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make code-block formatting more consistent and align with documented conventions

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This commit is contained in:
Axel Kohlmeyer
2022-12-30 06:46:09 -05:00
parent 406289d0f9
commit 33711ac36e
19 changed files with 312 additions and 266 deletions
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4
doc/src/Build_basics.rst
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@ -276,7 +276,7 @@ LAMMPS.
Parallel build (see ``src/MAKE/Makefile.mpi``):
.. code-block:: bash
.. code-block:: make
CC = mpicxx
CCFLAGS = -g -O3
@ -296,7 +296,7 @@ LAMMPS.
If compilation stops with a message like the following:
.. code-block::
.. code-block:: output
g++ -g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I../STUBS -c ../main.cpp
In file included from ../pointers.h:24:0,

78
doc/src/Build_development.rst
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@ -154,32 +154,48 @@ for implementing the tests.
framework are more strict than for the main part of LAMMPS. For
example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
(version 4.8.x) are not sufficient. The CMake configuration will try
to detect compatible versions and either skip incompatible tests or
stop with an error.
to detect incompatible versions and either skip incompatible tests or
stop with an error. Also the number of tests will depend on
installed LAMMPS packages, development environment, operating system,
and configuration settings.
After compilation is complete, the unit testing is started in the build
folder using the ``ctest`` command, which is part of the CMake software.
The output of this command will be looking something like this::
The output of this command will be looking something like this:
[...]$ ctest
.. code-block:: console
$ ctest
Test project /home/akohlmey/compile/lammps/build-testing
Start 1: MolPairStyle:hybrid-overlay
1/109 Test #1: MolPairStyle:hybrid-overlay ......... Passed 0.02 sec
Start 2: MolPairStyle:hybrid
2/109 Test #2: MolPairStyle:hybrid ................. Passed 0.01 sec
Start 3: MolPairStyle:lj_class2
Start 1: RunLammps
1/563 Test #1: RunLammps .......................................... Passed 0.28 sec
Start 2: HelpMessage
2/563 Test #2: HelpMessage ........................................ Passed 0.06 sec
Start 3: InvalidFlag
3/563 Test #3: InvalidFlag ........................................ Passed 0.06 sec
Start 4: Tokenizer
4/563 Test #4: Tokenizer .......................................... Passed 0.05 sec
Start 5: MemPool
5/563 Test #5: MemPool ............................................ Passed 0.05 sec
Start 6: ArgUtils
6/563 Test #6: ArgUtils ........................................... Passed 0.05 sec
[...]
Start 107: PotentialFileReader
107/109 Test #107: PotentialFileReader ................ Passed 0.04 sec
Start 108: EIMPotentialFileReader
108/109 Test #108: EIMPotentialFileReader ............. Passed 0.03 sec
Start 109: TestSimpleCommands
109/109 Test #109: TestSimpleCommands ................. Passed 0.02 sec
Start 561: ImproperStyle:zero
561/563 Test #561: ImproperStyle:zero ................................. Passed 0.07 sec
Start 562: TestMliapPyUnified
562/563 Test #562: TestMliapPyUnified ................................. Passed 0.16 sec
Start 563: TestPairList
563/563 Test #563: TestPairList ....................................... Passed 0.06 sec
100% tests passed, 0 tests failed out of 26
100% tests passed, 0 tests failed out of 563
Total Test time (real) = 25.57 sec
Label Time Summary:
generated = 0.85 sec*proc (3 tests)
noWindows = 4.16 sec*proc (2 tests)
slow = 78.33 sec*proc (67 tests)
unstable = 28.23 sec*proc (34 tests)
Total Test time (real) = 132.34 sec
The ``ctest`` command has many options, the most important ones are:
@ -210,11 +226,13 @@ Fortran) and testing different aspects of the LAMMPS software and its features.
The tests will adapt to the compilation settings of LAMMPS, so that tests
will be skipped if prerequisite features are not available in LAMMPS.
.. note::
.. admonition:: Work in Progress
:class: note
The unit test framework was added in spring 2020 and is under active
development. The coverage is not complete and will be expanded over
time.
time. Preference is given to parts of the code base that are easy to
test or commonly used.
Tests for styles of the same kind of style (e.g. pair styles or bond
styles) are performed with the same test executable using different
@ -248,9 +266,9 @@ the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
since this will skip the MPI initialization for each test run.
Below is an example command and output:
.. parsed-literal::
.. code-block:: console
[tests]$ test_pair_style mol-pair-lj_cut.yaml
$ test_pair_style mol-pair-lj_cut.yaml
[==========] Running 6 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 6 tests from PairStyle
@ -530,7 +548,7 @@ commands like the following:
.. code-block:: bash
$ clang-format -i some_file.cpp
clang-format -i some_file.cpp
The following target are available for both, GNU make and CMake:
@ -539,3 +557,19 @@ The following target are available for both, GNU make and CMake:
make format-src # apply clang-format to all files in src and the package folders
make format-tests # apply clang-format to all files in the unittest tree
----------
.. _gh-cli:
GitHub command line interface
-----------------------------
GitHub is developing a `tool for the command line
<https://cli.github.com>`_ that interacts with the GitHub website via a
command called ``gh``. This can be extremely convenient when working
with a Git repository hosted on GitHub (like LAMMPS). It is thus highly
recommended to install it when doing LAMMPS development.
The capabilities of the ``gh`` command is continually expanding, so
please see the documentation at https://cli.github.com/manual/

