Merge branch 'develop' into read_sourcefile

docs/source/quickinstall.rst

@@ -48,7 +48,12 @@ following commands in a terminal:
     sudo make install
 
 This will build an executable named ``openmc`` and install it (by default in
-/usr/local/bin).
+/usr/local/bin). If you do not have administrator privileges, the last command
+can be replaced with a local install, e.g.
+
+.. code-block:: sh
+
+    make install -e prefix=$HOME/.local
 
 .. _GitHub: https://github.com/mit-crpg/openmc
 .. _git: http://git-scm.com

docs/source/releasenotes/index.rst

@@ -10,6 +10,7 @@ bugs fixed, and known issues for each successive release.
 .. toctree::
     :maxdepth: 1
 
+    notes_0.5.4
     notes_0.5.3
     notes_0.5.2
     notes_0.5.1

docs/source/releasenotes/notes_0.5.4.rst

@@ -0,0 +1,61 @@
+.. _notes_0.5.4:
+
+==============================
+Release Notes for OpenMC 0.5.4
+==============================
+
+.. note::
+    These release notes are for an upcoming release of OpenMC and are still
+    subject to change.
+
+-------------------
+System Requirements
+-------------------
+
+There are no special requirements for running the OpenMC code. As of this
+release, OpenMC has been tested on a variety of Linux distributions, Mac OS X,
+and Microsoft Windows 7. Memory requirements will vary depending on the size of
+the problem at hand (mostly on the number of nuclides in the problem).
+
+------------
+New Features
+------------
+
+- New XML parsing backend (FoX)
+- Ability to write particle track files
+- Handle lost particles more gracefully (via particle track files)
+- Source sites outside geometry are resampled
+- Multiple random number generator streams
+- plot_mesh_tally.py utility converted to use Tkinter rather than PyQt
+- Script added to download ACE data from NNDC
+- Mixed ASCII/binary cross_sections.xml now allowed
+
+---------
+Bug Fixes
+---------
+
+- 32c03c_: Check for valid data in cross_sections.xml
+- c71ef5_: Fix bug in statepoint.py
+- 8884fb_: Check for all ZAIDs for S(a,b) tables
+- b38af0_: Fix XML reading on multiple levels of input
+- d28750_: Fix bug in convert_xsdir.py
+
+.. _32c03c: https://github.com/mit-crpg/openmc/commit/32c03c
+.. _c71ef5: https://github.com/mit-crpg/openmc/commit/c71ef5
+.. _8884fb: https://github.com/mit-crpg/openmc/commit/8884fb
+.. _b38af0: https://github.com/mit-crpg/openmc/commit/b38af0
+.. _d28750: https://github.com/mit-crpg/openmc/commit/d28750
+
+------------
+Contributors
+------------
+
+This release contains new contributions from the following people:
+
+- `Sterling Harper <smharper@mit.edu>`_
+- `Bryan Herman <bherman@mit.edu>`_
+- `Nick Horelik <nhorelik@mit.edu>`_
+- `Adam Nelson <nelsonag@umich.edu>`_
+- `Paul Romano <paul.k.romano@gmail.com>`_
+- `Tuomas Viitanen <tuomas.viitanen@vtt.fi>`_
+- `Jon Walsh <walshjon@mit.edu>`_

docs/source/usersguide/input.rst

@@ -1089,7 +1089,7 @@ sub-elements:
               the PNG format can often times reduce the file size by orders of
               magnitude without any loss of image quality. Likewise,
               high-resolution voxel files produced by OpenMC can be quite large,
-              but the equivalent SILO files will by significantly smaller.
+              but the equivalent SILO files will be significantly smaller.
 
     *Default*: "slice"
 

docs/source/usersguide/install.rst

@@ -189,7 +189,15 @@ the root directory of the source code:
     sudo make install
 
 This will build an executable named ``openmc`` and install it (by default in
-/usr/local/bin).
+/usr/local/bin). If you do not have administrative privileges, you can install
+OpenMC locally by replacing the last command with:
+
+.. code-block:: sh
+
+    make install -e prefix=$HOME/.local
+
+The ``prefix`` variable can be changed to any path for which you have
+write-access.
 
 Compiling on Windows
 --------------------

docs/source/usersguide/troubleshoot.rst

@@ -79,6 +79,14 @@ with the :envvar:`CROSS_SECTIONS` environment variable. It is recommended to add
 a line in your ``.profile`` or ``.bash_profile`` setting the
 :envvar:`CROSS_SECTIONS` environment variable.
 
