updates references to geodynamics

SPECFEM · Nov 17, 2022 · de57676 · de57676
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diff --git a/.travis/run_tests.sh b/.travis/run_tests.sh
@@ -193,7 +193,7 @@ echo
 echo -en 'travis_fold:end:tests\\r'
 echo
 
-# code coverage: https://codecov.io/gh/geodynamics/specfem2d/
+# code coverage: https://app.codecov.io/gh/SPECFEM/specfem2d/
 # additional runs for coverage
 #
 # note: log becomes too long, trying to fold each test output

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1 +1 @@
-Instruction for how to contribute to SPECFEM2D are available at https://github.com/geodynamics/specfem3d/wiki.
+Instruction for how to contribute to SPECFEM2D are available at https://github.com/SPECFEM/specfem3d/wiki.
diff --git a/README.md b/README.md
@@ -34,28 +34,32 @@ and check the output files in `./OUTPUT_FILES/`
 
 ## Development
 
-[![Actions Status](https://github.com/specfem/specfem2d/workflows/CI/badge.svg)](https://github.com/specfem/specfem2d/actions)
-[![Travis Status](https://app.travis-ci.com/specfem/specfem2d.svg?branch=devel)](https://app.travis-ci.com/specfem/specfem2d)
+Development is hosted on GitHub in the
+[geodynamics/specfem2d repository](https://github.com/SPECFEM/specfem2d).
+
+
+[![Actions Status](https://github.com/SPECFEM/specfem2d/workflows/CI/badge.svg)](https://github.com/SPECFEM/specfem2d/actions)
+[![Travis Status](https://app.travis-ci.com/SPECFEM/specfem2d.svg?branch=devel)](https://app.travis-ci.com/SPECFEM/specfem2d)
 [![Azure Status](https://dev.azure.com/danielpeter22/SPECFEM2D/_apis/build/status/geodynamics.specfem2d?branchName=devel)](https://dev.azure.com/danielpeter22/SPECFEM2D/_build/latest?definitionId=6&branchName=devel)
-[![codecov](https://codecov.io/gh/specfem/specfem2d/branch/devel/graph/badge.svg)](https://codecov.io/gh/specfem/specfem2d)
+[![codecov](https://codecov.io/gh/SPECFEM/specfem2d/branch/devel/graph/badge.svg)](https://codecov.io/gh/SPECFEM/specfem2d)
 [![Documentation Status](https://readthedocs.org/projects/specfem2d/badge/?version=latest)](https://specfem2d.readthedocs.io/en/latest/?badge=latest)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](LICENSE)
 
-* Actions tests: [github actions specfem2d](https://github.com/specfem/specfem2d/actions)
+* Actions tests: [github actions specfem2d](https://github.com/SPECFEM/specfem2d/actions)
 
-* Travis tests: [travis-ci specfem2d](https://travis-ci.com/specfem/specfem2d/builds)
+* Travis tests: [travis-ci specfem2d](https://travis-ci.com/SPECFEM/specfem2d/builds)
 
 
 Development is hosted on GitHub in the
-[geodynamics/specfem2d repository](https://github.com/specfem/specfem2d).
+[SPECFEM/specfem2d repository](https://github.com/SPECFEM/specfem2d).
 
 
 SPECFEM2D is a community project that lives by the participation of its
 members — i.e., including you! It is our goal to build an inclusive and
 participatory community so we are happy that you are interested in
 participating! We have collected a set of guidelines and advice on how to get
 involved in the community and keep them in the specfem3d github wiki:
-[specfem3d wiki](https://github.com/specfem/specfem3d/wiki)
+[specfem3d wiki](https://github.com/SPECFEM/specfem3d/wiki)
 
 
 ## Computational Infrastructure for Geodynamics (CIG)

diff --git a/doc/USER_MANUAL/01_introduction.tex b/doc/USER_MANUAL/01_introduction.tex
@@ -31,7 +31,7 @@ \chapter{Introduction}
 (an)elastic, and poroelastic media. The package also considers 2D SH
 and P-SV wave propagation. Finally, the solver can run
 both in serial and in parallel. See SPECFEM2D
-\urlwithparentheses{http://www.geodynamics.org/cig/software/packages/seismo/specfem2d}
+\urlwithparentheses{https://github.com/SPECFEM/specfem2d}
 for the source code.\\
 
