Updated documentation for CMFD merge.

_sources/devguide/index.txt

@@ -13,5 +13,7 @@ as debugging.
     :maxdepth: 2
 
     structures
+    styleguide
+    workflow
     xml-fortran
     statepoint

_sources/devguide/statepoint.txt

@@ -4,6 +4,621 @@
 State Point Binary File Specifications
 ======================================
 
+----------
+Revision 5
+----------
+
+**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.
+
+**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_CRITICALITY)
+
+    **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*
+
+        **real(8) k_batch(i)**
+
+             k-effective for the i-th batch
+
+    *do i = 1, current_batch*
+
+        **real(8) entropy(i)**
+
+            Shannon entropy for the i-th batch
+
+**integer(4) n_meshes**
+
+    Number of meshes in tallies.xml file
+
+*do i = 1, n_meshes*
+
+    **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) % 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).
+
+**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_CRITICALITY)
+
+    *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 4
+----------
+
+**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.
+
+**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_CRITICALITY)
+
+    **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*
+
+        **real(8) k_batch(i)**
+
+             k-effective for the i-th batch
+
+    *do i = 1, current_batch*
+
+        **real(8) entropy(i)**
+
+            Shannon entropy for the i-th batch
+
+**integer(4) n_meshes**
+
+    Number of meshes in tallies.xml file
+
+*do i = 1, n_meshes*
+
+    **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) 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).
+
+**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)
+
+    **integer(4) n_realizations**
+
+        Number of realizations for tally random variables.
+
+    *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_CRITICALITY)
+
+    *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 3
+----------
+
+**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.
+
+**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_CRITICALITY)
+
+    **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*
+
+        **real(8) k_batch(i)**
+
+             k-effective for the i-th batch
+
+    *do i = 1, current_batch*
+
+        **real(8) entropy(i)**
+
+            Shannon entropy for the i-th batch
+
+**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) n_meshes**
+
+    Number of meshes in tallies.xml file
+
+*do i = 1, n_meshes*
+
+    **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) 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).
+
+**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_CRITICALITY)
+
+    *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 2
 ----------
@@ -57,7 +672,9 @@ Revision 2
 
     if (entropy_on)
 
-        **real(8) entropy for the i-th batch**
+        **real(8) entropy(i)**
+
+            Shannon entropy for the i-th batch
 
 **integer(4) N_GLOBAL_TALLIES**
 
@@ -156,7 +773,9 @@ Revision 1
 
     if (entropy_on)
 
-        **real(8) entropy for the i-th batch**
+        **real(8) entropy(i)**
+
+            Shannon entropy for the i-th batch
 
 **integer(4) N_GLOBAL_TALLIES**
 

_sources/devguide/structures.txt

@@ -4,3 +4,86 @@
 Data Structures
 ===============
 
+The purpose of this section is to give you an overview of the major data
+structures in OpenMC and how they are logically related. A majority of variables
+in OpenMC are `derived types`_ (similar to a struct in C). These derived types
+are defined in the various header modules, e.g. src/geometry_header.F90. Most
+important variables are found in the `global module`_. Have a look through that
+module to get a feel for what variables you'll often come across when looking at
+OpenMC code.
+
+--------
+Particle
+--------
+
+Perhaps the variable that you will see most often is simply called ``p`` and is
+of type(Particle). This variable stores information about a particle's physical
+characteristics (coordinates, direction, energy), what cell and material it's
+currently in, how many collisions it has undergone, etc. In practice, only one
+particle is followed at a time so there is no array of type(Particle). The
+Particle type is defined in the `particle_header module`_.
+
+You will notice that the direction and angle of the particle is stored in a
+linked list of type(LocalCoord). In geometries with multiple :ref:`universes`,
+the coordinates in each universe are stored in this linked list. If universes or
+lattices are not used in a geometry, only one LocalCoord is present in the
+linked list.
+
+The LocalCoord type has a component called cell which gives the index in the
+``cells`` array in the `global module`_. The ``cells`` array is of type(Cell)
+and stored information about each region defined by the user.
+
+----
+Cell
+----
+
+The Cell type is defined in the `geometry_header module`_ along with other
+geometry-related derived types. Each cell in the problem is described in terms
+of its bounding surfaces, which are listed on the ``surfaces`` component. The
+absolute value of each item in the ``surfaces`` component contains the index of
+the corresponding surface in the ``surfaces`` array defined in the `global
+module`_. The sign on each item in the ``surfaces`` component indicates whether
+the cell exists on the positive or negative side of the surface (see
+:ref:`methods_geometry`).
+
+Each cell can either be filled with another universe/lattice or with a
+material. If it is filled with a material, the ``material`` component gives the
+index of the material in the ``materials`` array defined in the `global
+module`_.
+
+-------
+Surface
+-------
+
+The Surface type is defined in the `geometry_header module`_. A surface is
+defined by a type (sphere, cylinder, etc.) and a list of coefficients for that
+surface type. The simplest example would be a plane perpendicular to the xy, yz,
+or xz plane which needs only one parameter. The ``type`` component indicates the
+type through integer parameters such as SURF_SPHERE or SURF_CYL_Y (these are
+defined in the `constants module`_). The ``coeffs`` component gives the
+necessary coefficients to parameterize the surface type (see
+:ref:`surface_element`).
+
+--------
+Material
+--------
+
+The Material type is defined in the `material_header module`_. Each material
+contains a number of nuclides at a given atom density. Each item in the
+``nuclide`` component corresponds to the index in the global ``nuclides`` array
+(as usual, found in the `global module`_). The ``atom_density`` component is the
+same length as the ``nuclides`` component and lists the corresponding atom
+density in atom/barn-cm for each nuclide in the ``nuclides`` component.
+
+If the material contains nuclides for which binding effects are important in
+low-energy scattering, a :math:`S(\alpha,\beta)` can be associated with that
+material through the ``sab_table`` component. Again, this component contains the
+index in the ``sab_tables`` array from the `global module`_.
+
+
+.. _derived types: http://nf.nci.org.au/training/FortranAdvanced/slides/slides.025.html
+.. _global module: https://github.com/mit-crpg/openmc/blob/master/src/global.F90
+.. _particle_header module: https://github.com/mit-crpg/openmc/blob/master/src/particle_header.F90
+.. _geometry_header module: https://github.com/mit-crpg/openmc/blob/master/src/geometry_header.F90
+.. _constants module: https://github.com/mit-crpg/openmc/blob/master/src/constants.F90
+.. _material_header module: https://github.com/mit-crpg/openmc/blob/master/src/material_header.F90

_sources/devguide/styleguide.txt

@@ -0,0 +1,144 @@
+.. _devguide_styleguide:
+
+======================
+Style Guide for OpenMC
+======================
+
+In order to keep the OpenMC code base consistent in style, this guide specifies
+a number of rules which should be adhered to when modified existing code or
+adding new code in OpenMC.
+
+-------------
+General Rules
+-------------
+
+Conform to the Fortran 2008 standard.
+
+Make sure code can be compiled with most common compilers, especially gfortran
+and the Intel Fortran compiler. This supercedes the previous rule --- if a
+Fortran 2003/2008 feature is not implemented in a common compiler, do not use
+it.
+
+Do not use special extensions that can be only be used from certain compilers.
+
+In general, write your code in lower-case. Having code in all caps does not
+enhance code readability or otherwise.
+
+Always include comments to describe what your code is doing. Do not be afraid of
+using copious amounts of comments.
+
+Use <, >, <=, >=, ==, and /= rather than .lt., .gt., .le., .ge., .eq., and .ne.
+
+Try to keep code within 80 columns when possible.
+
+Don't use ``print *`` or ``write(*,*)``. If writing to a file, use a specific
+unit. Writing to standard output or standard error should be handled by the
+``write_message`` subroutine or functionality in the error module.
+
+-------------------------
+Subroutines and Functions
+-------------------------
+
+Above each subroutine/function, include a comment block giving a brief
+description of what the subroutine or function does.
+
+Arguments to subroutines/functions should be explicitly specified as intent(in),
+intent(out), or intent(inout).
+
+Include a comment describing what each argument to a subroutine/function is.
+
+---------
+Variables
+---------
+
+Never, under any circumstances, should implicit variables be used! Always
+include ``implicit none`` and define all your variables.
+
+Variable names should be all lower-case and descriptive, i.e. not a random
+assortment of letters that doesn't give any information to someone seeing it for
+the first time. Variables consisting of multiple words should be separated by
+underscores, not hyphens or in camel case.
+
+Constant (parameter) variables should be in ALL CAPITAL LETTERS and defined in
+in the constants.F90 module.
+
+32-bit reals (real(4)) should never be used. Always use 64-bit reals (real(8)).
+
+For arbitrary length character variables, use the pre-defined lengths
+MAX_LINE_LEN, MAX_WORD_LEN, and MAX_FILE_LEN if possible.
+
+Do not use old-style character/array length (e.g. character*80, real*8).
+
+Integer values being used to indicate a certain state should be defined as named
+constants (see the constants.F90 module for many examples).
+
+Yes:
+
+.. code-block:: fortran
+
+    if (boundary_condition == BC_VACUUM) then
+
+No:
+
+.. code-block:: fortran
+
+    if (boundary_condition == -10) then
+
+Avoid creating arrays with a pre-defined maximum length. Use dynamic memory
+allocation instead. Use allocatable variables instead of pointer variables when
+possible.
+
+Shared/Module Variables
+-----------------------
+
+Always put shared variables in modules. Access module variables through a
+``use`` statement. Always use the ``only`` specifier on the ``use`` statement
+except for variables from the global, constants, and various header modules.
+
+Never use ``equivalence`` statements, ``common`` blocks, or ``data`` statements.
+
+-------------------------
+Derived Types and Classes
+-------------------------
+
+Derived types and classes should have CamelCase names with words not separated
+by underscores or hyphens.
+
+-----------
+Indentation
+-----------
+
+Never use tab characters. Indentation should always be applied using
+spaces. Emacs users should include the following line in their .emacs file:
+
+.. code-block:: common-lisp
+
+    (setq-default indent-tabs-mode nil)
+
+vim users should include the following line in their .vimrc file::
+
+    set expandtab
+
+Use 2 spaces per indentation level. This applies to all constructs such as
+program, subroutine, function, if, associate, etc. Emacs users should set the
+variables f90-if-indent, f90-do-indent, f90-continuation-indent,
+f90-type-indent, f90-associate-indent, and f90-program indent to 2.
+
+Continuation lines should be indented by an extra 5 spaces. This is the default
+value of f90-continuation-indent in Emacs.
+
+-------------------------
+Whitespace in Expressions
+-------------------------
+
+Avoid extraneous whitespace in the following situations:
+
+- In subroutine/function calls::
+
+    Yes: call somesub(x, y(2), z)
+    No:  call somesub( x, y( 2 ), z )
+
+- In logical expressions, use one space around operators but nowhere else::
+
+    Yes: if (variable == 2) then
+    No:  if ( variable==2 ) then

