Work on documentation.

doc/conf.py

@@ -207,9 +207,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.0'
+version = '3.1'
 # The full version, including alpha/beta/rc tags.
-release = '2.0'
+release = '3.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/src/about-hermes.rst

@@ -3,16 +3,14 @@ About Hermes
 
 Hermes is a free C++ library for rapid development of
 adaptive *hp*-FEM and *hp*-DG solvers for partial differential equations (PDE)
-and multiphysics PDE systems. The development team includes the 
-`hp-FEM group <http://hpfem.org/>`_ at the `University of Nevada, Reno <http://www.unr.edu>`_ 
-and their `collaborators <http://git.hpfem.org/hermes.git/blob/HEAD:/AUTHORS>`_ 
-from numerous places around the globe.
+and multiphysics PDE systems. The development team now includes mostly the department of Theory of Electrical Engineering at the University of West Bohemia in Pilsen (contact: korous@rice.zcu.cz), in the past the main development was done by the `hp-FEM group <http://hpfem.org/hermes>`_ at the `University of Nevada, Reno <http://www.unr.edu>`_.
+Information about further collaborators from numerous places around the globe can be found at `<http://www.hpfem.org/citing/>`_.
 
 A standard way to use Hermes is to write short C++ user programs 
 that use the functionality provided by the library, but for 
 those who prefer to use a graphical interface, the group located at the 
-University of West Bohemia develops a graphical Engineering tool based on Hermes2D: 
-`Agros2D <http://hpfem.org/agros2d/>`_. 
+University of West Bohemia also develops a graphical Engineering tool based on Hermes2D: 
+`Agros2D <http://agros2d.org/>`_. 
 
 .. figure:: img/agros.png
    :align: center 

doc/src/citing-hermes.rst

@@ -346,10 +346,8 @@ If you use Hermes for your work, please be so kind to include some of the refere
 
 .. only:: html
 
-   Other papers that may be still closer to what you need can be found in the `publications section  <http://hpfem.org/people/>`_ of the hp-FEM group home page or on `Pavel Solin's home page <http://hpfem.org/~pavel>`_.
+   Other papers that may be still closer to what you need can be found in the `citing section  <http://www.hpfem.org/citing/>`_ of the hp-FEM group home page.
 
 .. only:: latex 
 
-      Other papers that may be still closer to what you need can be found in the `publications section  
-      <http://hpfem.org/people/>`_ of the hp-FEM group home page or on `Pavel Solin's home page 
-      <http://hpfem.org/~pavel>`_.
+      Other papers that may be still closer to what you need can be found in the `citing section  <http://www.hpfem.org/citing/>`_ of the hp-FEM group home page.

doc/src/collaboration.rst

@@ -250,7 +250,7 @@ Git and Github are very powerful tools and we covered just a tiny part
 of the story. After you familiarize yourself with the contents of
 this simple primer, read more in `Pro Git <http://progit.org/book/>`_.
 
-Also watch this `YouTube video <http://www.youtube.com/watch?v=OFkgSjRnay4>`_
+Also watch this `YouTube video <http://www.youtube.com/watch?v=OFkgSjRnay4>`_.
 by Scott Chacon.
 
 Good luck and let us know if you think that this document could be improved!

doc/src/documentation.rst

@@ -32,15 +32,15 @@ Developer Documentation (in Doxygen)
 ------------------------------------
 The documentation is accessible online.
 
-     `Hermes - common code <http://hpfem.org/~hermes/hermes/hermes_common/doc/html/index.html>`_
+     `Hermes - common code <http://hpfem.org/~hermes/hermes/hermes_common/doc/html/index.html>`_.
 
-     `Hermes - 2D specific code <http://hpfem.org/~hermes/hermes/hermes2d/doc/html/index.html>`_
+     `Hermes - 2D specific code <http://hpfem.org/~hermes/hermes/hermes2d/doc/html/index.html>`_.
 
 
 In order to build developers documentation, install Doxygen::
 
     Linux: sudo apt-get install doxygen
-    Windows: http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.2-setup.exe
+    Windows: `<http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.2-setup.exe>`_.
 
