Merge commit 'mitcrpgopenmc/develop' into res_scat

Conflicts:

	src/DEPENDENCIES

docs/source/devguide/statepoint.rst

@@ -4,6 +4,296 @@
 State Point Binary File Specifications
 ======================================
 
+-----------
+Revision 11
+-----------
+
+**integer(4) FILETYPE_STATEPOINT**
+
+    Flags whether this file is a statepoint file or a particle restart file.
+
+**integer(4) REVISION_STATEPOINT**
+
+    Revision of the binary state point file. Any time a change is made in the
+    format of the state-point file, this integer is incremented.
+
+**integer(4) VERSION_MAJOR**
+
+    Major version number for OpenMC
+
+**integer(4) VERSION_MINOR**
+
+    Minor version number for OpenMC
+
+**integer(4) VERSION_RELEASE**
+
+    Release version number for OpenMC
+
+**character(19) time_stamp**
+
+    Date and time the state point was written.
+
+**character(255) path**
+
+    Absolute path to directory containing input files.
+
+**integer(8) seed**
+
+    Pseudo-random number generator seed.
+
+**integer(4) run_mode**
+
+    run mode used. The modes are described in constants.F90.
+
+**integer(8) n_particles**
+
+    Number of particles used per generation.
+
+**integer(4) n_batches**
+
+    Total number of batches (active + inactive).
+
+**integer(4) current_batch**
+
+    The number of batches already simulated.
+
+if (run_mode == MODE_EIGENVALUE)
+
+    **integer(4) n_inactive**
+
+        Number of inactive batches
+
+    **integer(4) gen_per_batch**
+
+        Number of generations per batch for criticality calculations
+
+    *do i = 1, current_batch \* gen_per_batch*
+
+        **real(8) k_generation(i)**
+
+             k-effective for the i-th total generation
+
+    *do i = 1, current_batch \* gen_per_batch*
+
+        **real(8) entropy(i)**
+
+            Shannon entropy for the i-th total generation
+
+    **real(8) k_col_abs**
+
+        Sum of product of collision/absorption estimates of k-effective
+
+    **real(8) k_col_tra**
+
+        Sum of product of collision/track-length estimates of k-effective
+
+    **real(8) k_abs_tra**
+
+        Sum of product of absorption/track-length estimates of k-effective
+
+    **real(8) k_combined(2)**
+
+        Mean and standard deviation of a combined estimate of k-effective
+
+    **integer(4) cmfd_on**
+
+        Flag that cmfd is on
+
+    if (cmfd_on)
+
+        **integer(4) cmfd % indices**
+
+            Indices for cmfd mesh (i,j,k,g)
+
+        **real(8) cmfd % k_cmfd(1:current_batch)**
+
+            CMFD eigenvalues
+
+        **real(8) cmfd % src(1:G,1:I,1:J,1:K)**
+
+            CMFD fission source
+
+        **real(8) cmfd % entropy(1:current_batch)**
+
+            CMFD estimate of Shannon entropy
+
+        **real(8) cmfd % balance(1:current_batch)**
+
+            RMS of the residual neutron balance equation on CMFD mesh
+
+        **real(8) cmfd % dom(1:current_batch)**
+
+            CMFD estimate of dominance ratio
+
+        **real(8) cmfd % scr_cmp(1:current_batch)**
+
+            RMS comparison of difference between OpenMC and CMFD fission source
+
+**integer(4) n_meshes**
+
+    Number of meshes in tallies.xml file
+
+*do i = 1, n_meshes*
+
+    **integer(4) meshes(i) % id**
+
+        Unique ID of mesh.
+
+    **integer(4) meshes(i) % type**
+
+        Type of mesh.
+
+    **integer(4) meshes(i) % n_dimension**
+
+        Number of dimensions for mesh (2 or 3).
+
+    **integer(4) meshes(i) % dimension(:)**
+
+        Number of mesh cells in each dimension.
+
+    **real(8) meshes(i) % lower_left(:)**
+
+        Coordinates of lower-left corner of mesh.
+
+    **real(8) meshes(i) % upper_right(:)**
+
+        Coordinates of upper-right corner of mesh.