_sources/devguide/workflow.txt

@@ -0,0 +1,45 @@
+.. _devguide_workflow:
+
+====================
+Development Workflow
+====================
+
+Anyone wishing to make contributions to OpenMC should be fully acquianted and
+comfortable working with git_ and GitHub_. The primary means of modifying and
+making contributions to OpenMC is through GitHub `pull requests`_. This is
+what's known as a fork and pull development model. The steps for this are as
+follows:
+
+1. Fork the main openmc repository from `mit-crpg/openmc`_. This will create a
+repository with the same name under your personal account. As such, you can
+commit to it as you please without disrupting other developers.
+
+2. Create a branch that you want merged back to `mit-crpg/openmc`_ and make
+commits that you intend to go back. If you have made other changes that should
+not be merged back, those changes should be on another branch.
+
+3. Issue a pull request from GitHub and select the branch you want merged.
+
+4. The OpenMC integration manager will review your pull request and make sure it
+conforms to the :ref:`devguide_styleguide`, compiles correctly, runs in parallel
+correctly, does not break other features in the code, etc. Any issues with the
+pull request can be discussed directly on the pull request page itself.
+
+5. After the pull request has been thoroughly vetted, it is merged back into
+`mit-crpg/openmc`_.
+
+While the process above depends on the fork of the OpenMC repository being
+publicly available on GitHub, you may also wish to do development on a private
+repository for research or commercial purposes. The proper way to do this is to
+create a complete copy of the OpenMC repository (not a fork from GitHub). The
+private repository can then either be stored just locally or in conjunction with
+a private repository on Github (this requires a `paid plan`_). If you want to
+merge some changes you've made in your private repository back to
+`mit-crpg/openmc`_ repository, simply follow the steps above with an extra step
+of pulling a branch from your private repository into your public fork.
+
+.. _git: http://git-scm.com/
+.. _GitHub: https://github.com/
+.. _pull requests: https://help.github.com/articles/using-pull-requests
+.. _mit-crpg/openmc: https://github.com/mit-crpg/openmc
+.. _paid plan: https://github.com/plans

_sources/devguide/xml-fortran.txt

@@ -4,3 +4,37 @@
 xml-fortran Input Parsing
 =========================
 
+OpenMC relies on the xml-fortran package for reading and intrepreting the XML
+input files for geometry, materials, settings, tallies, etc. The use of an XML
+format makes writing input files considerably more flexible than would otherwise
+be possible.
+
+With the xml-fortran package, extending the user input files to include new tags
+is fairly straightforward. A "template" file exists for each diferent type of
+input file that tells xml-fortran what to expect in a file. These template files
+can be found in the src/templates directory. The steps for modifying/adding
+input are as follows:
+
+1. Add a ``<variable>``` tag to the desired template file,
+e.g. src/templates/geometry_t.xml. See the `xml-fortran documentation`_ for a
+description of the acceptable fields.
+
+2. In the input_xml module, any input given in your new tag will be read
+automatically through a call to, e.g. read_xml_file_geometry_t. Whatever
+variable name you specified should have the data available.
+
+3. Add code in the appropriate subroutine to check the variable for any possible
+errors.
+
+4. Add a variable in OpenMC to copy the temporary variable into if there are no
+errors.
+
+A set of `RELAX NG`_ schemata exists that enables real-time validation of input
+files when using the GNU Emacs text editor. You should also modify the RELAX NG
+schema for the template you changed (e.g. src/templates/geometry.rnc) so that
+those who use Emacs can confirm whether their input is valid before they
+run. You will need to be familiar with RELAX NG `compact syntax`_.
+
+.. _xml-fortran documentation: http://xml-fortran.sourceforge.net/documentation.html
+.. _RELAX NG: http://relaxng.org/
+.. _compact syntax: http://relaxng.org/compact-tutorial-20030326.html

_sources/methods/geometry.txt

@@ -64,6 +64,8 @@ In OpenMC, any second-order surface of the form
 can be modeled in OpenMC. For example, the equation for a sphere centered at
 :math:`(\bar{x},\bar{y},\bar{z})` and of radius :math:`R` can be written as
 
+.. _universes:
+
 Universes
 ---------
 

_sources/publications.txt

@@ -5,18 +5,18 @@ Publications
 ============
 
 - Paul K. Romano and Benoit Forget, "Reducing Parallel Communication in Monte
-  Carlo Simulations via Batch Statistics," *Trans. Am. Nucl. Soc.*, Accepted
-  (2012).
+  Carlo Simulations via Batch Statistics," *Trans. Am. Nucl. Soc.*, **107**,
+  xxx--xxx (2012).
 
 - Paul K. Romano and Benoit Forget, "The OpenMC Monte Carlo Particle Transport
-  Code," *Annals of Nuclear Energy*, Accepted (2012).
+  Code," *Ann. Nucl. Energy*, **51**, 274--281
+  (2012). `<http://dx.doi.org/10.1016/j.anucene.2012.06.040>`_
 
 - Andrew R. Siegel, Kord Smith, Paul K. Romano, Benoit Forget, and Kyle Felker,
   "The effect of load imbalances on the performance of Monte Carlo codes in LWR
-  analysis", *Journal of Computational Physics*,
+  analysis", *J. Comput. Phys.*,
   `<http://dx.doi.org/10.1016/j.jcp.2012.06.012>`_ (2012).
 
 - Paul K. Romano and Benoit Forget, "Parallel Fission Bank Algorithms in Monte
-  Carlo Criticality Calculations," *Nuclear Science and Engineering*, **170**,
-  pp. 125--135 (2012). [`PDF
-  <http://web.mit.edu/romano7/www/nse_v170_n2_pp125-135.pdf>`_]
+  Carlo Criticality Calculations," *Nucl. Sci. Eng.*, **170**, 125--135
+  (2012). `<http://hdl.handle.net/1721.1/73569>`_

_sources/quickinstall.txt

@@ -18,11 +18,13 @@ and libraries may be needed. These include:
 - A Fortran compiler such as gfortran_
 - git_ version control software for obtaining source code (*optional*)
 - An MPI implementation for parallel runs (*optional*)
-- HDF5_ Library for improved output format (*optional*)
+- HDF5_ Library for portable binary output format (*optional*)
+- PETSc_ for CMFD acceleration (*optional*)
 
 .. _gfortran: http://gcc.gnu.org/wiki/GFortran
 .. _git: http://git-scm.com
 .. _HDF5: http://www.hdfgroup.org/HDF5/
+.. _PETSc: http://www.mcs.anl.gov/petsc/
 
 --------------------
 Obtaining the Source

_sources/usersguide/input.txt

@@ -37,16 +37,19 @@ Overview of Files
 -----------------
 
 To assemble a complete model for OpenMC, one needs to create separate XML files
-for the geometry, materials, and settings. Additionally, there are two optional
+for the geometry, materials, and settings. Additionally, there are three optional
 input files. The first is a tallies XML file that specifies physical quantities
 to be tallied. The second is a plots XML file that specifies regions of geometry
-which should be plotted. OpenMC expects that these files are called:
+which should be plotted. The third is a CMFD XML file that specifies coarse mesh
+acceleration geometry and execution parameters. OpenMC expects that these 
+files are called:
 
 * ``geometry.xml``
 * ``materials.xml``
 * ``settings.xml``
 * ``tallies.xml``
 * ``plots.xml``
+* ``cmfd.xml``
 
 --------------------------------------
 Settings Specification -- settings.xml
@@ -454,6 +457,8 @@ could be written as:
 
     </geometry>
 
+.. _surface_element:
+
 ``<surface>`` Element
 ---------------------
 
@@ -519,6 +524,21 @@ The following quadratic surfaces can be modeled:
     A sphere of the form :math:`(x - x_0)^2 + (y - y_0)^2 + (z - z_0)^2 =
     R^2`. The coefficients specified are ":math:`x_0 \: y_0 \: z_0 \: R`".
 
