Merge branch 'master' into inactive_tallies

docs/source/usersguide/input.rst

@@ -938,6 +938,13 @@ sub-elements:
       Specifies the custom color for the cell or material.  Should be 3 integers separated
       by spaces.
 
+    As an example, if your plot is colored by material and you want material 23
+    to be blue, the corresponding ``col_spec`` element would look like:
+
+    .. code-block:: xml
+
+        <col_spec id="23" rgb="0 0 255" />
+
     *Default*: None
 
   :mask:

docs/source/usersguide/install.rst

@@ -179,3 +179,27 @@ Alternatively, you could run from any directory:
 
 Note that in the latter case, any output files will be placed in the present
 working directory which may be different from ``/home/username/somemodel``.
+
+-----------------------------------------------------
+Configuring Input Validation with GNU Emacs nXML mode
+-----------------------------------------------------
+
+The `GNU Emacs`_ text editor has a built-in mode that extends functionality for
+editing XML files. One of the features in nXML mode is the ability to perform
+real-time `validation`_ of XML files against a `RELAX NG`_ schema. The OpenMC
+source contains RELAX NG schemas for each type of user input file. In order for
+nXML mode to know about these schemas, you need to tell emacs where to find a
+"locating files" description. Adding the following lines to your ``~/.emacs``
+file will enable real-time validation of XML input files:
+
+.. code-block:: common-lisp
+
+    (require 'rng-loc)
+    (add-to-list 'rng-schema-locating-files "~/openmc/schemas.xml")
+
+Make sure to replace the last string on the second line with the path to the
+schemas.xml file in your own OpenMC source directory.
+
+.. _GNU Emacs: http://www.gnu.org/software/emacs/
+.. _validation: http://en.wikipedia.org/wiki/XML_validation
+.. _RELAX NG: http://relaxng.org/

schemas.xml

@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<locatingRules xmlns="http://thaiopensource.com/ns/locating-rules/1.0">
+  <documentElement localName="geometry" uri="src/templates/geometry.rnc"/>
+  <documentElement localName="materials" uri="src/templates/materials.rnc"/>
+  <documentElement localName="settings" uri="src/templates/settings.rnc"/>
+  <documentElement localName="tallies" uri="src/templates/tallies.rnc"/>
+  <documentElement localName="plots" uri="src/templates/plots.rnc"/>
+  <documentElement localName="cross_sections" uri="src/templates/cross_sections.rnc"/>
+</locatingRules>

src/ace.F90

@@ -217,10 +217,14 @@ contains
        ! Read XSS array
        read(UNIT=in, FMT='(4E20.0)') XSS
 
+       ! Close ACE file
+       close(UNIT=in)
+
     elseif (filetype == BINARY) then
        ! =======================================================================
        ! READ ACE TABLE IN BINARY FORMAT
 
+       ! Open ACE file
        open(UNIT=in, FILE=filename, STATUS='old', ACTION='read', &
             ACCESS='direct', RECL=record_length)
 
@@ -238,6 +242,9 @@ contains
           j2 = min(length, j1 + entries - 1)
           read(UNIT=IN, REC=location + i) (XSS(j), j=j1,j2)
        end do
+
+       ! Close ACE file
+       close(UNIT=in)
     end if
 
     ! ==========================================================================
@@ -287,8 +294,6 @@ contains
     if(associated(nuc)) nullify(nuc)
     if(associated(sab)) nullify(sab)
 
-    close(UNIT=in)
-
   end subroutine read_ace_table
 
 !===============================================================================

src/datatypes.F90

@@ -156,12 +156,14 @@ contains
     type(ListInt), pointer :: current
     type(ListInt), pointer :: next
 
-    current => list
-    do while (associated(current%next))
-       next => current%next
-       deallocate(current)
-       current => next
-    enddo
+    if (associated(list)) then
+       current => list
+       do while (associated(current%next))
+          next => current%next
+          deallocate(current)
+          current => next
+       end do
+    end if
 
   end subroutine list_int_delete
 
@@ -175,12 +177,14 @@ contains
     type(ListReal), pointer :: current
     type(ListReal), pointer :: next
 
-    current => list
-    do while (associated(current%next))
-       next => current%next
-       deallocate(current)
-       current => next
-    enddo
+    if (associated(list)) then
+       current => list
+       do while (associated(current%next))
+          next => current%next
+          deallocate(current)
+          current => next
+       end do
+    end if
 
   end subroutine list_real_delete
 
@@ -194,12 +198,14 @@ contains
     type(ListKeyValueCI), pointer  :: current
     type(ListKeyValueCI), pointer  :: next
 