+
+    **real(8) meshes(i) % width(:)**
+
+        Width of each mesh cell in each dimension.
+
+**integer(4) n_tallies**
+
+*do i = 1, n_tallies*
+
+    **integer(4) tallies(i) % id**
+
+        Unique ID of tally.
+
+    **integer(4) tallies(i) % n_realizations**
+
+        Number of realizations for the i-th tally.
+
+    **integer(4) size(tallies(i) % scores, 1)**
+
+        Total number of score bins for the i-th tally
+
+    **integer(4) size(tallies(i) % scores, 2)**
+
+        Total number of filter bins for the i-th tally
+
+    **integer(4) tallies(i) % n_filters**
+
+    *do j = 1, tallies(i) % n_filters*
+
+        **integer(4) tallies(i) % filter(j) % type**
+
+            Type of tally filter.
+
+        **integer(4) tallies(i) % filter(j) % n_bins**
+
+            Number of bins for filter.
+
+        **integer(4)/real(8) tallies(i) % filter(j) % bins(:)**
+
+            Value for each filter bin of this type.
+
+    **integer(4) tallies(i) % n_nuclide_bins**
+
+        Number of nuclide bins. If none are specified, this is just one.
+
+    *do j = 1, tallies(i) % n_nuclide_bins*
+
+        **integer(4) tallies(i) % nuclide_bins(j)**
+
+            Values of specified nuclide bins
+
+    **integer(4) tallies(i) % n_score_bins**
+
+        Number of scoring bins.
+
+    *do j = 1, tallies(i) % n_score_bins*
+
+        **integer(4) tallies(i) % score_bins(j)**
+
+            Values of specified scoring bins (e.g. SCORE_FLUX).
+            
+    *do j = 1, tallies(i) % n_score_bins*
+
+        **integer(4) tallies(i) % scatt_order(j)**
+
+            Scattering Order specified scoring bins.
+            
+    **integer(4) tallies(i) % n_score_bins**
+
+        Number of scoring bins without accounting for those added by
+        the scatter-pn command.
+
+**integer(4) source_present**
+
+    Flag indicated if source bank is present in the file
+
+**integer(4) n_realizations**
+
+    Number of realizations for global tallies.
+
+**integer(4) N_GLOBAL_TALLIES**
+
+    Number of global tally scores
+
+*do i = 1, N_GLOBAL_TALLIES*
+
+    **real(8) global_tallies(i) % sum**
+
+        Accumulated sum for the i-th global tally
+
+    **real(8) global_tallies(i) % sum_sq**
+
+        Accumulated sum of squares for the i-th global tally
+
+**integer(4) tallies_on**
+
+    Flag indicated if tallies are present in the file.
+
+if (tallies_on > 0)
+
+    *do i = 1, n_tallies*
+
+        *do k = 1, size(tallies(i) % scores, 2)*
+
+            *do j = 1, size(tallies(i) % scores, 1)*
+
+                **real(8) tallies(i) % scores(j,k) % sum**
+            
+                    Accumulated sum for the j-th score and k-th filter of the
+                    i-th tally
+
+                **real(8) tallies(i) % scores(j,k) % sum_sq**
+
+                    Accumulated sum of squares for the j-th score and k-th
+                    filter of the i-th tally
+
+if (run_mode == MODE_EIGENVALUE and source_present)
+
+    *do i = 1, n_particles*
+
+        **real(8) source_bank(i) % wgt**
+
+            Weight of the i-th source particle
+
+        **real(8) source_bank(i) % xyz(1:3)**
+
+            Coordinates of the i-th source particle.
+
+        **real(8) source_bank(i) % uvw(1:3)**
+
+            Direction of the i-th source particle
+
+        **real(8) source_bank(i) % E**
+
+            Energy of the i-th source particle.
+
 -----------
 Revision 10 
 -----------

docs/source/releasenotes/notes_0.5.4.rst

@@ -4,10 +4,6 @@
 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
 -------------------
@@ -21,16 +17,17 @@ the problem at hand (mostly on the number of nuclides in the problem).
 New Features
 ------------
 