+  :x-cone:
+    A cone parallel to the x-axis of the form :math:`(y - y_0)^2 + (z - z_0)^2 =
+    R^2 (x - x_0)^2`. The coefficients specified are ":math:`x_0 \: y_0 \: z_0
+    \: R^2`".
+
+  :y-cone:
+    A cone parallel to the y-axis of the form :math:`(x - x_0)^2 + (z - z_0)^2 =
+    R^2 (y - y_0)^2`. The coefficients specified are ":math:`x_0 \: y_0 \: z_0
+    \: R^2`".
+
+  :z-cone:
+    A cone parallel to the x-axis of the form :math:`(x - x_0)^2 + (y - y_0)^2 =
+    R^2 (z - z_0)^2`. The coefficients specified are ":math:`x_0 \: y_0 \: z_0
+    \: R^2`".
+
 ``<cell>`` Element
 ------------------
 
@@ -962,3 +982,184 @@ sub-elements:
       materials to plot.  This overrides any ``col_spec`` color specifications.
 
     *Default*: None
+
+--------------------------------------------
+CMFD Specification -- cmfd.xml
+--------------------------------------------
+    
+Coarse mesh finite difference acceleration method has been implemented in OpenMC.
+Currently, it allows users to accelerate fission source convergence during 
+inactive neutron batches. To run CMFD, the ``<run_cmfd>`` element in 
+``settings.xml`` should be set to ``.true.``.
+
+``<active_flush>`` Element
+--------------------------
+
+The ``<active_flush>`` element controls the batch where CMFD tallies should be
+reset. CMFD tallies should be reset before active batches so they are accumulated 
+without bias.
+
+  *Default*: 0 
+
+``<begin>`` Element
+-------------------
+
+The ``<begin>`` element controls what batch CMFD calculations should begin.
+
+  *Default*: 1
+
+``<feedback>`` Element
+----------------------
+
+The ``<feedback>`` element controls whether or not the CMFD diffusion result is 
+used to adjust the weight of fission source neutrons on the next OpenMC batch. 
+It can be turned on with ".true." and off with ".false.". 
+
+  *Default*: .false.
+
+``<inactive>`` Element
+----------------------
+
+The ``<inactive>`` element controls if cmfd tallies should be accumulated 
+during inactive batches. For some applications, CMFD tallies may not be 
+needed until the start of active batches. This option can be turned on 
+with ".true." and off with ".false."
+
+  *Default*: .true.
+
+``<keff_tol>`` Element
+----------------------
+
+The ``<keff_tol>`` element specifies acceptance criteria of a CMFD eigenvalue.
+If the CMFD eigenvalue and OpenMC batch eigenvalue are within this tolerance, 
+CMFD is allowed to modify source neutron weights. 
+
+  *Default*: 0.005
+
+``<ksp_monitor>`` Element
+-------------------------
+
+The ``<ksp_monitor>`` element is used to view the convergence of linear GMRES 
+iterations in PETSc. This option can be turned on with ".true." and turned off 
+with ".false.".
+
+
+  *Default*: .false. 
+
+``<mesh>`` Element
+------------------
+
+If a structured mesh is desired as a filter for a tally, it must be specified in
+a separate element with the tag name ``<mesh>``. This element has the following
+attributes/sub-elements:
+
+  :type:
+    The type of structured mesh. Only "rectangular" is currently supported.
+
+  :lower_left:
+    The lower-left corner of the structured mesh. If only two coordinate are
+    given, it is assumed that the mesh is an x-y mesh.
+
+  :upper_right:
+    The upper-right corner of the structrued mesh. If only two coordinate are 
+    given, it is assumed that the mesh is an x-y mesh.
+
+  :dimension:
+    The number of mesh cells in each direction.
+
+  :width:
+    The width of mesh cells in each direction.
+
+  :energy:
+    Energy bins [in MeV], listed in ascending order (e.g. 0.0 0.625e-7 20.0)
+    for CMFD tallies and acceleration. If no energy bins are listed, OpenMC 
+    automatically assumes a one energy group calculation over the entire 
+    energy range.
+
+  :albedo:
+    Surface ratio of incoming to outgoing partial currents on global boundary
+    conditions. They are listed in the following order: -x +x -y +y -z +z.
+
+    *Default*: 1.0 1.0 1.0 1.0 1.0 1.0
+
+  :map:
+    An optional acceleration map can be specified to overlay on the coarse 
+    mesh spatial grid. If this option is used a ``1`` is used for a 
+    non-accelerated region and a ``2`` is used for an accelerated region.
+    For a simple 4x4 coarse mesh with a 2x2 fuel lattice surrounded by 
+    reflector, the map is:
+
+      ``1 1 1 1``
+
+      ``1 2 2 1``
+
+      ``1 2 2 1``
+
+      ``1 1 1 1``
+
+    Therefore a 2x2 system of equations is solved rather than a 4x4. This 
+    is extremely important to use in reflectors as neutrons will not 
+    contribute to any tallies far away from fission source neutron regions.
+    A ``2`` must be used to identify any fission source region.
+
+    .. note:: Only two of the following three sub-elements are needed: 
+              ``lower_left``, ``upper_right`` and ``width``. Any combination 
+              of two of these will yield the third.
+
+``<norm>`` Element
+------------------
+
+The ``<norm>`` element is used to normalize the CMFD fission source distribution 
+to a particular value. For example, if a fission source is calculated for a 
+17 x 17 lattice of pins, the fission source may be normalized to the number of 
+fission source regions, in this case 289. This is useful when visualizing this 
+distribution as the average peaking factor will be unity. This parameter will 
+not impact the calculation. 
+
+  *Default*: 1.0
+
+``<n_procs_cmfd>`` Element
+--------------------------
+
+The ``<n_procs_cmfd>`` element is used to set the number of processors used 
+for CMFD calculation. It should be less than or equal to the number of 
+processors used during OpenMC. 
+
+  *Default*: 1
+
+``<power_monitor>`` Element
+---------------------------
+
+The ``<power_monitor>`` element is used to view the convergence of power iteration. 
+This option can be turned on with ".true." and turned off with ".false.".
+
+
+  *Default*: .false.
+
+``<write_balance>`` Element
+---------------------------
+
+The ``<write_balance>`` element is used to view the balance of OpenMC tally
+residuals for every coarse mesh region and energy group. This option can be 
+turned on with ".true." and off with ".false.". 
+
+
+  *Default*: .false.
+
+``<write_hdf5>`` Element
+------------------------
+
+The ``<write_hdf5>`` element can be turned on with ".true." to get an 
+HDF5 output file of CMFD results. 
+
+  *Default*: .false.
+
+``<write_matrices>`` Element
+----------------------------
+
+The ``<write_matrices>`` element is used to view the PETSc sparse matrices
+created when solving CMFD equations. These binary output files can be imported
+into MATLAB using PETSc-MATLAB utilities. This option can be
+turned on with ".true." and off with ".false.".
+
+  *Default*: .false.

_sources/usersguide/install.txt

@@ -32,10 +32,15 @@ To compile with support for HDF5_ output (highly recommended), you will need to
 have HDF5 installed on your computer. The installed version will need to have
 been compiled with the same compiler you intend to compile OpenMC with.
 
