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get rid of references to USER-MISC in the general discussion

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This commit is contained in:
Axel Kohlmeyer
2021-07-25 10:03:16 -04:00
parent 9d162d865a
commit 9d9b089700
8 changed files with 77 additions and 78 deletions
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2
doc/src/Developer_org.rst
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@ -17,7 +17,7 @@ currently supports building with :doc:`conventional makefiles
differ in how packages are enabled or disabled for inclusion into a
LAMMPS binary so they cannot be mixed. The source files for each
package are in all-uppercase sub-directories of the ``src`` folder, for
example ``src/MOLECULE`` or ``src/USER-MISC``. The ``src/STUBS``
example ``src/MOLECULE`` or ``src/EXTRA-MOLECULE``. The ``src/STUBS``
sub-directory is not a package but contains a dummy MPI library, that is
used when building a serial version of the code. The ``src/MAKE``
directory and its sub-directories contain makefiles with settings and

5
doc/src/Errors_bugs.rst
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@ -17,8 +17,9 @@ the steps outlined below:
if your issue has already been reported and if it is still open.
* Check the `GitHub Pull Requests page <https://github.com/lammps/lammps/pulls>`_
to see if there is already a fix for your bug pending.
* Check the `mailing list archives <https://www.lammps.org/mail.html>`_
to see if the issue has been discussed before.
* Check the `mailing list archives <https://www.lammps.org/mail.html>`_ or
the `LAMMPS forum <https://www.lammps.org/forum.html>`_ to see if the
issue has been discussed before.
If none of these steps yields any useful information, please file a new
bug report on the `GitHub Issue page <https://github.com/lammps/lammps/issues>`_.

7
doc/src/Examples.rst
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@ -207,14 +207,12 @@ Uppercase directories
+------------+--------------------------------------------------------------------------------------------------+
| MC | using LAMMPS in a Monte Carlo mode to relax the energy of a system |
+------------+--------------------------------------------------------------------------------------------------+
| PACKAGES | examples for specific packages and contributed commands in USER-MISC |
| PACKAGES | examples for specific packages and contributed commands |
+------------+--------------------------------------------------------------------------------------------------+
| SPIN | examples for features of the SPIN package |
+------------+--------------------------------------------------------------------------------------------------+
| UNITS | examples that run the same simulation in lj, real, metal units |
+------------+--------------------------------------------------------------------------------------------------+
| USER-MISC | examples for commands in the USER-MISC packages |
+------------+--------------------------------------------------------------------------------------------------+
| VISCOSITY | compute viscosity via several methods |
+------------+--------------------------------------------------------------------------------------------------+
@ -228,7 +226,4 @@ of the sub-directories have their own README files which give further
instructions. See the :doc:`Packages_details <Packages_details>` doc
page for more info on specific packages.
Similarly the USER-MISC directory has sub-directories for examples
corresponding to individual commands or styles in the USER-MISC package.
.. _openkim: https://openkim.org

2
doc/src/Howto_cmake.rst
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@ -362,7 +362,7 @@ have to be enabled to be included into a LAMMPS executable. Packages
are enabled through setting variables of the kind ``PKG_<NAME>`` to
``on`` and disabled by setting them to ``off`` (or using ``yes``,
``no``, ``1``, ``0`` correspondingly). ``<NAME>`` has to be replaced by
the name of the package, e.g. ``MOLECULE`` or ``USER-MISC``.
the name of the package, e.g. ``MOLECULE`` or ``EXTRA-PAIR``.
Using presets

