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Merge pull request #1864 from akohlmey/doc-remove-redundant-links 

More documentation ReStructuredText cleanup
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Axel Kohlmeyer 2020-01-31 17:32:51 -05:00 committed by GitHub
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5
doc/src/Build.rst
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@ -21,8 +21,3 @@ as described on the :doc:`Install <Install>` doc page.
Build_extras
Build_windows
Build_development
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_basics.rst
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@ -430,8 +430,3 @@ you want to copy files to is protected.
There is no "install" option in the src/Makefile for LAMMPS. If you
wish to do this you will need to first build LAMMPS, then manually
copy the desired LAMMPS files to the appropriate system directories.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_cmake.rst
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@ -238,8 +238,3 @@ enough version, you can download the latest version at
`https://cmake.org/download/ <https://cmake.org/download/>`_.
Instructions on how to install it on various platforms can be found
`on this page <https://cmake.org/install/>`_.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

6
doc/src/Build_development.rst
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@ -112,9 +112,3 @@ These reports require GCOVR to be installed. The easiest way to do this to insta
.. parsed-literal::
pip install git+https://github.com/gcovr/gcovr.git
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_extras.rst
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@ -1414,8 +1414,3 @@ the settings are not valid for your system, check if one of the other
lib/vtk/Makefile.lammps.\* files is compatible and copy it to
Makefile.lammps. If none of the provided files work, you will need to
edit the Makefile.lammps file. See lib/vtk/README for details.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_link.rst
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@ -84,8 +84,3 @@ See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS through its library interface.
Other examples in the COUPLE directory use coupling ideas discussed on
the :doc:`Howto couple <Howto_couple>` doc page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_make.rst
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@ -87,8 +87,3 @@ settings may become outdated:
make kokkos_omp # build with the KOKKOS package for OpenMP
make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
make kokkos_phi # build with the KOKKOS package for KNLs
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_package.rst
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@ -258,8 +258,3 @@ sub-directories with src files.
Type "make package-diff" to list all differences between pairs of
files in both the src dir and a package dir.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_settings.rst
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@ -488,8 +488,3 @@ e.g. to Python.
.. parsed-literal::
LMP_INC = -DLAMMPS_EXCEPTIONS
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Build_windows.rst
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@ -104,8 +104,3 @@ Support for the Visual C++ compilers is currently not available. The
CMake build system is capable of creating suitable a Visual Studio
style build environment, but the LAMMPS code itself is not fully ported
to support Visual C++. Volunteers to take on this task are welcome.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

1
doc/src/Commands_all.rst
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@ -136,4 +136,3 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`write_data <write_data>`
* :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>`

1
doc/src/Commands_compute.rst
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@ -163,4 +163,3 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`vcm/chunk <compute_vcm_chunk>`
* :doc:`voronoi/atom <compute_voronoi_atom>`
* :doc:`xrd <compute_xrd>`

5
doc/src/Commands_removed.rst
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@ -60,8 +60,3 @@ LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For added
convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Errors.rst
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@ -15,8 +15,3 @@ additional details for many of them.
Errors_bugs
Errors_messages
Errors_warnings
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

