||
----------
|
||||
@ -690,7 +701,8 @@ library. Building the MS-CG library requires that the GSL
|
||||
machine. See the ``lib/mscg/README`` and ``MSCG/Install`` files for
|
||||
more details.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -705,7 +717,8 @@ filename (plus path) of the MSCG library file, not the directory the
|
||||
library file is in. ``MSCG_INCLUDE_DIR`` is the directory the MSCG
|
||||
include file is in.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
You can download and build the MS-CG library manually if you prefer;
|
||||
follow the instructions in ``lib/mscg/README``\ . You can also do it in one
|
||||
@ -733,16 +746,18 @@ not need to edit the ``lib/mscg/Makefile.lammps`` file.
|
||||
OPT package
|
||||
---------------------
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
No additional settings are needed besides ``-D PKG_OPT=yes``
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
The compile flag "-restrict" must be used to build LAMMPS with the OPT
|
||||
The compile flag ``-restrict`` must be used to build LAMMPS with the OPT
|
||||
package when using Intel compilers. It should be added to the CCFLAGS
|
||||
line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for
|
||||
an example.
|
||||
line of your ``Makefile.machine``. See
|
||||
``src/MAKE/OPTIONS/Makefile.opt`` for an example.
|
||||
|
||||
----------
|
||||
|
||||
@ -751,11 +766,13 @@ an example.
|
||||
POEMS package
|
||||
-------------------------
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
No additional settings are needed besides ``-D PKG_OPT=yes``
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
Before building LAMMPS, you must build the POEMS library in ``lib/poems``\ .
|
||||
You can do this manually if you prefer; follow the instructions in
|
||||
@ -771,8 +788,8 @@ dir, using a command like these, which simply invoke the
|
||||
$ make lib-poems args="-m icc" # build with Intel icc compiler
|
||||
|
||||
The build should produce two files: ``lib/poems/libpoems.a`` and
|
||||
``lib/poems/Makefile.lammps``\ . The latter is copied from an existing
|
||||
``Makefile.lammps.\*`` and has settings needed to build LAMMPS with the
|
||||
``lib/poems/Makefile.lammps``. The latter is copied from an existing
|
||||
``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
|
||||
POEMS library (though typically the settings are just blank). If
|
||||
necessary, you can edit/create a new ``lib/poems/Makefile.machine`` file
|
||||
for your system, which should define an ``EXTRAMAKE`` variable to specify
|
||||
@ -790,7 +807,8 @@ library available on your system, which needs to be a Python 2.7
|
||||
version or a Python 3.x version. See ``lib/python/README`` for more
|
||||
details.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -803,11 +821,12 @@ 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.
|
||||
|
||||
**Traditional make**\ :
|
||||
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
|
||||
``Makefile.lammps.*`` file (and copy it to ``Makefile.lammps``) if
|
||||
the LAMMPS build fails.
|
||||
|
||||
----------
|
||||
@ -821,7 +840,8 @@ To build with this package, you must download and build the `Voro++ library <vor
|
||||
|
||||
.. _voro-home: http://math.lbl.gov/voro++
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -829,19 +849,20 @@ To build with this package, you must download and build the `Voro++ library <vor
|
||||
-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
|
||||
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
|
||||
``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**\ :
|
||||
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
|
||||
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
|
||||
@ -851,10 +872,10 @@ args:
|
||||
$ 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++ src 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.
|
||||
|
||||
----------
|
||||
|
||||
@ -863,23 +884,28 @@ the lib/voronoi/Makefile.lammps file.
|
||||
USER-ADIOS package
|
||||
-----------------------------------
|
||||
|
||||
The USER-ADIOS package requires the `ADIOS I/O library <https://github.com/ornladios/ADIOS2>`_,
|
||||
version 2.3.1 or newer. Make sure that you have ADIOS built either with or
|
||||
without MPI to match if you build LAMMPS with or without MPI.
|
||||
ADIOS compilation settings for LAMMPS are automatically detected, if the PATH
|
||||
and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS
|
||||
installation and the instructions below are followed for the respective build systems.
