Loading doc/src/Build_extras.rst +107 −84 Original line number Diff line number Diff line Loading @@ -7,8 +7,13 @@ in addition to: .. code-block:: bash -D PKG_NAME=yes # CMake make yes-name # make $ cmake -D PKG_NAME=yes or .. code-block:: bash $ make yes-name as described on the :doc:`Build\_package <Build_package>` doc page. Loading @@ -20,18 +25,35 @@ You may need to tell LAMMPS where it is found on your system. This is the list of packages that may require additional steps. +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` | +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` | +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>` | +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` | +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | | | +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ .. table_from_list:: :columns: 6 * :ref:`COMPRESS <compress>` * :ref:`GPU <gpu>` * :ref:`KIM <kim>` * :ref:`KOKKOS <kokkos>` * :ref:`LATTE <latte>` * :ref:`MESSAGE <message>` * :ref:`MSCG <mscg>` * :ref:`OPT <opt>` * :ref:`POEMS <poems>` * :ref:`PYTHON <python>` * :ref:`VORONOI <voronoi>` * :ref:`USER-ADIOS <user-adios>` * :ref:`USER-ATC <user-atc>` * :ref:`USER-AWPMD <user-awpmd>` * :ref:`USER-COLVARS <user-colvars>` * :ref:`USER-H5MD <user-h5md>` * :ref:`USER-INTEL <user-intel>` * :ref:`USER-MOLFILE <user-molfile>` * :ref:`USER-NETCDF <user-netcdf>` * :ref:`USER-PLUMED <user-plumed>` * :ref:`USER-OMP <user-omp>` * :ref:`USER-QMMM <user-qmmm>` * :ref:`USER-QUIP <user-quip>` * :ref:`USER-SCAFACOS <user-scafacos>` * :ref:`USER-SMD <user-smd>` * :ref:`USER-VTK <user-vtk>` ---------- Loading Loading @@ -127,10 +149,10 @@ script with the specified args: .. code-block:: bash make lib-gpu # print help message make lib-gpu args="-b" # build GPU library with default Makefile.linux make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi $ make lib-gpu # print help message $ make lib-gpu args="-b" # build GPU library with default Makefile.linux $ make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision $ make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi Note that this procedure starts with a Makefile.machine in lib/gpu, as specified by the "-m" switch. For your convenience, machine makefiles Loading Loading @@ -181,7 +203,8 @@ use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>` command, you also need to have libcurl installed with the matching development headers and the curl-config tool. See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to See the `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ web page to learn how to install a pre-build binary of the OpenKIM Repository of Models. See the list of all KIM models here: https://openkim.org/browse/models Loading Loading @@ -231,13 +254,13 @@ invoke the lib/kim/Install.py script with the specified args. .. code-block:: bash make lib-kim # print help message make lib-kim args="-b " # (re-)install KIM API lib with only example models make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model make lib-kim args="-b -a everything" # install KIM API lib with all models make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver $ make lib-kim # print help message $ make lib-kim args="-b " # (re-)install KIM API lib with only example models $ make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model $ make lib-kim args="-b -a everything" # install KIM API lib with all models $ make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver $ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location $ 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 Loading Loading @@ -410,10 +433,10 @@ args: .. code-block:: bash make lib-latte # print help message make lib-latte args="-b" # download and build in lib/latte/LATTE-master make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte make lib-latte args="-b -m gfortran" # download and build in lib/latte and $ make lib-latte # print help message $ make lib-latte args="-b" # download and build in lib/latte/LATTE-master $ make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte $ 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 Loading Loading @@ -455,9 +478,9 @@ simply invoke the lib/message/Install.py script with the specified args: .. code-block:: bash make lib-message # print help message make lib-message args="-m -z" # build with MPI and socket (ZMQ) support make lib-message args="-s" # build as serial lib with no ZMQ support $ make lib-message # print help message $ make lib-message args="-m -z" # build with MPI and socket (ZMQ) support $ 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 Loading Loading @@ -505,12 +528,12 @@ invoke the lib/mscg/Install.py script with the specified args: .. code-block:: bash make lib-mscg # print help message make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master $ make lib-mscg # print help message $ make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master # with the settings compatible with "make serial" make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master $ make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master # with the settings compatible with "make mpi" make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release $ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg to point to the MS-CG src/installation dir. Loading Loading @@ -561,10 +584,10 @@ lib/poems/Install.py script with the specified args: .. code-block:: bash make lib-poems # print help message make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") make lib-poems args="-m icc" # build with Intel icc compiler $ make lib-poems # print help message $ make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") $ make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") $ 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 Loading Loading @@ -651,10 +674,10 @@ args: .. 