Merge pull request #75 from OpenSEMBA/dev

Foxes bug with intel parsing files with many elements

Author: lmdiazangulo

CMakeLists.txt

@@ -116,6 +116,8 @@ if (SEMBA_FDTD_MAIN_LIB)
 		"src_main_pub/timestepping.F90"
 		"src_main_pub/observation.F90"
 		"src_main_pub/vtk.F90"
+		"src_main_pub/xdmf.F90"
+		"src_main_pub/xdmf_h5.F90"
 		"src_wires_pub/wires.F90"
 		"src_wires_pub/wires_mtln.F90"
 	)
@@ -140,13 +142,6 @@ add_definitions(
 -DCompileWithInt2 
 -DCompileWithReal4 
 -DCompileWithOpenMP 
--DCompileWithAnisotropic 
--DCompileWithEDispersives
--DCompileWithNF2FF
--DCompileWithNodalSources
--DCompileWithDMMA
--DCompileWithSGBC
--DCompileWithWires
 )
 
 

doc/smbjson.md

@@ -634,15 +634,15 @@ If not `magnitudeFile` is specified and only one `source` is defined, the `magni
 
 Probes of type `movie` record a vector field in a volume region indicated by `elementIds`. `[field]` can be `electric`, `magnetic`, or `currentDensity`; defaults to `electric`.
 `currentDensity` will store only the surface density currents on `pec` or lossy surfaces.
-The stored values can be selected using `[components]`, which stores an array of the following labels `x`, `y`, `z`, or `magnitude`; if no components are specified, defaults to `magnitude`.
+The stored values can be selected using the `[component]` entry, which stores one of the following labels `x`, `y`, `z`, or `magnitude`; if no component is specified, defaults to `magnitude`.
 
 An example follows:
 ```json
 {
     "name": "electric_field_movie",
     "type": "movie",
     "field": "electric",
-    "components": ["x"],
+    "component": "x",
     "elementIds": [4]
 }
 ```

src_json_parser/CMakeLists.txt

@@ -13,7 +13,7 @@ add_library (jsonfortran
 )
 
 add_library(smbjson 
-	"labels_mod.F90"
+	"smbjson_labels.F90"
 	"cells.F90"
 	"smbjson.F90"
 	"idchildtable.F90"

src_json_parser/idchildtable.F90

@@ -2,8 +2,8 @@ module idchildtable_mod
 
 #ifdef CompileWithSMBJSON    
    use json_module
+   use smbjson_labels_mod, only: J_ID
    use fhash, only: fhash_tbl_t, key=>fhash_key
-   use labels_mod
    use parser_tools_mod, only: json_value_ptr
 
    type :: IdChildTable_t
@@ -29,10 +29,13 @@ function ctor(core, root, path) result(res)
       integer :: id
       integer :: i
       logical :: found
+      integer :: numberOfEntries
 
       call core%get(root, path, jentries, found)
       if (.not. found) return
-      do i = 1, core%count(jentries)
+      numberOfEntries = core%count(jentries)
+      call res%idToChilds%allocate(10*numberOfEntries)
+      do i = 1, numberOfEntries
          call core%get_child(jentries, i, jentry)
          call core%get(jentry, J_ID, id)
          call res%idToChilds%set(key(id), json_value_ptr(jentry))

src_json_parser/mesh.F90

@@ -40,10 +40,10 @@ module mesh_mod
       procedure :: checkId => mesh_checkId
 
       procedure :: addElement => mesh_addElement
+      procedure :: addCellRegion  => mesh_addCellRegion
+      
       procedure :: getNode => mesh_getNode
       procedure :: getPolyline => mesh_getPolyline
-      
-      procedure :: addCellRegion  => mesh_addCellRegion
       procedure :: getCellRegion  => mesh_getCellRegion
       procedure :: getCellRegions => mesh_getCellRegions
 
@@ -54,6 +54,7 @@ module mesh_mod
 
       procedure :: printCoordHashInfo => mesh_printCoordHashInfo
       procedure :: allocateCoordinates => mesh_allocateCoordinates
+      procedure :: allocateElements => mesh_allocateElements
    end type
 
 
@@ -65,6 +66,13 @@ subroutine mesh_allocateCoordinates(this, buck)
       integer :: buck
       call this%coordinates%allocate(buck)
    end subroutine
+   
+   subroutine mesh_allocateElements(this, buck)
+      class(mesh_t) :: this
+      integer :: buck
+      call this%elements%allocate(buck)
+   end subroutine
+
 
    subroutine mesh_printCoordHashInfo(this)
       class(mesh_t) :: this
@@ -193,12 +201,26 @@ function mesh_getCellRegions(this, ids) result (res)
       integer, dimension(:), intent(in) :: ids
       type(cell_region_t) :: cR
       logical :: found
-      integer :: i
+      integer :: i, j
+      integer :: numberOfCellRegions
 
