Index: For_developers/Sphinx/source/Documentation/Input/fortran_makefile.rst
===================================================================
--- For_developers/Sphinx/source/Documentation/Input/fortran_makefile.rst	(revision 5920b7f7de7d2f322abca005714c549cca869fed)
+++ For_developers/Sphinx/source/Documentation/Input/fortran_makefile.rst	(revision a9d33f6eed246594f5e81d80ffcb3fb420c694b2)
@@ -16,6 +16,6 @@
 | Files to be used as they are!
     
-    | **makefile_ecgate**: For  use on ECMWF's server **ecgate**.
-    | **makefile_cray**:   For  use on ECMWF's server **cca/ccb**. 
+    | **makefile_ecgate**: For  use on the ECMWF server **ecgate**.
+    | **makefile_cray**:   For  use on the ECMWF servers **cca/ccb**. 
     
 | **Local mode**
@@ -24,10 +24,47 @@
     | **makefile_fast**:  For use with the gfortran compiler and optimisation mode.
     | **makefile_debug**: For use with the gfortran compiler and debugging mode. Primarily for developers.
+    | **makefile_local_gfortran**: Linked to makefile_fast. Default value.
+
+They can be found at ``flex_extract_vX.X/Source/Fortran/``, where ``vX.X`` should be substituted by the current flex_extract version number.
+
+.. caution::   
+   It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** in these
+   ``makefiles`` if other than standard paths are used.
+
+Thus, go to the ``Fortran`` source directory and open the ``makefile`` of your 
+choice, and check / modify with an editor of your choice:
+
+.. code-block:: bash 
+
+   cd flex_extract_vX.X/Source/Fortran
+   nedit makefile_fast
+ 
+Set the paths to the ``eccodes`` library on your local machine, if necessary.
+
+.. caution::
+   This can vary from system to system. 
+   It is suggested to use a command like 
+
+   .. code-block:: bash
+
+      # for the ECCODES_INCLUDE_DIR path do:
+      $ dpkg -L libeccodes-dev | grep eccodes.mod
+      # for the ECCODES_LIB path do:
+      $ dpkg -L libeccodes-dev | grep libeccodes.so
+      
+   to find out the path to the ``eccodes`` library.
+   
+Assign these paths to the parameters **ECCODES_INCLUDE_DIR**
+and **ECCODES_LIB** in the makefile, and save it.
+
+.. code-block:: bash
+
+   # these are the paths on Debian Buster:
+   ECCODES_INCLUDE_DIR=/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
+   ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm  
+   
 
 If you want to use another compiler than gfortran locally, you can still take ``makefile_fast``,
 and adapt everything that is compiler-specific in this file.
-
-For instructions on how to adapt the ``makefile`` (local application mode only),
-please see :ref:`ref-install-local`.
 
    
Index: For_developers/Sphinx/source/Documentation/Input/jobscript.rst
===================================================================
--- For_developers/Sphinx/source/Documentation/Input/jobscript.rst	(revision 5920b7f7de7d2f322abca005714c549cca869fed)
+++ For_developers/Sphinx/source/Documentation/Input/jobscript.rst	(revision a9d33f6eed246594f5e81d80ffcb3fb420c694b2)
@@ -139,5 +139,4 @@
     mailfail ${USER} 
     mailops ${USER} 
-    makefile Makefile.gfortran
     marsclass EP
     maxstep 0
Index: For_developers/Sphinx/source/Documentation/Input/setup.rst
===================================================================
--- For_developers/Sphinx/source/Documentation/Input/setup.rst	(revision 550435b6360f19b96c22737be3a5c1dfd17bc6b4)
+++ For_developers/Sphinx/source/Documentation/Input/setup.rst	(revision a9d33f6eed246594f5e81d80ffcb3fb420c694b2)
@@ -174,6 +174,7 @@
                             Valid targets: local | ecgate | cca , the latter two
                             are at ECMWF (default: None)
-      --makefile MAKEFILE   Name of Makefile to use for compiling the Fortran
-                            program (default: None)
+      --makefile MAKEFILE   Name of makefile to compile the Fortran
+                            code. (default depends on `target`: local - makefile_local_gfortran,
+                            ecgate - makefile_ecgate, cca - makefile_cray)
       --ecuid ECUID         The user id at ECMWF. (default: None)
       --ecgid ECGID         The group id at ECMWF. (default: None)
Index: For_developers/Sphinx/source/Documentation/disagg.rst
===================================================================
--- For_developers/Sphinx/source/Documentation/disagg.rst	(revision f20342a474e36967cf41b6e992ab0fd6992624c4)
+++ For_developers/Sphinx/source/Documentation/disagg.rst	(revision a9d33f6eed246594f5e81d80ffcb3fb420c694b2)
@@ -17,10 +17,10 @@
     :widths: 5,15,5,10
     
