Merge commit '19224455c5a589343b351bab3ae48351a9c1b807'

MD-CWI · Jun 2, 2024 · e2eed95 · e2eed95
2 parents 01af4dd + 1922445
commit e2eed95
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Showing 22 changed files with 39 additions and 231 deletions.
diff --git a/afivo/Doxyfile b/afivo/Doxyfile
@@ -684,7 +684,7 @@ FILE_VERSION_FILTER =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE = documentation/my_customlayout.xml
+LAYOUT_FILE =
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -827,7 +827,7 @@ EXCLUDE_SYMLINKS = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS = */m_aX_*.f90 */*_Xd.f90
+EXCLUDE_PATTERNS =
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -844,7 +844,7 @@ EXCLUDE_SYMBOLS =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH = examples
+EXAMPLE_PATH = examples src
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
@@ -938,7 +938,7 @@ 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.

diff --git a/afivo/Makefile b/afivo/Makefile
@@ -1,4 +1,4 @@
-SRC_DIRS := lib_1d lib_2d lib_3d examples tests
+SRC_DIRS := lib_1d lib_2d lib_3d examples tests tools
 
 # Directories with altered names (useful for cleaning)
 CLEANSRC := $(SRC_DIRS:%=clean-%)

diff --git a/afivo/documentation/my_customlayout.xml b/afivo/documentation/my_customlayout.xml
diff --git a/afivo/documentation/time_integration.md b/afivo/documentation/time_integration.md
@@ -6,9 +6,7 @@ The `m_af_advance` module can be used to perform time integration.
 
 Currently, the following explicit methods are included:
 
-* [Forward Euler](https://en.wikipedia.org/wiki/Euler_method) (`af_forward_euler`)
-* [Midpoint method](https://en.wikipedia.org/wiki/Midpoint_method) (`af_midpoint_method`)
-* [Heun's method](https://en.wikipedia.org/wiki/Heun%27s_method) (`af_heuns_method`)
+\snippet m_af_advance.f90 time_integration_schemes
 
 New integrators can be added relatively easily by modifying the `af_advance` routine.
 

diff --git a/afivo/src/m_af_advance.f90 b/afivo/src/m_af_advance.f90
@@ -1,12 +1,14 @@
-#include "cpp_macros.h"
 !> Module with methods to perform time integration
 module m_af_advance
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none
  private
 
  integer, parameter, public :: af_num_integrators = 8
+
+ !< [time_integration_schemes]
  !> Forward Euler method
  integer, parameter, public :: af_forward_euler = 1
  !> Heun's method (AKA modified Euler's method, explicit trapezoidal rule), CFL
@@ -27,6 +29,7 @@ module m_af_advance
  !> Classic 4th order Runge Kutta method, see e.g.
  !> https://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods
  integer, parameter, public :: af_rk4_method = 8
+ !< [time_integration_schemes]
 
  character(len=af_nlen), public :: af_integrator_names(af_num_integrators) = &
  [character(len=af_nlen) :: "forward_euler", "heuns_method", &

diff --git a/afivo/src/m_af_core.f90 b/afivo/src/m_af_core.f90
@@ -1,7 +1,7 @@
-#include "cpp_macros.h"
 !> This module contains the core routines of Afivo, namely those that deal with
 !> initializing and changing the quadtree/octree mesh.
 module m_af_core
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none

diff --git a/afivo/src/m_af_flux_schemes.f90 b/afivo/src/m_af_flux_schemes.f90
@@ -1,7 +1,7 @@
-#include "cpp_macros.h"
 !> Module containing a couple flux schemes for solving hyperbolic problems
 !> explicitly, as well as handling diffusion explicitly.
 module m_af_flux_schemes
+#include "cpp_macros.h"
  use m_af_types
  use m_af_limiters
 

diff --git a/afivo/src/m_af_ghostcell.f90 b/afivo/src/m_af_ghostcell.f90
@@ -1,7 +1,7 @@
-#include "cpp_macros.h"
 !> This module contains routines related to the filling of ghost cells. Note that
 !> corner ghost cells are not used in Afivo.
 module m_af_ghostcell
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none

diff --git a/afivo/src/m_af_interp.f90 b/afivo/src/m_af_interp.f90
@@ -1,8 +1,8 @@
-#include "cpp_macros.h"
 !> This module contains routines related to interpolation, which can interpolate
 !> 'to' the grid and 'from' the grid (useful for e.g. particle simulations). The
 !> interpolation for meshes is called prolongation, see m_aX_prolong.
 module m_af_interp
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none

diff --git a/afivo/src/m_af_limiters.f90 b/afivo/src/m_af_limiters.f90
@@ -1,6 +1,6 @@
-#include "cpp_macros.h"
 !> Module containing slope limiters
 module m_af_limiters
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none

diff --git a/afivo/src/m_af_multigrid.f90 b/afivo/src/m_af_multigrid.f90
@@ -1,8 +1,8 @@
-#include "../src/cpp_macros.h"
 !> This module contains the geometric multigrid routines that come with Afivo
 !>
 !> @todo How to use box tag with different types of operators?
 module m_af_multigrid
+#include "../src/cpp_macros.h"
  use m_af_types
  use m_af_stencil
  use m_af_ghostcell

diff --git a/afivo/src/m_af_output.f90 b/afivo/src/m_af_output.f90
@@ -1,8 +1,7 @@
-#include "cpp_macros.h"
 !> This module contains routines for writing output files with Afivo. The Silo
 !> format should probably be used for larger files, especially in 3D.
 module m_af_output
-
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none

diff --git a/afivo/src/m_af_particles.f90 b/afivo/src/m_af_particles.f90
@@ -1,4 +1,3 @@
-#include "cpp_macros.h"
 !> This module contains routines related to , which can interpolate
 !> 'to' the grid and 'from' the grid (useful for e.g. particle simulations). The
 !> interpolation for meshes is called prolongation, see m_aX_prolong.
@@ -7,6 +6,7 @@
 !> two advantages: first, data does not need to be copied, saving memory.
 !> Second, the particle id can be cached in the particle's data structured.
 module m_af_particles
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none

diff --git a/afivo/src/m_af_prolong.f90 b/afivo/src/m_af_prolong.f90
@@ -1,7 +1,7 @@
-#include "cpp_macros.h"
 !> This module contains the routines related to prolongation: going from
 !> coarse to fine variables.
 module m_af_prolong
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none

diff --git a/afivo/src/m_af_restrict.f90 b/afivo/src/m_af_restrict.f90
@@ -1,8 +1,7 @@
-#include "cpp_macros.h"
 !> This module contains routines for restriction: going from fine to coarse
 !> variables.
 module m_af_restrict
-
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none

diff --git a/afivo/src/m_af_stencil.f90 b/afivo/src/m_af_stencil.f90
@@ -1,6 +1,6 @@
-#include "cpp_macros.h"
 !> This module contains functionality for dealing with numerical stencils
 module m_af_stencil
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none

diff --git a/afivo/src/m_af_surface.f90 b/afivo/src/m_af_surface.f90
@@ -1,8 +1,8 @@
-#include "cpp_macros.h"
 !> This module contains routines for including flat surfaces between changes in
 !> epsilon (some material property). This can for example be used to include
 !> flat dielectrics in electrostatic computations.
 module m_af_surface
+#include "cpp_macros.h"
  use m_af_types
 
  implicit none

diff --git a/afivo/src/m_af_types.f90 b/afivo/src/m_af_types.f90
@@ -1,7 +1,7 @@
-#include "cpp_macros.h"
 !> This module contains the basic types and constants that are used in the
 !> NDIM-dimensional version of Afivo, together with some basic routines.
 module m_af_types
+#include "cpp_macros.h"
  use iso_c_binding, only: c_ptr
 
  implicit none