192
doc/src/Build_extras.rst
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@ -12,11 +12,11 @@ in addition to
- Traditional make
* - .. code-block:: bash
$ cmake -D PKG_NAME=yes
cmake -D PKG_NAME=yes
- .. code-block:: bash
- .. code-block:: console
$ make yes-name
make yes-name
as described on the :doc:`Build_package <Build_package>` page.
@ -242,10 +242,10 @@ 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
@ -358,13 +358,13 @@ minutes to hours) to build. Of course you only need to do that once.)
.. 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
When using the "-b " option, the KIM library is built using its native
cmake build system. The ``lib/kim/Install.py`` script supports a
@ -376,7 +376,7 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: bash
$ CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b " # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b " # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
Settings for debugging OpenKIM web queries discussed below need to
be applied by adding them to the ``LMP_INC`` variable through
@ -859,10 +859,10 @@ library.
.. 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``
@ -962,12 +962,12 @@ more details.
.. 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
@ -1019,10 +1019,10 @@ POEMS package
.. 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
@ -1108,10 +1108,10 @@ binary package provided by your operating system.
.. 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++
@ -1152,13 +1152,13 @@ systems.
.. code-block:: bash
$ make yes-adios
make yes-adios
otherwise, set ADIOS2_DIR environment variable when turning on the package:
.. code-block:: bash
$ ADIOS2_DIR=path make yes-adios # path is where ADIOS 2.x is installed
ADIOS2_DIR=path make yes-adios # path is where ADIOS 2.x is installed
----------
@ -1187,10 +1187,10 @@ The ATC package requires the MANYBODY package also be installed.
.. 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
@ -1209,10 +1209,10 @@ The ATC package requires the MANYBODY package also be installed.
.. 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
----------
@ -1238,10 +1238,10 @@ AWPMD package
.. 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
@ -1260,10 +1260,10 @@ AWPMD package
.. 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
----------
@ -1301,10 +1301,10 @@ be built for the most part with all major versions of the C++ language.
.. 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
@ -1316,8 +1316,8 @@ be built for the most part with all major versions of the C++ language.
.. 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
@ -1351,9 +1351,9 @@ This package depends on the KSPACE package.
.. code-block:: bash
$ make lib-electrode # print help message
$ make lib-electrode args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-electrode args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-electrode # print help message
make lib-electrode args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-electrode args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
Note that the ``Makefile.lammps`` file has settings for the BLAS
@ -1364,10 +1364,10 @@ This package depends on the KSPACE package.
.. 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
The package itself is activated with ``make yes-KSPACE`` and
``make yes-ELECTRODE``
@ -1407,8 +1407,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
.. code-block:: bash
$ make lib-pace # print help message
$ make lib-pace args="-b" # download and build the default version in lib/pace
make lib-pace # print help message
make lib-pace args="-b" # download and build the default version in lib/pace
You should not need to edit the ``lib/pace/Makefile.lammps`` file.
@ -1435,10 +1435,10 @@ ML-POD package
.. code-block:: bash
$ make lib-mlpod # print help message
$ make lib-mlpod args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-mlpod args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-mlpod args="-m mpi -e linalg" # same as above but use the bundled linalg lib
make lib-mlpod # print help message
make lib-mlpod args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-mlpod args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-mlpod args="-m mpi -e linalg" # same as above but use the bundled linalg lib
Note that the ``Makefile.lammps`` file has settings to use the BLAS
and LAPACK linear algebra libraries. These can either exist on
@ -1448,10 +1448,10 @@ ML-POD package
.. 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
The package itself is activated with ``make yes-ML-POD``.
@ -1550,10 +1550,10 @@ LAMMPS build.
.. 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``
@ -1566,8 +1566,8 @@ LAMMPS build.
.. code-block:: bash
$ make yes-plumed
$ make machine
make yes-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
@ -1619,8 +1619,8 @@ the HDF5 library.
.. 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
@ -1674,10 +1674,10 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
.. code-block:: bash
$ make lib-hdnnp # print help message
$ make lib-hdnnp args="-b" # download and build in lib/hdnnp/n2p2-...
$ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
$ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
make lib-hdnnp # print help message
make lib-hdnnp args="-b" # download and build in lib/hdnnp/n2p2-...
make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
@ -1777,8 +1777,8 @@ MDI package
.. code-block:: bash
$ python Install.py -m gcc # build using gcc compiler
$ python Install.py -m icc # build using icc compiler
python Install.py -m gcc # build using gcc compiler
python Install.py -m icc # build using icc compiler
The build should produce two files: ``lib/mdi/includelink/mdi.h``
and ``lib/mdi/liblink/libmdi.so``\ .
@ -1812,9 +1812,9 @@ they will be downloaded the first time this package is installed.
.. code-block:: bash
$ make lib-mesont # print help message
$ make lib-mesont args="-m gfortran" # build with GNU g++ compiler (settings as with "make serial")
$ make lib-mesont args="-m ifort" # build with Intel icc compiler
make lib-mesont # print help message
make lib-mesont args="-m gfortran" # build with GNU g++ compiler (settings as with "make serial")
make lib-mesont args="-m ifort" # build with Intel icc compiler
The build should produce two files: ``lib/mesont/libmesont.a`` and
``lib/mesont/Makefile.lammps``\ . The latter is copied from an
@ -1981,10 +1981,10 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
.. 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
@ -2133,9 +2133,9 @@ Eigen3 is a template library, so you do not need to build it.
.. 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