-    LSP,  "large-scale precipitation",          ":math:`m`",          "modified linear interpolation"
-    CP,   "convective precipitation",           ":math:`m`",          "modified linear interpolation"
-    SSHF, "surface sensible heat flux",         ":math:`J m^{-2}`",   "bicubic interpolation"
-    EWSS, "eastward turbulent surface stress",  ":math:`N m^{-2} s`", "bicubic interpolation"
-    NSSS, "northward turbulent surface stress", ":math:`N m^{-2} s`", "bicubic interpolation"
-    SSR,  "surface net solar radiation",        ":math:`J m^{-2}`",   "bicubic interpolation"
+    LSP,  "large-scale precipitation",          "m",          "modified linear interpolation"
+    CP,   "convective precipitation",           "m",          "modified linear interpolation"
+    SSHF, "surface sensible heat flux",         "J m:math:`^{-2}`",   "bicubic interpolation"
+    EWSS, "eastward turbulent surface stress",  "N m:math:`^{-2}` s", "bicubic interpolation"
+    NSSS, "northward turbulent surface stress", "N m:math:`^{-2}` s", "bicubic interpolation"
+    SSR,  "surface net solar radiation",        "J m:math:`^{-2}`",   "bicubic interpolation"
     
 
@@ -62,17 +62,17 @@
 
 
-Disaggregation is done for four adjacent timespans (:math:`a_0, a_1, a_2, a_3`) which generates a new, disaggregated value which is output at the central point of the four adjacent timespans. 
+Disaggregation is done for four adjacent time intervals (:math:`a_0, a_1, a_2, a_3`) which generates a new, disaggregated value which is output at the central point of the four adjacent time intervals. 
 
 .. math::
 
-       p_{ac} &= 0.5 * a_1\\
+       p_{ac} &= 0.5  a_1\\
             m &= a_0 + a_2 > 0.\\
-    p_{ac}(m) &= a_1(m) * a_2(m) / (a_0(m) + a_2(m))\\
+    p_{ac}(m) &= a_1(m) a_2(m) / (a_0(m) + a_2(m))\\
        p_{bd} &= 0.5 * a_2\\
             m &= a_1 + a_3 > 0.\\
-    p_{bd}(m) &= a_1(m) * a_2(m) / (a_1(m) + a_3(m))\\
+    p_{bd}(m) &= a_1(m)  a_2(m) / (a_1(m) + a_3(m))\\
 
 
-This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards. If one of the four original timespans has a value below 0, it is set to 0 prior to the calculation.
+This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards. If one of the four original time intervals has a value below 0, it is set to 0 prior to the calculation.
     