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++ src dir. When LAMMPS Loading Loading @@ -692,14 +715,14 @@ Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software .. code-block:: bash make yes-user-adios $ make yes-user-adios otherwise, set ADIOS2\_DIR environment variable when turning on the package: .. code-block:: bash ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed $ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed ---------- Loading Loading @@ -728,10 +751,10 @@ lib/atc/Install.py script with the specified args: .. code-block:: bash 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 $ 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 The build should produce two files: lib/atc/libatc.a and lib/atc/Makefile.lammps. The latter is copied from an existing Loading @@ -750,10 +773,10 @@ lib/linalg with a command like these: .. 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 $ 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 ---------- Loading @@ -779,10 +802,10 @@ lib/awpmd/Install.py script with the specified args: .. code-block:: bash 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 $ 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 The build should produce two files: lib/awpmd/libawpmd.a and lib/awpmd/Makefile.lammps. The latter is copied from an existing Loading @@ -801,10 +824,10 @@ library in lib/linalg with a command like these: .. 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 $ 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 ---------- Loading Loading @@ -853,10 +876,10 @@ the specified args: .. code-block:: bash 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 $ 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 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 Loading @@ -867,8 +890,8 @@ Optional flags may be specified as environment variables: .. code-block:: bash 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) $ 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 Loading Loading @@ -968,10 +991,10 @@ from the src folder through the following make args: .. code-block:: bash 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 $ 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 Note that 2 symbolic (soft) links, "includelink" and "liblink" are Loading @@ -984,8 +1007,8 @@ package and compile LAMMPS in the usual manner: .. code-block:: bash make yes-user-plumed make machine $ make yes-user-plumed $ make machine 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 Loading Loading @@ -1035,8 +1058,8 @@ 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 $ 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 Loading Loading @@ -1264,10 +1287,10 @@ lib/qmmm/Install.py script with the specified args: .. code-block:: bash make lib-qmmm # print help message make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") 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 $ make lib-qmmm # print help message $ make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") $ 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 Loading Loading @@ -1402,9 +1425,9 @@ the lib/smd/Install.py script with the specified args: .. code-block:: bash make lib-smd # print help message 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 $ make lib-smd # print help message $ 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 Loading doc/src/Manual_build.rst +7 −7 Original line number Diff line number Diff line Loading @@ -19,9 +19,9 @@ sub-directories and optionally 2 PDF files and 2 e-book format files: If you downloaded LAMMPS as a tarball from the web site, all these directories and files should be included. If you downloaded LAMMPS from the public git repository, then the HTML and PDF files are not included. Instead you need to create them, in one of two ways: If you downloaded LAMMPS from the public git repository, then the HTML and PDF files are not included. Instead you need to create them, in one of two ways: a. You can "fetch" the current HTML and PDF files from the LAMMPS web site. Just type "make fetch". This should download a html\_www Loading @@ -41,10 +41,10 @@ b. You can build the HTML and PDF files yourself, by typing "make html" be able to view the math offline, some extra data and javascript code needs to be downloaded and the HTML generation needs to be changed to reference them. When typing "make html-offline" this is done automatically. Same as for the sphinx tool, this download is required only once. After that also the processing of the documentation can be done without internet access. To generate the PDF version of the manual, additionally the PDFLaTeX software and automatically. Same as for the sphinx tool and its extensions, this