added doxygen documentation files

.gitignore

@@ -69,6 +69,5 @@ main
 *.snm
 *.nlo
 
-html/
 test
 DoxygenWarningLog.txt

Doxyfile

@@ -32,26 +32,26 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "PRISMS Phase Field"
+PROJECT_NAME           = "PRISMS PhaseField" 
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         =
+PROJECT_NUMBER         = "1.0"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          =
+PROJECT_BRIEF          = 
 
 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55
 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
 # the logo to the output directory.
 
-PROJECT_LOGO           =
+PROJECT_LOGO           = 
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is
@@ -299,7 +299,7 @@ MARKDOWN_SUPPORT       = YES
 # globally by setting AUTOLINK_SUPPORT to NO.
 # The default value is: YES.
 
-AUTOLINK_SUPPORT       = YES
+AUTOLINK_SUPPORT       = NO
 
 # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
 # to include (a tag file for) the STL sources as input, then you should set this
@@ -512,7 +512,7 @@ CASE_SENSE_NAMES       = NO
 # scope will be hidden.
 # The default value is: NO.
 
-HIDE_SCOPE_NAMES       = NO
+HIDE_SCOPE_NAMES       = YES
 
 # If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
 # append additional text to a page's title, such as Class Reference. If set to
@@ -661,7 +661,7 @@ SHOW_FILES             = YES
 # Folder Tree View (if specified).
 # The default value is: YES.
 
-SHOW_NAMESPACES        = YES
+SHOW_NAMESPACES        = NO
 
 # The FILE_VERSION_FILTER tag can be used to specify a program or script that
 # doxygen should invoke to get the current version for each file (typically from
@@ -932,7 +932,7 @@ INLINE_SOURCES         = NO
 # Fortran comments will always remain visible.
 # The default value is: YES.
 
-STRIP_CODE_COMMENTS    = YES
+STRIP_CODE_COMMENTS    = NO
 
 # If the REFERENCED_BY_RELATION tag is set to YES then for each documented
 # function all documented functions referencing it will be listed.
@@ -1062,7 +1062,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            =
+HTML_HEADER            = 
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1107,7 +1107,7 @@ HTML_EXTRA_STYLESHEET  =
 # files will be copied as-is; there are no commands or markers available.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_FILES       = applications/mechanics/README.pdf
+HTML_EXTRA_FILES       = 
 
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to

LICENSE

@@ -1,4 +1,4 @@
-This directory contains the Phase Field Code developed by the PRISMS Center
+This directory contains the PhaseField Code developed by the PRISMS Center
 at the University of Michigan, Ann Arbor, USA.
 
 (c) 2014 The Regents of the University of Michigan

README.md

@@ -1,107 +1,113 @@
-What is phaseField_PRISMS?
+<B>Code repository:</B> https://github.com/prisms-center/phaseField
 
-  phaseField_PRISMS is a C++ code implementing various phase field and
-  mechanics models and its applications to some physical problems
-  (spinodal decomposition, precipitate growth, coupled
-  transport+mechanics, etc)
+<B>What is PRISMS PhaseField?</B>
 
-  It is a Finite Element Method (FEM) code and is build on top of the
-  deal.II open source finite element library (http://www.dealii.org)
+  It is a Finite Element Method (FEM) code implementing various phase field 
+  and coupled mechanics models and its applications to some physical problems
+  (spinodal decomposition, coupled transport and mechanics, precipitate evolution, etc.).
+  It is build on top of the deal.II open source finite element library [http://www.dealii.org]
 