 .. math::
@@ -162,5 +162,5 @@
 The accumulated values for the other variables are first divided by the number of hours and
 then interpolated to the exact times using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
-Disaggregation is done for four adjacent timespans (:math:`p_a, p_b, p_c, p_d`) which produces a new, disaggregated value that is the output at the central point of the four adjacent timespans.
+Disaggregation is done for four adjacent time intervals (:math:`p_a, p_b, p_c, p_d`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
 
 .. math::
Index: For_developers/Sphinx/source/Installation/local.rst
===================================================================
--- For_developers/Sphinx/source/Installation/local.rst	(revision f20342a474e36967cf41b6e992ab0fd6992624c4)
+++ For_developers/Sphinx/source/Installation/local.rst	(revision a9d33f6eed246594f5e81d80ffcb3fb420c694b2)
@@ -11,13 +11,11 @@
          
     
-.. _Python 3: https://docs.python.org/3/
-.. _Python3: https://www.python.org/downloads/
-.. _Anaconda Python3: https://www.anaconda.com/distribution/#download-section
-
+.. _Python3: https://www.python.org/
+.. _Anaconda Python3: https://www.anaconda.com/distribution/
 .. _numpy: http://www.numpy.org/
 .. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
 .. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
 .. _genshi: https://genshi.edgewall.org/
-.. _eccodes for python: https://packages.debian.org/sid/python3-eccodes 
+.. _eccodes for python: https://pypi.org/project/eccodes-python/
 .. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
 .. _gfortran: https://gcc.gnu.org/wiki/GFortran
@@ -30,17 +28,11 @@
 .. _ECMWF ectrans site: https://confluence.ecmwf.int/display/ECAC/Unattended+file+transfer+-+ectrans
 .. _ECaccess Presentation: https://confluence.ecmwf.int/download/attachments/45759146/ECaccess.pdf
-.. _ECMWF's instructions on gateway server: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home
+.. _ECMWF instructions on gateway servers: https://confluence.ecmwf.int/display/ECAC/ECaccess+Home
 .. _Computing Representative: https://www.ecmwf.int/en/about/contact-us/computing-representatives
 .. _MARS access: https://confluence.ecmwf.int//display/WEBAPI/Access+MARS
-
 .. _download section: https://www.flexpart.eu/downloads
 
- 
-    
-    
-    
+     
 .. _ref-local-mode:
-
-
 
 .. _ref-req-local: 
@@ -54,14 +46,14 @@
 and libraries, since the preparation of the extraction and the post-processing is done on the local machine:
 
-+-------------------------------------------------+-----------------+
-|  Python part                                    | Fortran part    |
-+-------------------------------------------------+-----------------+
-| 1. `Python3`_                                   | 1. `gfortran`_  |
-| 2. `numpy`_                                     | 2. `fftw3`_     |
-| 3. `genshi`_                                    | 3. `eccodes`_   |
-| 4. `eccodes for python`_                        | 4. `emoslib`_   |
-| 5. `ecmwf-api-client`_ (everything except ERA5) |                 |
-| 6. `cdsapi`_ (just for ERA5 and member user)    |                 |
-+-------------------------------------------------+-----------------+
++------------------------------------------------+----------------+
+|  Python code                                   | Fortran code   |
++------------------------------------------------+----------------+
+| * `Python3`_                                   | * `gfortran`_  |
+| * `numpy`_                                     | * `fftw3`_     |
+| * `genshi`_                                    | * `eccodes`_   |
+| * `eccodes for python`_                        | * `emoslib`_   |
+| * `ecmwf-api-client`_ (everything except ERA5) |                |
+| * `cdsapi`_ (just for ERA5 and member user)    |                |
++------------------------------------------------+----------------+
 
 
@@ -265,5 +257,4 @@
 
 
-
 .. _ref-install-local:
 