 There are separate Doxygen files for hermes-common (dimension-independent functionality
 such as matrix solvers) and for Hermes2D. To build the former, go to the directory 
@@ -58,7 +58,7 @@ Other Resources
 
 See the section "Citing Hermes" in this document for a representative selection of 
 books and scientific papers about Hermes. A more complete overview of publications 
-about Hermes and adaptive *hp*-FEM can be found in the `publications section <http://hpfem.org/people/>`_
+about Hermes and adaptive *hp*-FEM can be found in the `publications section <http://hpfem.org/people/>`_.
 at hpfem.org. The most recent list is probably the one 
 on `Pavel Solin's publications page <http://hpfem.org/~pavel/public/papers.html>`_.
 

doc/src/getting_started.rst

@@ -21,18 +21,23 @@ If something is not clear enough from the comments in the code, please see the s
 
 These examples (located in hermes2d/test_examples) are::
 
+    00-quickShow
     01-poisson
     02-poisson-newton
     03-navier-stokes
     04-complex-adapt
     05-hcurl-adapt
     06-system-adapt
     07-newton-heat-rk
-    08-eigenvalue
+    08-nonlinearity
     09-trilinos-nonlinear
     10-linear-advection-dg-adapt
-    11-FCT
-    12-transient-adapt
+    11-transient-adapt
+    12-picard
+    13-FCT
+    14-error-calculation
+    15-adaptivity-matrix-reuse-simple
+    16-adaptivity-matrix-reuse-layer-interior
     
 And these examples are well-documented showcase examples of how to use Hermes.
 

doc/src/hermesOO.rst

@@ -1,6 +1,10 @@
 Hermes C++ object model - deriving your own specialized classes
 ---------------------------------------------------------------
 
+.. admonition:: DOXYGEN documentation
+
+    Anything that is written here can be much faster and in much more complex way read and understood from the Doxygen documentation - please, please, use it - many an hour has been spent to make Doxygen documentation a useful resource for programmers.
+
 There are several classes that represent some piece of the whole FEM discretization and calculation process that hold the custom informaion for a specific problem.
 
 Be sure to have checked the section "Typical example" that will give you an idea of the basics. This section is more technically focused.

doc/src/installation/linux.rst

@@ -4,7 +4,19 @@ Linux
 Download and compilation
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-[NEW] You can download a package directly from **`Hermes launchpad repository<https://launchpad.net/~lukas-korous/+archive/ubuntu/hermes>`_**
+.. figure:: ../hermes2d/img/redRow.jpg
+   :align: center
+   :scale: 100% 
+   :figclass: align-center
+
+.. admonition:: [NEW] - debian packages on Launchpad
+
+    You can download a package directly from `<https://launchpad.net/~lukas-korous/+archive/ubuntu/hermes>`_.
+
+.. figure:: ../hermes2d/img/redRow.jpg
+   :align: center
+   :scale: 100% 
+   :figclass: align-center
 
 The rest of the instructions here are for building Hermes from source.
 
@@ -26,7 +38,7 @@ For thread caching memory allocator from Google, see
 
   - TCMalloc
 
-      - Get TCMalloc from the SVN repository at http://code.google.com/p/gperftools/source/checkout
+      - Get TCMalloc from the SVN repository at `<http://code.google.com/p/gperftools/source/checkout>`_.
       - Make & install
 
 To obtain the source code, clone the Git repository from Github::

doc/src/installation/mac.rst

@@ -19,7 +19,7 @@ application which allows you to easily install and manage UNIX
 libraries and applications on your Mac) by doing the following:
 
   (a) Download and install MacPorts from 
-      http://www.macports.org/install.php.
+      `<http://www.macports.org/install.php>`_.
   (b) Do 'sudo port install suitesparse glew'.
   (c) If you don't already have git installed, do 
       'sudo port install git'.
@@ -31,7 +31,7 @@ above. Change to the directory where you want
 to download the Hermes source and clone the git repository either
 from the hpfem.org server::
 
-    git clone http://git.hpfem.org/git/hermes.git
+    git clone `<http://git.hpfem.org/git/hermes.git>`_.
 
 or from Github::
 

doc/src/installation/matrix_solvers/mumps.rst

@@ -1,9 +1,7 @@
 Mumps
 -----
 
-.. _MUMPS home page: http://graal.ens-lyon.fr/MUMPS/index.php
-.. _solvers repository: https://github.com/hpfem/solvers
-.. _manual: https://github.com/hpfem/solvers/raw/master/manuals/MUMPS_4.9.2.pdf
+.. _MUMPS home page: `<http://graal.ens-lyon.fr/MUMPS/index.php>`_.
 