|
||||
The USER-ADIOS package requires the `ADIOS I/O library
|
||||
<https://github.com/ornladios/ADIOS2>`_, version 2.3.1 or newer. Make
|
||||
sure that you have ADIOS built either with or without MPI to match if
|
||||
you build LAMMPS with or without MPI. ADIOS compilation settings for
|
||||
LAMMPS are automatically detected, if the PATH and LD_LIBRARY_PATH
|
||||
environment variables have been updated for the local ADIOS installation
|
||||
and the instructions below are followed for the respective build
|
||||
systems.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
|
||||
-D PKG_USER-ADIOS=yes
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
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:
|
||||
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:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -900,18 +926,20 @@ USER-ATC package
|
||||
|
||||
The USER-ATC package requires the MANYBODY package also be installed.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
No additional settings are needed besides "-D PKG_USER-ATC=yes"
|
||||
and "-D PKG_MANYBODY=yes".
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
Before building LAMMPS, you must build the ATC library in lib/atc.
|
||||
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:
|
||||
``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:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -920,19 +948,19 @@ lib/atc/Install.py script with the specified args:
|
||||
$ 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
|
||||
|
||||
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.
|
||||
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.
|
||||
|
||||
Note that the Makefile.lammps file has settings for the BLAS and
|
||||
LAPACK linear algebra libraries. As explained in lib/atc/README these
|
||||
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:
|
||||
``lib/linalg``. In the latter case you also need to build the library in
|
||||
``lib/linalg`` with a command like these:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -946,19 +974,21 @@ lib/linalg with a command like these:
|
||||
.. _user-awpmd:
|
||||
|
||||
USER-AWPMD package
|
||||
-----------------------------------
|
||||
------------------
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
No additional settings are needed besides "-D PKG_USER-AQPMD=yes".
|
||||
No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
Before building LAMMPS, you must build the AWPMD library in lib/awpmd.
|
||||
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
|
||||
``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:
|
||||
``lib/awpmd/Install.py`` script with the specified args:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -967,19 +997,19 @@ lib/awpmd/Install.py script with the specified args:
|
||||
$ 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
|
||||
|
||||
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
|
||||
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.
|
||||
``lib/awpmd/Makefile.machine`` file for your system, which should define
|
||||
an ``EXTRAMAKE`` variable to specify a corresponding
|
||||
``Makefile.lammps.<machine>`` file.
|
||||
|
||||
Note that the Makefile.lammps file has settings for the BLAS and
|
||||
LAPACK linear algebra libraries. As explained in lib/awpmd/README
|
||||
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:
|
||||
provided in ``lib/linalg``. In the latter case you also need to build the
|
||||
library in ``lib/linalg`` with a command like these:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -998,36 +1028,26 @@ 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.
|
||||
|
||||
A few of the most recent features require C++11 support. In particular, the
|
||||
library is optionally built together with the
|
||||
`Lepton <https://simtk.org/projects/lepton>`_ library, a copy of which is also
|
||||
included in the LAMMPS distribution. Lepton implements the
|
||||
`customFunction <http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction>`_
|
||||
feature, and requires C++11 support.
|
||||
|
||||
See `here <https://colvars.github.io/README-c++11.html>`_ for a detailed list of
|
||||
C++11-only features.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
This is the recommended build recipe: no additional settings are normally
|
||||
needed besides "-D PKG_USER-COLVARS=yes".
|
||||
needed besides ``-D PKG_USER-COLVARS=yes``.
|
||||
|
||||
Building and linking of Lepton (or other C++11-only features) is enabled
|
||||
automatically when compilation is carried out with C++11 support, and disabled
|
||||
otherwise. Optionally, Lepton build may be manually controlled with the flag
|
||||
"-D COLVARS_LEPTON=yes\|no".