+To enable CMFD acceleration, you will need to have PETSc_ installed on your
+computer. The installed version will need to have been compiled with the same
+compiler you intend to compile OpenMC with.
+
 .. _gfortran: http://gcc.gnu.org/wiki/GFortran
 .. _OpenMPI: http://www.open-mpi.org
 .. _MPICH2: http://www.mcs.anl.gov/mpi/mpich/
 .. _HDF5: http://www.hdfgroup.org/HDF5/
+.. _PETSc: http://www.mcs.anl.gov/petsc/
 
 --------------------
 Obtaining the Source

devguide/index.html

@@ -58,11 +58,30 @@ structure of the OpenMC source code and how to do various development tasks such
 as debugging.</p>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="structures.html">1. Data Structures</a></li>
-<li class="toctree-l1"><a class="reference internal" href="xml-fortran.html">2. xml-fortran Input Parsing</a></li>
-<li class="toctree-l1"><a class="reference internal" href="statepoint.html">3. State Point Binary File Specifications</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="statepoint.html#revision-2">3.1. Revision 2</a></li>
-<li class="toctree-l2"><a class="reference internal" href="statepoint.html#revision-1">3.2. Revision 1</a></li>
+<li class="toctree-l1"><a class="reference internal" href="structures.html">1. Data Structures</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="structures.html#particle">1.1. Particle</a></li>
+<li class="toctree-l2"><a class="reference internal" href="structures.html#cell">1.2. Cell</a></li>
+<li class="toctree-l2"><a class="reference internal" href="structures.html#surface">1.3. Surface</a></li>
+<li class="toctree-l2"><a class="reference internal" href="structures.html#material">1.4. Material</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="styleguide.html">2. Style Guide for OpenMC</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="styleguide.html#general-rules">2.1. General Rules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="styleguide.html#subroutines-and-functions">2.2. Subroutines and Functions</a></li>
+<li class="toctree-l2"><a class="reference internal" href="styleguide.html#variables">2.3. Variables</a></li>
+<li class="toctree-l2"><a class="reference internal" href="styleguide.html#derived-types-and-classes">2.4. Derived Types and Classes</a></li>
+<li class="toctree-l2"><a class="reference internal" href="styleguide.html#indentation">2.5. Indentation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="styleguide.html#whitespace-in-expressions">2.6. Whitespace in Expressions</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="workflow.html">3. Development Workflow</a></li>
+<li class="toctree-l1"><a class="reference internal" href="xml-fortran.html">4. xml-fortran Input Parsing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="statepoint.html">5. State Point Binary File Specifications</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="statepoint.html#revision-5">5.1. Revision 5</a></li>
+<li class="toctree-l2"><a class="reference internal" href="statepoint.html#revision-4">5.2. Revision 4</a></li>
+<li class="toctree-l2"><a class="reference internal" href="statepoint.html#revision-3">5.3. Revision 3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="statepoint.html#revision-2">5.4. Revision 2</a></li>
+<li class="toctree-l2"><a class="reference internal" href="statepoint.html#revision-1">5.5. Revision 1</a></li>
 </ul>
 </li>
 </ul>

devguide/statepoint.html

@@ -8,7 +8,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>3. State Point Binary File Specifications &mdash; OpenMC Documentation</title>
+    <title>5. State Point Binary File Specifications &mdash; OpenMC Documentation</title>
     
     <link rel="stylesheet" href="../_static/haiku.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -30,7 +30,7 @@
     <link rel="top" title="OpenMC Documentation" href="../index.html" />
     <link rel="up" title="Developer’s Guide" href="index.html" />
     <link rel="next" title="Publications" href="../publications.html" />
-    <link rel="prev" title="2. xml-fortran Input Parsing" href="xml-fortran.html" /> 
+    <link rel="prev" title="4. xml-fortran Input Parsing" href="xml-fortran.html" /> 
   </head>
   <body>
       <div class="header">
@@ -41,7 +41,7 @@
       <div class="topnav">
       
         <p>
-        «&#160;&#160;<a href="xml-fortran.html">2. xml-fortran Input Parsing</a>
+        «&#160;&#160;<a href="xml-fortran.html">4. xml-fortran Input Parsing</a>
         &#160;&#160;::&#160;&#160;
         <a class="uplink" href="../index.html">Contents</a>
         &#160;&#160;::&#160;&#160;
@@ -53,9 +53,537 @@
         