@@ -271,47 +262,13 @@
 ==================
 
-First, adapt the Fortran ``makefile`` for your environment (if necessary) and insert it into ``setup.sh`` script (see :ref:`Fortran Makefile <ref-convert>` for more information).
-They can be found at ``flex_extract_vX.X/Source/Fortran/``, where ``vX.X`` should be substituted by the current flex_extract version number.
-
-.. caution::   
-   It is necessary to adapt **ECCODES_INCLUDE_DIR** and **ECCODES_LIB** in these
-   ``makefiles`` if other than standard paths are used.
-
-Thus, go to the ``Fortran`` source directory and open the ``makefile`` of your 
-choice, and check / modify with an editor of your choice:
-
-.. code-block:: bash 
-
-   cd flex_extract_vX.X/Source/Fortran
-   nedit makefile_fast
+   
+The Fortran program called ``calc_etadot`` will be compiled during the 
+installation process. A suitable makefile (``makefile_local_gfortran``) for the compilation is set by default.
+This may be overwritten by the ``MAKEFILE`` parameter in ``setup.sh``.
+
+However, you may have to adapt the makefile for your environment (the current default makefile works on Debian stretch and similar GNU/Linux distributions). If you use a new name for it, you will have to insert it into ``setup.sh``
+For details on the makefile and how to adapt them, see :ref:`Fortran Makefile <ref-convert>`.
+
  
-Set the paths to the ``eccodes`` library on your local machine, if necessary.
-
-.. caution::
-   This can vary from system to system. 
-   It is suggested to use a command like 
-
-   .. code-block:: bash
-
-      # for the ECCODES_INCLUDE_DIR path do:
-      $ dpkg -L libeccodes-dev | grep eccodes.mod
-      # for the ECCODES_LIB path do:
-      $ dpkg -L libeccodes-dev | grep libeccodes.so
-      
-   to find out the path to the ``eccodes`` library.
-   
-Assign these paths to the parameters **ECCODES_INCLUDE_DIR**
-and **ECCODES_LIB** in the makefile, and save it.
-
-.. code-block:: bash
-
-   # these are the paths on Debian Buster:
-   ECCODES_INCLUDE_DIR=/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/
-   ECCODES_LIB= -L/usr/lib -leccodes_f90 -leccodes -lm  
-   
-    
-The Fortran program called ``calc_etadot`` will be compiled during the 
-installation process. Therefore, the name of the ``makefile`` to be used needs to be given in  ``setup.sh``.
-
 In the root directory of ``flex_extract``, open the ``setup.sh`` script 
 with an editor and adapt the installation parameters in the section labelled with 
@@ -330,5 +287,4 @@
    #
    TARGET='local'
-   MAKEFILE='makefile_fast'
    ECUID=None
    ECGID=None
@@ -357,5 +313,5 @@
 	Install flex_extract_v7.1 software at local in directory <path-to-flex_extract>/flex_extract_v7.1
 
-	Using makefile: makefile_fast
+	Using makefile: makefile_local_gfortran
 	gfortran   -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c	./rwgrib2.f90
 	gfortran   -O3 -march=native -Bstatic -leccodes_f90 -leccodes -Bdynamic -lm -ljasper -lemosR64 -I. -I/usr/local/include -fdefault-real-8 -fopenmp -fconvert=big-endian   -c	./phgrreal.f90
Index: For_developers/Sphinx/source/Installation/remote.rst
===================================================================
--- For_developers/Sphinx/source/Installation/remote.rst	(revision b1674ed9a3275890229aaf2e958f2ea7db4f28ac)
+++ For_developers/Sphinx/source/Installation/remote.rst	(revision a9d33f6eed246594f5e81d80ffcb3fb420c694b2)
@@ -48,5 +48,5 @@
     
 +---------------------------+-----------------+
-|  Python part              | Fortran part    |
+|  Python code              | Fortran code    |
 +---------------------------+-----------------+
 | * `Python3`_              | * `gfortran`_   |
Index: For_developers/Sphinx/source/documentation.rst
===================================================================
--- For_developers/Sphinx/source/documentation.rst	(revision f20342a474e36967cf41b6e992ab0fd6992624c4)
+++ For_developers/Sphinx/source/documentation.rst	(revision a9d33f6eed246594f5e81d80ffcb3fb420c694b2)
@@ -1,9 +1,9 @@
-*************
-Documentation
-*************
+************************
+Code-Level Documentation
+************************
         