59
doc/src/Errors_bugs.rst
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@ -1,32 +1,45 @@
Reporting bugs
==============
If you are confident that you have found a bug in LAMMPS, follow these
steps.
If you are confident that you have found a bug in LAMMPS, please follow the steps outlined below:
Check the `New features and bug fixes <http://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site <lws_>`_ to see if the bug has already been reported or fixed or the
`Unfixed bug <http://lammps.sandia.gov/unbug.html>`_ to see if a fix is
pending.
* Check the `New features and bug fixes
<http://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
<lws_>`_ to see if the bug has already been addressed in a patch.
* Check that your issue can be reproduced with the latest development
version of LAMMPS.
* Check the manual carefully to verify that the unexpected behavior you
are observing is indeed in conflict with the documentation
* Check the `GitHub Issue page <gip_>`_
if your issue has already been reported and if it is still open.
* Check the `GitHub Pull Requests page <https://github.com/lammps/pulls>`_
if there is already a fix for your bug pending.
* Check the `mailing list archives <http://lammps.sandia.gov/mail.html>`_
to see if the issue has been discussed before.
Check the `mailing list <http://lammps.sandia.gov/mail.html>`_ to see if
it has been discussed before.
If none of these steps yields any useful information, please file
a new bug report on the `GitHub Issue page <gip_>`_\ .
The website will offer you to select a suitable template with explanations
and then you should replace those explanations with the information
that you can provide to reproduce your issue.
If not, send an email to the mailing list describing the problem with
any ideas you have as to what is causing it or where in the code the
problem might be. The developers will ask for more info if needed,
such as an input script or data files.
The most useful thing you can do to help us fix the bug is to isolate
the problem. Run it on the smallest number of atoms and fewest number
of processors and with the simplest input script that reproduces the
bug and try to identify what command or combination of commands is
causing the problem.
.. note::
this page needs to have GitHub issues info added
The most useful thing you can do to help us verify and fix a bug is to
isolate the problem. Run it on the smallest number of atoms and fewest
number of processors with the simplest input script that reproduces the
bug. Try to identify what command or combination of commands is
causing the problem and upload the complete input deck as a tar or zip
archive. Please avoid using binary restart files unless the issue requires
it. In the latter case you should also include an input deck to quickly
generate this restart from a data file or a simple additional input.
You may also send an email to the LAMMPS mailing list at
"lammps-users at lists.sourceforge.net" describing the problem with the
same kind of information. The mailing list can provide a faster response,
especially if the bug reported is actually expected behavior. But because
of the high volume of the mailing list, it can happen that your e-mail
is overlooked and then forgotten. Issues on GitHub have to be explicitly
closed, so that will *guarantee* that at least one LAMMPS developer will
have looked at it.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
.. _gip: https://github.com/lammps/issues

5
doc/src/Errors_common.rst
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@ -121,8 +121,3 @@ implementations handle buffering of messages. If the code hangs
without an error message, it may be that you need to specify an MPI
setting or two (usually via an environment variable) to enable
buffering or boost the sizes of messages that can be buffered.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Errors_messages.rst
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@ -8415,10 +8415,3 @@ keyword to allow for additional bonds to be formed
*Zero-length lattice orient vector*
Self-explanatory.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Errors_warnings.rst
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@ -796,10 +796,3 @@ This will most likely cause errors in kinetic fluctuations.
*pair style reax is now deprecated and will soon be retired. Users should switch to pair\_style reax/c*
Self-explanatory.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

6
doc/src/Examples.rst
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@ -228,10 +228,4 @@ instructions. See the :doc:`Packages\_details <Packages_details>` doc
page for more info on specific USER packages.
.. _openkim: https://openkim.org
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto.rst
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@ -99,8 +99,3 @@ Packages howto
Howto_drude2
Howto_manifold
Howto_spins
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_2d.rst
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@ -41,8 +41,3 @@ are for 2d models.
and the *disc* option for the :doc:`fix nve/sphere <fix_nve_sphere>`,
:doc:`fix nvt/sphere <fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>`
commands.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_barostat.rst
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@ -61,8 +61,3 @@ explicitly via the :doc:`thermo_style custom <thermo_style>` command.
Or you can use the :doc:`thermo_modify <thermo_modify>` command to
re-define what pressure compute is used for default thermodynamic
output.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_bash.rst
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@ -284,8 +284,3 @@ the PATH variable should be
This should give you a jump start when trying to run LAMMPS on Windows.
To become effective in this environment I encourage you to look into Linux
tutorials explaining Bash and Basic Unix commands (e.g., `Linux Journey <https://linuxjourney.com>`_)
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_bioFF.rst
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@ -144,8 +144,3 @@ Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_body.rst
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@ -512,8 +512,3 @@ Particuology, 6, 455 (2008).
**(Wang)** J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
Matter, 13, 1 (2011).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_chunk.rst
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@ -212,8 +212,3 @@ using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an
average dipole moment vector for each bin. This example is explained
on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
command doc page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_client_server.rst
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@ -157,8 +157,3 @@ command-line option as their its option, where color is an integer
label that will be used to distinguish one executable from another in
the multiple executables that the mpirun command launches. In this
example the client was colored with a 0, and the server with a 1.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_coreshell.rst
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@ -264,8 +264,3 @@ The additional section in the date file would be formatted like this:
**(Fincham)** Fincham, Mackrodt and Mitchell, J Phys Condensed Matter,
6, 393-404 (1994).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_couple.rst
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@ -118,8 +118,3 @@ instances of LAMMPS to perform different calculations.
(4) Couple LAMMPS with another code in a client/server mode. This is
described on the :doc:`Howto client/server <Howto_client_server>` doc
page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