         
   <div class="section" id="state-point-binary-file-specifications">
-<span id="devguide-statepoint"></span><h1>3. State Point Binary File Specifications<a class="headerlink" href="#state-point-binary-file-specifications" title="Permalink to this headline">¶</a></h1>
+<span id="devguide-statepoint"></span><h1>5. State Point Binary File Specifications<a class="headerlink" href="#state-point-binary-file-specifications" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="revision-5">
+<h2>5.1. Revision 5<a class="headerlink" href="#revision-5" title="Permalink to this headline">¶</a></h2>
+<p><strong>integer(4) REVISION_STATEPOINT</strong></p>
+<blockquote>
+<div>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.</div></blockquote>
+<p><strong>integer(4) VERSION_MAJOR</strong></p>
+<blockquote>
+<div>Major version number for OpenMC</div></blockquote>
+<p><strong>integer(4) VERSION_MINOR</strong></p>
+<blockquote>
+<div>Minor version number for OpenMC</div></blockquote>
+<p><strong>integer(4) VERSION_RELEASE</strong></p>
+<blockquote>
+<div>Release version number for OpenMC</div></blockquote>
+<p><strong>character(19) time_stamp</strong></p>
+<blockquote>
+<div>Date and time the state point was written.</div></blockquote>
+<p><strong>integer(8) seed</strong></p>
+<blockquote>
+<div>Pseudo-random number generator seed.</div></blockquote>
+<p><strong>integer(4) run_mode</strong></p>
+<blockquote>
+<div>run mode used. The modes are described in constants.F90.</div></blockquote>
+<p><strong>integer(8) n_particles</strong></p>
+<blockquote>
+<div>Number of particles used per generation.</div></blockquote>
+<p><strong>integer(4) n_batches</strong></p>
+<blockquote>
+<div>Total number of batches (active + inactive).</div></blockquote>
+<p><strong>integer(4) current_batch</strong></p>
+<blockquote>
+<div>The number of batches already simulated.</div></blockquote>
+<p>if (run_mode == MODE_CRITICALITY)</p>
+<blockquote>
+<div><p><strong>integer(4) n_inactive</strong></p>
+<blockquote>
+<div>Number of inactive batches</div></blockquote>
+<p><strong>integer(4) gen_per_batch</strong></p>
+<blockquote>
+<div>Number of generations per batch for criticality calculations</div></blockquote>
+<p><em>do i = 1, current_batch</em></p>
+<blockquote>
+<div><p><strong>real(8) k_batch(i)</strong></p>
+<blockquote>
+<div>k-effective for the i-th batch</div></blockquote>
+</div></blockquote>
+<p><em>do i = 1, current_batch</em></p>
+<blockquote>
+<div><p><strong>real(8) entropy(i)</strong></p>
+<blockquote>
+<div>Shannon entropy for the i-th batch</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) n_meshes</strong></p>
+<blockquote>
+<div>Number of meshes in tallies.xml file</div></blockquote>
+<p><em>do i = 1, n_meshes</em></p>
+<blockquote>
+<div><p><strong>integer(4) meshes(i) % type</strong></p>
+<blockquote>
+<div>Type of mesh.</div></blockquote>
+<p><strong>integer(4) meshes(i) % n_dimension</strong></p>
+<blockquote>
+<div>Number of dimensions for mesh (2 or 3).</div></blockquote>
+<p><strong>integer(4) meshes(i) % dimension(:)</strong></p>
+<blockquote>
+<div>Number of mesh cells in each dimension.</div></blockquote>
+<p><strong>real(8) meshes(i) % lower_left(:)</strong></p>
+<blockquote>
+<div>Coordinates of lower-left corner of mesh.</div></blockquote>
+<p><strong>real(8) meshes(i) % upper_right(:)</strong></p>
+<blockquote>
+<div>Coordinates of upper-right corner of mesh.</div></blockquote>
+<p><strong>real(8) meshes(i) % width(:)</strong></p>
+<blockquote>
+<div>Width of each mesh cell in each dimension.</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) n_tallies</strong></p>
+<p><em>do i = 1, n_tallies</em></p>
+<blockquote>
+<div><p><strong>integer(4) tallies(i) % n_realizations</strong></p>
+<blockquote>
+<div>Number of realizations for the i-th tally.</div></blockquote>
+<p><strong>integer(4) size(tallies(i) % scores, 1)</strong></p>
+<blockquote>
+<div>Total number of score bins for the i-th tally</div></blockquote>
+<p><strong>integer(4) size(tallies(i) % scores, 2)</strong></p>
+<blockquote>
+<div>Total number of filter bins for the i-th tally</div></blockquote>
+<p><strong>integer(4) tallies(i) % n_filters</strong></p>
+<p><em>do j = 1, tallies(i) % n_filters</em></p>
+<blockquote>
+<div><p><strong>integer(4) tallies(i) % filter(j) % type</strong></p>
+<blockquote>
+<div>Type of tally filter.</div></blockquote>
+<p><strong>integer(4) tallies(i) % filter(j) % n_bins</strong></p>
+<blockquote>
+<div>Number of bins for filter.</div></blockquote>
+<p><strong>integer(4)/real(8) tallies(i) % filter(j) % bins(:)</strong></p>
+<blockquote>
+<div>Value for each filter bin of this type.</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) tallies(i) % n_nuclide_bins</strong></p>
+<blockquote>
+<div>Number of nuclide bins. If none are specified, this is just one.</div></blockquote>
+<p><em>do j = 1, tallies(i) % n_nuclide_bins</em></p>
+<blockquote>
+<div><p><strong>integer(4) tallies(i) % nuclide_bins(j)</strong></p>
+<blockquote>
+<div>Values of specified nuclide bins</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) tallies(i) % n_score_bins</strong></p>
+<blockquote>
+<div>Number of scoring bins.</div></blockquote>
+<p><em>do j = 1, tallies(i) % n_score_bins</em></p>
+<blockquote>
+<div><p><strong>integer(4) tallies(i) % score_bins(j)</strong></p>
+<blockquote>
+<div>Values of specified scoring bins (e.g. SCORE_FLUX).</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) n_realizations</strong></p>
+<blockquote>
+<div>Number of realizations for global tallies.</div></blockquote>
+<p><strong>integer(4) N_GLOBAL_TALLIES</strong></p>
+<blockquote>
+<div>Number of global tally scores</div></blockquote>
+<p><em>do i = 1, N_GLOBAL_TALLIES</em></p>
+<blockquote>
+<div><p><strong>real(8) global_tallies(i) % sum</strong></p>
+<blockquote>
+<div>Accumulated sum for the i-th global tally</div></blockquote>
+<p><strong>real(8) global_tallies(i) % sum_sq</strong></p>
+<blockquote>
+<div>Accumulated sum of squares for the i-th global tally</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) tallies_on</strong></p>
+<blockquote>
+<div>Flag indicated if tallies are present in the file.</div></blockquote>
+<p>if (tallies_on &gt; 0)</p>
+<blockquote>
+<div><p><em>do i = 1, n_tallies</em></p>
+<blockquote>
+<div><p><em>do k = 1, size(tallies(i) % scores, 2)</em></p>
+<blockquote>
+<div><p><em>do j = 1, size(tallies(i) % scores, 1)</em></p>
+<blockquote>
+<div><p><strong>real(8) tallies(i) % scores(j,k) % sum</strong></p>
+<blockquote>
+<div>Accumulated sum for the j-th score and k-th filter of the
+i-th tally</div></blockquote>
+<p><strong>real(8) tallies(i) % scores(j,k) % sum_sq</strong></p>
+<blockquote>
+<div>Accumulated sum of squares for the j-th score and k-th
+filter of the i-th tally</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+<p>if (run_mode == MODE_CRITICALITY)</p>
+<blockquote>
+<div><p><em>do i = 1, n_particles</em></p>
+<blockquote>
+<div><p><strong>real(8) source_bank(i) % wgt</strong></p>
+<blockquote>
+<div>Weight of the i-th source particle</div></blockquote>
+<p><strong>real(8) source_bank(i) % xyz(1:3)</strong></p>
+<blockquote>
+<div>Coordinates of the i-th source particle.</div></blockquote>
+<p><strong>real(8) source_bank(i) % uvw(1:3)</strong></p>
+<blockquote>
+<div>Direction of the i-th source particle</div></blockquote>
+<p><strong>real(8) source_bank(i) % E</strong></p>
+<blockquote>
+<div>Energy of the i-th source particle.</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+</div>
+<div class="section" id="revision-4">
+<h2>5.2. Revision 4<a class="headerlink" href="#revision-4" title="Permalink to this headline">¶</a></h2>
+<p><strong>integer(4) REVISION_STATEPOINT</strong></p>
+<blockquote>
+<div>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.</div></blockquote>
+<p><strong>integer(4) VERSION_MAJOR</strong></p>
+<blockquote>
+<div>Major version number for OpenMC</div></blockquote>
+<p><strong>integer(4) VERSION_MINOR</strong></p>
+<blockquote>
+<div>Minor version number for OpenMC</div></blockquote>
+<p><strong>integer(4) VERSION_RELEASE</strong></p>
+<blockquote>
+<div>Release version number for OpenMC</div></blockquote>
+<p><strong>character(19) time_stamp</strong></p>
+<blockquote>
+<div>Date and time the state point was written.</div></blockquote>
+<p><strong>integer(8) seed</strong></p>
+<blockquote>
+<div>Pseudo-random number generator seed.</div></blockquote>
+<p><strong>integer(4) run_mode</strong></p>
+<blockquote>
+<div>run mode used. The modes are described in constants.F90.</div></blockquote>
+<p><strong>integer(8) n_particles</strong></p>
+<blockquote>
+<div>Number of particles used per generation.</div></blockquote>
+<p><strong>integer(4) n_batches</strong></p>
+<blockquote>
+<div>Total number of batches (active + inactive).</div></blockquote>
+<p><strong>integer(4) current_batch</strong></p>
+<blockquote>
+<div>The number of batches already simulated.</div></blockquote>
+<p>if (run_mode == MODE_CRITICALITY)</p>
+<blockquote>
+<div><p><strong>integer(4) n_inactive</strong></p>
+<blockquote>
+<div>Number of inactive batches</div></blockquote>
+<p><strong>integer(4) gen_per_batch</strong></p>
+<blockquote>
+<div>Number of generations per batch for criticality calculations</div></blockquote>
+<p><em>do i = 1, current_batch</em></p>
+<blockquote>
+<div><p><strong>real(8) k_batch(i)</strong></p>
+<blockquote>
+<div>k-effective for the i-th batch</div></blockquote>
+</div></blockquote>
+<p><em>do i = 1, current_batch</em></p>
+<blockquote>
+<div><p><strong>real(8) entropy(i)</strong></p>
+<blockquote>
+<div>Shannon entropy for the i-th batch</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) n_meshes</strong></p>
+<blockquote>
+<div>Number of meshes in tallies.xml file</div></blockquote>
+<p><em>do i = 1, n_meshes</em></p>
+<blockquote>
+<div><p><strong>integer(4) meshes(i) % type</strong></p>
+<blockquote>
+<div>Type of mesh.</div></blockquote>
+<p><strong>integer(4) meshes(i) % n_dimension</strong></p>
+<blockquote>
+<div>Number of dimensions for mesh (2 or 3).</div></blockquote>
+<p><strong>integer(4) meshes(i) % dimension(:)</strong></p>
+<blockquote>
+<div>Number of mesh cells in each dimension.</div></blockquote>
+<p><strong>real(8) meshes(i) % lower_left(:)</strong></p>
+<blockquote>
+<div>Coordinates of lower-left corner of mesh.</div></blockquote>
+<p><strong>real(8) meshes(i) % upper_right(:)</strong></p>
+<blockquote>
+<div>Coordinates of upper-right corner of mesh.</div></blockquote>
+<p><strong>real(8) meshes(i) % width(:)</strong></p>
+<blockquote>
+<div>Width of each mesh cell in each dimension.</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) n_tallies</strong></p>
+<p><em>do i = 1, n_tallies</em></p>
+<blockquote>
+<div><p><strong>integer(4) size(tallies(i) % scores, 1)</strong></p>
+<blockquote>
+<div>Total number of score bins for the i-th tally</div></blockquote>
+<p><strong>integer(4) size(tallies(i) % scores, 2)</strong></p>
+<blockquote>
+<div>Total number of filter bins for the i-th tally</div></blockquote>
+<p><strong>integer(4) tallies(i) % n_filters</strong></p>
+<p><em>do j = 1, tallies(i) % n_filters</em></p>
+<blockquote>
+<div><p><strong>integer(4) tallies(i) % filter(j) % type</strong></p>
+<blockquote>
+<div>Type of tally filter.</div></blockquote>
+<p><strong>integer(4) tallies(i) % filter(j) % n_bins</strong></p>
+<blockquote>
+<div>Number of bins for filter.</div></blockquote>
+<p><strong>integer(4)/real(8) tallies(i) % filter(j) % bins(:)</strong></p>
+<blockquote>
+<div>Value for each filter bin of this type.</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) tallies(i) % n_nuclide_bins</strong></p>