     Overview (under construction)
       
-    Control & input data 
+    Scripts, control & input data 
     
     Output data (under construction)
@@ -11,5 +11,5 @@
     Disaggregation of flux data (under construction)
     
-    Vertical coordinate (under construction)
+    Vertical wind (under construction)
       - methods (GAUSS, ETA, OMEGA)
       - calc_etadot 
Index: For_developers/Sphinx/source/index.rst
===================================================================
--- For_developers/Sphinx/source/index.rst	(revision 5920b7f7de7d2f322abca005714c549cca869fed)
+++ For_developers/Sphinx/source/index.rst	(revision a9d33f6eed246594f5e81d80ffcb3fb420c694b2)
@@ -4,7 +4,7 @@
    contain the root `toctree` directive.
 
-=================================================
-Welcome to ``flex_extract``'s user documentation!
-=================================================
+===================================================
+Welcome to the ``flex_extract`` Documentation!
+===================================================
 
 ``Flex_extract`` is an open-source software to retrieve meteorological fields from the MARS archive of the European Centre for Medium-Range Weather Forecasts (ECMWF) to serve as input for the FLEXTRA/FLEXPART atmospheric transport modelling system. 
@@ -14,15 +14,4 @@
     <table style="width:100%;">
       <tr>
-        <td style="width:30%;height:150px;">
-          <div style="width:100%;height:60px;margin-left:20%;position:relative;">
-            <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/install_icon.png">
-          </div>
-          <h2><a href="installation.html">Installation</a></h2>
-          <ul>
-            <li><a href="installation.html#ref-requirements">Environment requirements</a></li>
-            <li><a href="installation.html#ref-download">Download flex_extract</a></li>
-            <li><a href="installation.html#ref-install-fe">Install flex_extract</a></li>
-          </ul>
-        </td>          
         <td style="width:30%;height:150px;">
           <div style="width:100%;height:60px;margin-left:20%;position:relative;">
@@ -38,26 +27,36 @@
         <td style="width:30%;height:150px;">
           <div style="width:100%;height:60px;margin-left:20%;position:relative;">
-            <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/prog_icon.png">
+            <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/install_icon.png">
           </div>
-          <h2><a href="documentation.html">Documentation</a></h2>
+          <h2><a href="installation.html">Installation</a></h2>
           <ul>
-            <li><a href="Documentation/overview.html">Overview</a></li>
-            <li><a href="Documentation/input.html">Control & input data</a></li>
-            <li><a href="Documentation/output.html">Output data</a></li>
+            <li><a href="installation.html#ref-requirements">Dependencies</a></li>
+            <li><a href="installation.html#ref-download">Download flex_extract</a></li>
+            <li><a href="installation.html#ref-install-fe">Install flex_extract</a></li>
           </ul>
-        </td>
-      </tr>
-      <tr>   
+        </td>          
         <td style="width:30%;height:150px;">
           <div style="width:100%;height:60px;margin-left:20%;position:relative;">
             <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/guide_icon.png">
           </div>
-          <h2><a href="quick_start.html">Quick Start</a></h2>
+          <h2><a href="quick_start.html">Usage</a></h2>
           <ul>
             <li><a href="quick_start.html#job-preparation">Job preparation</a></li>
-            <li><a href="quick_start.html#selection-and-adjustment-of-control-files">Handling CONTROL files</a></li>
+            <li><a href="quick_start.html#selection-and-adjustment-of-control-files">CONTROL files</a></li>
             <li><a href="quick_start.html#hints-for-definition-of-some-parameter-combinations">Hints on parameter combinations</a></li>
           </ul>
-        </td>  
+        </td>        </tr>
+      <tr>   
+        <td style="width:30%;height:150px;">
+          <div style="width:100%;height:60px;margin-left:20%;position:relative;">
+            <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/prog_icon.png">
+          </div>
+          <h2><a href="documentation.html">Code-level documentation</a></h2>
+          <ul>
+            <li><a href="Documentation/overview.html">Overview</a></li>
+            <li><a href="Documentation/input.html">Scripts, control & input data</a></li>
+            <li><a href="Documentation/output.html">Output data</a></li>
+          </ul>
+        </td>
         <td style="width:30%;height:150px;">
           <div style="width:100%;height:60px;margin-left:20%;position:relative;">
@@ -75,7 +74,7 @@
             <img style="position:absolute;height:90%;vertical-align:bottom;" src="_static/dev_icon.png">
           </div>
-          <h2><a href="dev_guide.html">Developer</a></h2>
+          <h2><a href="dev_guide.html">Developer guide</a></h2>
           <ul>
-            <li><a href="Developers/gen_docu.html">Updateing the documentation</a></li>
+            <li><a href="Developers/gen_docu.html">Updating the documentation</a></li>
             <li><a href=""></a><Placeholder></li>
             <li><a href=""></a><Placeholder></li>
@@ -132,7 +131,7 @@
    :caption: Table of Contents:
 