9
doc/src/Howto_diffusion.rst
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@ -21,12 +21,3 @@ diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the :doc:`fix vector <fix_vector>` command,
and time integrated via the :doc:`variable trap <variable>` function,
and thus extract D.
----------
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_dispersion.rst
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@ -98,8 +98,3 @@ This can be achieved using the *kspace\_modify mix/disp none* command.
Note that the code does not check automatically whether any mixing
rule is fulfilled. If mixing rules do not apply, the user will have
to specify this command explicitly.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_drude.rst
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@ -65,8 +65,3 @@ too close, which can cause numerical issues.
**(Lamoureux and Roux)** G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_drude2.rst
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@ -535,8 +535,3 @@ NPT ensemble using Nose-Hoover thermostat:
**(SWM4-NDP)** Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys
Let, 418, 245-249 (2006)
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_elastic.rst
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@ -42,8 +42,3 @@ converge and requires careful post-processing :ref:`(Shinoda) <Shinoda1>`
**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_github.rst
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@ -492,8 +492,3 @@ 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/master/doc/github-development-workflow.md>`_
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_granular.rst
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@ -48,8 +48,3 @@ computations between frozen atoms by using this command:
will be the same as in 3d. If you wish to model granular particles in
2d as 2d discs, see the note on this topic on the :doc:`Howto 2d <Howto_2d>`
doc page, where 2d simulations are discussed.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_kappa.rst
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@ -79,8 +79,3 @@ formalism.
**(Wirnsberger)** Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104
(2015).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_library.rst
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@ -245,8 +245,3 @@ lammps\_reset\_box()) to restore a previously extracted and saved state
of a simulation. Additional properties for the new atoms can then be
assigned via the lammps\_scatter\_atoms() or lammps\_extract\_atom()
functions.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_manifold.rst
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@ -50,8 +50,3 @@ to the relevant fixes.
**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_multiple.rst
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@ -96,8 +96,3 @@ on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each
partition. When one finished, that partition would then start
the 4th simulation, and so forth, until all 8 were completed.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_nemd.rst
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@ -53,8 +53,3 @@ using the :doc:`fix flow/gauss <fix_flow_gauss>` command.
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_output.rst
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@ -342,8 +342,3 @@ vector input could be a column of an array.
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
| :doc:`fix store/state <fix_store_state>` | per-atom vectors | per-atom vector/array |
+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_polarizable.rst
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@ -71,8 +71,3 @@ temperature is regulated using the velocities of the center of mass of
core+shell (or Drude) pairs, but in the Drude model the actual
relative core-Drude particle motion is thermostatted separately as
well.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_pylammps.rst
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@ -577,8 +577,3 @@ If you find this Python interface useful, please feel free to provide feedback
and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
and maybe their latest research results.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_replica.rst
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@ -53,8 +53,3 @@ 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.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_restart.rst
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@ -98,8 +98,3 @@ commands since the new data file lists the force field coefficients.
Also, the :doc:`reset_timestep <reset_timestep>` command is used to tell
LAMMPS the current timestep. This value is stored in restart files,
but not in data files.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_spc.rst
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@ -50,8 +50,3 @@ Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki
**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_spherical.rst
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@ -236,8 +236,3 @@ as single particles, though they can store internal state, such as a
list of sub-particles. Individual body particles are typically treated
as rigid bodies, and their motion integrated with a command like :doc:`fix nve/body <fix_nve_body>`. Interactions between pairs of body
particles are computed via a command like :doc:`pair_style body/nparticle <pair_body_nparticle>`.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_spins.rst
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@ -66,8 +66,3 @@ magnetic spin, or the magnetic force acting on this spin.
**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
Journal of Computational Physics, 372, 406-425, (2018).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_temperature.rst
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@ -31,8 +31,3 @@ They both allow for velocity biases indirectly, via an optional extra
argument which is another temperature compute that subtracts a
velocity bias. This allows the translational velocity of spherical or
aspherical particles to be adjusted in prescribed ways.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_thermostat.rst
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@ -92,8 +92,3 @@ temperature compute is used for default thermodynamic output.
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_tip3p.rst
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@ -74,8 +74,3 @@ Phys, 79, 926 (1983).
**(Price)** Price and Brooks, J Chem Phys, 121, 10096 (2004).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_tip4p.rst
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@ -109,8 +109,3 @@ Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

