Mark all subnodes processed when using readSpeciesList (dftbplus#1559)

src/dftbp/dftbplus/specieslist.F90

@@ -14,7 +14,7 @@ module dftbp_dftbplus_specieslist
   use dftbp_common_unitconversion, only : TUnit
   use dftbp_extlibs_xmlf90, only : char, fnode, string
   use dftbp_io_hsdutils, only : getChild, getChildValue
-  use dftbp_io_hsdutils2, only : convertUnitHsd
+  use dftbp_io_hsdutils2, only : convertUnitHsd, setProcessed
   implicit none
 
   private
@@ -32,26 +32,30 @@ module dftbp_dftbplus_specieslist
 
 
   !> Read a list of real valued species data
-  subroutine readSpeciesListReal(node, speciesNames, array, default, units)
+  subroutine readSpeciesListReal(node, speciesNames, array, default, units, markAllProcessed)
 
     !> Node to process
     type(fnode), pointer :: node
 
-    !> Data array to read
-    real(dp), intent(inout) :: array(:)
-
     !> Names of all species
     character(len=*), intent(in) :: speciesNames(:)
 
+    !> Data array to read
+    real(dp), intent(inout) :: array(:)
+
     !> Optional default values of data array to be read
     real(dp), intent(in), optional :: default(:)
 
     !> Conversion factor
     type(TUnit), intent(in), optional :: units(:)
 
+    !> Whether all unread subnodes should also be marked as processed (default: .true.)
+    logical, optional, intent(in) :: markAllProcessed
+
     type(fnode), pointer :: child
     type(string) :: modifier
     integer :: iSp
+    logical :: markAllProcessed_
 
     if (present(default)) then
       if (present(units)) then
@@ -79,25 +83,33 @@ subroutine readSpeciesListReal(node, speciesNames, array, default, units)
       end if
     end if
 
+    markAllProcessed_ = .true.
+    if (present(markAllProcessed)) markAllProcessed_ = markAllProcessed
+    if (markAllProcessed_) call setProcessed(node, recursive=.true.)
+
   end subroutine readSpeciesListReal
 
 
   !> Read a list of integer valued species data
-  subroutine readSpeciesListInt(node, speciesNames, array, default)
+  subroutine readSpeciesListInt(node, speciesNames, array, default, markAllProcessed)
 
     !> Node to process
     type(fnode), pointer :: node
 
-    !> Data array to read
-    integer, intent(out) :: array(:)
-
     !> Names of all species
     character(len=*), intent(in) :: speciesNames(:)
 
     !> Data array to read
-    integer, intent(in), optional :: default(:)
+    integer, intent(out) :: array(:)
+
+    !> Data array to read
+    integer, optional, intent(in) :: default(:)
+
+    !> Whether all unread subnodes should also be marked as processed (default: .true.)
+    logical, optional, intent(in) :: markAllProcessed
 
     integer :: iSp
+    logical :: markAllProcessed_
 
     if (present(default)) then
       do iSp = 1, size(speciesNames)
@@ -110,7 +122,10 @@ subroutine readSpeciesListInt(node, speciesNames, array, default)
       end do
     end if
 
-  end subroutine readSpeciesListInt
+    markAllProcessed_ = .true.
+    if (present(markAllProcessed)) markAllProcessed_ = markAllProcessed
+    if (markAllProcessed_) call setProcessed(node, recursive=.true.)
 
+  end subroutine readSpeciesListInt
 
 end module dftbp_dftbplus_specieslist

src/dftbp/io/hsdutils2.F90

@@ -16,7 +16,8 @@ module dftbp_io_hsdutils2
   use dftbp_common_unitconversion, only : TUnit, unitConvStat => statusCodes, convertUnit
   use dftbp_extlibs_xmlf90, only : fnode, fnodeList, string, trim, len, assignment(=), parsefile,&
       & getLength, item, char, removeAttribute, getAttribute, setAttribute, setTagName,&
-      & normalize, append_to_string, destroyNodeList, removeAttribute, getItem1
+      & normalize, append_to_string, destroyNodeList, removeAttribute, getItem1, getFirstChild,&
+      & getNextSibling
   use dftbp_io_charmanip, only : newline, tolower, i2c
   use dftbp_io_hsdparser, only : attrName, attrModifier
   use dftbp_io_hsdutils, only : attrProcessed, getChild, setChildValue, detailedError,&
@@ -30,7 +31,7 @@ module dftbp_io_hsdutils2
   public :: getUnprocessedNodes, warnUnprocessedNodes
   public :: readHSDAsXML
   public :: getNodeName2, setNodeName, removeModifier, splitModifier
-  public :: setUnprocessed, getDescendant
+  public :: setUnprocessed, getDescendant, setProcessed
   public :: convertUnitHsd
   public :: renameChildren
 
@@ -67,6 +68,40 @@ subroutine setUnprocessed(node)
   end subroutine setUnprocessed
 
 
+  !> Sets the processed flag on a node (and eventually on all its children)
+  recursive subroutine setProcessed(node, recursive)
+
+    !> The node to process
+    type(fnode), pointer, intent(in) :: node
+
+    !> Whether also all subnodes should be recursively included
+    logical, optional, intent(in) :: recursive
+
+    if (.not. associated(node)) return
+    call setAttribute(node, attrProcessed, "")
+    if (present(recursive)) then
+      if (recursive) call setChildrenProcessed_(node)
+    end if
+
+  contains
+
+    recursive subroutine setChildrenProcessed_(node)
+      type(fnode), pointer, intent(in) :: node
+
+      type(fnode), pointer :: child
+
+      child => getFirstChild(node)
+      do while (associated(child))
+        call setAttribute(node, attrProcessed, "")
+        call setChildrenProcessed_(child)
+        child => getNextSibling(child)
+      end do
+
+    end subroutine setChildrenProcessed_
+
+  end subroutine setProcessed
+
+
   !> Prints a warning message about unprocessed nodes
 
   subroutine getUnprocessedNodes(node, nodeList)