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
Before building LAMMPS, one must build the Colvars library in lib/colvars.
|
||||
|
||||
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 compiler.
|
||||
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).
|
||||
|
||||
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
|
||||
command like these, which simply invoke the ``lib/colvars/Install.py`` script with
|
||||
the specified args:
|
||||
|
||||
.. code-block:: bash
|
||||
@ -1038,7 +1058,7 @@ the specified args:
|
||||
$ make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
|
||||
|
||||
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
|
||||
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.
|
||||
|
||||
@ -1049,9 +1069,9 @@ 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)
|
||||
|
||||
The build should produce two files: the library lib/colvars/libcolvars.a
|
||||
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
|
||||
``lib/colvars/Makefile.lammps``. The latter is auto-generated, and normally does
|
||||
not need to be edited.
|
||||
|
||||
----------
|
||||
@ -1098,12 +1118,14 @@ 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**\ :
|
||||
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.
|
||||
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.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -1113,21 +1135,22 @@ the manner in which PLUMED is obtained and linked into LAMMPS.
|
||||
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.
|
||||
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
|
||||
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.
|
||||
please see above. When ``DOWNLOAD_PLUMED`` is enabled the static
|
||||
linkage mode is recommended.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
PLUMED needs to be installed before the USER-PLUMED package is installed
|
||||
so that LAMMPS can find the right settings when compiling and linking
|
||||
@ -1148,9 +1171,9 @@ from the src folder through the following make args:
|
||||
$ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
|
||||
# /usr/local and use shared linkage mode
|
||||
|
||||
Note that 2 symbolic (soft) links, "includelink" and "liblink" are
|
||||
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
|
||||
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:
|
||||
@ -1185,9 +1208,10 @@ 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**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
No additional settings are needed besides "-D PKG_USER-H5MD=yes".
|
||||
No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.
|
||||
|
||||
This should auto-detect the H5MD library on your system. Several
|
||||
advanced CMake H5MD options exist if you need to specify where it is
|
||||
@ -1195,26 +1219,27 @@ installed. Use the ccmake (terminal window) or cmake-gui (graphical)
|
||||
tools to see these options and set them interactively from their user
|
||||
interfaces.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
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:
|
||||
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:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
$ 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
|
||||
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.
|
||||
``lib/h5md/Makefile.machine`` file for your system, which should define
|
||||
an EXTRAMAKE variable to specify a corresponding
|
||||
``Makefile.lammps.<machine>`` file.
|
||||
|
||||
----------
|
||||
|
||||
@ -1229,7 +1254,8 @@ also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
|
||||
used in tandem with the USER-INTEL package to good effect, as explained
|
||||
on the :doc:`Speed intel <Speed_intel>` doc page.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -1248,11 +1274,12 @@ Best performance is achieved with Intel hardware, Intel compilers, as well as
|
||||
the Intel TBB and MKL libraries. However, the code also compiles, links, and
|
||||
runs with other compilers and without TBB and MKL.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
Choose which hardware to compile for in Makefile.machine via the
|
||||
following settings. See src/MAKE/OPTIONS/Makefile.intel_cpu\* and
|
||||
Makefile.knl files for examples. and src/USER-INTEL/README for
|
||||
following settings. See ``src/MAKE/OPTIONS/Makefile.intel_cpu*`` and
|
||||
``Makefile.knl`` files for examples. and ``src/USER-INTEL/README`` for
|
||||
additional information.
|
||||
|
||||
For CPUs:
|
||||
@ -1280,7 +1307,8 @@ For KNLs:
|
||||
USER-MOLFILE package
|
||||
---------------------------------------
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -1295,13 +1323,14 @@ folder of the local VMD installation in use. LAMMPS ships with a
|
||||
couple of default header files that correspond to a popular VMD
|
||||
version, usually the latest release.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
The lib/molfile/Makefile.lammps file has a setting for a dynamic
|
||||
The ``lib/molfile/Makefile.lammps`` file has a setting for a dynamic
|
||||
loading library libdl.a that is typically present on all systems. It
|
||||
is required for LAMMPS to link with this package. If the setting is
|
||||
not valid for your system, you will need to edit the Makefile.lammps
|
||||
file. See lib/molfile/README and lib/molfile/Makefile.lammps for
|
||||
file. See ``lib/molfile/README`` and ``lib/molfile/Makefile.lammps`` for
|
||||
details. It is also possible to configure a different folder with
|
||||
the VMD molfile plugin header files. LAMMPS ships with a couple of
|
||||
default headers, but these are not compatible with all VMD versions,
|
||||
@ -1318,22 +1347,24 @@ USER-NETCDF package
|
||||
To build with this package you must have the NetCDF library installed
|
||||
on your system.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
No additional settings are needed besides "-D PKG_USER-NETCDF=yes".