15
doc/src/Howto_triclinic.rst
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@ -1,17 +1,3 @@
:doc:`Higher level section <Howto>` - `LAMMPS WWW Site <lws_>`_ - `LAMMPS Documentation <ld_>`_ - `LAMMPS Commands <lc_>`_
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands\_all.html
Triclinic (non-orthogonal) simulation boxes
===========================================
@ -225,4 +211,3 @@ material. The :doc:`fix deform <fix_deform>` command can be used for
this purpose. It allows dynamic control of the xy, xz, yz tilt
factors as a simulation runs. This is discussed in the next section
on non-equilibrium MD (NEMD) simulations.

5
doc/src/Howto_viscosity.rst
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@ -141,8 +141,3 @@ with time at sufficiently long times.
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Howto_viz.rst
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@ -34,10 +34,3 @@ snapshots.
.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Howto_walls.rst
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@ -69,8 +69,3 @@ The only frictional idealized walls currently in LAMMPS are flat or
curved surfaces specified by the :doc:`fix wall/gran <fix_wall_gran>`
command. At some point we plan to allow regoin surfaces to be used as
frictional walls, as well as triangulated surfaces.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install.rst
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@ -51,8 +51,3 @@ These are the files and sub-directories in the LAMMPS distribution:
You will have all of these if you download source. You will only have
some of them if you download executables, as explained on the pages
listed above.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

4
doc/src/Install_conda.rst
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@ -42,7 +42,3 @@ up the Conda capability.
.. _conda: https://docs.conda.io/en/latest/index.html
.. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install_git.rst
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@ -121,8 +121,3 @@ The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
gmail.com) and Richard Berger (Temple U, richard.berger at
temple.edu).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install_linux.rst
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@ -262,8 +262,3 @@ Alternatively, you may use an AUR helper to install these packages.
Note that the AUR provides build-scripts that download the source and
the build the package on your machine.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

6
doc/src/Install_mac.rst
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@ -46,9 +46,3 @@ up the Homebrew capability.
.. _openkim: https://openkim.org
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install_patch.rst
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@ -61,8 +61,3 @@ up to date.
sub-dir of src, then re-install the package. The version in the src
dir is merely a copy and will be wiped out if you type "make
package-update".
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install_svn.rst
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@ -95,8 +95,3 @@ The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
gmail.com) and Richard Berger (Temple U, richard.berger at
temple.edu).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