download is required only once. After that also the processing of the documentation can be done without internet access. To generate the PDF version of the manual, additionally the PDFLaTeX software and several LaTeX packages are required. ---------- Loading doc/src/Run_basics.rst +34 −32 Original line number Diff line number Diff line Basics of running LAMMPS ======================== LAMMPS is run from the command line, reading commands from a file via the -in command line flag, or from standard input. LAMMPS is run from the command line, reading commands from a file via the -in command line flag, or from standard input. Using the "-in in.file" variant is recommended: .. parsed-literal:: .. code-block:: bash lmp_serial < in.file lmp_serial -in in.file /path/to/lammps/src/lmp_serial < in.file mpirun -np 4 lmp_mpi -in in.file mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file mpirun -np 6 /usr/local/bin/lmp -in in.file $ lmp_serial -in in.file $ lmp_serial < in.file $ /path/to/lammps/src/lmp_serial -i in.file $ mpirun -np 4 lmp_mpi -in in.file $ mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file $ mpirun -np 6 /usr/local/bin/lmp -in in.file You normally run the LAMMPS command in the directory where your input script is located. That is also where output files are produced by default, unless you provide specific other paths in your input script or on the command line. As in some of the examples above, the LAMMPS executable itself can be placed elsewhere. You normally run the LAMMPS command in the directory where your input script is located. That is also where output files are produced by default, unless you provide specific other paths in your input script or on the command line. As in some of the examples above, the LAMMPS executable itself can be placed elsewhere. .. note:: Loading @@ -27,7 +27,8 @@ examples above, the LAMMPS executable itself can be placed elsewhere. in parallel with mpirun; for those systems the -in form is required. As LAMMPS runs it prints info to the screen and a logfile named log.lammps. More info about output is given on the :doc:`Run output <Run_output>` doc page. *log.lammps*\ . More info about output is given on the :doc:`Run output <Run_output>` doc page. If LAMMPS encounters errors in the input script or while running a simulation it will print an ERROR message and stop or a WARNING Loading @@ -35,26 +36,27 @@ message and continue. See the :doc:`Errors <Errors>` doc page for a discussion of the various kinds of errors LAMMPS can or can't detect, a list of all ERROR and WARNING messages, and what to do about them. ---------- LAMMPS can run the same problem on any number of processors, including a single processor. In theory you should get identical answers on any LAMMPS can run the same problem on any number of processors, including a single processor. In theory you should get identical answers on any number of processors and on any machine. In practice, numerical round-off can cause slight differences and eventual divergence of molecular dynamics phase space trajectories. See the :doc:`Errors common <Errors_common>` doc page for discussion of this. round-off due to using floating-point math can cause slight differences and an eventual divergence of molecular dynamics trajectories. See the :doc:`Errors common <Errors_common>` doc page for discussion of this. LAMMPS can run as large a problem as will fit in the physical memory of one or more processors. If you run out of memory, you must run on more processors or define a smaller problem. LAMMPS can run as large a problem as will fit in the physical memory of one or more processors. If you run out of memory, you must run on more processors or define a smaller problem. The amount of memory needed and how well it can be distributed across processors may vary based on the models and settings and commands used. If you run LAMMPS in parallel via mpirun, you should be aware of the :doc:`processors <processors>` command which controls how MPI tasks are mapped to the simulation box, as well as mpirun options that control how MPI tasks are assigned to physical cores of the node(s) of the machine you are running on. These settings can improve performance, though the defaults are often adequate. :doc:`processors <processors>` command, which controls how MPI tasks are mapped to the simulation box, as well as mpirun options that control how MPI tasks are assigned to physical cores of the node(s) of the machine you are running on. These settings can improve performance, though the defaults are often adequate. For example, it is often important to bind MPI tasks (processes) to physical cores (processor affinity), so that the operating system does Loading @@ -67,10 +69,10 @@ can set the number of threads per MPI task via the environment variable OMP\_NUM\_THREADS, before you launch LAMMPS: .. parsed-literal:: .. code-block:: bash export OMP_NUM_THREADS=2 # bash setenv OMP_NUM_THREADS 2 # csh or tcsh $ export OMP_NUM_THREADS=2 # bash $ setenv OMP_NUM_THREADS 2 # csh or tcsh This can also be done via the :doc:`package <package>` command or via the :doc:`-pk command-line switch <Run_options>` which invokes the Loading doc/src/Run_options.rst +6 −7 File changed.Preview size limit exceeded, changes collapsed. Show changes Loading
