Merge remote-tracking branch 'origin/develop' into xml

docs/source/quickinstall.rst

@@ -43,6 +43,7 @@ following commands in a terminal:
 
     git clone git://github.com/mit-crpg/openmc.git
     cd openmc/src
+    git checkout master
     make
     sudo make install
 

docs/source/usersguide/install.rst

@@ -102,6 +102,12 @@ repository::
 
     git clone git://github.com/mit-crpg/openmc.git
 
+By default, the cloned repository will be set to the development branch. To
+switch to the source of the latest stable release, run the following commands::
+
+    cd openmc/src
+    git checkout master
+
 .. _GitHub: https://github.com/mit-crpg/openmc
 .. _git: http://git-scm.com
 .. _ssh: http://en.wikipedia.org/wiki/Secure_Shell

src/ace.F90

@@ -10,7 +10,7 @@ module ace
   use material_header,  only: Material
   use output,           only: write_message
   use set_header,       only: SetChar
-  use string,           only: str_to_int, str_to_real, lower_case, to_str
+  use string,           only: to_str
 
   implicit none
 

src/cmfd_slepc_solver.F90

@@ -1,6 +1,6 @@
 module cmfd_slepc_solver
 
-#ifdef PETSC
+#ifdef SLEPC
   use cmfd_loss_operator, only: loss_operator, init_M_operator, &
                                 build_loss_matrix, destroy_M_operator
   use cmfd_prod_operator, only: prod_operator, init_F_operator, &

src/eigenvalue.F90

@@ -98,6 +98,9 @@ contains
     ! END OF RUN WRAPUP
 
     if (master) call header("SIMULATION FINISHED", level=1)
+    
+    ! Clear particle
+    call p % clear()
 
   end subroutine run_eigenvalue
 

src/global.F90

@@ -409,6 +409,19 @@ contains
     if (allocated(xs_listings)) deallocate(xs_listings)
     if (allocated(micro_xs)) deallocate(micro_xs)
 
+    ! Deallocate external source
+    if (allocated(external_source % params_space)) &
+         deallocate(external_source % params_space)
+    if (allocated(external_source % params_angle)) &
+         deallocate(external_source % params_angle)
+    if (allocated(external_source % params_energy)) &
+         deallocate(external_source % params_energy)
+
+    ! Deallocate k and entropy
+    if (allocated(k_generation)) deallocate(k_generation)
+    if (allocated(entropy)) deallocate(entropy)
+    if (allocated(entropy_p)) deallocate(entropy_p)
+
     ! Deallocate tally-related arrays
     if (allocated(meshes)) deallocate(meshes)
     if (allocated(tallies)) then
@@ -450,6 +463,9 @@ contains
     call nuclide_dict % clear()
     call sab_dict % clear()
     call xs_listing_dict % clear()
+
+    ! Clear statepoint batch set
+    call statepoint_batch % clear()
     
   end subroutine free_memory
 

src/initialize.F90

@@ -417,6 +417,8 @@ contains
     integer, allocatable :: index_cell_in_univ(:) ! the index in the univ%cells
                                                   ! array for each universe
     type(ElemKeyValueII), pointer :: pair_list => null()
+    type(ElemKeyValueII), pointer :: current => null()
+    type(ElemKeyValueII), pointer :: next => null()
     type(Universe),       pointer :: univ => null()
     type(Cell),           pointer :: c => null()
 
@@ -428,11 +430,12 @@ contains
     ! cells_in_univ_dict, it's the id of the universe and the number of cells.
 
     pair_list => universe_dict % keys()
-    do while (associated(pair_list))
+    current => pair_list
+    do while (associated(current))
       ! find index of universe in universes array
-      i_univ = pair_list % value
+      i_univ = current % value
       univ => universes(i_univ)
-      univ % id = pair_list % key
+      univ % id = current % key
 
       ! check for lowest level universe
       if (univ % id == 0) BASE_UNIVERSE = i_univ
@@ -445,7 +448,9 @@ contains
       univ % n_cells = n_cells_in_univ
 