13
doc/src/Install_tarball.rst
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@ -5,15 +5,9 @@ You can download a current LAMMPS tarball from the `download page <download_>`_
of the `LAMMPS website <lws_>`_.
.. _download: http://lammps.sandia.gov/download.html
.. _bug: http://lammps.sandia.gov/bug.html
.. _older: http://lammps.sandia.gov/tars
.. _lws: http://lammps.sandia.gov
You have two choices of tarballs, either the most recent stable
@ -77,8 +71,3 @@ The patch files are posted on the `bug and feature page <bug_>`_ of the
website, along with a list of changed files and details about what is
in the new patch release. Instructions for applying a patch file are
on the :doc:`Install patch <Install_patch>` doc page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Install_windows.rst
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@ -42,8 +42,3 @@ automatically, so this should only be done for debugging purposes.
Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting
up this Windows capability.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Intro.rst
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@ -14,8 +14,3 @@ These pages provide a brief introduction to LAMMPS.
Intro_opensource
Intro_authors
Intro_website
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Intro_authors.rst
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@ -11,7 +11,7 @@ University:
* Richard Berger, richard.berger at temple.edu
.. _sjp: http://www.cs.sandia.gov/~sjplimp
.. _lws: http://lammps.sandia.gov
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
@ -62,8 +62,3 @@ version of LAMMPS were the following:
* Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)
* Steve Lustig (Dupont)
* Jim Belak and Roy Pollock (LLNL)
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Intro_features.rst
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@ -224,8 +224,3 @@ classical MD options:
* :doc:`Lattice Boltzmann fluid <fix_lb_fluid>`
* :doc:`targeted <fix_tmd>` and :doc:`steered <fix_smd>` molecular dynamics
* :doc:`two-temperature electron model <fix_ttm>`
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Intro_nonfeatures.rst
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@ -80,8 +80,3 @@ Here are suggestions on how to perform these tasks:
simulations. It thus provides some functionality for several of the
above bullets. Pizza.py is written in `Python <http://www.python.org>`_
and is available for download from `this page <http://www.cs.sandia.gov/~sjplimp/download.html>`_.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Intro_opensource.rst
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@ -42,8 +42,3 @@ of the GPL.
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should
remain part of the code.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

8
doc/src/Intro_overview.rst
View File

@ -16,8 +16,7 @@ shared-memory boxes and distributed-memory clusters and
supercomputers.
.. _mpi: http://www-unix.mcs.anl.gov/mpi
.. _lws: http://lammps.sandia.gov
LAMMPS is written in C++. Earlier versions were written in F77 and
F90. See the `History page <http://lammps.sandia.gov/history.html>`_ of
@ -47,8 +46,3 @@ partition the simulation domain into small sub-domains of equal
computational cost, one of which is assigned to each processor.
Processors communicate and store "ghost" atom information for atoms
that border their sub-domain.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Intro_website.rst
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@ -5,6 +5,8 @@ The `LAMMPS website <lws_>`_ has a variety of additional info about
LAMMPS, beyond what is in this manual. Some of the other pages in
this Intr are included in this list.
.. _lws: http://lammps.sandia.gov
* `Brief intro and recently added significant features <lws_>`_
* `List of features <http://lammps.sandia.gov/features.html>`_
* `List of non-features <http://lammps.sandia.gov/non_features.html>`_
@ -32,8 +34,3 @@ this Intr are included in this list.
* `Authors of LAMMPS <http://lammps.sandia.gov/authors.html>`_
* `History of LAMMPS development <http://lammps.sandia.gov/history.html>`_
* `Funding for LAMMPS <http://lammps.sandia.gov/funding.html>`_
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

