Merge branch 'develop' into atomic

docs/source/usersguide/input.rst

@@ -757,7 +757,10 @@ Each ``<cell>`` element can have the following attributes or sub-elements:
     is on the negative side of surface 3 and the positive side of surface 5, the
     bounding surfaces would be given as "-3 5".
 
-    *Default*: None
+    .. note:: The surface attribute/element can be omitted to make a cell fill
+              its entire universe.
+
+    *Default*: No surfaces
 
   :rotation:
     If the cell is filled with a universe, this element specifies the angles in
@@ -1170,7 +1173,7 @@ implemented in openMC:
 ``<plot>`` Element
 ------------------
 
-Each plot must contain a combination of the following attributes or
+Each plot is specified by a combination of the following attributes or
 sub-elements:
 
   :id:
@@ -1191,6 +1194,18 @@ sub-elements:
 
     *Default*: ``cell``
 
+  :level:
+    Universe depth to plot at (optional).  This parameter controls how many
+    universe levels deep to pull cell and material ids from when setting plot
+    colors.  If a given location does not have as many levels as specified,
+    colors will be taken from the lowest level at that location. For example, if
+    ``level`` is set to zero colors will be taken from top-level (universe zero)
+    cells only.  However, if ``level`` is set to 1 colors will be taken from
+    cells in universes that fill top-level fill-cells, and from top-level cells
+    that contain materials.
+
+    *Default*: Whatever the deepest universe is in the model
+
   :origin:
     Specifies the (x,y,z) coordinate of the center of the plot.  Should be three
     floats separated by spaces.

src/geometry.F90

@@ -59,7 +59,8 @@ contains
       end if
     end do SURFACE_LOOP
 
-    ! If we've reached here, then the sense matched on every surface
+    ! If we've reached here, then the sense matched on every surface or there
+    ! are no surfaces.
     in_cell = .true.
 
   end function simple_cell_contains

src/input_xml.F90

@@ -1011,17 +1011,18 @@ contains
         call fatal_error("Cannot specify material and fill simultaneously")
       end if
 
-      ! Check to make sure that surfaces were specified
-      if (.not. check_for_node(node_cell, "surfaces")) then
-        call fatal_error("No surfaces specified for cell " &
-             &// trim(to_str(c % id)))
-      end if
-
       ! Allocate array for surfaces and copy
-      n = get_arraysize_integer(node_cell, "surfaces")
+      if (check_for_node(node_cell, "surfaces")) then
+        n = get_arraysize_integer(node_cell, "surfaces")
+      else
+        n = 0
+      end if
       c % n_surfaces = n
-      allocate(c % surfaces(n))
-      call get_node_array(node_cell, "surfaces", c % surfaces)
+
+      if (n > 0) then
+        allocate(c % surfaces(n))
+        call get_node_array(node_cell, "surfaces", c % surfaces)
+      end if
 
       ! Rotation matrix
       if (check_for_node(node_cell, "rotation")) then
@@ -2730,16 +2731,14 @@ contains
       end select
 
       ! Set output file path
-      filename = "plot"
+      filename = trim(to_str(pl % id)) // "_plot"
       if (check_for_node(node_plot, "filename")) &
         call get_node_value(node_plot, "filename", filename)
       select case (pl % type)
       case (PLOT_TYPE_SLICE)
-        pl % path_plot = trim(path_input) // trim(to_str(pl % id)) // &
-             "_" // trim(filename) // ".ppm"
+        pl % path_plot = trim(path_input) // trim(filename) // ".ppm"
       case (PLOT_TYPE_VOXEL)
-        pl % path_plot = trim(path_input) // trim(to_str(pl % id)) // &
-             "_" // trim(filename) // ".voxel"
+        pl % path_plot = trim(path_input) // trim(filename) // ".voxel"
       end select
 
       ! Copy plot pixel size
@@ -2819,6 +2818,18 @@ contains
         end if
       end if
 
+      ! Copy plot cell universe level
+      if (check_for_node(node_plot, "level")) then
+        call get_node_value(node_plot, "level", pl % level)
+        
+        if (pl % level < 0) then
+          call fatal_error("Bad universe level in plot " &
+               &// trim(to_str(pl % id)))
+        end if
+      else
+        pl % level = PLOT_LEVEL_LOWEST
+      end if
+
       ! Copy plot color type and initialize all colors randomly
       temp_str = "cell"
       if (check_for_node(node_plot, "color")) &

src/output.F90

@@ -1428,6 +1428,12 @@ contains
       ! Plot id
       write(ou,100) "Plot ID:", trim(to_str(pl % id))
 