 The SEM is a continuous Galerkin technique \citep{TrKoLi08,PeKoLuMaLeCaLeMaLiBlNiBaTr11}, which can easily be made discontinuous \citep{BeMaPa94,Ch00,KoWoHu02,ChCaVi03,LaWaBe05,Kop06,WiStBuGh10,AcKo11}; it is then close to a particular case of the discontinuous Galerkin technique \citep{ReHi73,LeRa74,Arn82,JoPi86,BoMaHe91,FaRi99,HuHuRa99,CoKaSh00,GiHeWa02,RiWh03,MoRi05,GrScSc06,AiMoMu06,BeLaPi06,DuKa06,DeSeWh08,PuAmKa09,WiStBuGh10,DeSe10,EtChViGl10}, with optimized efficiency because of its tensorized basis functions \citep{WiStBuGh10,AcKo11}.

diff --git a/doc/USER_MANUAL/02_getting_started.tex b/doc/USER_MANUAL/02_getting_started.tex
@@ -6,7 +6,7 @@ \chapter{Getting Started}\label{cha:Getting-Started}
 
 To download the SPECFEM2D software package, type this:
 \begin{verbatim}
-git clone --recursive --branch devel https://github.com/geodynamics/specfem2d.git
+git clone --recursive --branch devel https://github.com/SPECFEM/specfem2d.git
 \end{verbatim}
 
 Note: for people who would like to run the package on Windows rather than on Unix machines, you can install Docker or VirtualBox (installing a Linux in VirtualBox in that latter case) and run it easily from inside that.
@@ -107,7 +107,7 @@ \section{Becoming a developer of the code, or making small modifications in the
 If you want to develop new features in the code, and/or if you want to make small changes, improvements, or bug fixes, you are very welcome to contribute.\\
 
 To do so, i.e. to access the development branch of the source code with read/write access (in a safe way, no need to worry too much about breaking the package, there is a robot called BuildBot that is in charge of checking and validating all new contributions and changes), please visit this Web page:\\
-\url{https://github.com/geodynamics/specfem2d/wiki}\\
+\url{https://github.com/SPECFEM/specfem2d/wiki}\\
 
 \noindent
 To visualize the call tree (calling tree) of the source code, you can see the Doxygen tool available in directory \texttt{doc/call\_trees\_of\_the\_source\_code}.

diff --git a/doc/USER_MANUAL/03_mesh_generation.tex b/doc/USER_MANUAL/03_mesh_generation.tex
@@ -27,7 +27,7 @@ \section{How to use SPECFEM2D}
 they contain may be obsolete or even wrong; thus refer to the default \texttt{DATA/Par\_file} instead for reliable explanations).}}\\
 If you need more details we do not have a detailed description of all the parameters for the 2D version in this manual
 but you can find useful information in the manuals of the 3D versions, since many parameters and the general philosophy is similar. They are available at
-\urlwithparentheses{https://github.com/geodynamics/specfem3d/tree/master/doc/USER_MANUAL}.\\
+\urlwithparentheses{https://github.com/SPECFEM/specfem3d/tree/master/doc/USER_MANUAL}.\\
 To create acoustic (fluid) regions, just set the S wave speed to zero and the code will see that these elements are fluid and switch to the right equations there automatically, and automatically match them with the solid regions
 
 \item if you are using an external mesher (like GiD or CUBIT / Trelis), you should set \texttt{read\_external\_mesh} to \texttt{.true.}:

diff --git a/doc/USER_MANUAL/08_informations_for_developers.tex b/doc/USER_MANUAL/08_informations_for_developers.tex
@@ -6,7 +6,7 @@ \chapter{Information for developers of the code, and for people who want to lear
 
 You can get a very simple 1D version of a demo code (there is one in Fortran and one in Python):
 \begin{verbatim}
-git clone --recursive https://github.com/geodynamics/specfem1d.git
+git clone --recursive https://github.com/SPECFEM/specfem1d.git
 \end{verbatim}
 
 \noindent We also have simple 3D demo source codes that implement the SEM in a single, small program, in directory\\
@@ -17,5 +17,5 @@ \chapter{Information for developers of the code, and for people who want to lear
 \texttt{utils/small\_SEM\_solver\_in\_Fortran\_without\_MPI\_to\_learn} of the specfem2d package.\\
 