11
doc/src/Manual.rst
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@ -22,23 +22,21 @@ It includes links to an on-line version of this manual, a `mailing list <http://
questions, and a `GitHub site <https://github.com/lammps/lammps>`_ where
all LAMMPS development is coordinated.
----------
The content for this manual is part of the LAMMPS distribution. You
can build a local copy of the Manual as HTML pages or a PDF file, by
following the steps on the :doc:`Manual build <Manual_build>` doc page.
There is also a `Developer.pdf <Developer.pdf>`_ document which gives
a brief description of the basic code structure of LAMMPS.
----------
Once you are familiar with LAMMPS, you may want to bookmark :doc:`this page <Commands>` since it gives quick access to a doc page for
every LAMMPS command.
.. _lws: http://lammps.sandia.gov
.. _lc: Commands_all.html
.. toctree::
:maxdepth: 2
@ -85,8 +83,3 @@ Indices and tables
.. raw:: html
</BODY>
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Manual_build.rst
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@ -134,8 +134,3 @@ For converting the generated ePUB file to a MOBI format file
also need to have the 'ebook-convert' tool from the "calibre"
software installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
You first create the ePUB file and then convert it with 'make mobi'
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Manual_version.rst
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@ -21,8 +21,3 @@ first page of the :doc:`manual <Manual>`.
describe the most current patch release of LAMMPS.
* If you browse the HTML doc pages included in your tarball, they
describe the version you have, which may be older.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify.rst
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@ -33,8 +33,3 @@ as a pull request on our `GitHub site <https://github.com/lammps/lammps>`_, afte
Modify_body
Modify_thermo
Modify_variable
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_atom.rst
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@ -117,8 +117,3 @@ accessed using the returned index as
Ivector or dvector are vectors of length Nlocal = # of owned atoms,
which store the attributes of individual atoms.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_body.rst
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@ -33,8 +33,3 @@ class. See body.h for details.
+----------------------+-----------------------------------------------------------+
| unpack\_border\_body | unpacking of those attributes |
+----------------------+-----------------------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_bond.rst
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@ -34,8 +34,3 @@ for details and specific additional methods.
+-----------------------+---------------------------------------------------------------------------+
| memory\_usage | tally memory allocated by the style (optional) |
+-----------------------+---------------------------------------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_command.rst
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@ -18,8 +18,3 @@ The single method your new class must define is as follows:
Of course, the new class can define other methods and variables as
needed.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_compute.rst
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@ -55,8 +55,3 @@ each pair after force and energy has been computed for this pair. Then
the tallied values are retrieved with the standard compute\_scalar or
compute\_vector or compute\_peratom methods. The USER-TALLY package
provides *examples*\ \_compute\_tally.html for utilizing this mechanism.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

7
doc/src/Modify_contribute.rst
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@ -69,6 +69,8 @@ unusual event).
`developers <http://lammps.sandia.gov/authors.html>`_ with info about
your package and we will post it there.
.. _lws: http://lammps.sandia.gov
The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
one or more new class files which are invoked as a new style within a
@ -196,8 +198,3 @@ Finally, as a general rule-of-thumb, the more clear and
self-explanatory you make your documentation and README files, and the
easier you make it for people to get started, e.g. by providing example
scripts, the more likely it is that users will try out your new feature.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_dump.rst
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@ -30,8 +30,3 @@ new quantities to dump.
Note that new keywords for atom properties are not typically
added to the :doc:`dump custom <dump>` command. Instead they are added
to the :doc:`compute property/atom <compute_property_atom>` command.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_fix.rst
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@ -151,8 +151,3 @@ command), the initial\_integrate, post\_force\_integrate, and
final\_integrate\_respa methods can be implemented. The thermo method
enables a fix to contribute values to thermodynamic output, as printed
quantities and/or to be summed to the potential energy of the system.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_kspace.rst
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@ -19,8 +19,3 @@ class. See kspace.h for details.
+---------------+----------------------------------------------+
| memory\_usage | tally of memory usage |
+---------------+----------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_min.rst
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@ -17,8 +17,3 @@ class. See min.h for details.
+---------------+------------------------------------------+
| memory\_usage | tally of memory usage |
+---------------+------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_overview.rst
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@ -100,8 +100,3 @@ functionality:
**(Foo)** Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_pair.rst
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@ -33,8 +33,3 @@ Here is a brief description of the class methods in pair.h:
+---------------------------------+-------------------------------------------------------------------+
The inner/middle/outer routines are optional.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_region.rst
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@ -20,8 +20,3 @@ class. See region.h for details.
+-------------------+---------------------------------------------------------------------+
| shape\_update | change region shape if set by time-dependent variable |
+-------------------+---------------------------------------------------------------------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_thermo.rst
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@ -25,8 +25,3 @@ for thermo output of quantities calculated by :doc:`fixes <fix>`,
:doc:`computes <compute>`, and :doc:`variables <variable>`. Thus, it may
be simpler to compute what you wish via one of those constructs, than
by adding a new keyword to the thermo command.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Modify_variable.rst
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@ -38,8 +38,3 @@ to find the appropriate location.
Adding new :doc:`compute styles <compute>` (whose calculated values can
then be accessed by variables) is discussed on the :doc:`Modify compute <Modify_compute>` doc page.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Packages.rst
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@ -18,8 +18,3 @@ LAMMPS build process.
Packages_standard
Packages_user
Packages_details
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