doc/src/Build_extras.rst +107 −84 Original line number Diff line number Diff line Loading @@ -7,8 +7,13 @@ in addition to: .. code-block:: bash -D PKG_NAME=yes # CMake make yes-name # make $ cmake -D PKG_NAME=yes or .. code-block:: bash $ make yes-name as described on the :doc:`Build\_package <Build_package>` doc page. Loading @@ -20,18 +25,35 @@ You may need to tell LAMMPS where it is found on your system. This is the list of packages that may require additional steps. +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` | +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` | +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>` | +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` | +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | | | +----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ .. table_from_list:: :columns: 6 * :ref:`COMPRESS <compress>` * :ref:`GPU <gpu>` * :ref:`KIM <kim>` * :ref:`KOKKOS <kokkos>` * :ref:`LATTE <latte>` * :ref:`MESSAGE <message>` * :ref:`MSCG <mscg>` * :ref:`OPT <opt>` * :ref:`POEMS <poems>` * :ref:`PYTHON <python>` * :ref:`VORONOI <voronoi>` * :ref:`USER-ADIOS <user-adios>` * :ref:`USER-ATC <user-atc>` * :ref:`USER-AWPMD <user-awpmd>` * :ref:`USER-COLVARS <user-colvars>` * :ref:`USER-H5MD <user-h5md>` * :ref:`USER-INTEL <user-intel>` * :ref:`USER-MOLFILE <user-molfile>` * :ref:`USER-NETCDF <user-netcdf>` * :ref:`USER-PLUMED <user-plumed>` * :ref:`USER-OMP <user-omp>` * :ref:`USER-QMMM <user-qmmm>` * :ref:`USER-QUIP <user-quip>` * :ref:`USER-SCAFACOS <user-scafacos>` * :ref:`USER-SMD <user-smd>` * :ref:`USER-VTK <user-vtk>` ---------- Loading Loading @@ -127,10 +149,10 @@ script with the specified args: .. code-block:: bash make lib-gpu # print help message make lib-gpu args="-b" # build GPU library with default Makefile.linux make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi $ make lib-gpu # print help message $ make lib-gpu args="-b" # build GPU library with default Makefile.linux $ make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision $ make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi Note that this procedure starts with a Makefile.machine in lib/gpu, as specified by the "-m" switch. For your convenience, machine makefiles Loading Loading @@ -181,7 +203,8 @@ use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>` command, you also need to have libcurl installed with the matching development headers and the curl-config tool. See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to See the `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ web page to learn how to install a pre-build binary of the OpenKIM Repository of Models. See the list of all KIM models here: https://openkim.org/browse/models Loading Loading @@ -231,13 +254,13 @@ invoke the lib/kim/Install.py script with the specified args. .. code-block:: bash make lib-kim # print help message make lib-kim args="-b " # (re-)install KIM API lib with only example models make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model make lib-kim args="-b -a everything" # install KIM API lib with all models make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver $ make lib-kim # print help message $ make lib-kim args="-b " # (re-)install KIM API lib with only example models $ make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model $ make lib-kim args="-b -a everything" # install KIM API lib with all models $ make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver $ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location $ 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 Loading Loading @@ -410,10 +433,10 @@ args: .. code-block:: bash make lib-latte # print help message make lib-latte args="-b" # download and build in lib/latte/LATTE-master make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte make lib-latte args="-b -m gfortran" # download and build in lib/latte and $ make lib-latte # print help message $ make lib-latte args="-b" # download and build in lib/latte/LATTE-master $ make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte $ 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 Loading Loading @@ -455,9 +478,9 @@ simply invoke the lib/message/Install.py script with the specified args: .. code-block:: bash make lib-message # print help message make lib-message args="-m -z" # build with MPI and socket (ZMQ) support make lib-message args="-s" # build as serial lib with no ZMQ support $ make lib-message # print help message $ make lib-message args="-m -z" # build with MPI and socket (ZMQ) support $ 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 Loading Loading @@ -505,12 +528,12 @@ invoke the lib/mscg/Install.py script with the specified args: .. code-block:: bash make lib-mscg # print help message make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master $ make lib-mscg # print help message $ make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master # with the settings compatible with "make serial" make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master $ make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master # with the settings compatible with "make mpi" make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release $ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg to point to the MS-CG src/installation dir. Loading Loading @@ -561,10 +584,10 @@ lib/poems/Install.py script with the specified args: .. code-block:: bash make lib-poems # print help message make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") make lib-poems args="-m icc" # build with Intel icc compiler $ make lib-poems # print help message $ make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") $ make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") $ 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 Loading Loading @@ -651,10 +674,10 @@ args: .. 