-      allocate(res(0))
+      ! Precounts
+      numberOfCellRegions = 0
       do i = 1, size(ids)
          cR = this%getCellRegion(ids(i), found)
-         if (found) res = [res, cR]
+         if (found) then
+             numberOfCellRegions = numberOfCellRegions + 1
+         end if
+      end do     
+      
+      allocate(res(numberOfCellRegions))
+      j = 1
+      do i = 1, size(ids)
+         cR = this%getCellRegion(ids(i), found)
+         if (found) then
+             res(j) = cR
+             j = j + 1
+         end if
       end do
 
    end function

src_json_parser/parser_tools.F90

@@ -1,7 +1,6 @@
 module parser_tools_mod
 
 #ifdef CompileWithSMBJSON
-   use labels_mod
    use mesh_mod
    use cells_mod
    use json_module

src_json_parser/smbjson.F90

@@ -4,7 +4,7 @@ module smbjson
    use NFDETypes
 
    use NFDETypes_extension
-   use labels_mod
+   use smbjson_labels_mod
    use mesh_mod
    use parser_tools_mod
    use idchildtable_mod
@@ -30,7 +30,6 @@ module smbjson
 
    contains
       procedure :: readProblemDescription
-      procedure :: initializeJson
 
       ! private
       procedure :: readGeneral
@@ -93,112 +92,96 @@ function parser_ctor(filename) result(res)
       type(parser_t) :: res
       character(len=*), intent(in) :: filename
       res%filename = filename
-   end function
-
-   subroutine initializeJson(this)
-      class(parser_t) :: this
-      integer :: stat
-
-      allocate(this%jsonfile)
-      call this%jsonfile%initialize()
-      if (this%jsonfile%failed()) then
-         call this%jsonfile%print_error_message(error_unit)
+      
+      allocate(res%jsonfile)
+      call res%jsonfile%initialize()
+      if (res%jsonfile%failed()) then
+         call res%jsonfile%print_error_message(error_unit)
          return
       end if
 
-      call this%jsonfile%load(filename = this%filename)
-      if (this%jsonfile%failed()) then
-         call this%jsonfile%print_error_message(error_unit)
+      call res%jsonfile%load(filename = res%filename)
+      if (res%jsonfile%failed()) then
+         call res%jsonfile%print_error_message(error_unit)
          return
       end if
 
-      allocate(this%core)
-      call this%jsonfile%get_core(this%core)
-      call this%jsonfile%get('.', this%root)
-   end subroutine
+      allocate(res%core)
+      call res%jsonfile%get_core(res%core)
+      call res%jsonfile%get('.', res%root)
+   end function
 
    function readProblemDescription(this) result (res)
       class(parser_t) :: this
       type(Parseador) :: res
       integer :: stat 
 
-      allocate(this%jsonfile)
-      call this%jsonfile%initialize()
-      if (this%jsonfile%failed()) then
-         call this%jsonfile%print_error_message(error_unit)
-         return
-      end if
-
-      call this%jsonfile%load(filename = this%filename)
-      if (this%jsonfile%failed()) then
-         call this%jsonfile%print_error_message(error_unit)
-         return
-      end if
-
-      allocate(this%core)
-      call this%jsonfile%get_core(this%core)
-      call this%jsonfile%get('.', this%root)
-
       this%mesh = this%readMesh()
       this%matTable = IdChildTable_t(this%core, this%root, J_MATERIALS)
-
+      
       call initializeProblemDescription(res)
-
+      
       ! Basics
       res%general = this%readGeneral()
       res%matriz = this%readMediaMatrix()
       res%despl = this%readGrid()
       res%front = this%readBoundary()
-
+      
       ! Materials
       res%pecRegs = this%readPECRegions()
       res%pmcRegs = this%readPMCRegions()
-
+      
       ! Sources
       res%plnSrc = this%readPlanewaves()
       res%nodSrc = this%readNodalSources()
-
+      
       ! Probes
       res%oldSonda = this%readProbes()
       res%sonda = this%readMoreProbes()
       res%BloquePrb = this%readBlockProbes()
       res%VolPrb = this%readVolumicProbes()
-
+      
       ! Thin elements
       res%tWires = this%readThinWires()
       res%mtln = this%readMTLN(res%despl)
 