-- New XML parsing backend (FoX)
+- Source sites outside geometry are resampled
+- XML-Fortran backend replaced by FoX XML
 - 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
+- Mesh tally plotting utility converted to use Tkinter rather than PyQt
 - Script added to download ACE data from NNDC
 - Mixed ASCII/binary cross_sections.xml now allowed
 - Expanded options for writing source bank
 - Re-enabled ability to use source file as starting source
+- S(a,b) recalculation avoided when same nuclide and S(a,b) table are accessed
 
 ---------
 Bug Fixes
@@ -41,12 +38,16 @@ Bug Fixes
 - 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
+- cf567c_: ENDF/B-VI data checked for compatibility
+- 6b9461_: Fix p_valid sampling inside of sample_energy
 
 .. _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
+.. _cf567c: https://github.com/mit-crpg/openmc/commit/cf567c
+.. _6b9461: https://github.com/mit-crpg/openmc/commit/6b9461
 
 ------------
 Contributors

docs/source/usersguide/input.rst

@@ -470,6 +470,8 @@ attributes/sub-elements:
     source bank will be available. It should be noted that a user can set both 
     this element to "true" and specify batches to write a permanent source bank.
 
+    *Default*: false
+
 ``<survival_biasing>`` Element
 ------------------------------
 

docs/source/usersguide/install.rst

@@ -50,6 +50,15 @@ Prerequisites
 
           sudo apt-get install gfortran
 
+    * CMake_ cross-platform build system
+
+      The compiling and linking of source files is handled by CMake in a
+      platform-independent manner. If you are using Debian or a Debian
+      derivative such as Ubuntu, you can install CMake using the following
+      command::
+
+          sudo apt-get install cmake
+
 .. admonition:: Optional
 
     * An MPI implementation for distributed-memory parallel runs
@@ -74,8 +83,8 @@ Prerequisites
       OpenMC with. HDF5_ must be built with parallel I/O features if you intend
       to use HDF5_ with MPI. An example of configuring HDF5_ is listed below::
 
-           FC=/opt/mpich/3.0.4-gnu/bin/mpif90 CC=/opt/mpich/3.0.4-gnu/bin/mpicc \
-           ./configure --prefix=/opt/hdf5/1.8.11-gnu --enable-fortran \
+           FC=/opt/mpich/3.1/bin/mpif90 CC=/opt/mpich/3.1/bin/mpicc \
+           ./configure --prefix=/opt/hdf5/1.8.12 --enable-fortran \
                        --enable-fortran2003 --enable-parallel
 
       You may omit ``--enable-parallel`` if you want to compile HDF5_ in serial.
@@ -88,8 +97,8 @@ Prerequisites
       requires PETSc_ to be configured with Fortran datatypes. An example of
       configuring PETSc_ is listed below::
 
-           ./configure --prefix=/opt/petsc/3.4.2-gnu --download-f-blas-lapack \
-                       --with-mpi-dir=/opt/mpich/3.0.4-gnu/ --with-shared-libraries=0 \
+           ./configure --prefix=/opt/petsc/3.4.4 --download-f-blas-lapack \
+                       --with-mpi-dir=/opt/mpich/3.1 --with-shared-libraries \
                        --with-fortran-datatypes
 
       The BLAS/LAPACK library is not required to be downloaded and can be linked
@@ -98,6 +107,7 @@ Prerequisites
     * git_ version control software for obtaining source code
 
 .. _gfortran: http://gcc.gnu.org/wiki/GFortran
+.. _CMake: http://www.cmake.org
 .. _OpenMPI: http://www.open-mpi.org
 .. _MPICH: http://www.mpich.org
 .. _HDF5: http://www.hdfgroup.org/HDF5/
@@ -131,50 +141,95 @@ switch to the source of the latest stable release, run the following commands::
 Build Configuration
 -------------------
 
