- replace ECCO_v4_r2 with ECCOv4 following the change of repository name

- reduce usage of quotes and acronyms in index.rst and introduction.rst

docs/eccov4r2_dirtree.rst

@@ -8,7 +8,7 @@
        genmake2        (shell script)
        build_options   (compiler options)
      mysetups/         (user created)
-       ECCO_v4_r2/
+       ECCOv4/
          build/                (build directory)
          code/                 (compile-time settings)
          input/                (run-time settings)

docs/eccov4r2_setup.rst

@@ -1,18 +1,18 @@
 
-Users can donwload the `MITgcm` from `this github repository <https://github.com/MITgcm/MITgcm/>`__ and the model setup there from `that github repository <https://github.com/gaelforget/ECCO_v4_r2/>`__ by typing:
+Users can donwload the `MITgcm` from `this github repository <https://github.com/MITgcm/MITgcm/>`__ and the model setup there from `that github repository <https://github.com/gaelforget/ECCOv4/>`__ by typing:
 
 ::
 
     git clone https://github.com/MITgcm/MITgcm
-    git clone https://github.com/gaelforget/ECCO_v4_r2
+    git clone https://github.com/gaelforget/ECCOv4
     mkdir MITgcm/mysetups
-    mv ECCO_v4_r2 MITgcm/mysetups/.
+    mv ECCOv4 MITgcm/mysetups/.
 
 Re-running `ECCO v4 r2` additionally requires downloading surface forcing input (96G of 6-hourly fields in `ECCO v4 r2`), initial condition, grid, etc. input (610M), and observational input (25G) either from the `Harvard Dataverse <https://dataverse.harvard.edu/dataverse/ECCOv4r2inputs>`__ permanent archive or directly from the `ECCO ftp server <ftp://mit.ecco-group.org/ecco_for_las/version_4/release2/>`__ as follows:
 
 ::
 
-    cd MITgcm/mysetups/ECCO_v4_r2
+    cd MITgcm/mysetups/ECCOv4
     wget --recursive ftp://mit.ecco-group.org/ecco_for_las/version_4/release2/input_forcing/
     wget --recursive ftp://mit.ecco-group.org/ecco_for_las/version_4/release2/input_init/
     wget --recursive ftp://mit.ecco-group.org/ecco_for_las/version_4/release2/input_ecco/

docs/index.rst

@@ -1,12 +1,12 @@
-.. ECCO v4 documentation master file, created by
+.. ECCOv4 documentation master file, created by
    sphinx-quickstart on Mon Jan 15 15:00:00 2018.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
 Welcome to ECCO version 4's documentation!
 ==========================================
 
-Here, you will learn about simple methods that are available to download, analyze, rerun, or modify `ECCO version 4` and `MITgcm` solutions. In the :ref:`downloads` and :ref:`runs` section, the `ECCO v4 r2` solution is taken as an example before reviewing other solutions and additional resources. For an overview of the `ECCO version 4` framework, please refer to :cite:`for-eta:15`.
+Here, you will learn about simple methods that are available to download, analyze, rerun, or modify `ECCO version 4` and `MITgcm` solutions. In the :ref:`downloads` and :ref:`runs` section, the `release 2` solution is taken as an example before reviewing other solutions and additional resources. For an overview of the `ECCO version 4` framework, please refer to :cite:`for-eta:15`.
 
 .. toctree::
    :maxdepth: 3

docs/introduction.rst

@@ -4,13 +4,13 @@
 Introduction
 ************
 
-`ECCO v4 r2` is an ocean state estimate and solution of the `MIT` general circulation model (`MITgcm`) that covers the period from 1992 to 2011 :cite:`dspace-eccov4r2`. It is a minor update of the original `ECCO v4 r1` solution :cite:`for-eta:15` that 
+ECCO version 4 release 2 (`ECCO v4 r2`) is an ocean state estimate and solution of the MIT general circulation model (`MITgcm`) that covers the period from 1992 to 2011 :cite:`dspace-eccov4r2`. It is a minor update of the original ECCO version 4 solution :cite:`for-eta:15` that 
 
 #. benefits from a few additional corrections listed in :cite:`dspace-eccov4r2`
 
 #. is provided with additional model-data misfit and model budget output
 
-#. has become easier to rerun than `ECCO v4 r1`. 
+#. has become easier to rerun than ECCO version 4 release 1. 
 