 \noindent For information on how to contribute to the code, i.e., for how to make your modifications, additions or improvements part of the
-official package, see \url{https://github.com/geodynamics/specfem3d/wiki} .
+official package, see \url{https://github.com/SPECFEM/specfem3d/wiki} .
 
diff --git a/doc/USER_MANUAL/manual_SPECFEM2D.pdf b/doc/USER_MANUAL/manual_SPECFEM2D.pdf
diff --git a/doc/USER_MANUAL/notes_and_acknowledgement.tex b/doc/USER_MANUAL/notes_and_acknowledgement.tex
@@ -11,8 +11,5 @@ \chapter*{Notes \& Acknowledgments}
 The non-structured global numbering software was provided by Paul
 F. Fischer (Brown University, Providence, Rhode Island, USA, now at Argonne National Laboratory, USA).\\
 
-Please e-mail your feedback, bug reports, questions, comments, and suggestions
-to the CIG Computational Seismology Mailing List \urlwithparentheses{[email protected]}.
-
-
+Please provide your feedback, questions, comments, and suggestions through the github repository.
 
diff --git a/doc/USER_MANUAL/translate_LaTeX_manual_to_wiki_markdown.sh b/doc/USER_MANUAL/translate_LaTeX_manual_to_wiki_markdown.sh
@@ -13,7 +13,7 @@ if [ ! -f translate_user_manual_to_markdown.pl ]; then
 ######## echo "translation script is not available, exiting..."
 ######## exit 1
 # if not, get it from GitHub
-  git clone https://github.com/geodynamics/specfem2d.wiki.git
+  git clone https://github.com/SPECFEM/specfem2d.wiki.git
   mv -f specfem2d.wiki/translate_user_manual_to_markdown.pl .
   mv -f specfem2d.wiki/*.md .
 fi

diff --git a/...es_about_tomography/Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt b/...es_about_tomography/Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt
@@ -47,7 +47,7 @@ discussed APPROXIMATE_HESS_KL (inversion), USER_T0 (inversion), and
 NGLLX (minimum resolvable period).
 
 constants file:
-https://github.com/geodynamics/specfem3d/blob/devel/setup/constants.h.in
+https://github.com/SPECFEM/specfem3d/blob/devel/setup/constants.h.in
 
 + Are the src/tomograhy/ files different in SPECFEM3D and SPECFEM3D_GLOBE?
 

diff --git a/flags.guess b/flags.guess
@@ -20,7 +20,7 @@
 # You can add -DFORCE_VECTORIZATION to the options below (for all compilers, except for IBM for which the syntax is -WF,-DFORCE_VECTORIZATION)
 # to speed up the code in the fluid (acoustic) parts (only; FORCE_VECTORIZATION support for elastic parts has been discontinued in the source code).
 # This works fine if (and only if) your computer always allocates a contiguous memory block for each allocatable array;
-# this is the case for most machines and most compilers, but not all. For more details see https://github.com/geodynamics/specfem3d/issues/81 .
+# this is the case for most machines and most compilers, but not all. For more details see https://github.com/SPECFEM/specfem3d/issues/81 .
 # To check if that option works fine on your machine, run the code with and without it for a model containing a significant fluid layer
 # (or entirely fluid) and make sure the seismograms are identical.
 

diff --git a/tests/run_all_tests.sh b/tests/run_all_tests.sh
@@ -9,7 +9,7 @@ echo "This script runs a set of compilation and unit tests in directory tests/"
 echo "It may take a few minutes to execute."
 echo
 echo "Please consider adding more test units to this directory here ..."
-echo "Contributions can be sent to: $(tput bold)http://github.com/geodynamics/specfem2d$(tput sgr0)"
+echo "Contributions can be sent to: $(tput bold)https://github.com/SPECFEM/specfem2d$(tput sgr0)"
 echo
 
 # directories
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		Instruction for how to contribute to SPECFEM2D are available at https://github.com/geodynamics/specfem3d/wiki.
		Instruction for how to contribute to SPECFEM2D are available at https://github.com/SPECFEM/specfem3d/wiki.