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small updates to the introduction

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This commit is contained in:
Axel Kohlmeyer
2021-07-25 21:05:33 -04:00
parent 7e6a06b1cc
commit ef244c3061
3 changed files with 27 additions and 18 deletions
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23
doc/src/Intro_features.rst
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@ -24,11 +24,15 @@ General features
^^^^^^^^^^^^^^^^
* runs on a single processor or in parallel
* distributed-memory message-passing parallelism (MPI)
* spatial-decomposition of simulation domain for parallelism
* open-source distribution
* highly portable C++
* optional libraries used: MPI and single-processor FFT
* distributed memory message-passing parallelism (MPI)
* shared memory multi-threading parallelism (OpenMP)
* spatial decomposition of simulation domain for MPI parallelism
* particle decomposition inside of spatial decomposition for OpenMP parallelism
* GPLv2 licensed open-source distribution
* highly portable C++-11
* modular code with most functionality in optional packages
* only depends on MPI library for basic parallel functionality
* other libraries are optional and only required for specific packages
* GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
* easy to extend with new features and functionality
* runs from an input script
@ -68,9 +72,9 @@ Interatomic potentials (force fields)
:doc:`improper style <improper_style>`, :doc:`kspace style <kspace_style>`
commands)
* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
* charged pairwise potentials: Coulombic, point-dipole
* many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
* many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
* long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
* polarization models: :doc:`QEq <fix_qeq>`, :doc:`core/shell model <Howto_coreshell>`, :doc:`Drude dipole model <Howto_drude>`
* charge equilibration (QEq via dynamic, point, shielded, Slater methods)
@ -170,9 +174,12 @@ Multi-replica models
^^^^^^^^^^^^^^^^^^^^
* :doc:`nudged elastic band <neb>`
* :doc:`hyperdynamics <hyper>`
* :doc:`parallel replica dynamics <prd>`
* :doc:`temperature accelerated dynamics <tad>`
* :doc:`parallel tempering <temper>`
* :doc:`path-integral MD <fix_pimd>`
* multi-walker collective variables with :doc:`Colvars <fix_colvars>` and :doc:`Plumed <fix_plumed>`
.. _prepost:
@ -187,7 +194,7 @@ Pre- and post-processing
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in `Python <python_>`_ and is available for download from `the Pizza.py WWW site <pizza_>`_.
.. _pizza: https://pizza.sandia.gov
.. _pizza: https://lammps.github.io/pizza
.. _python: http://www.python.org

2
doc/src/Intro_nonfeatures.rst
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@ -77,7 +77,7 @@ Here are suggestions on how to perform these tasks:
it easier to analyze and plot. See the :doc:`Tools <Tools>` doc page
for more discussion of the various tools.
* **Pizza.py:** Our group has also written a separate toolkit called
`Pizza.py <https://pizza.sandia.gov>`_ which can do certain kinds of
`Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
simulations. It thus provides some functionality for several of the
above bullets. Pizza.py is written in `Python <http://www.python.org>`_

20
doc/src/Intro_overview.rst
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@ -18,10 +18,11 @@ supercomputers.
.. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface
.. _lws: https://www.lammps.org
LAMMPS is written in C++. Earlier versions were written in F77 and
F90. See the `History page <https://www.lammps.org/history.html>`_ of
the website for details. All versions can be downloaded from the
`LAMMPS website <lws_>`_.
LAMMPS is written in C++ and requires a compiler that is at least
compatible with the C++-11 standard.
Earlier versions were written in F77 and F90. See the `History page
<https://www.lammps.org/history.html>`_ of the website for details. All
versions can be downloaded from the `LAMMPS website <lws_>`_.
LAMMPS is designed to be easy to modify or extend with new
capabilities, such as new force fields, atom types, boundary
@ -41,8 +42,9 @@ short distances, so that the local density of particles never becomes
too large. This is in contrast to methods used for modeling plasma
or gravitational bodies (e.g. galaxy formation).
On parallel machines, LAMMPS uses spatial-decomposition techniques to
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.
On parallel machines, LAMMPS uses spatial-decomposition techniques with
MPI parallelization to 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. Multi-threading
parallelization with with particle-decomposition can be used in addition.