       ! move to next universe
-      pair_list => pair_list % next
+      next => current % next
+      deallocate(current)
+      current => next
     end do
 
     ! Also allocate a list for keeping track of where cells have been assigned

src/particle_header.F90

@@ -77,6 +77,7 @@ module particle_header
 
   contains
     procedure :: initialize => initialize_particle
+    procedure :: clear => clear_particle
   end type Particle
 
 contains
@@ -110,6 +111,9 @@ contains
 
     class(Particle) :: this
 
+    ! Clear coordinate lists
+    call this % clear()
+
     ! Set particle to neutron that's alive
     this % type  = NEUTRON
     this % alive = .true.
@@ -126,9 +130,6 @@ contains
     this % wgt_bank      = ZERO
     this % n_collision   = 0
 
-    ! remove any original coordinates
-    call deallocate_coord(this % coord0)
-
     ! Set up base level coordinates
     allocate(this % coord0)
     this % coord0 % universe = BASE_UNIVERSE
@@ -136,4 +137,20 @@ contains
 
   end subroutine initialize_particle
 
+!===============================================================================
+! CLEAR_PARTICLE
+!===============================================================================
+
+  subroutine clear_particle(this)
+
+    class(Particle) :: this
+
+    ! remove any coordinate levels
+    call deallocate_coord(this % coord0)
+
+    ! Make sure coord pointer is nullified
+    nullify(this % coord)
+
+  end subroutine clear_particle
+
 end module particle_header

src/string.F90

@@ -322,49 +322,18 @@ contains
   end function str_to_int
 
 !===============================================================================
-! STR_TO_REAL converts an arbitrary string to a real(8). Generally this function
-! is intended for strings for which the exact format is not known. If the format
-! of the number is known a priori, the appropriate format descriptor should be
-! used in lieu of this routine because of the extra overhead.
-!
-! Arguments:
-!   string = character(*) containing number to convert
+! STR_TO_REAL converts an arbitrary string to a real(8)
 !===============================================================================
 
   function str_to_real(string) result(num)
 
     character(*), intent(in) :: string
-    real(8) :: num
+    real(8)                  :: num
 
-    integer      :: index_decimal  ! index of decimal point
-    integer      :: index_exponent ! index of exponent character
-    integer      :: w              ! total field width
-    integer      :: d              ! number of digits to right of decimal point
-    integer      :: ioError
-    character(8) :: fmt            ! format for reading string
-
-    ! Determine total field width
-    w = len_trim(string)
-
-    ! Determine number of digits to right of decimal point
-    index_decimal = index(string, '.')
-    index_exponent = max(index(string, 'd'), index(string, 'D'), &
-         index(string, 'e'), index(string, 'E'))
-    if (index_decimal > 0) then
-      if (index_exponent > 0) then
-        d = index_exponent - index_decimal - 1
-      else
-        d = w - index_decimal
-      end if
-    else
-      d = 0
-    end if
-
-    ! Create format specifier for reading string
-    write(fmt, '("(E",I2,".",I2,")")') w, d
+    integer :: ioError
 
     ! Read string
-    read(UNIT=string, FMT=fmt, IOSTAT=ioError) num
+    read(UNIT=string, FMT=*, IOSTAT=ioError) num
     if (ioError > 0) num = ERROR_REAL
 
   end function str_to_real

tests/test_survival_biasing/materials.xml

@@ -2,8 +2,9 @@
 <materials>
 
   <material id="1">
-    <density value="4.5" units="g/cc" />
-    <nuclide name="U-235" xs="70c" ao="1.0" />
+    <density value="19.5" units="g/cc" />
+    <nuclide name="U-235" xs="70c" ao="2.0" />
+    <nuclide name="U-238" xs="70c" ao="1.0" />
   </material>
 
 </materials>

tests/test_survival_biasing/results_true.dat

@@ -1,2 +1,2 @@
 k-combined:
-0.30487324 0.00983400
+0.96880768 0.06981246