Updated the documentation to reflect changes

Author: makeclean

doc/install/fludag.rst

@@ -10,21 +10,24 @@ Install FLUKA
 ~~~~~~~~~~~~~
 
 FluDAG uses FLUKA_ from CERN/INFN. In order to download FLUKA you need to become
-a registered user, which you can do at the `FLUKA registration
-<FLUKA_register_>`_ page.
+a registered user, which you can do at the `FLUKA-INFN registration
+<FLUKA_infn_register_>`_ page for FLUKA-INFN and `FLUKA-CERN registration page <FLUKA_cern_register>`_. 
 
 Save your user ID and password for future FLUKA updates. We recommend an x64
-worfklow and thus you should download the 64-bit executable. The name of the
-downloaded tarball is of the form ``fluka20xx.xx-linux-gfor64bitAA.tar.gz``.
-Refer to the `installation instructions <FLUKA_install_>`_ when building FLUKA.
+worfklow and thus you should download the 64-bit executable. For FLUKA-INFN, the
+name of the downloaded tarball is of the form ``fluka20xx.xx-linux-gfor64bitAA.tar.gz``.
+Refer to the `installation instructions <FLUKA_infn_install_>`_ when building FLUKA.
+
+For FLUKA-CERN, x64 is the only option and refer to `installation instructions <FLUKA_cern_install_>`_
 
 Take care to follow the FLUKA site instructions when setting the ``$FLUPRO`` and
 ``$FLUFOR`` environment variables.
 
 ..  include:: configure_dag-code_header.txt
 
 The following CMake command will build FluDAG. Note that ``$FLUPRO`` should have
-previously been defined as part of the FLUKA install.
+previously been defined as part of the FLUKA install. FLUPRO can also be set explictly
+to the base path of FLUKA, for example ``/home/user/fluka-cern/fluka4.01``
 ::
 
     $ cmake ../src -DMOAB_DIR=$HOME/dagmc_bld/MOAB \
@@ -60,5 +63,7 @@ like this:
 ..  include:: test_dagmc.txt
 
 ..  _FLUKA: http://www.fluka.org/fluka.php
-..  _FLUKA_register: https://www.fluka.org/fluka.php?id=secured_intro
-..  _FLUKA_install: http://www.fluka.org/fluka.php?id=ins_run
+..  _FLUKA_infn_register: https://www.fluka.org/fluka.php?id=secured_intro
+..  _FLUKA_cern_register: https://fluka.cern/home
+..  _FLUKA_infn_install: http://www.fluka.org/fluka.php?id=ins_run
+..  _FLUKA_cern_install: https://fluka.cern/documentation/installation

doc/usersguide/uw2.rst

@@ -147,7 +147,7 @@ run the ``mainfludag`` executable to produce the ``mat.inp`` file which contains
 all the detailed material assignments and compound descriptions.
 ::
 
-    $ mainfludag geom.h5m
+    $ mainfludag --dagmc geom.h5m
 
 The user should then paste the contents of ``mat.inp`` into the main FLUKA input
 deck. Now the user must make a symbolic link to the geometry file named