+   ecmwf_data
    installation
    quick_start
-   ecmwf_data
    documentation
    evaluation
Index: For_developers/Sphinx/source/installation.rst
===================================================================
--- For_developers/Sphinx/source/installation.rst	(revision b936fd3459713a8e34676303eb10ede41eded37d)
+++ For_developers/Sphinx/source/installation.rst	(revision a9d33f6eed246594f5e81d80ffcb3fb420c694b2)
@@ -135,10 +135,10 @@
 ============
 
-The software required for running ``flex_extract`` depends on the :doc:`Documentation/Overview/app_modes` and therefore is described in the respective specific installation sections. 
+The software required to run ``flex_extract`` depends on the :doc:`Documentation/Overview/app_modes` and therefore is described in the respective specific installation sections. 
     
 Generally speaking, ``flex_extract`` requires `Python 3`_ and Fortran together with certain modules / libraries.
-We tested ``flex_extract`` with the python3 package from the the GNU/Linux distribution and Anaconda Python. The required python3 modules should prefarably be installed as distribution packages, or alternatively using Python's own package manager ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.).
-
-Before installing the system packages check the availability with ``dpkg -s <package-name> |  grep Status`` or ``rpm -q <package_name>``, depending on your system. For example: 
+We tested ``flex_extract`` with the Python3 package from the the GNU/Linux distribution and Anaconda Python. The required Python3 modules should prefarably be installed as distribution packages, or alternatively using Python's own package manager ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.).
+
+Before installing the system packages check the availability with (Debian-based system) ``dpkg -s <package-name> |  grep Status`` or (Redhat-based system)``rpm -q <package_name>``. For example: 
 
 .. code-block:: sh
@@ -150,7 +150,4 @@
 
 
-
-
-
 .. _ref-install-fe:
 
@@ -183,21 +180,4 @@
     Installation/local
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-    
-    
     
 
@@ -206,11 +186,4 @@
 
 Some users might wish to incorporate ``flex_extract`` directly into the ``FLEXPART`` distribution. Then the installation path has to be changed by setting the parameter `installdir` in the ``setup.sh`` file to the ``script`` directory in the ``FLEXPART`` root directoy. 
-
-
-
-
-
-
-
 
 
Index: For_developers/Sphinx/source/quick_start.rst
===================================================================
--- For_developers/Sphinx/source/quick_start.rst	(revision 5920b7f7de7d2f322abca005714c549cca869fed)
+++ For_developers/Sphinx/source/quick_start.rst	(revision a9d33f6eed246594f5e81d80ffcb3fb420c694b2)
@@ -1,5 +1,5 @@
-***********
-Quick Start
-***********
+*****
+Usage
+*****
 
 ``flex_extract`` is a command-line tool. In the first versions, it was started via a korn shell script and since version 6, the entry point was a python script. From version 7.1, a bash shell script was implemented to call ``flex_extract`` with the command-line parameters. 