|
||||
No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``.
|
||||
|
||||
This should auto-detect the NETCDF library if it is installed on your
|
||||
system at standard locations. Several advanced CMake NETCDF options
|
||||
exist if you need to specify where it was installed. Use the ccmake
|
||||
(terminal window) or cmake-gui (graphical) tools to see these options
|
||||
and set them interactively from their user interfaces.
|
||||
exist if you need to specify where it was installed. Use the ``ccmake``
|
||||
(terminal window) or ``cmake-gui`` (graphical) tools to see these
|
||||
options and set them interactively from their user interfaces.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
The lib/netcdf/Makefile.lammps file has settings for NetCDF include
|
||||
The ``lib/netcdf/Makefile.lammps`` file has settings for NetCDF include
|
||||
and library files which LAMMPS needs to build with this package. If
|
||||
the settings are not valid for your system, you will need to edit the
|
||||
Makefile.lammps file. See lib/netcdf/README for details.
|
||||
``Makefile.lammps`` file. See ``lib/netcdf/README`` for details.
|
||||
|
||||
----------
|
||||
|
||||
@ -1342,18 +1373,20 @@ Makefile.lammps file. See lib/netcdf/README for details.
|
||||
USER-OMP package
|
||||
-------------------------------
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
No additional settings are required besides "-D PKG_USER-OMP=yes". If
|
||||
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**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
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.
|
||||
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.
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
@ -1363,8 +1396,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
|
||||
LINKFLAGS: -qopenmp # for Intel compilers on Linux
|
||||
|
||||
For other platforms and compilers, please consult the documentation
|
||||
about OpenMP support for your compiler. Please see the note about
|
||||
how to address compatibility :ref:`issues with the 'default(none)' directive <default-none-issues>` of some compilers.
|
||||
about OpenMP support for your compiler.
|
||||
|
||||
----------
|
||||
|
||||
@ -1374,19 +1406,20 @@ USER-QMMM package
|
||||
---------------------------------
|
||||
|
||||
For using LAMMPS to do QM/MM simulations via the USER-QMMM package you
|
||||
need to build LAMMPS as a library. A LAMMPS executable with fix qmmm
|
||||
included can be built, but will not be able to do a QM/MM simulation
|
||||
on as such. You must also build a QM code - currently only Quantum
|
||||
ESPRESSO (QE) is supported - and create a new executable which links
|
||||
LAMMPS and the QM code together. Details are given in the
|
||||
lib/qmmm/README file. It is also recommended to read the instructions
|
||||
for :doc:`linking with LAMMPS as a library <Build_link>` for
|
||||
background information. This requires compatible Quantum Espresso
|
||||
and LAMMPS versions. The current interface and makefiles have last
|
||||
been verified to work in February 2020 with Quantum Espresso versions
|
||||
6.3 to 6.5.