-    current => list
-    do while (associated(current%next))
-       next => current%next
-       deallocate(current)
-       current => next
-    enddo
+    if (associated(list)) then
+       current => list
+       do while (associated(current%next))
+          next => current%next
+          deallocate(current)
+          current => next
+       end do
+    end if
 
   end subroutine list_kvci_delete
 
@@ -213,12 +219,14 @@ contains
     type(ListKeyValueII), pointer  :: current
     type(ListKeyValueII), pointer  :: next
 
-    current => list
-    do while (associated(current%next))
-       next => current%next
-       deallocate(current)
-       current => next
-    enddo
+    if (associated(list)) then
+       current => list
+       do while (associated(current%next))
+          next => current%next
+          deallocate(current)
+          current => next
+       end do
+    end if
 
   end subroutine list_kvii_delete
 

src/fixed_source.F90

@@ -117,18 +117,16 @@ contains
     call timer_stop(time_ic_tallies)
 
     ! Write out state point if it's been specified for this batch
-    if (master) then
-       do i = 1, n_state_points
-          if (current_batch == statepoint_batch(i)) then
+    do i = 1, n_state_points
+       if (current_batch == statepoint_batch(i)) then
 #ifdef HDF5
-             call hdf5_write_state_point()
+          call hdf5_write_state_point()
 #else
-             call write_state_point()
+          call write_state_point()
 #endif
-             exit
-          end if
-       end do
-    end if
+          exit
+       end if
+    end do
 
   end subroutine finalize_batch
 

src/plot.F90

@@ -115,9 +115,16 @@ contains
            if (pl % color_by == PLOT_COLOR_MATS) then
               ! Assign color based on material
               c => cells(p % coord % cell)
-              r = pl % colors(c % material) % rgb(1)
-              g = pl % colors(c % material) % rgb(2)
-              b = pl % colors(c % material) % rgb(3)
+              if (c % material == MATERIAL_VOID) then
+                 ! By default, color void cells white
+                 r = 255
+                 g = 255
+                 b = 255
+              else
+                 r = pl % colors(c % material) % rgb(1)
+                 g = pl % colors(c % material) % rgb(2)
+                 b = pl % colors(c % material) % rgb(3)
+              end if
            else if (pl % color_by == PLOT_COLOR_CELLS) then
               ! Assign color based on cell
               r = pl % colors(p % coord % cell) % rgb(1)

src/templates/cross_sections.rnc

@@ -0,0 +1,23 @@
+element cross_sections {
+  element ace_table {
+    (element name { xsd:string { maxLength = "15" } } |
+      attribute name { xsd:string { maxLength = "15" } }) &
+    (element alias { xsd:string { maxLength = "15" } } |
+      attribute alias { xsd:string { maxLength = "15" } })? &
+    (element zaid { xsd:int } | attribute zaid { xsd:int }) &
+    (element metastable { xsd:int } | attribute metastable { xsd:int })? &
+    (element awr { xsd:double } | attribute awr { xsd:double }) &
+    (element temperature { xsd:double } | attribute temperature { xsd:double }) &
+    (element path { xsd:string { maxLength = "255" } } |
+      attribute path { xsd:string { maxLength = "255" } }) &
+    (element location { xsd:int } | attribute location { xsd:int })?
+  }* &
+
+  element directory { xsd:string { maxLength = "255" } }? &
+
+  element filetype { ( "ascii" | "binary" ) } &
+
+  element record_length { xsd:int }? &
+
+  element entries { xsd:int }?
+}

src/templates/geometry.rnc

@@ -0,0 +1,32 @@
+element geometry {
+  element cell {
+    (element id { xsd:int } | attribute id { xsd:int }) &
+    (element universe { xsd:int } | attribute universe { xsd:int })? &
+    (
+      (element fill { xsd:int } | attribute fill { xsd:int }) |
+      (element material { xsd:int } | attribute material { 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+ } })?
+  }*
+
+  & element surface {
+    (element id { xsd:int } | attribute id { xsd:int }) &
+    (element type { xsd:string { maxLength = "15" } } | 
+     attribute type { xsd:string { maxLength = "15" } }) &
+    (element coeffs { list { xsd:double+ } } | attribute coeffs { list { xsd:double+ } }) &
+    (element boundary { ( "transmit" | "reflective" | "vacuum" ) } |
+     attribute boundary { ( "transmit" | "reflective" | "vacuum" ) })?
+  }*
+
+  & element lattice {
+    (element id { xsd:int } | attribute id { xsd:int }) &
+    (element type { ( "rectangular" | "hexagonal" ) } | 
+     attribute type { ( "rectangular" | "hexagonal" ) })? &
+    (element dimension { list { xsd:int+ } } | attribute dimension { list { xsd:int+ } }) &
+    (element lower_left { list { xsd:double+ } } | attribute lower_left { list { xsd:double+ } }) &
+    (element width { list { xsd:double+ } } | attribute width { list { xsd:double+ } }) &
+    (element universes { list { xsd:int+ } } | attribute universes { list { xsd:int+ } })
+  }*
+}