-      ! Cleanup
-      call this%core%destroy()
-      call this%jsonfile%destroy()
-      nullify(this%root)
+      !! Cleanup
+      !call this%core%destroy()
+      !call this%jsonfile%destroy()
+      !nullify(this%root)
 
    end function
 
    function readMesh(this) result(res)
       class(parser_t) :: this
       type(Mesh_t) :: res
-      type(json_value), pointer :: jcs, jc
-      integer :: id, i
-      real, dimension(:), allocatable :: pos
-      type(coordinate_t) :: c
-      integer :: stat
-      logical :: found
-
-      call this%core%get(this%root, J_MESH//'.'//J_COORDINATES, jcs, found=found)
-      if (found) then
-         call res%allocateCoordinates(10*this%core%count(jcs))
-         do i = 1, this%core%count(jcs)
-            call this%core%get_child(jcs, i, jc)
-            call this%core%get(jc, J_ID, id)
-            call this%core%get(jc, J_COORDINATE_POS, pos)
-            c%position = pos
-            call res%addCoordinate(id, c)
-         end do
-      end if
+      call addCoordinates(res)
       call addElements(res)
 
    contains
+      subroutine addCoordinates(mesh)
+          type(mesh_t), intent(inout) :: mesh
+          type(json_value), pointer :: jcs, jc
+          integer :: id, i
+          real, dimension(:), allocatable :: pos
+          type(coordinate_t) :: c
+          integer :: numberOfCoordinates 
+          logical :: found
+          
+          call this%core%get(this%root, J_MESH//'.'//J_COORDINATES, jcs, found=found)
+          if (found) then
+             numberOfCoordinates = this%core%count(jcs)
+             call res%allocateCoordinates(10*numberOfCoordinates)
+             do i = 1, numberOfCoordinates
+                call this%core%get_child(jcs, i, jc)
+                call this%core%get(jc, J_ID, id)
+                call this%core%get(jc, J_COORDINATE_POS, pos)
+                c%position = pos
+                call mesh%addCoordinate(id, c)
+             end do
+          end if
+      end subroutine
+   
       subroutine addElements(mesh)
          type(mesh_t), intent(inout) :: mesh
          character (len=:), allocatable :: elementType
@@ -207,10 +190,15 @@ subroutine addElements(mesh)
          type(node_t) :: node
          type(polyline_t) :: polyline
          integer, dimension(:), allocatable :: coordIds
+         integer :: numberOfElements
          logical :: found
+         
          call this%core%get(this%root, J_MESH//'.'//J_ELEMENTS, jes, found=found)
+         numberOfElements = this%core%count(jes)
+         call res%allocateElements(10*numberOfElements)
+             
          if (found) then
-            do i = 1, this%core%count(jes)
+            do i = 1, numberOfElements
                call this%core%get_child(jes, i, je)
                call this%core%get(je, J_ID, id)
                call this%core%get(je, J_TYPE, elementType)
@@ -985,19 +973,13 @@ function readVolProbe(p) result(res)
          cs = cellIntervalsToCoords(cRs(1)%intervals)
 
          fieldType = this%getStrAt(p, J_FIELD, default=J_FIELD_ELECTRIC)
-         call this%core%get(p, J_PR_MOVIE_COMPONENTS, compsPtr, found=componentsFound)
+         call this%core%get(p, J_PR_MOVIE_COMPONENT, compsPtr, found=componentsFound)
+         allocate(res%cordinates(1))
          if (componentsFound) then
-            numberOfComponents = this%core%count(compsPtr)
-            allocate(res%cordinates(numberOfComponents))
-            do i = 1, numberOfComponents
-               call this%core%get_child(compsPtr, i, compPtr)
-               call this%core%get(compPtr, component)
-               res%cordinates(i) = cs(1)
-               res%cordinates(i)%Or  = buildVolProbeType(fieldType, component)
-            end do
-         else 
-            allocate(res%cordinates(1))
+            call this%core%get(compsPtr, component)
             res%cordinates(1) = cs(1)
+            res%cordinates(1)%Or  = buildVolProbeType(fieldType, component)
+         else 
             component = J_DIR_M
             res%cordinates(1)%Or  = buildVolProbeType(fieldType, component)
          endif

src_json_parser/labels_mod.F90 src_json_parser/smbjson_labels.F90src_json_parser/labels_mod.F90 renamed to src_json_parser/smbjson_labels.F90

@@ -1,4 +1,4 @@
-module labels_mod
+module smbjson_labels_mod
 
 #ifdef CompileWithSMBJSON    
    ! LABELS
@@ -155,7 +155,7 @@ module labels_mod
 
    character (len=*), parameter :: J_PR_POINT_DIRECTIONS = "directions"
 
-   character (len=*), parameter :: J_PR_MOVIE_COMPONENTS = "components"
+   character (len=*), parameter :: J_PR_MOVIE_COMPONENT = "component"
 
    character (len=*), parameter :: J_PR_FAR_FIELD_THETA = "theta"
    character (len=*), parameter :: J_PR_FAR_FIELD_PHI = "phi"

src_main_pub/anisotropic.F90

@@ -32,9 +32,6 @@
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 module Anisotropic
-
-#ifdef CompileWithAnisotropic
-
    use fdetypes
    implicit none
    private
@@ -1581,6 +1578,4 @@ Subroutine CalculateCoeff(epr,mur,sigma,sigmam,dt,coeff)
 
    end subroutine
 
-#endif
-
 end module Anisotropic