|
||||
need to build LAMMPS as a library. A LAMMPS executable with :doc:`fix
|
||||
qmmm <fix_qmmm>` included can be built, but will not be able to do a
|
||||
QM/MM simulation on as such. You must also build a QM code - currently
|
||||
only Quantum ESPRESSO (QE) is supported - and create a new executable
|
||||
which links LAMMPS and the QM code together. Details are given in the
|
||||
``lib/qmmm/README`` file. It is also recommended to read the
|
||||
instructions for :doc:`linking with LAMMPS as a library <Build_link>`
|
||||
for background information. This requires compatible Quantum Espresso
|
||||
and LAMMPS versions. The current interface and makefiles have last been
|
||||
verified to work in February 2020 with Quantum Espresso versions 6.3 to
|
||||
6.5.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
When using CMake, building a LAMMPS library is required and it is
|
||||
recommended to build a shared library, since any libraries built from
|
||||
@ -1403,17 +1436,18 @@ would be:
|
||||
|
||||
After completing the LAMMPS build and also configuring and compiling
|
||||
Quantum ESPRESSO with external library support (via "make couple"),
|
||||
go back to the lib/qmmm folder and follow the instructions on the
|
||||
go back to the ``lib/qmmm` folder and follow the instructions on the
|
||||
README file to build the combined LAMMPS/QE QM/MM executable
|
||||
(pwqmmm.x) in the lib/qmmm folder. You need to make certain, that
|
||||
(pwqmmm.x) in the ``lib/qmmm`` folder. You need to make certain, that
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
Before building LAMMPS, you must build the QMMM library in lib/qmmm.
|
||||
Before building LAMMPS, you must build the QMMM library in ``lib/qmmm``.
|
||||
You can do this manually if you prefer; follow the first two steps
|
||||
explained in lib/qmmm/README. You can also do it in one step from the
|
||||
lammps/src dir, using a command like these, which simply invoke the
|
||||
lib/qmmm/Install.py script with the specified args:
|
||||
explained in ``lib/qmmm/README``. You can also do it in one step from
|
||||
the ``lammps/src`` dir, using a command like these, which simply invoke
|
||||
the ``lib/qmmm/Install.py`` script with the specified args:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -1422,18 +1456,18 @@ lib/qmmm/Install.py script with the specified args:
|
||||
$ make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
|
||||
$ make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler
|
||||
|
||||
The build should produce two files: lib/qmmm/libqmmm.a and
|
||||
lib/qmmm/Makefile.lammps. The latter is copied from an existing
|
||||
Makefile.lammps.\* and has settings needed to build LAMMPS with the
|
||||
The build should produce two files: ``lib/qmmm/libqmmm.a`` and
|
||||
``lib/qmmm/Makefile.lammps``. The latter is copied from an existing
|
||||
``Makefile.lammps.*`` and has settings needed to build LAMMPS with the
|
||||
QMMM library (though typically the settings are just blank). If
|
||||
necessary, you can edit/create a new lib/qmmm/Makefile.machine file
|
||||
for your system, which should define an EXTRAMAKE variable to specify
|
||||
a corresponding Makefile.lammps.machine file.
|
||||
necessary, you can edit/create a new ``lib/qmmm/Makefile.<machine>`` file
|
||||
for your system, which should define an ``EXTRAMAKE`` variable to
|
||||
specify a corresponding ``Makefile.lammps.<machine>`` file.
|
||||
|
||||
You can then install QMMM package and build LAMMPS in the usual
|
||||
manner. After completing the LAMMPS build and compiling Quantum
|
||||
ESPRESSO with external library support (via "make couple"), go back to
|
||||
the lib/qmmm folder and follow the instructions in the README file to
|
||||
the ``lib/qmmm`` folder and follow the instructions in the README file to
|
||||
build the combined LAMMPS/QE QM/MM executable (pwqmmm.x) in the
|
||||
lib/qmmm folder.
|
||||
|
||||
@ -1448,26 +1482,28 @@ To build with this package, you must download and build the QUIP
|
||||
library. It can be obtained from GitHub. For support of GAP
|
||||
potentials, additional files with specific licensing conditions need
|
||||
to be downloaded and configured. See step 1 and step 1.1 in the
|
||||
lib/quip/README file for details on how to do this.