49
doc/src/Howto_replica.rst
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@ -8,34 +8,33 @@ periodically.
These are the relevant commands:
* :doc:`neb <neb>` for nudged elastic band calculations
* :doc:`hyper <hyper>` for bond boost hyperdynamics (HD)
* :doc:`neb <neb>` for nudged elastic band calculations (NEB)
* :doc:`neb_spin <neb_spin>` for magnetic nudged elastic band calculations
* :doc:`prd <prd>` for parallel replica dynamics
* :doc:`tad <tad>` for temperature accelerated dynamics
* :doc:`temper <temper>` for parallel tempering
* :doc:`prd <prd>` for parallel replica dynamics (PRD)
* :doc:`tad <tad>` for temperature accelerated dynamics (TAD)
* :doc:`temper <temper>` for parallel tempering with fixed volume
* :doc:`temper/npt <temper_npt>` for parallel tempering extended for NPT
* :doc:`temper/grem <temper_grem>` for parallel tempering with generalized replica exchange (gREM)
* :doc:`fix pimd <fix_pimd>` for path-integral molecular dynamics (PIMD)
NEB is a method for finding transition states and barrier energies.
PRD and TAD are methods for performing accelerated dynamics to find
and perform infrequent events. Parallel tempering or replica exchange
runs different replicas at a series of temperature to facilitate
rare-event sampling.
NEB is a method for finding transition states and barrier potential energies.
HD, PRD, and TAD are methods for performing accelerated dynamics to find and
perform infrequent events. Parallel tempering or replica exchange runs
different replicas at a series of temperature to facilitate rare-event
sampling. PIMD runs different replicas whose individual particles in different
replicas are coupled together by springs to model a system of ring-polymers which
can represent the quantum nature of atom cores.
These commands can only be used if LAMMPS was built with the REPLICA
package. See the :doc:`Build package <Build_package>` doc page for more
info.
PIMD runs different replicas whose individual particles are coupled
together by springs to model a system or ring-polymers.
This commands can only be used if LAMMPS was built with the USER-MISC
package. See the :doc:`Build package <Build_package>` doc page for more
info.
In all these cases, you must run with one or more processors per
replica. The processors assigned to each replica are determined at
run-time by using the :doc:`-partition command-line switch <Run_options>` to launch LAMMPS on multiple partitions,
which in this context are the same as replicas. E.g. these commands:
run-time by using the :doc:`-partition command-line switch
<Run_options>` to launch LAMMPS on multiple partitions, which in this
context are the same as replicas. E.g. these commands:
.. code-block:: bash
@ -46,9 +45,11 @@ would each run 8 replicas, on either 16 or 8 processors. Note the use
of the :doc:`-in command-line switch <Run_options>` to specify the input
script which is required when running in multi-replica mode.
Also note that with MPI installed on a machine (e.g. your desktop),
you can run on more (virtual) processors than you have physical
processors. Thus the above commands could be run on a
single-processor (or few-processor) desktop so that you can run
a multi-replica simulation on more replicas than you have
physical processors.
Also note that with MPI installed on a machine (e.g. your desktop), you
can run on more (virtual) processors than you have physical processors.
Thus the above commands could be run on a single-processor (or
few-processor) desktop so that you can run a multi-replica simulation on
more replicas than you have physical processors. This is useful for
testing and debugging, since with most modern processors and MPI
libraries the efficiency of a calculation can severely diminish when
oversubscribing processors.

3
doc/src/Intro_website.rst
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@ -20,7 +20,8 @@ available online are listed below.
* `Glossary of terms relevant to LAMMPS <https://www.lammps.org/glossary.html>`_
* `LAMMPS highlights with images <https://www.lammps.org/pictures.html>`_
* `LAMMPS highlights with movies <https://www.lammps.org/movies.html>`_
* `Mail list <https://www.lammps.org/mail.html>`_
* `Mailing list <https://www.lammps.org/mail.html>`_
* `LAMMPS forum <https://www.lammps.org/forum.html>`_
* `Workshops <https://www.lammps.org/workshops.html>`_
* `Tutorials <https://www.lammps.org/tutorials.html>`_