4
doc/src/Build_link.rst
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@ -209,7 +209,7 @@ You can verify whether all required shared libraries are found with the
.. code-block:: bash
$ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
linux-vdso.so.1 (0x00007ffe729e0000)
liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
@ -222,7 +222,7 @@ If a required library is missing, you would get a 'not found' entry:
.. code-block:: bash
$ ldd caller
ldd caller
linux-vdso.so.1 (0x00007ffd672fe000)
liblammps.so => not found
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)

6
doc/src/Developer_unittest.rst
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@ -489,7 +489,7 @@ to update the YAML files. Running a command like
.. code-block:: bash
$ test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml
test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml
will read the settings from the ``mol-pair-lennard_mdf.yaml`` file and then compute
the reference data and write a new file with to ``new.yaml``. If this step fails,
@ -500,13 +500,13 @@ It is also possible to do an update in place with:
.. code-block:: bash
$ test_pair_style mol-pair-lennard_mdf.yaml -u
test_pair_style mol-pair-lennard_mdf.yaml -u
And one can finally run the full set of tests with:
.. code-block:: bash
$ test_pair_style mol-pair-lennard_mdf.yaml
test_pair_style mol-pair-lennard_mdf.yaml
This will just print a summary of the groups of tests. When using the "-v" flag
the test will also keep any LAMMPS output and when using the "-s" flag, there

13
doc/src/Errors_debug.rst
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@ -40,7 +40,7 @@ We use it to show how to identify the origin of a segmentation fault.
After recompiling LAMMPS and running the input you should get something like this:
.. code-block::
.. code-block:: console
$ ./lmp -in in.melt
LAMMPS (19 Mar 2020)
@ -90,8 +90,9 @@ it. When it reaches the code causing the segmentation fault, it will
stop with a message why it stopped, print the current line of code, and
drop back to the GDB prompt.
.. code-block::
.. code-block:: console
(gdb) run
[...]
Setting up Verlet run ...
Unit style : lj
@ -106,7 +107,7 @@ drop back to the GDB prompt.
Now typing the command "where" will show the stack of functions starting from
the current function back to "main()".
.. code-block::
.. code-block:: console
(gdb) where
#0 0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
@ -124,7 +125,7 @@ You can also print the value of variables and see if there is anything
unexpected. Segmentation faults, for example, commonly happen when a
pointer variable is not assigned and still initialized to NULL.
.. code-block::
.. code-block:: console
(gdb) print x
$1 = (double **) 0x7ffff7ca1010
@ -153,7 +154,7 @@ utility to the current folder. Example: ``coredumpctl -o core dump lmp``.
Now you can launch the debugger to load the executable, its debug info
and the core dump and drop you to a prompt like before.
.. code-block::
.. code-block:: console
$ gdb lmp core
Reading symbols from lmp...
@ -186,7 +187,7 @@ recommended to redirect the valgrind output to a file (e.g. with
process ID) so that the messages of the multiple valgrind instances to
the console are not mixed.
.. code-block::
.. code-block:: console
$ valgrind ./lmp -in in.melt
==1933642== Memcheck, a memory error detector

