Merge branch 'fast-list-append' into 'development'

Performance improvements when storing/retrieving data from YAML

Closes #180

See merge request damask/DAMASK!561

src/C_routines.c

@@ -88,7 +88,7 @@ void inflate_c(const uLong *s_deflated, const uLong *s_inflated, const Byte defl
 #ifdef FYAML
 void to_flow_c(char **flow, int* length_flow, const char *mixed){
   struct fy_document *fyd = NULL;
-  enum fy_emitter_cfg_flags emit_flags = FYECF_MODE_FLOW_ONELINE | FYECF_STRIP_LABELS | FYECF_STRIP_DOC;
+  enum fy_emitter_cfg_flags emit_flags = FYECF_MODE_FLOW_ONELINE | FYECF_STRIP_LABELS | FYECF_STRIP_TAGS |FYECF_STRIP_DOC;
 
   fyd = fy_document_build_from_string(NULL, mixed, -1);
   if (!fyd) {

src/YAML_parse.f90

@@ -83,7 +83,7 @@ recursive function parse_flow(YAML_flow) result(node)
     s, &                                                                                            ! start position of dictionary or list
     d                                                                                               ! position of key: value separator (':')
 
-  flow_string = trim(adjustl(YAML_flow(:)))
+  flow_string = trim(adjustl(YAML_flow))
   if (len_trim(flow_string) == 0) then
     node => emptyDict
     return
@@ -168,8 +168,11 @@ logical function quotedString(line)
 
   character(len=*), intent(in) :: line
 
+
   quotedString = .false.
 
+  if (len(line) == 0) return
+
   if (scan(line(:1),IO_QUOTES) == 1) then
     quotedString = .true.
     if(line(len(line):len(line)) /= line(:1)) call IO_error(710,ext_msg=line)
@@ -198,7 +201,7 @@ function to_flow(mixed) result(flow)
   block
     character(len=strlen,kind=c_char), pointer :: s
     call c_f_pointer(str_ptr,s)
-    flow = s
+    flow = s(:len(s)-1)
   end block
 
   call free_C(str_ptr)

src/YAML_types.f90

@@ -119,7 +119,8 @@ module YAML_types
 
   type, extends(tNode), public :: tList
 
-    class(tItem), pointer  :: first => NULL()
+    class(tItem), pointer :: first => NULL(), &
+                             last => NULL()
 
     contains
     procedure :: asFormattedString => tList_asFormattedString
@@ -144,7 +145,7 @@ module YAML_types
   end type tDict
 
 
-  type :: tItem
+  type, public :: tItem
     character(len=:), allocatable :: key
     class(tNode),     pointer     :: node => NULL()
     class(tItem),     pointer     :: next => NULL()
@@ -1348,15 +1349,13 @@ subroutine tList_append(self,node)
   type(tItem), pointer :: item
 
   if (.not. associated(self%first)) then
-    allocate(self%first)
+    allocate(item)
-    item => self%first
+    self%first => item
+    self%last => item
   else
-    item => self%first
+    allocate(self%last%next)
-    do while (associated(item%next))
+    item => self%last%next
-      item => item%next
+    self%last => item
-    enddo
-    allocate(item%next)
-    item => item%next
   end if
 
   item%node => node

src/material.f90

@@ -91,9 +91,13 @@ subroutine parse()
                            homogenizations, &
                            homogenization
 
+  class(tItem), pointer :: item
   integer, dimension(:), allocatable :: &
     counterPhase, &
-    counterHomogenization
+    counterHomogenization, &
+    ho_of
+  integer, dimension(:,:), allocatable :: ph_of
+  real(pReal), dimension(:,:), allocatable :: v_of
 
   real(pReal) :: v
   integer :: &
@@ -102,11 +106,14 @@ subroutine parse()
     co, ce, &
     ma
 
+
   materials       => config_material%get('material')
   phases          => config_material%get('phase')
   homogenizations => config_material%get('homogenization')
 
-  call sanityCheck(materials, homogenizations)
+
+  if (maxval(discretization_materialAt) > materials%length) &
+    call IO_error(155,ext_msg='More materials requested than found in material.yaml')
 
 #if defined (__GFORTRAN__)
   material_name_phase          = getKeys(phases)
@@ -123,6 +130,49 @@ subroutine parse()
   end do
   homogenization_maxNconstituents = maxval(homogenization_Nconstituents)
 
