[batch 1 of 100] developers documenation

docs/Doxyfile

@@ -833,7 +833,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = "README.md" "../src/vmc"  "../src/dmc" "../src/include"
+INPUT                  = "README.md" "../src/vmc"  "../src/dmc" "../src/module" "../src/parser"
 
 # 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
@@ -1202,15 +1202,15 @@ 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    = 0
 
 # 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
 # value of 255 will produce the most vivid colors.
 # Minimum value: 0, maximum value: 255, default value: 100.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_COLORSTYLE_SAT    = 100
+HTML_COLORSTYLE_SAT    = 0
 
 # The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
 # luminance component of the colors in the HTML output. Values below 100
@@ -1221,7 +1221,7 @@ HTML_COLORSTYLE_SAT    = 100
 # Minimum value: 40, maximum value: 240, default value: 80.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_COLORSTYLE_GAMMA  = 80
+HTML_COLORSTYLE_GAMMA  = 100
 
 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
 # page will contain the date and time when the page was generated. Setting this
@@ -1230,7 +1230,7 @@ HTML_COLORSTYLE_GAMMA  = 80
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_TIMESTAMP         = NO
+HTML_TIMESTAMP         = YES
 
 # If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
 # documentation will contain a main index with vertical navigation menus that
@@ -1241,15 +1241,15 @@ HTML_TIMESTAMP         = NO
 # The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_DYNAMIC_MENUS     = NO
+HTML_DYNAMIC_MENUS     = YES
 
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_DYNAMIC_SECTIONS  = NO
+HTML_DYNAMIC_SECTIONS  = YES
 
 # With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
 # shown in the various tree structured indices initially; the user can expand
@@ -1262,7 +1262,7 @@ HTML_DYNAMIC_SECTIONS  = NO
 # Minimum value: 0, maximum value: 9999, default value: 100.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_INDEX_NUM_ENTRIES = 100
+HTML_INDEX_NUM_ENTRIES = 1000
 
 # If the GENERATE_DOCSET tag is set to YES, additional index files will be
 # generated that can be used as input for Apple's Xcode 3 integrated development
@@ -1478,7 +1478,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
@@ -1666,7 +1666,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = YES
+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
@@ -2315,7 +2315,7 @@ UML_LIMIT_NUM_FIELDS   = 10
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-TEMPLATE_RELATIONS     = NO
+TEMPLATE_RELATIONS     = YES
 
 # If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
 # YES then doxygen will generate a graph for each documented file showing the
@@ -2357,7 +2357,7 @@ CALL_GRAPH             = YES
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALLER_GRAPH           = NO
+CALLER_GRAPH           = YES
 
 # If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
 # hierarchy of all classes instead of a textual one.
@@ -2388,7 +2388,7 @@ DIRECTORY_GRAPH        = YES
 # The default value is: png.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_IMAGE_FORMAT       = png
+DOT_IMAGE_FORMAT       = svg
 
 # If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
 # enable generation of interactive SVG images that allow zooming and panning.

src/vmc/array_utils.f90

@@ -1,3 +1,9 @@
+!> Utility module for array manipulation
+!> @author Viktor Azizi
+!> @author Alice Cuzzocrea
+!> @author Ravindra Shinde
+!> @author Nico Renaud
+!> @date 24/05/2022
 module array_utils
 
       use lapack_wrapper, only: lapack_matrix_vector,lapack_sort
@@ -14,8 +20,8 @@ module array_utils
 
 contains
 
+    !> Create an identity matrix
     pure function eye(m, n, alpha)
-        !> Create a matrix with ones in the diagonal and zero everywhere else
         !> \param m: number of rows
         !> \param n: number of colums
         !> \param alpha: optional diagonal value
@@ -53,6 +59,7 @@ pure function eye(m, n, alpha)
 
     end function eye
 
+    !> Create a diagnoal matrix from a vector
     pure function diag_mat(vec)
         real(dp), dimension(:), intent(in) :: vec
         real(dp), dimension(size(vec, 1), size(vec, 1)) :: diag_mat
@@ -65,18 +72,17 @@ pure function diag_mat(vec)
 
     end function diag_mat
 
+    !> compute the norm-2 of a vector
     pure function norm(vector)
-        !> compute the norm-2 of a vector
         real(dp), dimension(:), intent(in) :: vector
         real(dp) :: norm
 
         norm = sqrt(sum(vector**2.d0))
 
     end function norm
 
+    !> Concatenate two matrices
     subroutine concatenate(arr, brr)
-
-        !> Concatenate two matrices
         !> \param arr: first array
         !> \param brr: second array
         !>
@@ -106,8 +112,8 @@ subroutine concatenate(arr, brr)
 
     end subroutine concatenate
 
+    !> Generate a diagonal dominant square matrix of dimension m
     function generate_diagonal_dominant(m, sparsity, diag_val) result(arr)
-        !> Generate a diagonal dominant square matrix of dimension m
         !> \param m dimension of the matrix
         !> \param sparsity magnitude order of the off-diagonal values
 
@@ -135,8 +141,9 @@ function generate_diagonal_dominant(m, sparsity, diag_val) result(arr)
 
     end function generate_diagonal_dominant
 
+    !> return the diagonal of a matrix
     function diagonal(matrix)
-        !> return the diagonal of a matrix
+        !> \param matrix: input matrix
         real(dp), dimension(:, :), intent(in) :: matrix
         real(dp), dimension(size(matrix, 1)) :: diagonal
 
@@ -156,9 +163,8 @@ function diagonal(matrix)
 
     end function diagonal
 
+    !> Brief generates a diagonal preconditioner for .
     function initialize_subspace(diag, dim_sub, dim_base) result(precond)
-        !> Brief generates a diagonal preconditioner for .
-        !>
         !> return diagonal matrix
 
         ! input variable
@@ -183,10 +189,9 @@ function initialize_subspace(diag, dim_sub, dim_base) result(precond)
 
     end function initialize_subspace
 
+    !> Brief use modifed gram-schmidt orthogonalization on mat
+    !> Brief nstart is the index of the first vector to orthogonalize
     subroutine modified_gram_schmidt(mat, nstart)
-        !> Brief use modifed gram-schmidt orthogonalization on mat
-        !> Brief nstart is the index of the first vector to orthogonalize
-
         ! input
         real(dp), dimension(:, :), intent(inout) :: mat
         integer, optional, intent(in) :: nstart
@@ -217,8 +222,8 @@ subroutine modified_gram_schmidt(mat, nstart)
 
     end subroutine modified_gram_schmidt
 
+    !> Brief Search for a given index  in a vector
     function search_key(keys, i) result(k)
-        !> Brief Search for a given index  in a vector
         !> \param keys Vector of index
         !> \param i Index to search for
         !>
@@ -238,8 +243,8 @@ function search_key(keys, i) result(k)
 
     end function search_key
 
+    !> Write matrix to path_file
     subroutine write_matrix(path_file, mtx)
-        !> Write matrix to path_file
         character(len=*), intent(in) :: path_file
         real(dp), dimension(:, :), intent(in) :: mtx
         integer :: i, j
@@ -254,8 +259,8 @@ subroutine write_matrix(path_file, mtx)
 
     end subroutine write_matrix
 
+    !> Write vector to path_file
     subroutine write_vector(path_file, vector)
-        !> Write vector to path_file
         character(len=*), intent(in) :: path_file
         real(dp), dimension(:), intent(in) :: vector
         integer :: i
@@ -268,9 +273,9 @@ subroutine write_vector(path_file, vector)
 
     end subroutine write_vector
 
+    !> deallocate a matrix if allocated
     subroutine check_deallocate_matrix(mtx)
 
-        !> deallocate a matrix if allocated
         real(dp), dimension(:, :), allocatable, intent(inout) ::  mtx
 
         if (allocated(mtx)) then
@@ -279,9 +284,10 @@ subroutine check_deallocate_matrix(mtx)
 
     end subroutine check_deallocate_matrix
 
+    !> deallocate a vector if allocated
     subroutine check_deallocate_vector(vec)
 
-        !> deallocate a matrix if allocated
+
         real(dp), dimension(:), allocatable, intent(inout) ::  vec
 
         if (allocated(vec)) then
@@ -290,9 +296,9 @@ subroutine check_deallocate_vector(vec)
 
     end subroutine check_deallocate_vector
 
+    !> Returns the unique elements of a vector
+    !> Also returns the number of unique elements, their indices in the original vector.
     subroutine unique_elements(n, arr, res, count, frequency, ind)
-        !> Returns the unique elements of a vector
-        !> Also returns the number of unique elements, their indices in the original vector.
         !> \param[in] n: size of the vector
         !> \param[in] arr: vector to be processed
         !> \param[out] res: vector of unique elements
@@ -343,10 +349,9 @@ subroutine unique_elements(n, arr, res, count, frequency, ind)
 
     end subroutine unique_elements
 
-
+    !> Returns the unique elements of a vector
+    !> Also returns the number of unique elements, their indices in the original vector.
     subroutine unique_string_elements(n, arr, res, count)
-        !> Returns the unique elements of a vector
-        !> Also returns the number of unique elements, their indices in the original vector.
         !> \param[in] n: size of the vector
         !> \param[in] arr: vector to be processed
         !> \param[out] res: vector of unique elements
@@ -399,8 +404,15 @@ subroutine unique_string_elements(n, arr, res, count)
     end subroutine unique_string_elements
 
 
-
+    !> find "indices", the list of unique numbers in "list"
+    !> and return the sorted unique numbers in "sorted"
     subroutine sortedunique(list, n, indices, sorted)
+        !> \param[in] list: input list
+        !> \param[in] n: size of the list
+        !> \param[out] indices: indices of the unique elements
+        !> \param[out] sorted: sorted unique elements
+        !> @author: Ravindra Shinde
+        !> @date: 24/05/2022
         implicit none
         !   find "indices", the list of unique numbers in "list"
 

src/vmc/slm.f90

@@ -1,3 +1,7 @@
+!> Compute the zero-th, first, second, and third derivatives of a Ylm function
+!> @author Claudia Filippi
+!> @author Ravindra Shinde
+!> @date 2022-02-11
 module slm_mod
 contains
 subroutine slm(l,rvec,r2,y,dy,ddy,ddy_lap,dlapy,ider)