+<blockquote>
+<div>Number of nuclide bins. If none are specified, this is just one.</div></blockquote>
+<p><em>do j = 1, tallies(i) % n_nuclide_bins</em></p>
+<blockquote>
+<div><p><strong>integer(4) tallies(i) % nuclide_bins(j)</strong></p>
+<blockquote>
+<div>Values of specified nuclide bins</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) tallies(i) % n_score_bins</strong></p>
+<blockquote>
+<div>Number of scoring bins.</div></blockquote>
+<p><em>do j = 1, tallies(i) % n_score_bins</em></p>
+<blockquote>
+<div><p><strong>integer(4) tallies(i) % score_bins(j)</strong></p>
+<blockquote>
+<div>Values of specified scoring bins (e.g. SCORE_FLUX).</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) N_GLOBAL_TALLIES</strong></p>
+<blockquote>
+<div>Number of global tally scores</div></blockquote>
+<p><em>do i = 1, N_GLOBAL_TALLIES</em></p>
+<blockquote>
+<div><p><strong>real(8) global_tallies(i) % sum</strong></p>
+<blockquote>
+<div>Accumulated sum for the i-th global tally</div></blockquote>
+<p><strong>real(8) global_tallies(i) % sum_sq</strong></p>
+<blockquote>
+<div>Accumulated sum of squares for the i-th global tally</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) tallies_on</strong></p>
+<blockquote>
+<div>Flag indicated if tallies are present in the file.</div></blockquote>
+<p>if (tallies_on &gt; 0)</p>
+<blockquote>
+<div><p><strong>integer(4) n_realizations</strong></p>
+<blockquote>
+<div>Number of realizations for tally random variables.</div></blockquote>
+<p><em>do i = 1, n_tallies</em></p>
+<blockquote>
+<div><p><em>do k = 1, size(tallies(i) % scores, 2)</em></p>
+<blockquote>
+<div><p><em>do j = 1, size(tallies(i) % scores, 1)</em></p>
+<blockquote>
+<div><p><strong>real(8) tallies(i) % scores(j,k) % sum</strong></p>
+<blockquote>
+<div>Accumulated sum for the j-th score and k-th filter of the
+i-th tally</div></blockquote>
+<p><strong>real(8) tallies(i) % scores(j,k) % sum_sq</strong></p>
+<blockquote>
+<div>Accumulated sum of squares for the j-th score and k-th
+filter of the i-th tally</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+<p>if (run_mode == MODE_CRITICALITY)</p>
+<blockquote>
+<div><p><em>do i = 1, n_particles</em></p>
+<blockquote>
+<div><p><strong>real(8) source_bank(i) % wgt</strong></p>
+<blockquote>
+<div>Weight of the i-th source particle</div></blockquote>
+<p><strong>real(8) source_bank(i) % xyz(1:3)</strong></p>
+<blockquote>
+<div>Coordinates of the i-th source particle.</div></blockquote>
+<p><strong>real(8) source_bank(i) % uvw(1:3)</strong></p>
+<blockquote>
+<div>Direction of the i-th source particle</div></blockquote>
+<p><strong>real(8) source_bank(i) % E</strong></p>
+<blockquote>
+<div>Energy of the i-th source particle.</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+</div>
+<div class="section" id="revision-3">
+<h2>5.3. Revision 3<a class="headerlink" href="#revision-3" title="Permalink to this headline">¶</a></h2>
+<p><strong>integer(4) REVISION_STATEPOINT</strong></p>
+<blockquote>
+<div>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.</div></blockquote>
+<p><strong>integer(4) VERSION_MAJOR</strong></p>
+<blockquote>
+<div>Major version number for OpenMC</div></blockquote>
+<p><strong>integer(4) VERSION_MINOR</strong></p>
+<blockquote>
+<div>Minor version number for OpenMC</div></blockquote>
+<p><strong>integer(4) VERSION_RELEASE</strong></p>
+<blockquote>
+<div>Release version number for OpenMC</div></blockquote>
+<p><strong>character(19) time_stamp</strong></p>
+<blockquote>
+<div>Date and time the state point was written.</div></blockquote>
+<p><strong>integer(8) seed</strong></p>
+<blockquote>
+<div>Pseudo-random number generator seed.</div></blockquote>
+<p><strong>integer(4) run_mode</strong></p>
+<blockquote>
+<div>run mode used. The modes are described in constants.F90.</div></blockquote>
+<p><strong>integer(8) n_particles</strong></p>
+<blockquote>
+<div>Number of particles used per generation.</div></blockquote>
+<p><strong>integer(4) n_batches</strong></p>
+<blockquote>
+<div>Total number of batches (active + inactive).</div></blockquote>
+<p><strong>integer(4) current_batch</strong></p>
+<blockquote>
+<div>The number of batches already simulated.</div></blockquote>
+<p>if (run_mode == MODE_CRITICALITY)</p>
+<blockquote>
+<div><p><strong>integer(4) n_inactive</strong></p>
+<blockquote>
+<div>Number of inactive batches</div></blockquote>
+<p><strong>integer(4) gen_per_batch</strong></p>
+<blockquote>
+<div>Number of generations per batch for criticality calculations</div></blockquote>
+<p><em>do i = 1, current_batch</em></p>
+<blockquote>
+<div><p><strong>real(8) k_batch(i)</strong></p>
+<blockquote>
+<div>k-effective for the i-th batch</div></blockquote>
+</div></blockquote>
+<p><em>do i = 1, current_batch</em></p>
+<blockquote>
+<div><p><strong>real(8) entropy(i)</strong></p>
+<blockquote>
+<div>Shannon entropy for the i-th batch</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) N_GLOBAL_TALLIES</strong></p>
+<blockquote>
+<div>Number of global tally scores</div></blockquote>
+<p><em>do i = 1, N_GLOBAL_TALLIES</em></p>
+<blockquote>
+<div><p><strong>real(8) global_tallies(i) % sum</strong></p>
+<blockquote>
+<div>Accumulated sum for the i-th global tally</div></blockquote>
+<p><strong>real(8) global_tallies(i) % sum_sq</strong></p>
+<blockquote>
+<div>Accumulated sum of squares for the i-th global tally</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) n_meshes</strong></p>
+<blockquote>
+<div>Number of meshes in tallies.xml file</div></blockquote>
+<p><em>do i = 1, n_meshes</em></p>
+<blockquote>
+<div><p><strong>integer(4) meshes(i) % type</strong></p>
+<blockquote>
+<div>Type of mesh.</div></blockquote>
+<p><strong>integer(4) meshes(i) % n_dimension</strong></p>
+<blockquote>
+<div>Number of dimensions for mesh (2 or 3).</div></blockquote>
+<p><strong>integer(4) meshes(i) % dimension(:)</strong></p>
+<blockquote>
+<div>Number of mesh cells in each dimension.</div></blockquote>
+<p><strong>real(8) meshes(i) % lower_left(:)</strong></p>
+<blockquote>
+<div>Coordinates of lower-left corner of mesh.</div></blockquote>
+<p><strong>real(8) meshes(i) % upper_right(:)</strong></p>
+<blockquote>
+<div>Coordinates of upper-right corner of mesh.</div></blockquote>
+<p><strong>real(8) meshes(i) % width(:)</strong></p>
+<blockquote>
+<div>Width of each mesh cell in each dimension.</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) n_tallies</strong></p>
+<p><em>do i = 1, n_tallies</em></p>
+<blockquote>
+<div><p><strong>integer(4) size(tallies(i) % scores, 1)</strong></p>
+<blockquote>
+<div>Total number of score bins for the i-th tally</div></blockquote>
+<p><strong>integer(4) size(tallies(i) % scores, 2)</strong></p>
+<blockquote>
+<div>Total number of filter bins for the i-th tally</div></blockquote>
+<p><strong>integer(4) tallies(i) % n_filters</strong></p>
+<p><em>do j = 1, tallies(i) % n_filters</em></p>
+<blockquote>
+<div><p><strong>integer(4) tallies(i) % filter(j) % type</strong></p>
+<blockquote>
+<div>Type of tally filter.</div></blockquote>
+<p><strong>integer(4) tallies(i) % filter(j) % n_bins</strong></p>
+<blockquote>
+<div>Number of bins for filter.</div></blockquote>
+<p><strong>integer(4)/real(8) tallies(i) % filter(j) % bins(:)</strong></p>
+<blockquote>
+<div>Value for each filter bin of this type.</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) tallies(i) % n_nuclide_bins</strong></p>
+<blockquote>
+<div>Number of nuclide bins. If none are specified, this is just one.</div></blockquote>
+<p><em>do j = 1, tallies(i) % n_nuclide_bins</em></p>
+<blockquote>
+<div><p><strong>integer(4) tallies(i) % nuclide_bins(j)</strong></p>
+<blockquote>
+<div>Values of specified nuclide bins</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) tallies(i) % n_score_bins</strong></p>
+<blockquote>
+<div>Number of scoring bins.</div></blockquote>
+<p><em>do j = 1, tallies(i) % n_score_bins</em></p>
+<blockquote>
+<div><p><strong>integer(4) tallies(i) % score_bins(j)</strong></p>
+<blockquote>
+<div>Values of specified scoring bins (e.g. SCORE_FLUX).</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+<p><strong>integer(4) tallies_on</strong></p>
+<blockquote>
+<div>Flag indicated if tallies are present in the file.</div></blockquote>
+<p>if (tallies_on &gt; 0)</p>
+<blockquote>
+<div><p><em>do i = 1, n_tallies</em></p>
+<blockquote>
+<div><p><em>do k = 1, size(tallies(i) % scores, 2)</em></p>
+<blockquote>
+<div><p><em>do j = 1, size(tallies(i) % scores, 1)</em></p>
+<blockquote>
+<div><p><strong>real(8) tallies(i) % scores(j,k) % sum</strong></p>
+<blockquote>
+<div>Accumulated sum for the j-th score and k-th filter of the
+i-th tally</div></blockquote>
+<p><strong>real(8) tallies(i) % scores(j,k) % sum_sq</strong></p>
+<blockquote>
+<div>Accumulated sum of squares for the j-th score and k-th
+filter of the i-th tally</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+<p>if (run_mode == MODE_CRITICALITY)</p>
+<blockquote>
+<div><p><em>do i = 1, n_particles</em></p>
+<blockquote>
+<div><p><strong>real(8) source_bank(i) % wgt</strong></p>
+<blockquote>
+<div>Weight of the i-th source particle</div></blockquote>
+<p><strong>real(8) source_bank(i) % xyz(1:3)</strong></p>
+<blockquote>
+<div>Coordinates of the i-th source particle.</div></blockquote>
+<p><strong>real(8) source_bank(i) % uvw(1:3)</strong></p>
+<blockquote>
+<div>Direction of the i-th source particle</div></blockquote>
+<p><strong>real(8) source_bank(i) % E</strong></p>
+<blockquote>
+<div>Energy of the i-th source particle.</div></blockquote>
+</div></blockquote>
+</div></blockquote>
+</div>
 <div class="section" id="revision-2">
-<h2>3.1. Revision 2<a class="headerlink" href="#revision-2" title="Permalink to this headline">¶</a></h2>
+<h2>5.4. Revision 2<a class="headerlink" href="#revision-2" title="Permalink to this headline">¶</a></h2>
 <p><strong>integer(4) REVISION_STATEPOINT</strong></p>
 <blockquote>
 <div>Revision of the binary state point file. Any time a change is made in the
@@ -94,7 +622,10 @@ format of the state-point file, this integer is incremented.</div></blockquote>
 <div>k-effective for the i-th batch</div></blockquote>
 <p>if (entropy_on)</p>
 <blockquote>
-<div><strong>real(8) entropy for the i-th batch</strong></div></blockquote>
+<div><p><strong>real(8) entropy(i)</strong></p>
+<blockquote>
+<div>Shannon entropy for the i-th batch</div></blockquote>
+</div></blockquote>
 </div></blockquote>
 <p><strong>integer(4) N_GLOBAL_TALLIES</strong></p>
 <blockquote>
@@ -140,7 +671,7 @@ the i-th tally</div></blockquote>
 </div></blockquote>
 </div>
 <div class="section" id="revision-1">
-<h2>3.2. Revision 1<a class="headerlink" href="#revision-1" title="Permalink to this headline">¶</a></h2>
+<h2>5.5. Revision 1<a class="headerlink" href="#revision-1" title="Permalink to this headline">¶</a></h2>
 <p><strong>integer(4) REVISION_STATEPOINT</strong></p>
 <blockquote>
 <div>Revision of the binary state point file. Any time a change is made in the
@@ -179,7 +710,10 @@ format of the state-point file, this integer is incremented.</div></blockquote>
 <div>k-effective for the i-th batch</div></blockquote>
 <p>if (entropy_on)</p>
 <blockquote>
-<div><strong>real(8) entropy for the i-th batch</strong></div></blockquote>
+<div><p><strong>real(8) entropy(i)</strong></p>
+<blockquote>
+<div>Shannon entropy for the i-th batch</div></blockquote>
+</div></blockquote>
 </div></blockquote>
 <p><strong>integer(4) N_GLOBAL_TALLIES</strong></p>
 <blockquote>
@@ -234,7 +768,7 @@ the i-th tally</div></blockquote>
       <div class="bottomnav">
       