|
||||
``lib/quip/README`` file for details on how to do this.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
|
||||
|
||||
CMake will not download and build the QUIP library. But once you have
|
||||
done that, a CMake build of LAMMPS with "-D PKG_USER-QUIP=yes" should
|
||||
done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should
|
||||
work. Set QUIP_LIBRARY if CMake cannot find the QUIP library.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
The download/build procedure for the QUIP library, described in
|
||||
lib/quip/README file requires setting two environment variables,
|
||||
``lib/quip/README`` file requires setting two environment variables,
|
||||
QUIP_ROOT and QUIP_ARCH. These are accessed by the
|
||||
lib/quip/Makefile.lammps file which is used when you compile and link
|
||||
LAMMPS with this package. You should only need to edit
|
||||
Makefile.lammps if the LAMMPS build can not use its settings to
|
||||
``Makefile.lammps`` if the LAMMPS build can not use its settings to
|
||||
successfully build on your system.
|
||||
|
||||
----------
|
||||
@ -1477,11 +1513,13 @@ successfully build on your system.
|
||||
USER-SCAFACOS package
|
||||
-----------------------------------------
|
||||
|
||||
To build with this package, you must download and build the `ScaFaCoS Coulomb solver library <scafacos-home_>`_
|
||||
To build with this package, you must download and build the `ScaFaCoS
|
||||
Coulomb solver library <scafacos-home_>`_
|
||||
|
||||
.. _scafacos-home: http://www.scafacos.de
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -1496,22 +1534,23 @@ SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library
|
||||
file, not the directory the library file is in. SCAFACOS_INCLUDE_DIR
|
||||
is the directory the ScaFaCoS include file is in.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
You can download and build the ScaFaCoS library manually if you
|
||||
prefer; follow the instructions in lib/scafacos/README. You can also
|
||||
do it in one step from the lammps/src dir, using a command like these,
|
||||
which simply invoke the lib/scafacos/Install.py script with the
|
||||
prefer; follow the instructions in ``lib/scafacos/README``. You can also
|
||||
do it in one step from the ``lammps/src`` dir, using a command like these,
|
||||
which simply invoke the ``lib/scafacos/Install.py`` script with the
|
||||
specified args:
|
||||
|
||||
make lib-scafacos # print help message
|
||||
make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version>
|
||||
make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
|
||||
|
||||
Note that 2 symbolic (soft) links, "includelink" and "liblink", are
|
||||
created in lib/scafacos to point to the ScaFaCoS src dir. When LAMMPS
|
||||
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
|
||||
created in ``lib/scafacos`` to point to the ScaFaCoS src dir. When LAMMPS
|
||||
builds in src it will use these links. You should not need to edit
|
||||
the lib/scafacos/Makefile.lammps file.
|
||||
the ``lib/scafacos/Makefile.lammps`` file.
|
||||
|
||||
----------
|
||||
|
||||
@ -1523,24 +1562,26 @@ USER-SMD package
|
||||
To build with this package, you must download the Eigen3 library.
|
||||
Eigen3 is a template library, so you do not need to build it.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
|
||||
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location)
|
||||
|
||||
If DOWNLOAD_EIGEN3 is set, the Eigen3 library will be downloaded and
|
||||
If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be downloaded and
|
||||
inside the CMake build directory. If the Eigen3 library is already on
|
||||
your system (in a location CMake cannot find it), EIGEN3_INCLUDE_DIR
|
||||
your system (in a location CMake cannot find it), ``EIGEN3_INCLUDE_DIR``
|
||||
is the directory the Eigen3++ include file is in.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
You can download the Eigen3 library manually if you prefer; follow the
|
||||
instructions in lib/smd/README. You can also do it in one step from
|
||||
the lammps/src dir, using a command like these, which simply invoke
|
||||
the lib/smd/Install.py script with the specified args:
|
||||
instructions in ``lib/smd/README``. You can also do it in one step from
|
||||
the ``lammps/src`` dir, using a command like these, which simply invoke
|
||||
the ``lib/smd/Install.py`` script with the specified args:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -1548,9 +1589,9 @@ the lib/smd/Install.py script with the specified args:
|
||||
$ make lib-smd args="-b" # download to lib/smd/eigen3
|
||||
$ make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
|
||||
|
||||
Note that a symbolic (soft) link named "includelink" is created in
|
||||
lib/smd to point to the Eigen dir. When LAMMPS builds it will use
|
||||
this link. You should not need to edit the lib/smd/Makefile.lammps
|
||||
Note that a symbolic (soft) link named ``includelink`` is created in
|
||||
``lib/smd`` to point to the Eigen dir. When LAMMPS builds it will use
|
||||
this link. You should not need to edit the ``lib/smd/Makefile.lammps``
|
||||
file.