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++ src dir. When LAMMPS Loading Loading @@ -692,14 +715,14 @@ Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software .. code-block:: bash make yes-user-adios $ make yes-user-adios otherwise, set ADIOS2\_DIR environment variable when turning on the package: .. code-block:: bash ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed $ ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed ---------- Loading Loading @@ -728,10 +751,10 @@ lib/atc/Install.py script with the specified args: .. code-block:: bash 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 $ 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 The build should produce two files: lib/atc/libatc.a and lib/atc/Makefile.lammps. The latter is copied from an existing Loading @@ -750,10 +773,10 @@ lib/linalg with a command like these: .. 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 $ 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 ---------- Loading @@ -779,10 +802,10 @@ lib/awpmd/Install.py script with the specified args: .. code-block:: bash 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 $ 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 The build should produce two files: lib/awpmd/libawpmd.a and lib/awpmd/Makefile.lammps. The latter is copied from an existing Loading @@ -801,10 +824,10 @@ library in lib/linalg with a command like these: .. 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 $ 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 ---------- Loading Loading @@ -853,10 +876,10 @@ the specified args: .. code-block:: bash 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 $ 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 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 Loading @@ -867,8 +890,8 @@ Optional flags may be specified as environment variables: .. code-block:: bash 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) $ 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 Loading Loading @@ -968,10 +991,10 @@ from the src folder through the following make args: .. code-block:: bash 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 $ 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 Note that 2 symbolic (soft) links, "includelink" and "liblink" are Loading @@ -984,8 +1007,8 @@ package and compile LAMMPS in the usual manner: .. code-block:: bash make yes-user-plumed make machine $ make yes-user-plumed $ make machine 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 Loading Loading @@ -1035,8 +1058,8 @@ 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 $ 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 Loading Loading @@ -1264,10 +1287,10 @@ lib/qmmm/Install.py script with the specified args: .. code-block:: bash make lib-qmmm # print help message make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") 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 $ make lib-qmmm # print help message $ make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") $ 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 Loading Loading @@ -1402,9 +1425,9 @@ the lib/smd/Install.py script with the specified args: .. code-block:: bash make lib-smd # print help message 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 $ make lib-smd # print help message $ 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 Loading
doc/src/Manual_build.rst +7 −7 Original line number Diff line number Diff line Loading @@ -19,9 +19,9 @@ sub-directories and optionally 2 PDF files and 2 e-book format files: If you downloaded LAMMPS as a tarball from the web site, all these directories and files should be included. If you downloaded LAMMPS from the public git repository, then the HTML and PDF files are not included. Instead you need to create them, in one of two ways: If you downloaded LAMMPS from the public git repository, then the HTML and PDF files are not included. Instead you need to create them, in one of two ways: a. You can "fetch" the current HTML and PDF files from the LAMMPS web site. Just type "make fetch". This should download a html\_www Loading @@ -41,10 +41,10 @@ b. You can build the HTML and PDF files yourself, by typing "make html" be able to view the math offline, some extra data and javascript code needs to be downloaded and the HTML generation needs to be changed to reference them. When typing "make html-offline" this is done automatically. Same as for the sphinx tool, this download is required only once. After that also the processing of the documentation can be done without internet access. To generate the PDF version of the manual, additionally the PDFLaTeX software and automatically. Same as for the sphinx tool and its extensions, this download is required only once. After that also the processing of the documentation can be done without internet access. To generate the PDF version of the manual, additionally the PDFLaTeX software and several LaTeX packages are required. ---------- Loading