+ERROR: Invalid usage of L(I) in ACE data; Consider using more recent data set.
+******************************************************************************
+
+The cross-sections requested in ``materials.xml`` do not conform to the current
+standard format.  This typically happens with fissionable nuclides in a ``.6*c``
+library as distributed with MCNP.  Please try a newer library such as any from
+the ``.7*c`` set.
+
 Geometry Debugging
 ******************
 
@@ -107,8 +115,8 @@ have many particles travelling through them there will not be many locations
 where overlaps are checked for in that region.  The user should refer to the
 output after a geometry debug run to see how many checks were performed in each
 cell, and then adjust the number of starting particles or starting source
-distributions accordingly to achieve good coverage. 
- 
+distributions accordingly to achieve good coverage.
+
 ERROR: After particle __ crossed surface __ it could not be located in any cell and it did not leak.
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

src/ace.F90

@@ -942,6 +942,7 @@ contains
     integer :: NEa   ! number of energies for Watt 'a'
     integer :: NRb   ! number of interpolation regions for Watt 'b'
     integer :: NEb   ! number of energies for Watt 'b'
+    real(8), allocatable :: L(:)  ! locations of distributions for each Ein
 
     ! initialize length
     length = 0
@@ -966,6 +967,22 @@ contains
       ! Continuous tabular distribution
       NR = int(XSS(lc + 1))
       NE = int(XSS(lc + 2 + 2*NR))
+      ! Before progressing, check to see if data set uses L(I) values
+      ! in a way inconsistent with the current form of the ACE Format Guide
+      ! (MCNP5 Manual, Vol 3)
+      allocate(L(NE))
+      L = int(XSS(lc + 3 + 2*NR + NE: lc + 3 + 2*NR + 2*NE - 1))
+      do i = 1,NE
+        ! Now check to see if L(i) is equal to any other entries
+        ! If so, then we must exit
+        if (count(L == L(i)) > 1) then
+          message = "Invalid usage of L(I) in ACE data; &
+                    &Consider using more recent data set."
+          call fatal_error()
+        end if
+      end do
+      deallocate(L)
+      ! Continue with finding data length
       length = length + 2 + 2*NR + 2*NE
       do i = 1,NE
         ! determine length
@@ -1008,6 +1025,22 @@ contains
       ! Kalbach-Mann correlated scattering
       NR = int(XSS(lc + 1))
       NE = int(XSS(lc + 2 + 2*NR))
+      ! Before progressing, check to see if data set uses L(I) values
+      ! in a way inconsistent with the current form of the ACE Format Guide
+      ! (MCNP5 Manual, Vol 3)
+      allocate(L(NE))
+      L = int(XSS(lc + 3 + 2*NR + NE: lc + 3 + 2*NR + 2*NE - 1))
+      do i = 1,NE
+        ! Now check to see if L(i) is equal to any other entries
+        ! If so, then we must exit
+        if (count(L == L(i)) > 1) then
+          message = "Invalid usage of L(I) in ACE data; &
+                    &Consider using more recent data set."
+          call fatal_error()
+        end if
+      end do
+      deallocate(L)
+      ! Continue with finding data length
       length = length + 2 + 2*NR + 2*NE
       do i = 1,NE
         NP = int(XSS(lc + length + 2))
@@ -1022,6 +1055,22 @@ contains
       ! Correlated energy and angle distribution
       NR = int(XSS(lc + 1))
       NE = int(XSS(lc + 2 + 2*NR))
+      ! Before progressing, check to see if data set uses L(I) values
+      ! in a way inconsistent with the current form of the ACE Format Guide
+      ! (MCNP5 Manual, Vol 3)
+      allocate(L(NE))
+      L = int(XSS(lc + 3 + 2*NR + NE: lc + 3 + 2*NR + 2*NE - 1))
+      do i = 1,NE
+        ! Now check to see if L(i) is equal to any other entries
+        ! If so, then we must exit
+        if (count(L == L(i)) > 1) then
+          message = "Invalid usage of L(I) in ACE data; &
+                    &Consider using more recent data set."
+          call fatal_error()
+        end if
+      end do
+      deallocate(L)
+      ! Continue with finding data length
       length = length + 2 + 2*NR + 2*NE
       do i = 1,NE
         ! outgoing energy distribution
@@ -1054,6 +1103,22 @@ contains
       ! Laboratory energy-angle law
       NR  = int(XSS(lc + 1))
       NE  = int(XSS(lc + 2 + 2*NR))
+      ! Before progressing, check to see if data set uses L(I) values
+      ! in a way inconsistent with the current form of the ACE Format Guide
+      ! (MCNP5 Manual, Vol 3)
+      allocate(L(NE))
+      L = int(XSS(lc + 3 + 2*NR + NE: lc + 3 + 2*NR + 2*NE - 1))
+      do i = 1,NE
+        ! Now check to see if L(i) is equal to any other entries
+        ! If so, then we must exit
+        if (count(L == L(i)) > 1) then
+          message = "Invalid usage of L(I) in ACE data; &
+                    &Consider using more recent data set."
+          call fatal_error()
+        end if
+      end do
+      deallocate(L)
+      ! Continue with finding data length
       NMU = int(XSS(lc + 4 + 2*NR + 2*NE))
       length = 4 + 2*(NR + NE + NMU)
 

src/constants.F90

@@ -11,7 +11,7 @@ module constants
   integer, parameter :: VERSION_RELEASE = 3
 
   ! Revision numbers for binary files
-  integer, parameter :: REVISION_STATEPOINT       = 10
+  integer, parameter :: REVISION_STATEPOINT       = 11
   integer, parameter :: REVISION_PARTICLE_RESTART = 1
 
   ! Binary file types

src/initialize.F90

@@ -390,7 +390,7 @@ contains
               ! It is a source file
               path_source_point = argv(i)
 
-            else
+            else ! Different option is specified not a source file
 
               ! Source is in statepoint file
               path_source_point = path_state_point
@@ -399,6 +399,12 @@ contains
               i = i - 1
 
             end if
+
+          else ! No command line arg after statepoint
+
+            ! Source is assumed to be in statepoint file
+            path_source_point = path_state_point
+
           end if
 
         case ('-g', '-geometry-debug', '--geometry-debug')

src/input_xml.F90

@@ -58,7 +58,6 @@ contains
     integer(8) :: temp_long
     integer :: n_tracks
     logical :: file_exists
-    logical :: check
     character(MAX_FILE_LEN) :: env_variable
     character(MAX_WORD_LEN) :: type
     character(MAX_LINE_LEN) :: filename
@@ -670,14 +669,14 @@ contains
       end if
 
       ! Check if the user has specified to write binary source file
-      if (check_for_node(node_sp, "source_separate")) then
-        call get_node_value(node_sp, "source_separate", temp_str)
+      if (check_for_node(node_sp, "separate")) then
+        call get_node_value(node_sp, "separate", temp_str)
         call lower_case(temp_str)
         if (trim(temp_str) == 'true' .or. &
              trim(temp_str) == '1') source_separate = .true.
       end if
-      if (check_for_node(node_sp, "source_write")) then
-        call get_node_value(node_sp, "source_write", temp_str)
+      if (check_for_node(node_sp, "write")) then
+        call get_node_value(node_sp, "write", temp_str)
         call lower_case(temp_str)
         if (trim(temp_str) == 'false' .or. &
              trim(temp_str) == '0') source_write = .false.
@@ -702,10 +701,9 @@ contains
     ! make sure that the sourcepoint batch numbers are contained in the
     ! statepoint list
     if (.not. source_separate) then
-      check = .true.
       do i = 1, n_source_points
-        check = statepoint_batch % contains(sourcepoint_batch % get_item(i))
-        if (.not. check) then
+        if (.not. statepoint_batch % contains(sourcepoint_batch % &
+            get_item(i))) then
           message = 'Sourcepoint batches are not a subset&
                     & of statepoint batches.'
           call fatal_error()

src/relaxng/settings.rnc

@@ -101,11 +101,11 @@ element settings {
         attribute batches { list { xsd:positiveInteger+ } }) |
       (element interval { xsd:positiveInteger } | 
         attribute interval { xsd:positiveInteger })
-    ) &
-    (element source_separate { xsd:boolean } | 
-      attribute source_separate { xsd:boolean })? &
-    (element source_write { xsd:boolean } | 
-      attribute source_write { xsd:boolean })? &
+    )? &
+    (element separate { xsd:boolean } | 
+      attribute separate { xsd:boolean })? &
+    (element write { xsd:boolean } | 
+      attribute write { xsd:boolean })? &
     (element overwrite_latest { xsd:boolean} |
       attribute overwrite_latest {xsd:boolean})?
   }? &

src/state_point.F90

@@ -232,6 +232,13 @@ contains
 
     end if
 
+    ! Indicate where source bank is stored in statepoint
+    if (source_separate) then
+      call sp % write_data(0, "source_present")
+    else
+      call sp % write_data(1, "source_present")
+    end if
+
     ! Check for the no-tally-reduction method
     if (.not. reduce_tallies) then
       ! If using the no-tally-reduction method, we need to collect tally
@@ -518,6 +525,7 @@ contains
     integer                 :: length(4)
     integer                 :: int_array(3)
     integer, allocatable    :: temp_array(:)
+    logical                 :: source_present
     real(8)                 :: real_array(3) 
     type(TallyObject), pointer :: t => null()
 