-All configuration for OpenMC is done within the Makefile located in
-``src/Makefile``. In the Makefile, you will see that there are a number of User
-Options which can be changed. It is recommended that you do not change anything
-else in the Makefile unless you are experienced with compiling and building
-software using Makefiles. The following parameters can be set from the User
-Options sections in the Makefile:
+Compiling OpenMC with CMake is carried out in two steps. First, ``cmake`` is run
+to determine the compiler, whether optional packages (MPI, HDF5, PETSc) are
+available, to generate a list of dependencies between source files so that they
+may be compiled in the correct order, and to generate a normal Makefile. The
+Makefile is then used by ``make`` to actually carry out the compile and linking
+commands. A typical out-of-source build would thus look something like the
+following
 
-COMPILER
-  This variable tells the Makefile which compiler to use. Valid options are
-  gnu, intel, pgi, ibm, and cray. The default is gnu (gfortran).
+.. code-block:: sh
 
-DEBUG
+    mkdir src/build
+    cd src/build
+    cmake ..
+    make
+
+Note that first a build directory is created as a subdirectory of the source
+directory. The Makefile in ``src/`` will automatically perform an out-of-source
+build with default options.
+
+CMakeLists.txt Options
+++++++++++++++++++++++
+
+The following options are available in the CMakeLists.txt file:
+
+debug
   Enables debugging when compiling. The flags added are dependent on which
   compiler is used.
 
-PROFILE
+profile
   Enables profiling using the GNU profiler, gprof.
 
-OPTIMIZE
+optimize
   Enables high-optimization using compiler-dependent flags. For gfortran and
   Intel Fortran, this compiles with -O3.
 
-MPI
-  Enables parallel runs using the Message Passing Interface. The MPI_DIR
-  variable should be set to the base directory of the MPI implementation.
-
-OPENMP
+openmp
   Enables shared-memory parallelism using the OpenMP API. The Fortran compiler
   being used must support OpenMP.
 
-HDF5
-  Enables HDF5 output in addition to normal screen and text file output. The
-  HDF5_DIR variable should be set to the base directory of the HDF5
-  installation.
-
-PETSC
+petsc
   Enables PETSc for use in CMFD acceleration. The PETSC_DIR variable should be
   set to the base directory of the PETSc installation.
 
-It is also possible to change these options from the command line itself. For
-example, if you want to compile with DEBUG turned on without actually change the
-Makefile, you can enter the following from a terminal::
+To set any of these options (e.g. turning on debug mode), the following form
+should be used:
 
-    make DEBUG=yes
+.. code-block:: sh
+
+    cmake -Ddebug=on /path/to/src
+
+Compiling with MPI
+++++++++++++++++++
+
+To compile with MPI, set the :envvar:`FC` environment variable to the path to
+the MPI Fortran wrapper. For example, in a bash shell:
+
+.. code-block:: sh
+
+    export FC=mpif90
+    cmake /path/to/src
+
+Note that in many shells, an environment variable can be set for a single
+command, i.e.
+
+.. code-block:: sh
+
+    FC=mpif90 cmake /path/to/src
+
+Compiling with HDF5
++++++++++++++++++++
+
+To compile with MPI, set the :envvar:`FC` environment variable to the path to
+the HDF5 Fortran wrapper. For example, in a bash shell:
+
+.. code-block:: sh
+
+    export FC=h5fc
+    cmake /path/to/src
+
+As noted above, an environment variable can typically be set for a single
+command, i.e.
+
+.. code-block:: sh
+
+    FC=h5fc cmake /path/to/src
+
+To compile with support for both MPI and HDF5, use the parallel HDF5 wrapper
+``h5pfc`` instead. Note that this requires that your HDF5 installation be
+compiled with ``--enable-parallel``.
 
 Compiling on Linux and Mac OS X
 -------------------------------
@@ -210,9 +265,10 @@ a Linux-like environment for Windows. You will need to first `install
 Cygwin`_. When you are asked to select packages, make sure the following are
 selected:
 
-* Devel: gcc4-core
-* Devel: gcc4-fortran
+* Devel: gcc-core
+* Devel: gcc-fortran
 * Devel: make
+* Devel: cmake
 
 If you plan on obtaining the source code directly using git, select the
 following packages: