doc: correction in doxyfile (all warnings). creating build folder for…

… compiling

.github/workflows/c-cpp.yml

@@ -20,7 +20,7 @@ jobs:
       run: sudo apt-get update && sudo apt-get install -y build-essential
 
     - name: Build with Makefile
-      run: make -f make/makefile
+      run: make -f build/make/makefile
 
     - name: Upload compiled binaries
       uses: actions/upload-artifact@v3

.github/workflows/msbuild.yml

@@ -13,7 +13,7 @@ on:
 
 env:
   # Path to the solution file relative to the root of the project.
-  SOLUTION_FILE_PATH: ./make/VS/MPM-Geomechanics.sln
+  SOLUTION_FILE_PATH: ./build/msbuild/MPM-Geomechanics.sln
 
   # Configuration type to build.
   # You can convert this to a build matrix if you need coverage of multiple configuration types.

doxygen/Doxyfile → Doxyfile.bak

@@ -24,41 +24,41 @@
 # https://www.gnu.org/software/libiconv/ for the list of possible encodings.
 # The default value is: UTF-8.
 
-DOXYFILE_ENCODING      = UTF-8
+DOXYFILE_ENCODING = UTF-8
 
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
 # double-quotes, unless you are using Doxywizard) that should identify the
 # project for which the documentation is generated. This name is used in the
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "MPM-Geomechanics"
+PROJECT_NAME = "MPM-Geomechanics"
 
 # 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 = ""
 
 # 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          = "This project provides a platform for developing the Material Point Method for simulating geo-materials under large deformation conditions."
+PROJECT_BRIEF = "Material Point Method for simulating geo-materials under large deformation conditions"
 
 # 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
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       =
+OUTPUT_DIRECTORY =
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and
@@ -68,15 +68,15 @@ OUTPUT_DIRECTORY       =
 # performance problems for the file system.
 # The default value is: NO.
 
-CREATE_SUBDIRS         = NO
+CREATE_SUBDIRS = NO
 
 # If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
 # characters to appear in the names of generated files. If set to NO, non-ASCII
 # characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
 # U+3044.
 # The default value is: NO.
 
-ALLOW_UNICODE_NAMES    = NO
+ALLOW_UNICODE_NAMES = NO
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all
 # documentation generated by doxygen is written. Doxygen will use this
@@ -91,7 +91,7 @@ ALLOW_UNICODE_NAMES    = NO
 # Ukrainian and Vietnamese.
 # The default value is: English.
 
-OUTPUT_LANGUAGE        = English
+OUTPUT_LANGUAGE = English
 
 # The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all
 # documentation generated by doxygen is written. Doxygen will use this
@@ -106,7 +106,7 @@ OUTPUT_TEXT_DIRECTION  = None
 # documentation (similar to Javadoc). Set to NO to disable this.
 # The default value is: YES.
 
-BRIEF_MEMBER_DESC      = YES
+BRIEF_MEMBER_DESC  = YES
 
 # If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
 # description of a member or function before the detailed description
@@ -467,31 +467,31 @@ LOOKUP_CACHE_SIZE      = 0
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            = NO
+EXTRACT_ALL  = YES
 
 # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
 # be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIVATE        = YES
+EXTRACT_PRIVATE = YES
 
 # If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
 # methods of a class will be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIV_VIRTUAL   = NO
+EXTRACT_PRIV_VIRTUAL  = NO
 
 # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
 # scope will be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PACKAGE        = NO
+EXTRACT_PACKAGE = NO
 
 # If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
 # included in the documentation.
 # The default value is: NO.
 
-EXTRACT_STATIC         = NO
+EXTRACT_STATIC = YES
 
 # If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
 # locally in source files will be included in the documentation. If set to NO,
@@ -576,7 +576,7 @@ HIDE_SCOPE_NAMES       = NO
 # YES the compound reference will be hidden.
 # The default value is: NO.
 
-HIDE_COMPOUND_REFERENCE= NO
+HIDE_COMPOUND_REFERENCE = NO
 
 # If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
 # the files that are included by a file in the documentation of that file.
@@ -680,13 +680,13 @@ GENERATE_BUGLIST       = YES
 # the documentation.
 # The default value is: YES.
 
-GENERATE_DEPRECATEDLIST= YES
+GENERATE_DEPRECATEDLIST = YES
 
 # The ENABLED_SECTIONS tag can be used to enable conditional documentation
 # sections, marked by \if <section_label> ... \endif and \cond <section_label>
 # ... \endcond blocks.
 
-ENABLED_SECTIONS       =
+ENABLED_SECTIONS  = YES
 
 # The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
 # initial value of a variable or macro / define can have for it to appear in the
@@ -704,21 +704,21 @@ MAX_INITIALIZER_LINES  = 30
 # list will mention the files that were used to generate the documentation.
 # The default value is: YES.
 
-SHOW_USED_FILES        = YES
+SHOW_USED_FILES = YES
 
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
 # will remove the Files entry from the Quick Index and from the Folder Tree View
 # (if specified).
 # The default value is: YES.
 
-SHOW_FILES             = YES
+SHOW_FILES = YES
 
 # Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
 # page. This will remove the Namespaces entry from the Quick Index and from the
 # Folder Tree View (if specified).
 # The default value is: YES.
 