84
doc/src/Modify_contribute.rst
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@ -25,13 +25,16 @@ the work of others (and possibly get scooped by them) or have your work
duplicated by others.
For informal communication with (some of) the LAMMPS developers you may
ask to join the `LAMMPS developers on Slack <https://lammps.slack.com>`_.
This slack work space is by invitation only. Thus for access, please
send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
you are working on. Only discussions related to LAMMPS development are
tolerated, so this is **NOT** for people that look for help with compiling,
installing, or using LAMMPS. Please contact the `lammps-users mailing
list <https://www.lammps.org/mail.html>`_ for those purposes instead.
ask to join the `LAMMPS developers on Slack
<https://lammps.slack.com>`_. This slack work space is by invitation
only. Thus for access, please send an e-mail to ``slack@lammps.org``
explaining what part of LAMMPS you are working on. Only discussions
related to LAMMPS development are tolerated, so this is **NOT** for
people that look for help with compiling, installing, or using
LAMMPS. Please contact the
`lammps-users mailing list <https://www.lammps.org/mail.html>`_ or the
`LAMMPS forum <https://www.lammps.org/forum.html>`_ for those purposes
instead.
How quickly your contribution will be integrated depends largely on how
much effort it will cause to integrate and test it, how many and what
@ -49,11 +52,9 @@ with gzip. Please only use gzip compression, as this works well and is
available on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a :doc:`package <Packages_list>`. The
USER-MISC package is simply a collection of (mostly) unrelated single
files, which is the simplest way to have your contribution quickly added
to the LAMMPS distribution. All packages are listed and described
on the :doc:`Packages details <Packages_details>` doc page.
files to LAMMPS or as part of a :doc:`package <Packages_list>`. All
packages are listed and described on the :doc:`Packages details
<Packages_details>` doc page.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL
@ -92,7 +93,7 @@ trivial change is making a parent-class method "virtual" when you derive
a new child class from it.
Here is a checklist of steps you need to follow to submit a single file
or user package for our consideration. Following these steps will save
or package for our consideration. Following these steps will save
both you and us time. Please have a look at the existing files in
packages in the src directory for examples. If you are uncertain, please ask.
@ -150,37 +151,40 @@ packages in the src directory for examples. If you are uncertain, please ask.
You may also use ``// clang-format on/off`` throughout your file
to protect sections of the file from being reformatted.
* If you want your contribution to be added as a user-contributed
feature, and it's a single file (actually a \*.cpp and \*.h file) it can
rapidly be added to the USER-MISC directory. Send us the one-line
entry to add to the USER-MISC/README file in that dir, along with the
2 source files. You can do this multiple times if you wish to
contribute several individual features.
* Please review the list of :doc:`available Packages <Packages_details>`
to see if your contribution could be added to be added to one of them.
It should fit into the general purposed of that package. If it does not
fit well, it can be added to one of the EXTRA- packages or the MISC package.
* If you want your contribution to be added and it has several related
features or is dependent on an external or bundled library, it is best
to make it a package directory with a name like FOO. In addition to
your new files, the directory should contain a README text file. The
README should contain your name and contact information and a brief
description of what your new package does. If your files depend on
other LAMMPS style files also being installed (e.g. because your file
is a derived class from the other LAMMPS class), then an Install.sh
file is also needed to check for those dependencies. See other README
and Install.sh files in other directories as examples. Submit a pull
request on GitHub or send us a tarball of this FOO directory. Pull
requests are strongly encouraged since the greatly reduce the effort
to integrate a contribution and simplify the process of adjusting the
contributed code to cleanly integrate into the LAMMPS distribution.
* If your contribution has several related features that are not covered
by one of the existing packages or is dependent on a library (bundled
or external), it is best to make it a package directory with a name
like FOO. In addition to your new files, the directory should contain
a README text file. The README should contain your name and contact
information and a brief description of what your new package does. If
your files depend on other LAMMPS style files also being installed
(e.g. because your file is a derived class from the other LAMMPS
class), then an Install.sh file is also needed to check for those
dependencies and modifications to src/Depend.sh to trigger the checks.
See other README and Install.sh files in other directories as examples.
Similarly for CMake support changes need to be made to cmake/CMakeLists.txt,
the files in cmake/presets, and possibly a file to cmake/Modules/Packages/
added. Please check out how this is handled for existing packages and
ask the LAMMPS developers if you need assistance. Please submit a pull
request on GitHub or send us a tarball of this FOO directory and all
modified files. Pull requests are strongly encouraged since they greatly
reduce the effort required to integrate a contribution and simplify the
process of adjusting the contributed code to cleanly fit into the
LAMMPS distribution.
* Your new source files need to have the LAMMPS copyright, GPL notice,
and your name and email address at the top, like other
user-contributed LAMMPS source files. They need to create a class
that is inside the LAMMPS namespace. If the file is for one of the
USER packages, including USER-MISC, then we are not as picky about the
coding style (see above). I.e. the files do not need to be in the
same stylistic format and syntax as other LAMMPS files, though that
would be nice for developers as well as users who try to read your
code.
that is inside the LAMMPS namespace. To simplify maintenance, we
may ask to adjust the progamming style and formatting style to closer
match the rest of LAMMPS. We bundle a clang-format configuration file
that can help with adjusting the formatting, although this is not a
strict requirement.
* You **must** also create a **documentation** file for each new command
or style you are adding to LAMMPS. For simplicity and convenience,
@ -205,7 +209,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
cite itself. Citation labels must be unique across all .rst files.
The "Restrictions" section of the doc page should indicate if your
command is only available if LAMMPS is built with the appropriate
USER-MISC or FOO package. See other package doc files for examples of
FOO package. See other package doc files for examples of
how to do this. Please run at least "make html" and "make spelling"
and carefully inspect and proofread the resulting HTML format doc page
before submitting your code. Upon submission of a pull request,

3
doc/src/Packages_details.rst
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@ -2781,6 +2781,3 @@ which discuss the `QuickFF <quickff_>`_ methodology.
* :doc:`pair_style mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* examples/PACKAGES/yaff
----------