+  allocate(material_v(homogenization_maxNconstituents,discretization_Ncells),source=0.0_pReal)
+
+  allocate(material_O_0(materials%length))
+  allocate(material_F_i_0(materials%length))
+
+  allocate(ho_of(materials%length))
+  allocate(ph_of(materials%length,homogenization_maxNconstituents),source=-1)
+  allocate( v_of(materials%length,homogenization_maxNconstituents),source=0.0_pReal)
+
+  ! parse YAML structure
+  select type(materials)
+
+    class is(tList)
+
+      item => materials%first
+      do ma = 1, materials%length
+        material => item%node
+        ho_of(ma) = homogenizations%getIndex(material%get_asString('homogenization'))
+        constituents => material%get('constituents')
+
+        homogenization => homogenizations%get(ho_of(ma))
+        if (constituents%length /= homogenization%get_asInt('N_constituents')) call IO_error(148)
+
+        allocate(material_O_0(ma)%data(constituents%length))
+        allocate(material_F_i_0(ma)%data(1:3,1:3,constituents%length))
+
+        do co = 1, constituents%length
+          constituent => constituents%get(co)
+           v_of(ma,co) = constituent%get_asFloat('v')
+          ph_of(ma,co) = phases%getIndex(constituent%get_asString('phase'))
+
+          call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4))
+          material_F_i_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('F_i',defaultVal=math_I3,requiredShape=[3,3])
+
+        end do
+        if (dNeq(sum(v_of(ma,:)),1.0_pReal,1.e-9_pReal)) call IO_error(153,ext_msg='constituent')
+
+        item => item%next
+      end do
+
+  end select
+
+
   allocate(counterPhase(phases%length),source=0)
   allocate(counterHomogenization(homogenizations%length),source=0)
 
@@ -132,12 +182,13 @@ subroutine parse()
   allocate(material_phaseID(homogenization_maxNconstituents,discretization_Ncells),source=0)
   allocate(material_phaseEntry(homogenization_maxNconstituents,discretization_Ncells),source=0)
 
-  allocate(material_v(homogenization_maxNconstituents,discretization_Ncells),source=0.0_pReal)
 
+  ! build mappings
   do el = 1, discretization_Nelems
-    material => materials%get(discretization_materialAt(el))
 
-    ho = homogenizations%getIndex(material%get_asString('homogenization'))
+    ma = discretization_materialAt(el)
+    ho = ho_of(ma)
+
     do ip = 1, discretization_nIPs
       ce = (el-1)*discretization_nIPs + ip
       material_homogenizationID(ce) = ho
@@ -145,13 +196,11 @@ subroutine parse()
       material_homogenizationEntry(ce) = counterHomogenization(ho)
     end do
 
-    constituents => material%get('constituents')
+    do co = 1, size(ph_of(ma,:)>0)
-    do co = 1, constituents%length
-      constituent => constituents%get(co)
 
-      v = constituent%get_asFloat('v')
+      v  =  v_of(ma,co)
+      ph = ph_of(ma,co)
 
-      ph = phases%getIndex(constituent%get_asString('phase'))
       do ip = 1, discretization_nIPs
         ce = (el-1)*discretization_nIPs + ip
         material_phaseID(co,ce) = ph
@@ -161,54 +210,11 @@ subroutine parse()
       end do
 
     end do
-    if (dNeq(sum(material_v(1:constituents%length,ce)),1.0_pReal,1.e-9_pReal)) &
-      call IO_error(153,ext_msg='constituent')
-
-  end do
-
-  allocate(material_O_0(materials%length))
-  allocate(material_F_i_0(materials%length))
-
-  do ma = 1, materials%length
-    material     => materials%get(ma)
-    constituents => material%get('constituents')
-    allocate(material_O_0(ma)%data(constituents%length))
-    allocate(material_F_i_0(ma)%data(1:3,1:3,constituents%length))
-    do co = 1, constituents%length
-      constituent => constituents%get(co)
-      call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4))
-      material_F_i_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('F_i',defaultVal=math_I3,requiredShape=[3,3])
-    enddo
   end do
 
 end subroutine parse
 
 
-!--------------------------------------------------------------------------------------------------
-!> @brief Check if material.yaml is consistent and contains sufficient # of materials
-!--------------------------------------------------------------------------------------------------
-subroutine sanityCheck(materials,homogenizations)
-
-  class(tNode), intent(in) :: materials, &
-                              homogenizations
-
-  class(tNode), pointer :: material, &
-                           homogenization, &
-                           constituents
-  integer :: m
-
-  if (maxval(discretization_materialAt) > materials%length) &
-    call IO_error(155,ext_msg='More materials requested than found in material.yaml')
-
-  do m = 1, materials%length
-    material => materials%get(m)
-    constituents   => material%get('constituents')
-    homogenization => homogenizations%get(material%get_asString('homogenization'))
-    if (constituents%length /= homogenization%get_asInt('N_constituents')) call IO_error(148)
-  end do
-
-end subroutine sanityCheck
-
 #if defined (__GFORTRAN__)
 !--------------------------------------------------------------------------------------------------
 !> @brief %keys() is broken on gfortran