 Linux
 ~~~~~
@@ -46,9 +44,9 @@ Installation of MUMPS using MSVC is rather easy:
   - preparation
 
     - download MUMPS from http://mumps.enseeiht.fr/MUMPS_4.10.0.tar.gz (if the link does not work, look for 4.10 version of MUMPS)
-    - download WinMUMPS utility from http://sourceforge.net/projects/winmumps/
-    - download a Fortran compiler (e.g. http://software.intel.com/en-us/intel-fortran-studio-xe-evaluation-options)
-    - download BLAS (Debug/Release, static/dynamic, 32-bit/64-bit as you like) from http://icl.cs.utk.edu/lapack-for-windows/lapack/index.html#libraries
+    - download WinMUMPS utility from `<http://sourceforge.net/projects/winmumps/>`_.
+    - download a Fortran compiler (e.g. `<http://software.intel.com/en-us/intel-fortran-studio-xe-evaluation-options)>`_.
+    - download BLAS (Debug/Release, static/dynamic, 32-bit/64-bit as you like) from `<http://icl.cs.utk.edu/lapack-for-windows/lapack/index.html#libraries>`_.
     - you have to have Visual Studio version >= 2008
     - you have to have Python 2.6 or 2.7 available
 

doc/src/installation/matrix_solvers/paralution.rst

@@ -1,25 +1,32 @@
 PARALUTION
--------
+----------
 
-.. _PARALUTION home page: http://www.paralution.com
+1.  Download PARALUTION from `<http://www.paralution.com/>`_.
+2.  Compile, build PARALUTION, and copy headers, and libraries so that Hermes's CMake system can find them (as with other dependencies)
+
+    1.  On Linux, installing PARALUTION to default install directories is sufficient, on Windows some paths have to be set
+
+3.  In your CMake.vars file (or directly in CMakeLists.txt) in the root of Hermes (see step 0) add "set(WITH_PARALUTION YES)"
+
+    1.  It is on by default, so by default one has to include PARALUTION to build Hermes
+
+4.  That is it, build Hermes, it will automatically link to PARALUTION, include headers and make it usable.
 
-1) Download PARALUTION from http://www.paralution.com/
-2) Compile, build PARALUTION, and copy headers, and libraries so that Hermes's CMake system can find them (as with other dependencies)
-2.1) On Linux, installing PARALUTION to default install directories is sufficient, on Windows some paths have to be set
-3) In your CMake.vars file (or directly in CMakeLists.txt) in the root of Hermes (see step 0) add "set(WITH_PARALUTION YES)"
-3.1) It is on by default, so by default one has to include PARALUTION to build Hermes
-4) That is it, build Hermes, it will automatically link to PARALUTION, include headers and make it usable.
 
 How to use PARALUTION
---------------
-5) Read the doxygen manual of the classes
-5.1) Hermes::Algebra::ParalutionMatrix
-5.2) Hermes::Algebra::ParalutionVector
-5.3) Hermes::Preconditioners::ParalutionPrecond
-5.4) Hermes::Solvers::IterativeParalutionLinearMatrixSolver
-5.5) Hermes::Solvers::AMGParalutionLinearMatrixSolver
-5.6) and all classes that these inherit from
-6) If you want to see Hermes & PARALUTION readily work together, take any test example in the /hermes2d folder in the Hermes root and add one of these lines at the beginning of your main()
-6.1) HermesCommonApi.set_integral_param_value(matrixSolverType, SOLVER_PARALUTION_ITERATIVE); // to use iterative solver
-6.2) HermesCommonApi.set_integral_param_value(matrixSolverType, SOLVER_PARALUTION_AMG); // to use AMG solver
-7) Solver classes of Hermes (NewtonSolver, PicardSolver, LinearSolver, ...) will then take this API setting into account and use PARALUTION as the matrix solver.
+---------------------
+5.  Read the doxygen manual of the classes
+
+    1. Hermes::Algebra::ParalutionMatrix
+    2. Hermes::Algebra::ParalutionVector
+    3. Hermes::Preconditioners::ParalutionPrecond
+    4. Hermes::Solvers::IterativeParalutionLinearMatrixSolver
+    5. Hermes::Solvers::AMGParalutionLinearMatrixSolver
+    6. and all classes that these inherit from / use
+
+6.  If you want to see Hermes & PARALUTION readily work together, take any test example in the /hermes2d folder in the Hermes root and add one of these lines at the beginning of your main()
+
+    1.  HermesCommonApi.set_integral_param_value(matrixSolverType, SOLVER_PARALUTION_ITERATIVE); // to use iterative solver
+    2.  HermesCommonApi.set_integral_param_value(matrixSolverType, SOLVER_PARALUTION_AMG); // to use AMG solver
+
+7.  Solver classes of Hermes (NewtonSolver, PicardSolver, LinearSolver, ...) will then take this API setting into account and use PARALUTION as the matrix solver.

doc/src/installation/matrix_solvers/petsc.rst

@@ -1,9 +1,7 @@
 PETSc
 -----
 
-.. _PETSc home page: http://www.mcs.anl.gov/petsc/
-.. _solvers repository: https://github.com/hpfem/solvers
-.. _manual: https://github.com/hpfem/solvers/raw/master/manuals/petsc.pdf
+.. _PETSc home page: `<http://www.mcs.anl.gov/petsc/>`_.
 
 Linux
 ~~~~~