|
||||
|
||||
----------
|
||||
@ -1563,21 +1604,23 @@ USER-VTK package
|
||||
To build with this package you must have the VTK library installed on
|
||||
your system.
|
||||
|
||||
**CMake build**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
No additional settings are needed besides "-D PKG_USER-VTK=yes".
|
||||
No additional settings are needed besides ``-D PKG_USER-VTK=yes``.
|
||||
|
||||
This should auto-detect the VTK library if it is installed on your
|
||||
system at standard locations. Several advanced VTK options exist if
|
||||
you need to specify where it was installed. Use the ccmake (terminal
|
||||
window) or cmake-gui (graphical) tools to see these options and set
|
||||
you need to specify where it was installed. Use the ``ccmake`` (terminal
|
||||
window) or ``cmake-gui`` (graphical) tools to see these options and set
|
||||
them interactively from their user interfaces.
|
||||
|
||||
**Traditional make**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
The lib/vtk/Makefile.lammps file has settings for accessing VTK files
|
||||
The ``lib/vtk/Makefile.lammps`` file has settings for accessing VTK files
|
||||
and its library, which LAMMPS needs to build with this package. If
|
||||
the settings are not valid for your system, check if one of the other
|
||||
lib/vtk/Makefile.lammps.\* files is compatible and copy it to
|
||||
``lib/vtk/Makefile.lammps.*`` files is compatible and copy it to
|
||||
Makefile.lammps. If none of the provided files work, you will need to
|
||||
edit the Makefile.lammps file. See lib/vtk/README for details.
|
||||
edit the ``Makefile.lammps`` file. See ``lib/vtk/README`` for details.
|
||||
|
||||
@ -44,7 +44,8 @@ require use of an FFT library to compute 1d FFTs. The KISS FFT
|
||||
library is included with LAMMPS but other libraries can be faster.
|
||||
LAMMPS can use them if they are available on your system.
|
||||
|
||||
**CMake variables**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -74,7 +75,12 @@ to assist:
|
||||
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
|
||||
-D MKL_LIBRARIES=path
|
||||
|
||||
**Makefile.machine settings**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
To change the FFT library to be used and its options, you have to edit
|
||||
your machine Makefile. Below are examples how the makefile variables
|
||||
could be changed.
|
||||
|
||||
.. code-block:: make
|
||||
|
||||
@ -104,7 +110,8 @@ As with CMake, you do not need to set paths in ``FFT_INC`` or ``FFT_PATH``, if
|
||||
the compiler can find the FFT header and library files in its default search path.
|
||||
You must specify ``FFT_LIB`` with the appropriate FFT libraries to include in the link.
|
||||
|
||||
**CMake and make info**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
|
||||
distribution. It is portable across all platforms. Depending on the size
|
||||
@ -127,7 +134,7 @@ download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
|
||||
version 3.X; the legacy version 2.1.X is no longer supported.
|
||||
|
||||
Building FFTW for your box should be as simple as ``./configure; make;
|
||||
make install``\ . The install command typically requires root privileges
|
||||
make install``. The install command typically requires root privileges
|
||||
(e.g. invoke it via sudo), unless you specify a local directory with
|
||||
the "--prefix" option of configure. Type ``./configure --help`` to see
|
||||
various options.
|
||||
@ -176,13 +183,18 @@ LAMMPS has a few integer data types which can be defined as either
|
||||
4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
|
||||
The default setting of "smallbig" is almost always adequate.