         <p>
-        «&#160;&#160;<a href="xml-fortran.html">2. xml-fortran Input Parsing</a>
+        «&#160;&#160;<a href="xml-fortran.html">4. xml-fortran Input Parsing</a>
         &#160;&#160;::&#160;&#160;
         <a class="uplink" href="../index.html">Contents</a>
         &#160;&#160;::&#160;&#160;

devguide/structures.html

@@ -29,7 +29,7 @@
     <script type="text/javascript" src="../_static/theme_extras.js"></script>
     <link rel="top" title="OpenMC Documentation" href="../index.html" />
     <link rel="up" title="Developer’s Guide" href="index.html" />
-    <link rel="next" title="2. xml-fortran Input Parsing" href="xml-fortran.html" />
+    <link rel="next" title="2. Style Guide for OpenMC" href="styleguide.html" />
     <link rel="prev" title="Developer’s Guide" href="index.html" /> 
   </head>
   <body>
@@ -45,7 +45,7 @@
         &#160;&#160;::&#160;&#160;
         <a class="uplink" href="../index.html">Contents</a>
         &#160;&#160;::&#160;&#160;
-        <a href="xml-fortran.html">2. xml-fortran Input Parsing</a>&#160;&#160;»
+        <a href="styleguide.html">2. Style Guide for OpenMC</a>&#160;&#160;»
         </p>
 
       </div>
@@ -54,6 +54,69 @@
         
   <div class="section" id="data-structures">
 <span id="devguide-structures"></span><h1>1. Data Structures<a class="headerlink" href="#data-structures" title="Permalink to this headline">¶</a></h1>
+<p>The purpose of this section is to give you an overview of the major data
+structures in OpenMC and how they are logically related. A majority of variables
+in OpenMC are <a class="reference external" href="http://nf.nci.org.au/training/FortranAdvanced/slides/slides.025.html">derived types</a> (similar to a struct in C). These derived types
+are defined in the various header modules, e.g. src/geometry_header.F90. Most
+important variables are found in the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/global.F90">global module</a>. Have a look through that
+module to get a feel for what variables you&#8217;ll often come across when looking at
+OpenMC code.</p>
+<div class="section" id="particle">
+<h2>1.1. Particle<a class="headerlink" href="#particle" title="Permalink to this headline">¶</a></h2>
+<p>Perhaps the variable that you will see most often is simply called <tt class="docutils literal"><span class="pre">p</span></tt> and is
+of type(Particle). This variable stores information about a particle&#8217;s physical
+characteristics (coordinates, direction, energy), what cell and material it&#8217;s
+currently in, how many collisions it has undergone, etc. In practice, only one
+particle is followed at a time so there is no array of type(Particle). The
+Particle type is defined in the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/particle_header.F90">particle_header module</a>.</p>
+<p>You will notice that the direction and angle of the particle is stored in a
+linked list of type(LocalCoord). In geometries with multiple <a class="reference internal" href="../methods/geometry.html#universes"><em>Universes</em></a>,
+the coordinates in each universe are stored in this linked list. If universes or
+lattices are not used in a geometry, only one LocalCoord is present in the
+linked list.</p>
+<p>The LocalCoord type has a component called cell which gives the index in the
+<tt class="docutils literal"><span class="pre">cells</span></tt> array in the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/global.F90">global module</a>. The <tt class="docutils literal"><span class="pre">cells</span></tt> array is of type(Cell)
+and stored information about each region defined by the user.</p>
+</div>
+<div class="section" id="cell">
+<h2>1.2. Cell<a class="headerlink" href="#cell" title="Permalink to this headline">¶</a></h2>
+<p>The Cell type is defined in the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/geometry_header.F90">geometry_header module</a> along with other
+geometry-related derived types. Each cell in the problem is described in terms
+of its bounding surfaces, which are listed on the <tt class="docutils literal"><span class="pre">surfaces</span></tt> component. The
+absolute value of each item in the <tt class="docutils literal"><span class="pre">surfaces</span></tt> component contains the index of
+the corresponding surface in the <tt class="docutils literal"><span class="pre">surfaces</span></tt> array defined in the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/global.F90">global
+module</a>. The sign on each item in the <tt class="docutils literal"><span class="pre">surfaces</span></tt> component indicates whether
+the cell exists on the positive or negative side of the surface (see
+<a class="reference internal" href="../methods/geometry.html#methods-geometry"><em>Geometry</em></a>).</p>
+<p>Each cell can either be filled with another universe/lattice or with a
+material. If it is filled with a material, the <tt class="docutils literal"><span class="pre">material</span></tt> component gives the
+index of the material in the <tt class="docutils literal"><span class="pre">materials</span></tt> array defined in the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/global.F90">global
+module</a>.</p>
+</div>
+<div class="section" id="surface">
+<h2>1.3. Surface<a class="headerlink" href="#surface" title="Permalink to this headline">¶</a></h2>
+<p>The Surface type is defined in the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/geometry_header.F90">geometry_header module</a>. A surface is
+defined by a type (sphere, cylinder, etc.) and a list of coefficients for that
+surface type. The simplest example would be a plane perpendicular to the xy, yz,
+or xz plane which needs only one parameter. The <tt class="docutils literal"><span class="pre">type</span></tt> component indicates the
+type through integer parameters such as SURF_SPHERE or SURF_CYL_Y (these are
+defined in the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/constants.F90">constants module</a>). The <tt class="docutils literal"><span class="pre">coeffs</span></tt> component gives the
+necessary coefficients to parameterize the surface type (see
+<a class="reference internal" href="../usersguide/input.html#surface-element"><em>&lt;surface&gt; Element</em></a>).</p>
+</div>
+<div class="section" id="material">
+<h2>1.4. Material<a class="headerlink" href="#material" title="Permalink to this headline">¶</a></h2>
+<p>The Material type is defined in the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/material_header.F90">material_header module</a>. Each material
+contains a number of nuclides at a given atom density. Each item in the
+<tt class="docutils literal"><span class="pre">nuclide</span></tt> component corresponds to the index in the global <tt class="docutils literal"><span class="pre">nuclides</span></tt> array
+(as usual, found in the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/global.F90">global module</a>). The <tt class="docutils literal"><span class="pre">atom_density</span></tt> component is the
+same length as the <tt class="docutils literal"><span class="pre">nuclides</span></tt> component and lists the corresponding atom
+density in atom/barn-cm for each nuclide in the <tt class="docutils literal"><span class="pre">nuclides</span></tt> component.</p>
+<p>If the material contains nuclides for which binding effects are important in
+low-energy scattering, a <img class="math" src="../_images/math/610a7fba4c1d89de40e26ba8f6c2915102b17eae.png" alt="S(\alpha,\beta)"/> can be associated with that
+material through the <tt class="docutils literal"><span class="pre">sab_table</span></tt> component. Again, this component contains the
+index in the <tt class="docutils literal"><span class="pre">sab_tables</span></tt> array from the <a class="reference external" href="https://github.com/mit-crpg/openmc/blob/master/src/global.F90">global module</a>.</p>
+</div>
 </div>
 
