Merge branch 'master' into multi_epcc
This commit is contained in:
Axel Kohlmeyer
@ -15,6 +15,8 @@ This section documents the following functions:
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- :cpp:func:`lammps_config_package_count`
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- :cpp:func:`lammps_config_package_name`
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- :cpp:func:`lammps_config_accelerator`
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- :cpp:func:`lammps_has_gpu_device`
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- :cpp:func:`lammps_gpu_device_info`
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- :cpp:func:`lammps_has_style`
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- :cpp:func:`lammps_style_count`
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- :cpp:func:`lammps_style_name`
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@ -132,6 +134,16 @@ approach.
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-----------------------
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.. doxygenfunction:: lammps_has_gpu_device
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:project: progguide
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-----------------------
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.. doxygenfunction:: lammps_get_gpu_device_info
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:project: progguide
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-----------------------
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.. doxygenfunction:: lammps_has_style
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:project: progguide
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@ -94,6 +94,7 @@ Miscellaneous tools
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* :ref:`kate <kate>`
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* :ref:`LAMMPS shell <lammps_shell>`
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* :ref:`LAMMPS magic patterns for file(1) <magic>`
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* :ref:`Offline build tool <offline>`
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* :ref:`singularity <singularity_tool>`
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* :ref:`SWIG interface <swig>`
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* :ref:`vim <vim>`
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@ -756,6 +757,103 @@ See the README file in the tools/msi2lmp folder for more information.
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----------
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.. _offline:
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Scripts for building LAMMPS when offline
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----------------------------------------
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In some situations it might be necessary to build LAMMPS on a system
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without direct internet access. The scripts in ``tools/offline`` folder
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allow you to pre-load external dependencies for both the documentation
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build and for building LAMMPS with CMake.
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It does so by
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#. downloading necessary ``pip`` packages,
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#. cloning ``git`` repositories
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#. downloading tarballs
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to a designated cache folder.
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As of April 2021, all of these downloads make up around 600MB. By
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default, the offline scripts will download everything into the
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``$HOME/.cache/lammps`` folder, but this can be changed by setting the
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``LAMMPS_CACHING_DIR`` environment variable.
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Once the caches have been initialized, they can be used for building the
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LAMMPS documentation or compiling LAMMPS using CMake on an offline
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system.
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The ``use_caches.sh`` script must be sourced into the current shell
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to initialize the offline build environment. Note that it must use
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the same ``LAMMPS_CACHING_DIR``. This script does the following:
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#. Set up environment variables that modify the behavior of both,
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``pip`` and ``git``
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#. Start a simple local HTTP server using Python to host files for CMake
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Afterwards, it will print out instruction on how to modify the CMake
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command line to make sure it uses the local HTTP server.
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To undo the environment changes and shutdown the local HTTP server,
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run the ``deactivate_caches`` command.
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Examples
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^^^^^^^^
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For all of the examples below, you first need to create the cache, which
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requires an internet connection.
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.. code-block:: bash
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./tools/offline/init_caches.sh
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Afterwards, you can disconnect or copy the contents of the
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``LAMMPS_CACHING_DIR`` folder to an offline system.
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Documentation Build
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^^^^^^^^^^^^^^^^^^^
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The documentation build will create a new virtual environment that
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typically first installs dependencies from ``pip``. With the offline
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environment loaded, these installations will instead grab the necessary
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packages from your local cache.
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.. code-block:: bash
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# if LAMMPS_CACHING_DIR is different from default, make sure to set it first
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# export LAMMPS_CACHING_DIR=path/to/folder
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source tools/offline/use_caches.sh
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cd doc/
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make html
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deactivate_caches
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CMake Build
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^^^^^^^^^^^
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When compiling certain packages with external dependencies, the CMake
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build system will download necessary files or sources from the web. For
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more flexibility the CMake configuration allows users to specify the URL
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of each of these dependencies. What the ``init_caches.sh`` script does
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is create a CMake "preset" file, which sets the URLs for all of the known
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dependencies and redirects the download to the local cache.