   This code is developed by the PRedictive Integrated Structural
-  Materials Science (PRISMS) Center at University of Michigan which is
-  supported by the U.S. Department of Energy, Office of Basic Energy
-  Sciences, Division of Materials Sciences and Engineering under Award
-  #DE-SC0008637
-
-Installation and Use:
-
-  1) Configure, compile and install the deal.II library. No additional
-     libraries are required besides the installation of deal.ii with
-     the following configuration flags:
-     -DDEAL_II_WITH_MPI=ON  
-     -DDEAL_II_WITH_P4EST=ON 
-     -DDEAL_II_WITH_LAPACK=ON
-
-     Download: http://www.dealii.org/download.html
-     Detailed instructions: http://www.dealii.org/8.1.0/readme.html
-      
-  2) Fork the repo https://github.com/prisms-center/phaseField on
-  GitHub (How to fork: https://help.github.com/articles/fork-a-repo/)
-  and clone the phaseField repository using your GitHub username:
-
-  $ git clone [email protected]:username/phaseField.git 
-  (OR)
-  $ git clone https://github.com/username/phaseField.git  
-
-  [Note: phaseField is currently a private repository on GitHub and
-  hence you need to be authorised to access the repository. Contact
-  the developers/Mailing-List for requesting access]
-
-  3) Running phaseField applications, for example cahnHilliard 
-  $ cd applications/cahnHilliard
-  $ cmake CMakeLists.txt
-  For debug mode [default mode]:
-  $ make debug
-  For optimized mode:
-  $ make release 
-  Execution (serial runs):
-  $ make run
-  Execution (parallel runs):
-  $ mpiexec -np nprocs ./main
+  Materials Science (PRISMS) Center [http://www.prisms-center.org/]
+  at University of Michigan which is supported by the U.S. Department 
+  of Energy (DOE), Office of Basic Energy Sciences, Division of Materials Sciences 
+  and Engineering under Award #DE-SC0008637
+
+<B>Installation:</B>
+
+  1) Install deal.II (version 8.2.1 currently supported)<br>
+  + Download Binaries (OSX and Linux) or  Virtual Machine (VMI) from https://www.dealii.org/download.html <br>
+  (OR) <br>
+  + Configure, compile and install the deal.II library with the 
+  following configuration flags. Dependencies are MPI, p4est, PETSc libraries.<br>
+     -DDEAL_II_WITH_MPI=ON, -DDEAL_II_WITH_LAPACK=ON, -DDEAL_II_WITH_P4EST=ON, -DDEAL_II_WITH_PETSC=ON
+
+     Download: http://www.dealii.org/download.html <br>
+     Installation instructions: http://www.dealii.org/8.2.1/readme.html <br>
+     Installation instructions for external packages (P4EST, PETSC): https://www.dealii.org/developer/external-libs/
+
+  2) Clone the PRISMS PhaseField GitHub repo https://github.com/prisms-center/phaseField<br>
+  + $ git clone https://github.com/prisms-center/phaseField.git <br>
+  (OR) <br>
+  + $ git clone [email protected]:prisms-center/phaseField.git <br>
+  and <br>
+  + $ cd phaseField <br>
+  + $ git checkout master <br>
+
+<B>Usage:</B>
+
+  Running phaseField applications, for example Cahn-Hilliard spinodal decomposition problem :<br> 
+  + $ cd applications/cahnHilliard <br>
+  For debug mode [default mode, very slow]: <br>
+  + $ cmake CMakeLists.txt -DCMAKE_BUILD_TYPE=Debug <br>
+  For optimized mode:<br>
+  + $ cmake CMakeLists.txt -DCMAKE_BUILD_TYPE=Release <br>
+  and <br>
+  + $ make <br><br>
+  Execution (serial runs): <br>
+  + $ make run <br>
+  Execution (parallel runs): <br>
+  + $ mpirun -np nprocs ./main <br>
   [here nprocs denotes the number of processors]
 
-  4) Updates: Since phaseField code is still under active development,
+  Updates: Since phaseField code is still under active development,
   regular code and documentation updates are pushed to the upstream
   repo (https://github.com/prisms-center/phaseField) and we strongly
-  recommend users to synchronize their respective forks at regular
+  recommend users to synchronize their respective clones/forks at regular
   intervals or when requested by the developers through the
   announcements on the mailing list. 
-  (How to sync: https://help.github.com/articles/syncing-a-fork/)
 
-  5) Visualization: Results are written out in standard vtk/vtu/vts
-  formats which can be visualized with the following open source
-  applications:
+<B>Visualization</B> 
+
+  Output of the primal fields and postprocessed fields is in standard vtk 
+  format (parallel:*.pvtu, serial:*.vtu files) which can be visualized with the 
+  following open source applications:
   1. VisIt (https://wci.llnl.gov/simulation/computer-codes/visit/downloads)
   2. Paraview (http://www.paraview.org/download/)
 
-Getting started:
+<B>Getting started:</B>
 
-  The applications are located under /applications and each
-  application has a detailed README with instructions and related
-  documentation.
+  Examples of various initial boundary value problems (IBVP's) are located under the 
+  applications/ folder. Easiest way to get started on the code is to 
+  run the applications.
 
   Applications are intended to serve as (1) Demonstration of the
   capabilities of this library, (2) Provide a framework for
   further development of specialized/advanced applications by
-  users. Currently the following applications are provided:
-
-  cahnHilliard
-  allenCahn
-  mechanics	
-  coupledCahnHilliardAllenCahn
-  betaPrimePrecipitate
+  users. 
 
+  Application or code under development/testing is preceded by an
+  underscore. 
 
-  Applications under development/testing are preceded by an
-  underscore, such as:
-  _fickianFlux
-  _coupledFickianFluxMechanics
-  _coupledCahnHilliardMechanics
+  List of folders:
+  + include/: header files
+  + src/: models (diffusion, mechanics and coupled models),
+  matrixfree (base class for parallel implementation of parabolic and elliptic 
+  intial boundary value problems)
+  + applications/: Various phase field and mechanics example problems
+  + docs/: Formulations, user manuals, etc in PDF format
+  + html/: HTML documentation generated by doxygen
 
+<B>Documentation:</B>
 
-License:
+  Detailed mathematical formulations, example simulations, code documentation, etc, provided:
+  + Open html/index.html in any web browser <br>
+  (OR)<br>
+  + https://htmlpreview.github.io/?https://raw.githubusercontent.com/prisms-center/phaseField/master/html/index.html
+
+<B>License:</B>
 
   GNU Lesser General Public License (LGPL). Please see the file
   LICENSE for details.
 
-Mailing List:
+<B>Mailing List:</B>
 
-  [email protected]
+ + [email protected]	
+ + [email protected]  
 
-Further information, questions, issues and bugs:
+<B>Further information, questions, issues and bugs:</B>
 
-  Contact the phaseField mailing list at PRISMS.phaseField@umich.edu  
+  Contact the developers at prismsphaseField.dev@umich.edu