4
doc/src/Fortran.rst
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@ -2391,7 +2391,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
mode. The function should have Fortran language bindings with the following
interface, which depends on how LAMMPS was compiled:
.. code-block:: Fortran
.. code-block:: fortran
ABSTRACT INTERFACE
SUBROUTINE external_callback(caller, timestep, ids, x, fexternal)
@ -2450,7 +2450,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
with ``-DLAMMPS_SMALLBIG``) that applies something akin to Hooke's Law
(with each atom having a different *k* value) is shown below.
.. code-block:: Fortran
.. code-block:: fortran
MODULE stuff
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double, c_int64_t

4
doc/src/Howto_cmake.rst
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@ -56,7 +56,7 @@ You should change into the top level directory of the LAMMPS source tree all
paths mentioned in the tutorial are relative to that. Immediately after downloading
it should look like this:
.. code-block:: bash
.. code-block:: console
$ ls
bench doc lib potentials README tools
@ -104,7 +104,7 @@ the progress of the configuration printed to the screen followed by a
summary of the enabled features, options and compiler settings. A typical
summary screen will look like this:
.. code-block::
.. code-block:: console
$ cmake ../cmake/
-- The CXX compiler identification is GNU 8.2.0

61
doc/src/Howto_github.rst
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@ -78,13 +78,13 @@ machine via HTTPS:
.. code-block:: bash
$ git clone https://github.com/<your user name>/lammps.git <some name>
git clone https://github.com/<your user name>/lammps.git <some name>
or, if you have set up your GitHub account for using SSH keys, via SSH:
.. code-block:: bash
$ git clone git@github.com:<your user name>/lammps.git
git clone git@github.com:<your user name>/lammps.git
You can find the proper URL by clicking the "Clone or download"-button:
@ -103,21 +103,21 @@ and use git pull:
.. code-block:: bash
$ cd mylammps
$ git checkout develop
$ git pull https://github.com/lammps/lammps develop
cd mylammps
git checkout develop
git pull https://github.com/lammps/lammps develop
You can also add this URL as a remote:
.. code-block:: bash
$ git remote add upstream https://www.github.com/lammps/lammps
git remote add upstream https://www.github.com/lammps/lammps
From then on you can update your upstream branches with:
.. code-block:: bash
$ git fetch upstream
git fetch upstream
and then refer to the upstream repository branches with
`upstream/develop` or `upstream/release` and so on.
@ -129,8 +129,8 @@ workflow that updated this tutorial, and hence we will call the branch
.. code-block:: bash
$ git fetch upstream
$ git checkout -b github-tutorial-update upstream/develop
git fetch upstream
git checkout -b github-tutorial-update upstream/develop
Now that we have changed branches, we can make our changes to our local
repository. Just remember that if you want to start working on another,
@ -150,8 +150,8 @@ After everything is done, add the files to the branch and commit them:
.. code-block:: bash
$ git add doc/src/Howto_github.txt
$ git add doc/src/JPG/tutorial*.png
git add doc/src/Howto_github.txt
git add doc/src/JPG/tutorial*.png
.. warning::
@ -174,13 +174,13 @@ useful message that explains the change.
.. code-block:: bash
$ git commit -m 'Finally updated the GitHub tutorial'
git commit -m 'Finally updated the GitHub tutorial'
After the commit, the changes can be pushed to the same branch on GitHub:
.. code-block:: bash
$ git push
git push
Git will ask you for your user name and password on GitHub if you have
not configured anything. If your local branch is not present on GitHub yet,
@ -188,7 +188,7 @@ it will ask you to add it by running
.. code-block:: bash
$ git push --set-upstream origin github-tutorial-update
git push --set-upstream origin github-tutorial-update
If you correctly type your user name and
password, the feature branch should be added to your fork on GitHub.
@ -198,13 +198,13 @@ If you want to make really sure you push to the right repository
.. code-block:: bash
$ git push origin
git push origin
or using an explicit URL:
.. code-block:: bash
$ git push git@github.com:Pakketeretet2/lammps.git
git push git@github.com:Pakketeretet2/lammps.git
----------
@ -412,10 +412,10 @@ we need to pull Axel's change back into our branch, and merge them:
.. code-block:: bash
$ git add Howto_github.txt
$ git add JPG/tutorial_reverse_pull_request*.png
$ git commit -m "Updated text and images on reverse pull requests"
$ git pull
git add Howto_github.txt
git add JPG/tutorial_reverse_pull_request*.png
git commit -m "Updated text and images on reverse pull requests"
git pull
In this case, the merge was painless because git could auto-merge:
@ -428,10 +428,10 @@ commit and push again:
.. code-block:: bash
$ git add Howto_github.txt
$ git add JPG/tutorial_reverse_pull_request6.png
$ git commit -m "Merged Axel's suggestions and updated text"
$ git push git@github.com:Pakketeretet2/lammps
git add Howto_github.txt
git add JPG/tutorial_reverse_pull_request6.png
git commit -m "Merged Axel's suggestions and updated text"
git push git@github.com:Pakketeretet2/lammps
This merge also shows up on the lammps GitHub page:
@ -456,9 +456,9 @@ branch!
.. code-block:: bash
$ git checkout develop
$ git pull https://github.com/lammps/lammps develop
$ git branch -d github-tutorial-update
git checkout develop
git pull https://github.com/lammps/lammps develop
git branch -d github-tutorial-update
If you do not pull first, it is not really a problem but git will warn
you at the next statement that you are deleting a local branch that
@ -472,7 +472,7 @@ to your remote(s) as well:
.. code-block:: bash
$ git push origin :github-tutorial-update
git push origin :github-tutorial-update
**Recent changes in the workflow**
@ -486,5 +486,6 @@ simplify comparisons between releases. Finally, all patches and
submissions are subject to automatic testing and code checks to make
sure they at the very least compile.
A discussion of the LAMMPS developer GitHub workflow can be found in the file
`doc/github-development-workflow.md <https://github.com/lammps/lammps/blob/develop/doc/github-development-workflow.md>`_
A discussion of the LAMMPS developer GitHub workflow can be found in the
file `doc/github-development-workflow.md
<https://github.com/lammps/lammps/blob/develop/doc/github-development-workflow.md>`_

