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Updating README #2826

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Updating README #2826

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Updating the readme file
bendudson Dec 20, 2023
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Remove comment about m4
dschwoerer Jan 2, 2024
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Update README.md
bendudson Jan 2, 2024
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Expand Up @@ -26,8 +26,11 @@ For example, the following set of equations for magnetohydrodynamics
(MHD):

![ddt_rho](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Crho%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Crho%20-%20%5Crho%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D)

![ddt_p](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20p%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%20p%20-%20%5Cgamma%20p%5Cnabla%5Ccdot%5Cmathbf%7Bv%7D)

![ddt_v](http://latex.codecogs.com/png.latex?%5Cfrac%7B%5Cpartial%20%5Cmathbf%7Bv%7D%7D%7B%5Cpartial%20t%7D%20%3D%20-%5Cmathbf%7Bv%7D%5Ccdot%5Cnabla%5Cmathbf%7Bv%7D%20+%20%5Cfrac%7B1%7D%7B%5Crho%7D%28-%5Cnabla%20p%20+%20%28%5Cnabla%5Ctimes%5Cmathbf%7BB%7D%29%5Ctimes%5Cmathbf%7BB%7D%29)

![ddt_B](http://latex.codecogs.com/png.latex?%7B%7B%5Cfrac%7B%5Cpartial%20%5Cmathbf%7BB%7D%7D%7B%5Cpartial%20t%7D%7D%7D%20%3D%20%5Cnabla%5Ctimes%28%5Cmathbf%7Bv%7D%5Ctimes%5Cmathbf%7BB%7D%29)

can be written simply as:
Expand All @@ -43,7 +46,7 @@ The full code for this example can be found in the [orszag-tang
example](examples/orszag-tang/mhd.cxx).

Jointly developed by University of York (UK), LLNL, CCFE, DCU, DTU,
and other international partners.
and other international partners. See the Git logs for author details.


Homepage found at [http://boutproject.github.io/](http://boutproject.github.io/)
Expand All @@ -52,7 +55,6 @@ Homepage found at [http://boutproject.github.io/](http://boutproject.github.io/)
* [Requirements](#requirements)
* [Usage and installation](#usage-and-installation)
* [Terms of use](#terms-of-use)
* [Overview of files](#overview-of-files)
* [Contributing](#contributing)
* [License](#license)

Expand All @@ -66,18 +68,17 @@ BOUT++ needs the following:

BOUT++ has the following optional dependencies:

* FFTW3 (strongly recommended!)
* OpenMP
* PETSc
* SLEPc
* ARKODE
* IDA
* CVODE
* [FFTW3](https://www.fftw.org/) (strongly recommended!)
* [SUNDIALS](https://computing.llnl.gov/projects/sundials): CVODE, IDA, ARKODE
* [PETSc](https://petsc.org)
* [ADIOS2](https://adios2.readthedocs.io/)
* [SLEPc](https://slepc.upv.es/)
* LAPACK
* OpenMP
* Score-p (for performance diagnostics)

## Usage and installation
Please see the [users manual](http://bout-dev.readthedocs.io)
Please see the [users manual](http://bout-dev.readthedocs.io).

## Terms of use

Expand Down Expand Up @@ -105,58 +106,14 @@ You can convert the CITATION.cff file into a Bibtex file as follows:
pip3 install --user cffconvert
cffconvert -if CITATION.cff -f bibtex -of CITATION.bib

## Overview of files

This directory contains

* **bin** Files for setting the BOUT++ configuration
* **examples** Example models and test codes
* **externalpackages** External packages needed for installing BOUT++
* **include** Header files used in BOUT++
* **manual** Manuals and documentation (also [doxygen](http://www.stack.nl/~dimitri/doxygen/) documentation)
* **src** The main code directory
* **CITATION** Contains the paper citation for BOUT++
* **LICENSE** LGPL license
* **LICENSE.GPL** GPL license
* **tools** Tools for helping with analysis, mesh generation, and data managment

* **archiving** Routines for managing input/output files e.g. compressing data, converting formats, and managing runs
* **cyl_and_helimak_grids** IDL codes for generating cylindrical and helimak grids
* **eigensolver** Matlab routines for solving eigenmodes
* **idllib** Analysis codes in IDL. Add this to your IDL_PATH environment variable
* **line_tracing** IDL routines for line tracing of field lines
* **line_tracing_v2** Newer version of the IDL routines for line tracing of field lines
* **mathematicalib** Library for post processing using Mathematica
* **matlablib** Library for post processing using MATLAB
* **numlib** Numerical IDL routines
* **octave** Routines for post processing using octave
* **plasmalib** IDL routines for calculation of plasma parameters
* **pdb2idl** Library to read Portable Data Binary (PDB) files into IDL
* **pylib** Analysis codes in Python

* **boutdata** Routines to simplify accessing BOUT++ output
* **boututils** Some useful routines for accessing and plotting data
* **post_bout** Routines for post processing in BOUT++

* **slab** IDL routine for grid generation of a slab
* **tokamak_grids** Code to generate input grids for tokamak equilibria

* **gridgen** Grid generator in IDL. Hypnotoad GUI for converting G-EQDSK files into a flux-aligned orthogonal grid.
* **elite** Convert ELITE .eqin files into an intermediate binary file
* **gato** Convert DSKGATO files into intermediate binary format
* **all** Convert the intermediate binary file into BOUT++ input grid
* **coils** Routines for calculating the field due to external RMP coils and adding to existing equilibria
* **cyclone** Generate cyclone test cases (concentric circle "equilibrium" for local flux-surface calculations)
* **py_gridgen** Translation" into python of the corresponding IDL routines in the folder gridgen
* **shifted_circle** Produce shifted cirle equilibria input grids


## Contributing

See [CONTRIBUTING.md](CONTRIBUTING.md).
See [CONTRIBUTING.md](CONTRIBUTING.md) and the [manual page](https://bout-dev.readthedocs.io/en/stable/developer_docs/contributing.html)

## License
Copyright 2010 B.D.Dudson, S.Farley, M.V.Umansky, X.Q.Xu
Copyright 2010-2024 BOUT++ contributors

BOUT++ is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
Expand All @@ -171,15 +128,7 @@ GNU Lesser General Public License for more details.
A copy of the LGPL license is in [LICENSE](LICENSE). Since this is based
on (and refers to) the GPL, this is included in [LICENSE.GPL](LICENSE.GPL).

Some of the autoconf macros under [m4](m4) are licensed under
GPLv3. These are not necessary to either build or run BOUT++, but are
used in the creation of [configure](configure) from
[configure.ac](configure.ac), and are provided as a courtesy to
developers. You are free to substitute them with other autoconf macros
that provide equivalent functionality.

BOUT++ links by default with some GPL licensed libraries. Thus if you
compile BOUT++ with any of them, BOUT++ will automatically be licensed
as GPL. Thus if you want to use BOUT++ with GPL non-compatible code,
make sure to compile without GPLed code.

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