|
||||
|
||||
**CMake variable**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
|
||||
|
||||
**Makefile.machine setting**\ :
|
||||
Traditional build
|
||||
^^^^^^^^^^^^^^^^^
|
||||
|
||||
If you want a setting different from the default, you need to edit your
|
||||
machine Makefile.
|
||||
|
||||
.. code-block:: make
|
||||
|
||||
@ -190,7 +202,8 @@ The default setting of "smallbig" is almost always adequate.
|
||||
|
||||
The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
|
||||
|
||||
**CMake and make info**\ :
|
||||
CMake and make info
|
||||
^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
The default "smallbig" setting allows for simulations with:
|
||||
|
||||
@ -251,7 +264,8 @@ PNG image files. Likewise the :doc:`dump movie <dump_image>` command
|
||||
outputs movie files in MPEG format. Using these options requires the
|
||||
following settings:
|
||||
|
||||
**CMake variables**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -276,7 +290,8 @@ variables:
|
||||
-D ZLIB_LIBRARIES=path # path to libz.a (.so) file
|
||||
-D FFMPEG_EXECUTABLE=path # path to ffmpeg executable
|
||||
|
||||
**Makefile.machine settings**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
.. code-block:: make
|
||||
|
||||
@ -295,7 +310,8 @@ with a list of graphics libraries to include in the link. You must
|
||||
insure ffmpeg is in a directory where LAMMPS can find it at runtime,
|
||||
that is a directory in your PATH environment variable.
|
||||
|
||||
**CMake and make info**\ :
|
||||
CMake and make info
|
||||
^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
Using ``ffmpeg`` to output movie files requires that your machine
|
||||
supports the "popen" function in the standard runtime library.
|
||||
@ -318,7 +334,8 @@ If this option is enabled, large files can be read or written with
|
||||
gzip compression by several LAMMPS commands, including
|
||||
:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
|
||||
|
||||
**CMake variables**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -326,13 +343,15 @@ gzip compression by several LAMMPS commands, including
|
||||
# default is yes if CMake can find gzip, else no
|
||||
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
|
||||
|
||||
**Makefile.machine setting**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
.. code-block:: make
|
||||
|
||||
LMP_INC = -DLAMMPS_GZIP
|
||||
|
||||
**CMake and make info**\ :
|
||||
CMake and make info
|
||||
^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
This option requires that your machine supports the "popen()" function
|
||||
in the standard runtime library and that a gzip executable can be
|
||||
@ -363,7 +382,8 @@ pointers that are aligned to 16-byte boundaries. Using SSE vector
|
||||
instructions efficiently, however, requires memory blocks being
|
||||
aligned on 64-byte boundaries.
|
||||
|
||||
**CMake variable**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -374,7 +394,8 @@ and revert to using the malloc() C-library function instead. When
|
||||
compiling LAMMPS for Windows systems, malloc() will always be used
|
||||
and this setting ignored.
|
||||
|
||||
**Makefile.machine setting**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
.. code-block:: make
|
||||
|
||||
@ -398,13 +419,15 @@ types, the following setting will be needed. It converts "long long"
|
||||
to a "long" data type, which should be the desired 8-byte integer on
|
||||
those systems:
|
||||
|
||||
**CMake variable**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D LAMMPS_LONGLONG_TO_LONG=value # yes or no (default)
|
||||
|
||||
**Makefile.machine setting**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
.. code-block:: make
|
||||
|
||||
@ -423,13 +446,15 @@ Instead, the call stack is unwound and control returns to the caller,
|
||||
e.g. to Python. Of course, the calling code has to be set up to
|
||||
*catch* exceptions thrown from within LAMMPS.
|
||||
|
||||
**CMake variable**\ :
|
||||
CMake build
|
||||
^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D LAMMPS_EXCEPTIONS=value # yes or no (default)
|
||||
|
||||
**Makefile.machine setting**\ :
|
||||
Traditional make
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
.. code-block:: make
|
||||
|
||||
|
||||
Reference in New Issue
Block a user