-SHOW_NAMESPACES        = YES
+SHOW_NAMESPACES = YES
 
 # 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
@@ -728,7 +728,7 @@ SHOW_NAMESPACES        = YES
 # by doxygen. Whatever the program writes to standard output is used as the file
 # version. For an example see the documentation.
 
-FILE_VERSION_FILTER    =
+FILE_VERSION_FILTER =
 
 # The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
 # by doxygen. The layout file controls the global structure of the generated
@@ -829,7 +829,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../inc/ ../inc/Materials/ ../inc/Body/ ../inc/Particle/ ../inc/Mesh/ ../inc/Shape/ ../inc/Solver/
+INPUT  = ./inc/ ./inc/Materials/ ./inc/Body/ ./inc/Particle/ ./inc/Mesh/ ./inc/Shape/ ./inc/Solver/
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -838,7 +838,7 @@ INPUT                  = ../inc/ ../inc/Materials/ ../inc/Body/ ../inc/Particle/
 # possible encodings.
 # The default value is: UTF-8.
 
-INPUT_ENCODING         = UTF-8
+INPUT_ENCODING = UTF-8
 
 # If the value of the INPUT tag contains directories, you can use the
 # FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
@@ -908,7 +908,7 @@ FILE_PATTERNS          = *.c \
 # be searched for input files as well.
 # The default value is: NO.
 
-RECURSIVE              = NO
+RECURSIVE = NO
 
 # The EXCLUDE tag can be used to specify files and/or directories that should be
 # excluded from the INPUT source files. This way you can easily exclude a
@@ -1176,22 +1176,22 @@ IGNORE_PREFIX          =
 # If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
 # The default value is: YES.
 
-GENERATE_HTML          = YES
+GENERATE_HTML = YES
 
 # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
 # it.
 # The default directory is: html.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_OUTPUT            = docs
+HTML_OUTPUT  = docs
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
 # generated HTML page (for example: .htm, .php, .asp).
 # The default value is: .html.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FILE_EXTENSION    = .html
+HTML_FILE_EXTENSION  = .html
 
 # The HTML_HEADER tag can be used to specify a user-defined HTML header file for
 # each generated HTML page. If the tag is left blank doxygen will generate a
@@ -1246,7 +1246,7 @@ HTML_STYLESHEET        =
 # list). For an example see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  =
+HTML_EXTRA_STYLESHEET  = ./doxygen/custom.css
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
@@ -1267,7 +1267,7 @@ HTML_EXTRA_FILES       =
 # Minimum value: 0, maximum value: 359, default value: 220.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_COLORSTYLE_HUE    = 220
+HTML_COLORSTYLE_HUE = 210
 
 # The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
 # in the HTML output. For a value of 0 the output will use grayscales only. A
@@ -1737,15 +1737,15 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         =
+GENERATE_LATEX         = NO
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
 # it.
 # The default directory is: latex.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-LATEX_OUTPUT           = latex
+LATEX_OUTPUT =
 
 # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
 # invoked.

README.md

@@ -4,11 +4,13 @@
 [![CI](https://github.com/fabricix/MPM-Geomechanics/actions/workflows/c-cpp.yml/badge.svg)](https://github.com/fabricix/MPM-Geomechanics/actions/workflows/c-cpp.yml) 
 [![MSBuild](https://github.com/fabricix/MPM-Geomechanics/actions/workflows/msbuild.yml/badge.svg)](https://github.com/fabricix/MPM-Geomechanics/actions/workflows/msbuild.yml)
 
-## Motivation
+## Documentation
+
+See the documentation at [MPM-Geomechanics](https://fabricix.github.io/MPM-Geomechanics/).
 
-MPM-Geomechanics is a program that allows us to model the behavior of geo-materials, like soil and rock, when these materials are subjected to different initial and boundary conditions. Currently, the geo-materials are present in several areas of the society, like for example, in the slopes and excavation process in mining industry activities, or in the study of risk associated to naturals disasters.
+## Motivation
 
-This program uses the Material Point Method (MPM) to integrate the motion equation of continuum mechanics. In this method the motion equation is solved in an fixed mesh (Eulerian mesh) and the solution is interpolated to points that can move freely inside the mesh, carrying all the mechanical information like strain, stress, temperature, etc. The points allows us to transport all properties inside the mesh during the simulation (Lagrangian points).
+MPM-Geomechanics is a program that allows us to model the behavior of geo-materials, like soil and rock, when these materials are subjected to different initial and boundary conditions. Currently, the geo-materials are present in several areas of the society, like for example in the slopes and excavation process in mining industry activities, or in the study of risk associated to naturals disasters.
 
 The objective of this repository is to provide a platform for developing the MPM for the study of geomechanical problems involving large deformations and distortions.
 
@@ -44,25 +46,7 @@ The main features of the program in the actuality are:
 
 ## Documentation and Compilation
 
-To compile using make:
-
-```bash
-make -f make/makefile
-```
-Make sure you have installed OpenMP.
-
-To generate the code documentation using doxygen run: 
-
-```bash
-cd doxygen && doxygen
-```
-and the HTML documentation will be located in `/doxygen/html`.
-
-To generate the documentation in PDF, run the make command in `doxy/latex`.
-
-```bash
-cd /doxygen/latex && make
-```
+For generating documentation and compilation of the code please see the documentation at [MPM-Geomechanics](https://fabricix.github.io/MPM-Geomechanics/).
 
 ## Examples