26
doc/src/Install_git.rst
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@ -41,7 +41,7 @@ create a local copy of the LAMMPS repository with a command like:
.. code-block:: bash
$ git clone -b release https://github.com/lammps/lammps.git mylammps
git clone -b release https://github.com/lammps/lammps.git mylammps
where "mylammps" is the name of the directory you wish to create on
your machine and "release" is one of the 3 branches listed above.
@ -78,10 +78,10 @@ from within the "mylammps" directory:
.. code-block:: bash
$ git checkout release # not needed if you always stay in this branch
$ git checkout stable # use one of these 3 checkout commands
$ git checkout develop # to choose the branch to follow
$ git pull
git checkout release # not needed if you always stay in this branch
git checkout stable # use one of these 3 checkout commands
git checkout develop # to choose the branch to follow
git pull
Doing a "pull" will not change any files you have added to the LAMMPS
directory structure. It will also not change any existing LAMMPS
@ -97,7 +97,7 @@ this is as follows.
.. code-block:: bash
$ git checkout tagID
git checkout tagID
Stable versions and what tagID to use for a particular stable version
are discussed on `this page <https://www.lammps.org/bug.html#version>`_.
@ -138,13 +138,13 @@ changed. How to do this depends on the build system you are using.
.. code-block:: bash
$ make purge # remove any deprecated src files
$ make package-update # sync package files with src files
$ make foo # re-build for your machine (mpi, serial, etc)
make purge # remove any deprecated src files
make package-update # sync package files with src files
make foo # re-build for your machine (mpi, serial, etc)
to enforce consistency of the source between the src folder
and package directories. This is OK to do even if you don't
use any packages. The "make purge" command removes any deprecated
use any packages. The ``make purge`` command removes any deprecated
src files if they were removed by the patch from a package
sub-directory.
@ -160,9 +160,9 @@ changed. How to do this depends on the build system you are using.
:class: note
The servers at github.com support the "https://" access protocol for
anonymous, read-only access. If you have a suitably configured GitHub
account, you may also use SSH protocol with the
URL "git@github.com:lammps/lammps.git".
anonymous, read-only access. If you have a suitably configured
GitHub account, you may also use SSH protocol with the URL
"git@github.com:lammps/lammps.git".
The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
(Temple U, akohlmey at gmail.com).