doc/src/installation/matrix_solvers/superlu.rst

@@ -1,13 +1,9 @@
 SuperLU
 --------
 
-.. _SuperLU home page: http://crd.lbl.gov/~xiaoye/SuperLU/
-.. _solvers repository: https://github.com/hpfem/solvers
-.. _manual: https://github.com/hpfem/solvers/raw/master/manuals/SuperLU.pdf
-
 Hermes currently supports two versions of the SuperLU library - the sequential
 one and the multithreaded one. Support for the MPI version will be added in the 
-future. Please visit the `SuperLU home page`_ for more information about the
+future. Please visit `<http://crd.lbl.gov/~xiaoye/SuperLU/>`_ for more information about the
 library.
 
 Linux

doc/src/installation/matrix_solvers/trilinos.rst

@@ -1,9 +1,7 @@
 Trilinos
 --------
 
-.. _Trilinos home page: http://trilinos.sandia.gov/
-.. _solvers repository: https://github.com/hpfem/solvers
-.. _manual: https://github.com/hpfem/solvers/raw/master/manuals/Trilinos10.6Tutorial.pdf
+.. _Trilinos home page: `<http://trilinos.sandia.gov/>`_.
 
 Linux
 ~~~~~
@@ -38,8 +36,9 @@ First of all - to build Trilinos, one needs LAPACK (CLAPACK) (see the optional p
 | Go to the Trilinos source directory.
 | 
 | In the following, replace {TPL_LAPACK_LIBRARIES}, {TPL_BLAS_LIBRARIES} with the full path to your lapack.lib and blas.lib without any quotes.
-| Also, replace {CMAKE_INSTALL_PREFIX} with either your dependency root, or any other folder where you want to install Trilinos packages.::
+| Also, replace {CMAKE_INSTALL_PREFIX} with either your dependency root, or any other folder where you want to install Trilinos packages.
 
+::
 
     mkdir build_dir
     cd build_dir

doc/src/installation/matrix_solvers/umfpack.rst

@@ -1,7 +1,7 @@
 UMFpack
 -------
 
-.. _UMFPack home page: http://www.cise.ufl.edu/research/sparse/umfpack/
+.. _UMFPack home page: `<http://www.cise.ufl.edu/research/sparse/umfpack/>`_.
 
 Linux
 ~~~~~