src/templates/materials.rnc

@@ -0,0 +1,31 @@
+element materials {
+  element material {
+    (element id { xsd:int } | attribute id { xsd:int }) &
+
+    element density {
+      (element value { xsd:double } | attribute value { xsd:double })? &
+      (element units { xsd:string { maxLength = "10" } } |
+        attribute units { xsd:string { maxLength = "10" } })
+    } &
+
+    element nuclide {
+      (element name { xsd:string { maxLength = "7" } } | 
+        attribute name { xsd:string { maxLength = "7" } }) &
+      (element xs { xsd:string { maxLength = "3" } } |
+        attribute xs { xsd:string { maxLength = "3" } })? &
+      (
+        (element ao { xsd:double } | attribute ao { xsd:double }) |
+        (element wo { xsd:double } | attribute wo { xsd:double })
+      )
+    }*  &
+
+    element sab {
+      (element name { xsd:string { maxLength = "7" } } | 
+        attribute name { xsd:string { maxLength = "7" } }) &
+      (element xs { xsd:string { maxLength = "3" } } |
+        attribute xs { xsd:string { maxLength = "3" } })?
+    }*
+  }+ &
+
+  element default_xs { xsd:string { maxLength = "3" } }
+}

src/templates/plots.rnc

@@ -0,0 +1,31 @@
+element plots {
+  element plot {
+    (element id { xsd:int } | attribute id { xsd:int })? &
+    (element filename { xsd:string { maxLength = "50" } } |
+      attribute filename { xsd:string { maxLength = "50" } })? &
+    (element type { "slice" } | attribute type { "slice" })? &
+    (element color { ( "cell" | "mat" | "material" ) } |
+      attribute color { ( "cell" | "mat" | "material" ) })? &
+    (element origin { list { xsd:double+ } } | 
+      attribute origin { list { xsd:double+ } })? &
+    (element width { list { xsd:double+ } } | 
+      attribute width { list { xsd:double+ } })? &
+    (element basis { ( "xy" | "yz" | "xz" ) } |
+      attribute basis { ( "xy" | "yz" | "xz" ) })? &
+    (element pixels { list { xsd:int+ } } | 
+      attribute pixels { list { xsd:int+ } })? &
+    (element background { list { xsd:int+ } } |
+      attribute background { list { xsd:int+ } })? &
+    element col_spec {
+      (element id { xsd:int } | attribute id { xsd:int }) &
+      (element rgb { list { xsd:int+ } } | 
+        attribute rgb { list { xsd:int+ } })
+    }* &
+    element mask {
+      (element components { list { xsd:int+ } } | 
+        attribute components { list { xsd:int+ } }) &
+      (element background { list { xsd:int+ } } | 
+        attribute background { list { xsd:int+ } })
+    }*
+  }*
+}