+      ! Plot filename
+      write(ou,100) "Plot file:", trim(pl % path_plot)
+
+      ! Plot level
+      write(ou,100) "Universe depth:", trim(to_str(pl % level))
+
       ! Plot type
       if (pl % type == PLOT_TYPE_SLICE) then
         write(ou,100) "Plot Type:", "Slice"

src/plot.F90

@@ -7,7 +7,7 @@ module plot
   use global
   use mesh,            only: get_mesh_indices
   use output,          only: write_message
-  use particle_header, only: deallocate_coord, Particle
+  use particle_header, only: deallocate_coord, Particle, LocalCoord
   use plot_header
   use ppmlib,          only: Image, init_image, allocate_image, &
                              deallocate_image, set_pixel
@@ -32,7 +32,7 @@ contains
 
       ! Display output message
       call write_message("Processing plot " // trim(to_str(pl % id)) &
-           &// "...", 5)
+           &// ": " // trim(pl % path_plot) // " ...", 5)
 
       if (pl % type == PLOT_TYPE_SLICE) then
         ! create 2d image
@@ -58,7 +58,9 @@ contains
     integer, intent(out)                  :: id
     
     logical :: found_cell
-    type(Cell), pointer :: c => null()
+    integer :: level
+    type(Cell),       pointer :: c => null()
+    type(LocalCoord), pointer :: coord => null()
     
     call deallocate_coord(p % coord0 % next)
     p % coord => p % coord0
@@ -66,6 +68,16 @@ contains
     call find_cell(p, found_cell)
     if (check_overlaps) call check_cell_overlap(p)
 
+    ! Loop through universes and stop on any specified level
+    level = 0
+    coord => p % coord0
+    do
+      if (level == pl % level) exit
+      if (.not. associated(coord % next)) exit
+      coord => coord % next
+      level = level + 1
+    end do
+    
     if (.not. found_cell) then
       ! If no cell, revert to default color
       rgb = pl % not_found % rgb
@@ -73,19 +85,23 @@ contains
     else
       if (pl % color_by == PLOT_COLOR_MATS) then
         ! Assign color based on material
-        c => cells(p % coord % cell)
+        c => cells(coord % cell)
         if (c % material == MATERIAL_VOID) then
           ! By default, color void cells white
           rgb = 255
           id = -1
+        else if (c % type == CELL_FILL) then
+          ! If we stopped on a middle universe level, treat as if not found
+          rgb = pl % not_found % rgb
+          id = -1
         else
           rgb = pl % colors(c % material) % rgb
           id = materials(c % material) % id
         end if
       else if (pl % color_by == PLOT_COLOR_CELLS) then
         ! Assign color based on cell
-        rgb = pl % colors(p % coord % cell) % rgb
-        id = cells(p % coord % cell) % id
+        rgb = pl % colors(coord % cell) % rgb
+        id = cells(coord % cell) % id
       else
         rgb = 0
         id = -1

src/plot_header.F90

@@ -27,6 +27,7 @@ module plot_header
     integer :: basis                 ! direction of plot slice 
     integer :: pixels(3)             ! pixel width/height of plot slice
     integer :: meshlines_width       ! pixel width of meshlines
+    integer :: level                 ! universe depth to plot the cells of
     type(StructuredMesh), pointer :: meshlines_mesh => null() ! mesh to plot
     type(ObjectColor) :: meshlines_color ! Color for meshlines
     type(ObjectColor) :: not_found   ! color for positions where no cell found
@@ -36,6 +37,9 @@ module plot_header
   ! Plot type
   integer, parameter :: PLOT_TYPE_SLICE = 1
   integer, parameter :: PLOT_TYPE_VOXEL = 2
+  
+  ! Plot level
+  integer, parameter :: PLOT_LEVEL_LOWEST = -1
 
   ! Plot basis plane
   integer, parameter :: PLOT_BASIS_XY = 1

src/relaxng/geometry.rnc

@@ -7,7 +7,7 @@ element geometry {
       (element material { ( xsd:int | "void" ) } | 
         attribute material { ( xsd:int | "void" ) })
     ) &
-    (element surfaces { list { xsd:int+ } } | attribute surfaces { list { xsd:int+ } }) &
+    (element surfaces { list { xsd:int* } } | attribute surfaces { list { xsd:int* } })? &
     (element rotation { list { xsd:double+ } } | attribute rotation { list { xsd:double+ } })? &
     (element translation { list { xsd:double+ } } | attribute translation { list { xsd:double+ } })?
   }*
@@ -23,8 +23,8 @@ element geometry {
 