 
 The :ref:`downloads` section provides an installation guide and links to various analysis tools. The :ref:`runs` section provides simple instructions to rerun model solutions, which can be useful to generate additional output for example, and start experimenting with the model.

docs/runs.rst

@@ -12,7 +12,7 @@ This section first explains how the `MITgcm` can be used to re-run the `ECCO v4
 
 Running the model on a linux cluster requires `gcc` and `gfortran` (or alternative compilers), `mpi` libraries (for parallel computation), and `netcdf` libraries (e.g., for the `profiles` package) as explained in the `MITgcm documentations <http://mitgcm.org/public/docs.html>`__. In `ECCO v4 r2`, the 20-year model run typically takes between 6 to 12 hours when using 96 cores and modern on-premise clusters.
 
-Users who may lack on-premise computational resources or IT support can use `the included cloud computing recipe <https://github.com/gaelforget/ECCO_v4_r2/tree/master/example_scripts/>`__ to leverage `Amazon Web Services`'s ``cfncluster`` technology. This recipe sets up a complete computational environment in the `AWS` cloud (hardware, software, model, and inputs). When this recipe was tested in January 2017, the 20-year `ECCO v4 r2` model run took under 36h using 96 vCPUs and `AWS spot instances` for a cost of about 40$. 
+Users who may lack on-premise computational resources or IT support can use `the included cloud computing recipe <https://github.com/gaelforget/ECCOv4/tree/master/example_scripts/>`__ to leverage `Amazon Web Services`'s ``cfncluster`` technology. This recipe sets up a complete computational environment in the `AWS` cloud (hardware, software, model, and inputs). When this recipe was tested in January 2017, the 20-year `ECCO v4 r2` model run took under 36h using 96 vCPUs and `AWS spot instances` for a cost of about 40$. 
 
 .. _eccov4-baseline:
 
@@ -28,7 +28,7 @@ This section assumes that `MITgcm`, the `ECCO v4` setup, and model inputs have b
 ::
 
     #1) compile model
-    cd MITgcm/mysetups/ECCO_v4_r2/build
+    cd MITgcm/mysetups/ECCOv4/build
     ../../../tools/genmake2 -mods=../code -optfile \
          ../../../tools/build_options/linux_amd64_gfortran -mpi
     make depend
@@ -48,7 +48,7 @@ This section assumes that `MITgcm`, the `ECCO v4` setup, and model inputs have b
 
 .. note::
 
-   On most clusters, users would call ``mpiexec`` (or ``mpirun``) via a queuing system rather than directly from the command line. `The cloud computing recipe <https://github.com/gaelforget/ECCO_v4_r2/tree/master/example_scripts/>`__ provides an example.
+   On most clusters, users would call ``mpiexec`` (or ``mpirun``) via a queuing system rather than directly from the command line. `The cloud computing recipe <https://github.com/gaelforget/ECCOv4/tree/master/example_scripts/>`__ provides an example.
 
 Other compiler options, besides ``linux_amd64_gfortran``, are provided by the `MITgcm` development team in ``MITgcm/tools/build_options/`` for cases when `gfortran` is not available. The number of cores is 96 by default as seen in :ref:`baseline`. It can be reduced to, e.g., 24 simply by copying ``code/SIZE.h_24cores`` over ``code/SIZE.h`` before compiling the model and then running `MITgcm` with ``-np 24`` rather than ``-np 96`` in :ref:`baseline`. It can alternatively be increased to, e.g., 192 cores to speed up the model run or reduce memory requirements. In this case one needs to use ``code/SIZE.h_192cores`` at compile-time and ``input/data.exch2_192cores`` at run-time.
 
@@ -60,7 +60,7 @@ Other compiler options, besides ``linux_amd64_gfortran``, are provided by the `M
 
 ::
 
-    cd MITgcm/mysetups/ECCO_v4_r2;
+    cd MITgcm/mysetups/ECCOv4;
     p = genpath('gcmfaces/'); addpath(p); %this can be commented out if needed
     addpath results_itXX; %This adds necessary .m and .mat files to path
     mytest=testreport_ecco('run/'); %This compute tests and display results