doc/src/Run_basics.rst +34 −32 Original line number Diff line number Diff line Basics of running LAMMPS ======================== LAMMPS is run from the command line, reading commands from a file via the -in command line flag, or from standard input. LAMMPS is run from the command line, reading commands from a file via the -in command line flag, or from standard input. Using the "-in in.file" variant is recommended: .. parsed-literal:: .. code-block:: bash lmp_serial < in.file lmp_serial -in in.file /path/to/lammps/src/lmp_serial < in.file mpirun -np 4 lmp_mpi -in in.file mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file mpirun -np 6 /usr/local/bin/lmp -in in.file $ lmp_serial -in in.file $ lmp_serial < in.file $ /path/to/lammps/src/lmp_serial -i in.file $ mpirun -np 4 lmp_mpi -in in.file $ mpirun -np 8 /path/to//lammps/src/lmp_mpi -in in.file $ mpirun -np 6 /usr/local/bin/lmp -in in.file You normally run the LAMMPS command in the directory where your input script is located. That is also where output files are produced by default, unless you provide specific other paths in your input script or on the command line. As in some of the examples above, the LAMMPS executable itself can be placed elsewhere. You normally run the LAMMPS command in the directory where your input script is located. That is also where output files are produced by default, unless you provide specific other paths in your input script or on the command line. As in some of the examples above, the LAMMPS executable itself can be placed elsewhere. .. note:: Loading @@ -27,7 +27,8 @@ examples above, the LAMMPS executable itself can be placed elsewhere. in parallel with mpirun; for those systems the -in form is required. As LAMMPS runs it prints info to the screen and a logfile named log.lammps. More info about output is given on the :doc:`Run output <Run_output>` doc page. *log.lammps*\ . More info about output is given on the :doc:`Run output <Run_output>` doc page. If LAMMPS encounters errors in the input script or while running a simulation it will print an ERROR message and stop or a WARNING Loading @@ -35,26 +36,27 @@ message and continue. See the :doc:`Errors <Errors>` doc page for a discussion of the various kinds of errors LAMMPS can or can't detect, a list of all ERROR and WARNING messages, and what to do about them. ---------- LAMMPS can run the same problem on any number of processors, including a single processor. In theory you should get identical answers on any LAMMPS can run the same problem on any number of processors, including a single processor. In theory you should get identical answers on any number of processors and on any machine. In practice, numerical round-off can cause slight differences and eventual divergence of molecular dynamics phase space trajectories. See the :doc:`Errors common <Errors_common>` doc page for discussion of this. round-off due to using floating-point math can cause slight differences and an eventual divergence of molecular dynamics trajectories. See the :doc:`Errors common <Errors_common>` doc page for discussion of this. LAMMPS can run as large a problem as will fit in the physical memory of one or more processors. If you run out of memory, you must run on more processors or define a smaller problem. LAMMPS can run as large a problem as will fit in the physical memory of one or more processors. If you run out of memory, you must run on more processors or define a smaller problem. The amount of memory needed and how well it can be distributed across processors may vary based on the models and settings and commands used. If you run LAMMPS in parallel via mpirun, you should be aware of the :doc:`processors <processors>` command which controls how MPI tasks are mapped to the simulation box, as well as mpirun options that control how MPI tasks are assigned to physical cores of the node(s) of the machine you are running on. These settings can improve performance, though the defaults are often adequate. :doc:`processors <processors>` command, which controls how MPI tasks are mapped to the simulation box, as well as mpirun options that control how MPI tasks are assigned to physical cores of the node(s) of the machine you are running on. These settings can improve performance, though the defaults are often adequate. For example, it is often important to bind MPI tasks (processes) to physical cores (processor affinity), so that the operating system does Loading @@ -67,10 +69,10 @@ can set the number of threads per MPI task via the environment variable OMP\_NUM\_THREADS, before you launch LAMMPS: .. parsed-literal:: .. code-block:: bash export OMP_NUM_THREADS=2 # bash setenv OMP_NUM_THREADS 2 # csh or tcsh $ export OMP_NUM_THREADS=2 # bash $ setenv OMP_NUM_THREADS 2 # csh or tcsh This can also be done via the :doc:`package <package>` command or via the :doc:`-pk command-line switch <Run_options>` which invokes the Loading
doc/src/Run_options.rst +6 −7 File changed.Preview size limit exceeded, changes collapsed. Show changes