   & element lattice {
     (element id { xsd:int } | attribute id { xsd:int }) &
-    (element type { ( "rectangular" | "hexagonal" ) } | 
-     attribute type { ( "rectangular" | "hexagonal" ) })? &
+    (element type { ( "rect" | "rectangle" | "rectangular" | "hexagonal" ) } | 
+     attribute type { ( "rect" | "rectangle" | "rectangular" | "hexagonal" ) })? &
     (element dimension { list { xsd:positiveInteger+ } } | 
       attribute dimension { list { xsd:positiveInteger+ } }) &
     (element lower_left { list { xsd:double+ } } | attribute lower_left { list { xsd:double+ } }) &

src/relaxng/plots.rnc

@@ -7,6 +7,7 @@ element plots {
       attribute type { "slice" | "voxel" })? &
     (element color { ( "cell" | "mat" | "material" ) } |
       attribute color { ( "cell" | "mat" | "material" ) })? &
+    (element level { xsd:int } | attribute level { xsd:int })? &
     (element origin { list { xsd:double+ } } |
       attribute origin { list { xsd:double+ } })? &
     (element width { list { xsd:double+ } } |

tests/test_infinite_cell/geometry.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0"?>
+<geometry>
+  <cell id="11" universe="11" material="1"/>
+  <cell id="12" universe="12" material="2" surfaces=""/>
+
+  <lattice id="21" type="rect" dimension="2 2" lower_left="-2.0 -2.0"
+    width="2.0 2.0" outside="2">
+    <universes>
+      11 12
+      12 11
+    </universes>
+  </lattice>
+
+
+  <surface id="101" type="z-cylinder" coeffs="0.0 0.0 5.0" boundary="vacuum"/>
+  <cell id="101" universe="0" fill="21" surfaces="-101"/>
+</geometry>

tests/test_infinite_cell/materials.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<materials>
+
+  <material id="1">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-235" xs="71c" ao="1.0" />
+  </material>
+
+  <material id="2">
+    <density value="4.5" units="g/cc" />
+    <nuclide name="U-238" xs="71c" ao="1.0" />
+  </material>
+
+</materials>

tests/test_infinite_cell/results.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+
+import sys
+
+# import statepoint
+sys.path.insert(0, '../../src/utils')
+import statepoint
+
+# read in statepoint file
+if len(sys.argv) > 1:
+    sp = statepoint.StatePoint(sys.argv[1])
+else:
+    sp = statepoint.StatePoint('statepoint.10.binary')
+sp.read_results()
+
+# set up output string
+outstr = ''
+ 
+# write out k-combined
+outstr += 'k-combined:\n'
+outstr += "{0:12.6E} {1:12.6E}\n".format(sp.k_combined[0], sp.k_combined[1])
+
+# write results to file
+with open('results_test.dat','w') as fh:
+    fh.write(outstr)

tests/test_infinite_cell/results_true.dat

@@ -0,0 +1,2 @@
+k-combined:
+9.998895E-02 2.846817E-04

tests/test_infinite_cell/settings.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<settings>
+
+  <eigenvalue>
+    <batches>10</batches>
+    <inactive>5</inactive>
+    <particles>1000</particles>
+  </eigenvalue>
+
+  <source>
+    <space type="box">
+      <parameters>-4 -4 -4  4  4  4</parameters>
+    </space>
+  </source>
+
+</settings>

tests/test_infinite_cell/test_infinite_cell.py

@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+
+import os
+from subprocess import Popen, STDOUT, PIPE, call
+import filecmp
+import glob
+from optparse import OptionParser
+
+parser = OptionParser()
+parser.add_option('--mpi_exec', dest='mpi_exec', default='')
+parser.add_option('--mpi_np', dest='mpi_np', default='3')
+parser.add_option('--exe', dest='exe')
+(opts, args) = parser.parse_args()
+cwd = os.getcwd()
+
+def test_run():
+    if opts.mpi_exec != '':
+        proc = Popen([opts.mpi_exec, '-np', opts.mpi_np, opts.exe, cwd],
+               stderr=STDOUT, stdout=PIPE)
+    else:
+        proc = Popen([opts.exe, cwd], stderr=STDOUT, stdout=PIPE)
+    print(proc.communicate()[0])
+    returncode = proc.returncode
+    assert returncode == 0, 'OpenMC did not exit successfully.'
+
+def test_created_statepoint():
+    statepoint = glob.glob(os.path.join(cwd, 'statepoint.10.*'))
+    assert len(statepoint) == 1, 'Either multiple or no statepoint files exist.'
+    assert statepoint[0].endswith('binary') or statepoint[0].endswith('h5'),\
+        'Statepoint file is not a binary or hdf5 file.'
+
+def test_results():
+    statepoint = glob.glob(os.path.join(cwd, 'statepoint.10.*'))
+    call(['python', 'results.py', statepoint[0]])
+    compare = filecmp.cmp('results_test.dat', 'results_true.dat')
+    if not compare:
+      os.rename('results_test.dat', 'results_error.dat')
+    assert compare, 'Results do not agree.'
+
+def teardown():
+    output = glob.glob(os.path.join(cwd, 'statepoint.10.*'))
+    output.append(os.path.join(cwd, 'results_test.dat'))
+    for f in output:
+        if os.path.exists(f):
+            os.remove(f)
+
+if __name__ == '__main__':
+
+    # test for openmc executable
+    if opts.exe is None:
+        raise Exception('Must specify OpenMC executable from command line with --exe.')
+
+    # run tests
+    try:
+        test_run()
+        test_created_statepoint()
+        test_results()
+    finally:
+        teardown()