34
doc/src/Install_linux.rst
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@ -34,7 +34,7 @@ To install LAMMPS do the following once:
.. code-block:: bash
$ sudo apt-get install lammps
sudo apt-get install lammps
This downloads an executable named ``lmp`` to your box and multiple
packages with supporting data, examples and libraries as well as any
@ -43,13 +43,13 @@ to run input scripts:
.. code-block:: bash
$ lmp -in in.lj
lmp -in in.lj
To update LAMMPS to the latest packaged version, do the following:
.. code-block:: bash
$ sudo apt-get update
sudo apt-get update
which will also update other packages on your system.
@ -61,14 +61,14 @@ package
.. code-block:: bash
$ sudo apt-get install openkim-models
sudo apt-get install openkim-models
Or use the KIM-API commands to download and install individual models.
To un-install LAMMPS, do the following:
.. code-block:: bash
$ sudo apt-get remove lammps
sudo apt-get remove lammps
Please use ``lmp -help`` to see which compilation options, packages,
and styles are included in the binary.
@ -103,9 +103,9 @@ To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do:
.. code-block:: bash
$ dnf install lammps-openmpi
$ module load mpi/openmpi-x86_64
$ mpirun -np 2 lmp -in in.lj
dnf install lammps-openmpi
module load mpi/openmpi-x86_64
mpirun -np 2 lmp -in in.lj
The ``dnf install`` command is needed only once. In case of a new LAMMPS
stable release, ``dnf update`` will automatically update to the newer
@ -121,7 +121,7 @@ can install the `openkim-models` package
.. code-block:: bash
$ dnf install openkim-models
dnf install openkim-models
Please use ``lmp -help`` to see which compilation options, packages,
and styles are included in the binary.
@ -162,14 +162,14 @@ in OpenSuse as of Leap 15.0. You can install the package with:
.. code-block:: bash
$ zypper install lammps
zypper install lammps
This includes support for OpenMPI. The name of the LAMMPS executable
is ``lmp``. Thus to run an input in parallel on 2 CPUs you would do:
.. code-block:: bash
$ mpirun -np 2 lmp -in in.lj
mpirun -np 2 lmp -in in.lj
Please use ``lmp -help`` to see which compilation options, packages,
and styles are included in the binary.
@ -181,7 +181,7 @@ can install the `openkim-models` package
.. code-block:: bash
$ zypper install openkim-models
zypper install openkim-models
Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
@ -229,10 +229,10 @@ any of the above names in-place of lammps.
.. code-block:: bash
$ git clone https://aur.archlinux.org/lammps.git
$ cd lammps
$ makepkg -s
$ makepkg -i
git clone https://aur.archlinux.org/lammps.git
cd lammps
makepkg -s
makepkg -i
To update, you may repeat the above, or change into the cloned directory,
and execute the following, after which, if there are any changes, you may
@ -240,7 +240,7 @@ use makepkg as above.
.. code-block:: bash
$ git pull
git pull
Alternatively, you may use an AUR helper to install these packages.

4
doc/src/Install_tarball.rst
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@ -26,7 +26,7 @@ command:
.. code-block:: bash
$ tar -xzvf lammps*.tar.gz
tar -xzvf lammps*.tar.gz
This will create a LAMMPS directory with the version date
in its name, e.g. lammps-23Jun18.
@ -40,7 +40,7 @@ with the following command, to create a lammps-<version> dir:
.. code-block:: bash
$ unzip lammps*.zip
unzip lammps*.zip
This version corresponds to the selected LAMMPS patch or stable
release.

14
doc/src/Python_install.rst
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@ -214,7 +214,7 @@ folder that the dynamic loader searches or inside of the installed
.. code-block:: bash
$ python install.py -p <python package> -l <shared library> [-n]
python install.py -p <python package> -l <shared library> [-n]
* The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
* the ``-l`` flag points to the LAMMPS shared library file to be installed,
@ -343,7 +343,7 @@ Python interpreter, load the ``lammps`` Python module and create a
LAMMPS instance. This should not generate an error message and produce
output similar to the following:
.. code-block:: bash
.. code-block:: console
$ python
Python 3.8.5 (default, Sep 5 2020, 10:50:12)
@ -403,7 +403,7 @@ follows:
- Via ``pip`` into a virtual environment (see above):
.. code-block:: bash
.. code-block:: console
$ source $HOME/myenv/activate
(myenv)$ pip install mpi4py
@ -449,7 +449,7 @@ on a simple test script
.. code-block:: bash
$ mpirun -np 4 python3 test.py
mpirun -np 4 python3 test.py
where ``test.py`` contains the lines
@ -459,11 +459,11 @@ where ``test.py`` contains the lines
comm = MPI.COMM_WORLD
print("Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()))
and see one line of output for each processor you run on.
and see one line of output for each processor you run on. Please note
that the order of the lines is not deterministic
.. code-block:: bash
.. code-block:: console
# NOTE: the line order is not deterministic
$ mpirun -np 4 python3 test.py
Proc 0 out of 4 procs
Proc 1 out of 4 procs