src/templates/settings.rnc

@@ -0,0 +1,99 @@
+element settings {
+  element confidence_intervals { ( "on" | "off" ) }? &
+
+  (
+    element criticality {
+      (element batches { xsd:int } | attribute batches { xsd:int }) &
+      (element inactive { xsd:int } | attribute inactive { xsd:int }) &
+      (element particles { xsd:int } | attribute particles { xsd:int }) &
+      (element generations_per_batch { xsd:int } | attribute generations_per_batch { xsd:int })?
+    } |
+    element fixed_source {
+      (element batches { xsd:int } | attribute batches { xsd:int }) &
+      (element particles { xsd:int } | attribute particles { xsd:int })
+    }
+  ) &
+
+  element cross_sections { xsd:string { maxLength = "255" } }? &
+
+  element cutoff {
+    (element weight { xsd:double } | attribute weight { xsd:double })? &
+    (element weight_avg { xsd:double } | attribute weight_avg { xsd:double })?
+  }? &
+
+  element energy_grid { xsd:string { maxLength = "7" } }? &
+
+  element entropy {
+    (element dimension { list { xsd:int+ } } | 
+      attribute dimension { list { xsd:int+ } })? &
+    (element lower_left { list { xsd:double+ } } | 
+      attribute lower_left { list { xsd:double+ } }) &
+    (element upper_right { list { xsd:double+ } } | 
+      attribute upper_right { list { xsd:double+ } })
+  }? &
+
+  element no_reduce { ( "off" | "on" ) }? &
+
+  element output { list { 
+    ( "summary" | "cross_sections" | "tallies" )+ } }? &
+
+  element ptables { ( "off" | "on" ) }? &
+
+  element seed { xsd:integer }? &
+
+  element source {
+    element file { xsd:string { maxLength = "255" } }? &
+    element space {
+      (element type { xsd:string { maxLength = "10" } } |
+        attribute type { xsd:string { maxLength = "10" } }) &
+      (element length { xsd:int } | attribute length { xsd:int })? &
+      (element interpolation { xsd:string { maxLength = "10" } } |
+        attribute interplation { xsd:string { maxLength = "10" } })? &
+      (element parameters { list { xsd:double+ } } |
+        attribute parameters { list { xsd:double+ } })?
+    }? &
+    element angle {
+      (element type { xsd:string { maxLength = "10" } } |
+        attribute type { xsd:string { maxLength = "10" } }) &
+      (element length { xsd:int } | attribute length { xsd:int })? &
+      (element interpolation { xsd:string { maxLength = "10" } } |
+        attribute interplation { xsd:string { maxLength = "10" } })? &
+      (element parameters { list { xsd:double+ } } |
+        attribute parameters { list { xsd:double+ } })?
+    }? &
+    element energy {
+      (element type { xsd:string { maxLength = "10" } } |
+        attribute type { xsd:string { maxLength = "10" } }) &
+      (element length { xsd:int } | attribute length { xsd:int })? &
+      (element interpolation { xsd:string { maxLength = "10" } } |
+        attribute interplation { xsd:string { maxLength = "10" } })? &
+      (element parameters { list { xsd:double+ } } |
+        attribute parameters { list { xsd:double+ } })?
+    }?
+  }? &
+
+  element state_point {
+    (
+      (element batches { list { xsd:int } } |
+        attribute batches { list { xsd:int } }) |
+      (element interval { xsd:int} | attribute interval { xsd:int })
+    ) &
+    (element source_separate { ( "off" | "on" ) } | 
+      attribute source_separate { ( "off" | "on" ) })?
+  }? &
+
+  element survival_biasing { ( "off" | "on" ) }? &
+
+  element trace { list { xsd:int } }? &
+
+  element verbosity { xsd:int }? &
+
+  element uniform_fs{
+    (element dimension { list { xsd:int+ } } | 
+      attribute dimension { list { xsd:int+ } }) &
+    (element lower_left { list { xsd:double+ } } | 
+      attribute lower_left { list { xsd:double+ } }) &
+    (element upper_right { list { xsd:double+ } } | 
+      attribute upper_right { list { xsd:double+ } })
+  }?
+}

src/templates/tallies.rnc

@@ -0,0 +1,50 @@
+element tallies {
+  element mesh {
+    (element id { xsd:int } | attribute id { xsd:int }) &
+    (element type { ( "rectangular" | "hexagonal" ) } |
+      attribute type { ( "rectangular" | "hexagonal" ) }) &
+    (element dimension { list { xsd:int+ } } |
+      attribute dimension { list { xsd:int+ } }) &
+    (element lower_left { list { xsd:double+ } } |
+      attribute lower_left { list { xsd:double+ } }) &
+    (
+      (element upper_right { list { xsd:double+ } } |
+        attribute upper_right { list { xsd:double+ } }) |
+      (element width { list { xsd:double+ } } |
+        attribute width { list { xsd:double+ } })
+    )
+  }* &
+
+  element tally {
+    (element id { xsd:int } | attribute id { xsd:int }) &
+    (element label { xsd:string { maxLength="52" } } |
+      attribute label { xsd:string { maxLength="52" } })? &
+    (element estimator { ( "analog" | "tracklength" ) } |
+      attribute estimator { ( "analog" | "tracklength" ) })? &
+    element filters {
+      (element cell { list { xsd:string { maxLength = "20" } } } |
+        attribute cell { list { xsd:string { maxLength = "20" } } })? &
+      (element surface { list { xsd:string { maxLength = "20" } } } |
+        attribute surface { list { xsd:string { maxLength = "20" } } })? &
+      (element universe { list { xsd:string { maxLength = "20" } } } |
+        attribute universe { list { xsd:string { maxLength = "20" } } })? &
+      (element material { list { xsd:string { maxLength = "20" } } } |
+        attribute material { list { xsd:string { maxLength = "20" } } })? &
+      (element mesh { xsd:int } | attribute mesh { xsd:int })? &
+      (element cellborn { list { xsd:string { maxLength = "20" } } } |
+        attribute cellborn { list { xsd:string { maxLength = "20" } } })? &
+      (element energy { list { xsd:double+ } } |
+        attribute energy { list { xsd:double+ } })? &
+      (element energyout { list { xsd:double+ } } |
+        attribute energyout { list { xsd:double+ } })?
+    }? &
+    element nuclides {
+      list { xsd:string { maxLength = "20" }+ }
+    }? &
+    element scores { 
+      list { xsd:string { maxLength = "12" }+ }
+    }
+  }* &
+
+  element assume_separate { ( "off" | "on" ) }?
+}