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.. code-block:: bash
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# if LAMMPS_CACHING_DIR is different from default, make sure to set it first
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# export LAMMPS_CACHING_DIR=path/to/folder
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source tools/offline/use_caches.sh
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mkdir build
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cd build
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cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake
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make -j 8
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deactivate_caches
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----------
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.. _phonon:
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phonon tool
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@ -257,7 +257,7 @@ then overrides them with 0.0 only for CHARMM:
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.. code-block:: LAMMPS
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special_bonds amber
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pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
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pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
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pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
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The this input achieves the same effect:
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@ -265,7 +265,7 @@ The this input achieves the same effect:
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.. code-block:: LAMMPS
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special_bonds 0.0 0.0 0.1
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pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
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pair_style hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
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pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
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pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
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pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
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@ -279,7 +279,7 @@ effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA:
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.. code-block:: LAMMPS
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special_bonds lj/coul 1e-20 1e-20 0.5
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pair_hybrid tersoff lj/cut/coul/long 12.0
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pair_style hybrid tersoff lj/cut/coul/long 12.0
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pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
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For use with the various :doc:`compute \*/tally <compute_tally>`
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@ -417,7 +417,11 @@ assigned automatically to the sub-style defined for both I,I and J,J and
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its coefficients generated by the mixing rule used by that sub-style.
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For the *hybrid/overlay* and *hybrid/scaled* style, there is an
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additional requirement that both the I,I and J,J pairs are assigned to a
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single sub-style. See the :doc:`pair_modify <pair_modify>` command for
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single sub-style. If this requirement is not met, no I,J coeffs will be
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generated, even if the sub-styles support mixing, and I,J pair
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coefficients must be explicitly defined.
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See the :doc:`pair_modify <pair_modify>` command for
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details of mixing rules. See the See the doc page for the sub-style to
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see if allows for mixing.
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@ -11,12 +11,13 @@ Syntax
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thermo_modify keyword value ...
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* one or more keyword/value pairs may be listed
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* keyword = *lost* or *lost/bond* or *norm* or *flush* or *line* or *format* or *temp* or *press*
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* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *format* or *temp* or *press*
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.. parsed-literal::
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*lost* value = *error* or *warn* or *ignore*
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*lost/bond* value = *error* or *warn* or *ignore*
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*warn* value = *ignore* or *reset* or *default* or a number
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*norm* value = *yes* or *no*
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*flush* value = *yes* or *no*
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*line* value = *one* or *multi*
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@ -75,6 +76,43 @@ are drifting out of the box through a fixed boundary condition (see
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the :doc:`boundary <boundary>` command). In this case one atom may be
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deleted before the rest of the molecule is, on a later timestep.
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The *warn* keyword allows you to control whether LAMMPS will print
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warning messages and how many of them. Most warning messages are only
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printed by MPI rank 0. They are usually pointing out important issues
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that should be investigated, but LAMMPS cannot determine for
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certain whether they are an indication of an error.
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Some warning messages are printed during a run (or immediately before)
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each time a specific MPI rank encounters the issue, e.g. bonds that are
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stretched too far or dihedrals in extreme configurations. These number
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of these can quickly blow up the size of the log file and screen output.
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Thus a limit of 100 warning messages is applied by default. The warning
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count is applied to the entire input unless reset with a ``thermo_modify
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warn reset`` command. If there are more warnings than the limit, LAMMPS
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will print one final warning that it will not print any additional
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warning messages.
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.. note::
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The warning limit is enforced on either the per-processor count or
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the total count across all processors. For efficiency reasons,
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however, the total count is only updated at steps with thermodynamic
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output. Thus when running on a large number of processors in
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parallel, the total number of warnings printed can be significantly
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larger than the given limit.
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Any number after the keyword *warn* will change the warning limit
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accordingly. With the value *ignore* all warnings will be suppressed,
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with the value *always* no limit will be applied and warnings will
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always be printed, with the value *reset* the internal warning counter
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will be reset to zero, and with the value *default*, the counter is
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reset and the limit set to 100. An example usage of either *reset* or
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*default* would be to re-enable warnings that were disabled or have
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reached the limit during equilibration, where the warnings would be
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acceptable while the system is still adjusting, but then change
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to all warnings for the production run, where they would indicate
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problems that would require a closer look at what is causing them.
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The *norm* keyword determines whether various thermodynamic output
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values are normalized by the number of atoms or not, depending on
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whether it is set to *yes* or *no*\ . Different unit styles have
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@ -183,9 +221,9 @@ Related commands
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Default
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"""""""
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The option defaults are lost = error, norm = yes for unit style of
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*lj*\ , norm = no for unit style of *real* and *metal*\ , flush = no,
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and temp/press = compute IDs defined by thermo_style.
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The option defaults are lost = error, warn = 100, norm = yes for unit
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style of *lj*\ , norm = no for unit style of *real* and *metal*\ ,
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flush = no, and temp/press = compute IDs defined by thermo_style.
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The defaults for the line and format options depend on the thermo
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style. For styles "one" and "custom", the line and format defaults
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Reference in New Issue
Block a user