38
doc/src/Python_launch.rst
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@ -6,15 +6,15 @@ interactively from the ``bench`` directory:
.. code-block:: python
>>> from lammps import lammps
>>> lmp = lammps()
>>> lmp.file("in.lj")
from lammps import lammps
lmp = lammps()
lmp.file("in.lj")
Or put the same lines in the file ``test.py`` and run it as
.. code-block:: bash
$ python3 test.py
python3 test.py
Either way, you should see the results of running the ``in.lj`` benchmark
on a single processor appear on the screen, the same as if you had
@ -46,13 +46,13 @@ You can run the script in parallel as:
.. code-block:: bash
$ mpirun -np 4 python3 test.py
mpirun -np 4 python3 test.py
and you should see the same output as if you had typed
.. code-block:: bash
$ mpirun -np 4 lmp_mpi -in in.lj
mpirun -np 4 lmp_mpi -in in.lj
Note that without the mpi4py specific lines from ``test.py``
@ -82,9 +82,9 @@ one of several ways:
.. code-block:: bash
$ python script.py
$ python -i script.py
$ ./script.py
python script.py
python -i script.py
./script.py
The last command requires that the first line of the script be
something like this:
@ -92,17 +92,23 @@ something like this:
.. code-block:: bash
#!/usr/bin/python
#!/usr/bin/python -i
where the path points to where you have Python installed, and that you
have made the script file executable:
or
.. code-block:: bash
$ chmod +x script.py
#!/usr/bin/env python
where the path in the first case needs to point to where you have Python
installed (the second option is workaround for when this may change),
and that you have made the script file executable:
.. code-block:: bash
chmod +x script.py
Without the ``-i`` flag, Python will exit when the script finishes.
With the ``-i`` flag, you will be left in the Python interpreter when
the script finishes, so you can type subsequent commands. As
mentioned above, you can only run Python interactively when running
Python on a single processor, not in parallel.
the script finishes, so you can type subsequent commands. As mentioned
above, you can only run Python interactively when running Python on a
single processor, not in parallel.

18
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@ -32,7 +32,7 @@ standard Python distribution since version 2.5. You can check which
version of Python you have by simply typing "python" at a shell prompt.
Below is an example output for Python version 3.8.5.
.. code-block::
.. code-block:: console
$ python
Python 3.8.5 (default, Aug 12 2020, 00:00:00)
@ -43,12 +43,16 @@ Below is an example output for Python version 3.8.5.
.. warning::
The options described in this section of the manual for using Python with
LAMMPS currently support either Python 2 or 3. Specifically version 2.7 or
later and 3.6 or later. Since the Python community no longer maintains Python
2 (see `this notice <https://www.python.org/doc/sunset-python-2/>`_), we
recommend use of Python 3 with LAMMPS. While Python 2 code should continue to
work, that is not something we can guarantee long-term.
The options described in this section of the manual for using Python
with LAMMPS currently support either Python 2 or 3. Specifically
version 2.7 or later and 3.6 or later. Since the Python community no
longer maintains Python 2 (see `this notice
<https://www.python.org/doc/sunset-python-2/>`_), we recommend use of
Python 3 with LAMMPS. While Python 2 code should continue to work,
that is not something we can guarantee long-term. If you notice
Python code in the LAMMPS distribution that is not compatible with
Python 3, please contact the LAMMPS developers or submit `and issue
on GitHub <https://github.com/lammps/lammps/issues>`_
---------

22
doc/src/Run_basics.rst
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@ -12,15 +12,15 @@ build LAMMPS:
.. code-block:: bash
$ lmp_serial -in in.file
$ lmp_serial < in.file
$ lmp -in in.file
$ lmp < in.file
$ /path/to/lammps/src/lmp_serial -i in.file
$ mpirun -np 4 lmp_mpi -in in.file
$ mpiexec -np 4 lmp -in in.file
$ mpirun -np 8 /path/to/lammps/src/lmp_mpi -in in.file
$ mpiexec -n 6 /usr/local/bin/lmp -in in.file
lmp_serial -in in.file
lmp_serial < in.file
lmp -in in.file
lmp < in.file
/path/to/lammps/src/lmp_serial -i in.file
mpirun -np 4 lmp_mpi -in in.file
mpiexec -np 4 lmp -in in.file
mpirun -np 8 /path/to/lammps/src/lmp_mpi -in in.file
mpiexec -n 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
@ -78,8 +78,8 @@ variable OMP_NUM_THREADS, before you launch LAMMPS:
.. 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