18
doc/src/Packages_details.rst
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@ -24,6 +24,8 @@ page gives those details.
pair, bond, angle, etc correspond to commands with the same style name
as contained in the file name.
.. _lc: Commands_all.html
+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
| :ref:`ASPHERE <PKG-ASPHERE>` | :ref:`BODY <PKG-BODY>` | :ref:`CLASS2 <PKG-CLASS2>` | :ref:`COLLOID <PKG-COLLOID>` | :ref:`COMPRESS <PKG-COMPRESS>` | :ref:`CORESHELL <PKG-CORESHELL>` |
+------------------------------+--------------------------------+--------------------------------+------------------------------+--------------------------------+----------------------------------+
@ -2418,21 +2420,10 @@ The expressions and their use are discussed in the following papers
which discuss the `QuickFF <quickff_>`_ methodology.
.. _vanduyfhuys2015: http://dx.doi.org/10.1002/jcc.23877
.. _vanduyfhuys2018: http://dx.doi.org/10.1002/jcc.25173
.. _quickff: http://molmod.github.io/QuickFF
.. _yaff: https://github.com/molmod/yaff
**Author:** Steven Vandenbrande.
**Supporting info:**
@ -2446,8 +2437,3 @@ which discuss the `QuickFF <quickff_>`_ methodology.
* :doc:`pair_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* examples/USER/yaff
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Packages_standard.rst
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@ -89,8 +89,3 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
| :ref:`VORONOI <PKG-VORONOI>` | Voronoi tesselation | :doc:`compute voronoi/atom <compute_voronoi_atom>` | n/a | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+-----------------------------------------------------+---------+
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

4
doc/src/Packages_user.rst
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@ -114,7 +114,3 @@ package:
.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF
.. _PLUMED: http://www.plumed.org
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Python_call.rst
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@ -77,8 +77,3 @@ If you want to write Python code with callbacks to LAMMPS, then you
must also follow the steps summarized in the :doc:`Python run <Python_run>` doc page. I.e. you must build LAMMPS as a shared
library and insure that Python can find the python/lammps.py file and
the shared library.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Python_examples.rst
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@ -109,8 +109,3 @@ different visualization package options. Click to see larger images:
.. image:: JPG/screenshot_vmd_small.jpg
:target: JPG/screenshot_vmd.jpg
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Python_head.rst
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@ -42,8 +42,3 @@ interesting Python functions that can be called from a LAMMPS input
script, that you think would be generally useful, please post them as
a pull request to our `GitHub site <https://github.com/lammps/lammps>`_,
and they can be added to the LAMMPS distribution or webpage.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

5
doc/src/Python_install.rst
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@ -68,8 +68,3 @@ the LAMMPS shared library (see :doc:`this section <Python_shlib>`), you will
need to manually copy files like liblammps\_g++.so into the appropriate
system directory. This is not needed if you set the LD\_LIBRARY\_PATH
environment variable as described above.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

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