@@ -722,6 +730,20 @@ contains
 
     end do TALLY_METADATA
 
+    ! Check for source in statepoint if needed
+    call sp % read_data(int_array(1), "source_present")
+    if (int_array(1) == 1) then
+      source_present = .true.
+    else
+      source_present = .false.
+    end if
+
+    ! Check to make sure source bank is present
+    if (path_source_point == path_state_point .and. .not. source_present) then
+      message = "Source bank must be contained in statepoint restart file"
+      call fatal_error()
+    end if 
+
     ! Read tallies to master
     if (master) then
 
@@ -762,26 +784,17 @@ contains
     if (run_mode == MODE_EIGENVALUE) then
 
       ! Check if source was written out separately
-      if (source_separate) then
+      if (.not. source_present) then
 
         ! Close statepoint file 
         call sp % file_close()
 
-        ! Set filename for source
-        filename = trim(path_output) // 'source.' // &
-                   trim(to_str(restart_batch))
-#ifdef HDF5
-        filename = trim(filename) // '.h5'
-#else
-        filename = trim(filename) // '.binary'
-#endif
-
         ! Write message
         message = "Loading source file " // trim(filename) // "..."
         call write_message(1)
 
         ! Open source file 
-        call sp % file_open(filename, 'r', serial = .false.)
+        call sp % file_open(path_source_point, 'r', serial = .false.)
 
         ! Read file type
         call sp % read_data(int_array(1), "filetype")

src/utils/statepoint.py

@@ -151,7 +151,7 @@ class StatePoint(object):
 
         # Read statepoint revision
         self.revision = self._get_int(path='revision')[0]
-        if self.revision != 10:
+        if self.revision != 11:
           raise Exception('Statepoint Revision is not consistent.')
 
         # Read OpenMC version
@@ -298,6 +298,13 @@ class StatePoint(object):
                 f.stride = stride
                 stride *= f.length
 
+        # Source bank present
+        source_present = self._get_int(path='source_present')[0]
+        if source_present == 1:
+            self.source_present = True       
+        else:
+            self.source_present = False
+
         # Set flag indicating metadata has already been read
         self._metadata = True
 
@@ -342,6 +349,11 @@ class StatePoint(object):
         if not self._results:
             self.read_results()
 
+        # Check if source bank is in statepoint
+        if not self.source_present:
+            print('Source not in statepoint file.')
+            return
+
         # For HDF5 state points, copy entire bank
         if self._hdf5:
             source_sites = self._f['source_bank'].value

tests/cleanup

@@ -1,3 +1,5 @@
+#!/bin/bash
+
 # This simple script ensures that all binary
 # output files have been deleted in all the
 # folders. This can occur if a previous error
@@ -5,10 +7,4 @@
 # deleting left over binary files. This will
 # cause an assertion error in some of the 
 # tests.
-for i in ./*; do
-  if [ -d "$i" ]; then
-    cd $i
-    rm -f *.binary *.h5
-    cd ..
-  fi
-done
+find . \( -name "*.binary" -o -name "*.h5" \) -exec rm -f {} \;

tests/run_tests.py

@@ -117,6 +117,8 @@ if len(sys.argv) > 1:
                     if j.rfind(suffix) != -1:
                         if suffix == 'omp' and j == 'compile':
                             continue
+                        if j == 'compile':
+                            continue 
                         tests__.append(j)
         else:
             tests__.append(i)  # append specific test (e.g., mpi-debug)

tests/test_sourcepoint_latest/settings.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <settings>
 
-  <source_point batches="0" source_separate="true" overwrite_latest="true"/>
+  <source_point batches="0" separate="true" overwrite_latest="true"/>
 
   <eigenvalue>
     <batches>10</batches>

tests/test_sourcepoint_restart/settings.xml

@@ -2,7 +2,7 @@
 <settings>
 
   <state_point batches="7 10" />
-  <source_point batches="7" source_separate="true" />
+  <source_point batches="7" separate="true" />
 
   <eigenvalue>
     <batches>10</batches>

tests/test_statepoint_sourcesep/settings.xml

@@ -2,7 +2,7 @@
 <settings>
 
   <state_point batches="10" />
-  <source_point source_separate="true" />
+  <source_point separate="true" />
 
   <eigenvalue>
     <batches>10</batches>