4
doc/src/Run_options.rst
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@ -31,8 +31,8 @@ For example, the lmp_mpi executable might be launched as follows:
.. code-block:: bash
$ mpirun -np 16 lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
$ mpirun -np 16 lmp_mpi -var f tmp.out -log my.log -screen none -in in.alloy
mpirun -np 16 lmp_mpi -v f tmp.out -l my.log -sc none -i in.alloy
mpirun -np 16 lmp_mpi -var f tmp.out -log my.log -screen none -in in.alloy
----------

40
doc/src/Tools.rst
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@ -683,7 +683,7 @@ or (as administrator) to ``/etc/magic`` (for a system-wide
installation). Afterwards the ``file`` command should be able to
detect most LAMMPS restarts, dump, data and log files. Examples:
.. code-block:: bash
.. code-block:: console
$ file *.*
dihedral-quadratic.restart: LAMMPS binary restart file (rev 2), Version 10 Mar 2021, Little Endian
@ -1100,18 +1100,18 @@ for Tcl with:
.. code-block:: bash
$ swig -tcl -module tcllammps lammps.i
$ gcc -fPIC -shared $(pkgconf --cflags tcl) -o tcllammps.so \
swig -tcl -module tcllammps lammps.i
gcc -fPIC -shared $(pkgconf --cflags tcl) -o tcllammps.so \
lammps_wrap.c -L ../src/ -llammps
$ tclsh
tclsh
Or one can build an extended Tcl shell command with the wrapped
functions included with:
.. code-block:: bash
$ swig -tcl -module tcllmps lammps_shell.i
$ gcc -o tcllmpsh lammps_wrap.c -Xlinker -export-dynamic \
swig -tcl -module tcllmps lammps_shell.i
gcc -o tcllmpsh lammps_wrap.c -Xlinker -export-dynamic \
-DHAVE_CONFIG_H $(pkgconf --cflags tcl) \
$(pkgconf --libs tcl) -L ../src -llammps
@ -1142,20 +1142,20 @@ For illustration purposes below is a part of the Tcl example script.
.. code-block:: tcl
% load ./tcllammps.so
% set lmp [lammps_open_no_mpi 0 NULL NULL]
% lammps_command $lmp "units real"
% lammps_command $lmp "lattice fcc 2.5"
% lammps_command $lmp "region box block -5 5 -5 5 -5 5"
% lammps_command $lmp "create_box 1 box"
% lammps_command $lmp "create_atoms 1 box"
%
% set dt [doublep_value [voidp_to_doublep [lammps_extract_global $lmp dt]]]
% puts "LAMMPS version $ver"
% puts [format "Number of created atoms: %g" [lammps_get_natoms $lmp]]
% puts "Current size of timestep: $dt"
% puts "LAMMPS version: [lammps_version $lmp]"
% lammps_close $lmp
load ./tcllammps.so
set lmp [lammps_open_no_mpi 0 NULL NULL]
lammps_command $lmp "units real"
lammps_command $lmp "lattice fcc 2.5"
lammps_command $lmp "region box block -5 5 -5 5 -5 5"
lammps_command $lmp "create_box 1 box"
lammps_command $lmp "create_atoms 1 box"
set dt [doublep_value [voidp_to_doublep [lammps_extract_global $lmp dt]]]
puts "LAMMPS version $ver"
puts [format "Number of created atoms: %g" [lammps_get_natoms $lmp]]
puts "Current size of timestep: $dt"
puts "LAMMPS version: [lammps_version $lmp]"
lammps_close $lmp
----------

4
doc/src/read_dump.rst
View File

@ -161,7 +161,7 @@ snapshot was written on for the *native* or *adios* formats.
The list of timestamps available in an adios .bp file is stored in the
variable *ntimestep*:
.. parsed-literal::
.. parsed-literal:: console
$ bpls dump.bp -d ntimestep
uint64_t ntimestep 5*scalar
@ -253,7 +253,7 @@ except for the *q* charge field.
The list of fields stored in an adios .bp file is recorded in the attributes
*columns* (array of short strings) and *columnstr* (space-separated single string).
.. parsed-literal::
.. parsed-literal:: console
$ bpls -la dump.bp column*
string columns attr = {"id", "type", "x", "y", "z", "vx", "vy", "vz"}