 
@@ -65,7 +128,7 @@
         &#160;&#160;::&#160;&#160;
         <a class="uplink" href="../index.html">Contents</a>
         &#160;&#160;::&#160;&#160;
-        <a href="xml-fortran.html">2. xml-fortran Input Parsing</a>&#160;&#160;»
+        <a href="styleguide.html">2. Style Guide for OpenMC</a>&#160;&#160;»
         </p>
 
       </div>

devguide/styleguide.html

@@ -0,0 +1,195 @@
+
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>2. Style Guide for OpenMC &mdash; OpenMC Documentation</title>
+    
+    <link rel="stylesheet" href="../_static/haiku.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/print.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../',
+        VERSION:     '0.4.4',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="../_static/jquery.js"></script>
+    <script type="text/javascript" src="../_static/underscore.js"></script>
+    <script type="text/javascript" src="../_static/doctools.js"></script>
+    <script type="text/javascript" src="../_static/theme_extras.js"></script>
+    <link rel="top" title="OpenMC Documentation" href="../index.html" />
+    <link rel="up" title="Developer’s Guide" href="index.html" />
+    <link rel="next" title="3. Development Workflow" href="workflow.html" />
+    <link rel="prev" title="1. Data Structures" href="structures.html" /> 
+  </head>
+  <body>
+      <div class="header">
+        <a href="../index.html">
+          <img class="logo" src="../_static/openmc.png" alt="Logo"/>
+        </a>
+      </div>
+      <div class="topnav">
+      
+        <p>
+        «&#160;&#160;<a href="structures.html">1. Data Structures</a>
+        &#160;&#160;::&#160;&#160;
+        <a class="uplink" href="../index.html">Contents</a>
+        &#160;&#160;::&#160;&#160;
+        <a href="workflow.html">3. Development Workflow</a>&#160;&#160;»
+        </p>
+
+      </div>
+      <div class="content">
+        
+        
+  <div class="section" id="style-guide-for-openmc">
+<span id="devguide-styleguide"></span><h1>2. Style Guide for OpenMC<a class="headerlink" href="#style-guide-for-openmc" title="Permalink to this headline">¶</a></h1>
+<p>In order to keep the OpenMC code base consistent in style, this guide specifies
+a number of rules which should be adhered to when modified existing code or
+adding new code in OpenMC.</p>
+<div class="section" id="general-rules">
+<h2>2.1. General Rules<a class="headerlink" href="#general-rules" title="Permalink to this headline">¶</a></h2>
+<p>Conform to the Fortran 2008 standard.</p>
+<p>Make sure code can be compiled with most common compilers, especially gfortran
+and the Intel Fortran compiler. This supercedes the previous rule &#8212; if a
+Fortran 2003/2008 feature is not implemented in a common compiler, do not use
+it.</p>
+<p>Do not use special extensions that can be only be used from certain compilers.</p>
+<p>In general, write your code in lower-case. Having code in all caps does not
+enhance code readability or otherwise.</p>
+<p>Always include comments to describe what your code is doing. Do not be afraid of
+using copious amounts of comments.</p>
+<p>Use &lt;, &gt;, &lt;=, &gt;=, ==, and /= rather than .lt., .gt., .le., .ge., .eq., and .ne.</p>
+<p>Try to keep code within 80 columns when possible.</p>
+<p>Don&#8217;t use <tt class="docutils literal"><span class="pre">print</span> <span class="pre">*</span></tt> or <tt class="docutils literal"><span class="pre">write(*,*)</span></tt>. If writing to a file, use a specific
+unit. Writing to standard output or standard error should be handled by the
+<tt class="docutils literal"><span class="pre">write_message</span></tt> subroutine or functionality in the error module.</p>
+</div>
+<div class="section" id="subroutines-and-functions">
+<h2>2.2. Subroutines and Functions<a class="headerlink" href="#subroutines-and-functions" title="Permalink to this headline">¶</a></h2>
+<p>Above each subroutine/function, include a comment block giving a brief
+description of what the subroutine or function does.</p>
+<p>Arguments to subroutines/functions should be explicitly specified as intent(in),
+intent(out), or intent(inout).</p>
+<p>Include a comment describing what each argument to a subroutine/function is.</p>
+</div>
+<div class="section" id="variables">
+<h2>2.3. Variables<a class="headerlink" href="#variables" title="Permalink to this headline">¶</a></h2>
+<p>Never, under any circumstances, should implicit variables be used! Always
+include <tt class="docutils literal"><span class="pre">implicit</span> <span class="pre">none</span></tt> and define all your variables.</p>
+<p>Variable names should be all lower-case and descriptive, i.e. not a random
+assortment of letters that doesn&#8217;t give any information to someone seeing it for
+the first time. Variables consisting of multiple words should be separated by
+underscores, not hyphens or in camel case.</p>
+<p>Constant (parameter) variables should be in ALL CAPITAL LETTERS and defined in
+in the constants.F90 module.</p>
+<p>32-bit reals (real(4)) should never be used. Always use 64-bit reals (real(8)).</p>
+<p>For arbitrary length character variables, use the pre-defined lengths
+MAX_LINE_LEN, MAX_WORD_LEN, and MAX_FILE_LEN if possible.</p>
+<p>Do not use old-style character/array length (e.g. character*80, real*8).</p>
+<p>Integer values being used to indicate a certain state should be defined as named
+constants (see the constants.F90 module for many examples).</p>
+<p>Yes:</p>
+<div class="highlight-fortran"><div class="highlight"><pre><span class="k">if</span> <span class="p">(</span><span class="nv">boundary_condition</span> <span class="o">==</span> <span class="nv">BC_VACUUM</span><span class="p">)</span> <span class="k">then</span>
+</pre></div>
+</div>
+<p>No:</p>
+<div class="highlight-fortran"><div class="highlight"><pre><span class="k">if</span> <span class="p">(</span><span class="nv">boundary_condition</span> <span class="o">==</span> <span class="o">-</span><span class="mi">10</span><span class="p">)</span> <span class="k">then</span>
+</pre></div>
+</div>
+<p>Avoid creating arrays with a pre-defined maximum length. Use dynamic memory
+allocation instead. Use allocatable variables instead of pointer variables when
+possible.</p>
+<div class="section" id="shared-module-variables">
+<h3>2.3.1. Shared/Module Variables<a class="headerlink" href="#shared-module-variables" title="Permalink to this headline">¶</a></h3>
+<p>Always put shared variables in modules. Access module variables through a
+<tt class="docutils literal"><span class="pre">use</span></tt> statement. Always use the <tt class="docutils literal"><span class="pre">only</span></tt> specifier on the <tt class="docutils literal"><span class="pre">use</span></tt> statement
+except for variables from the global, constants, and various header modules.</p>
+<p>Never use <tt class="docutils literal"><span class="pre">equivalence</span></tt> statements, <tt class="docutils literal"><span class="pre">common</span></tt> blocks, or <tt class="docutils literal"><span class="pre">data</span></tt> statements.</p>
+</div>
+</div>
+<div class="section" id="derived-types-and-classes">
+<h2>2.4. Derived Types and Classes<a class="headerlink" href="#derived-types-and-classes" title="Permalink to this headline">¶</a></h2>
+<p>Derived types and classes should have CamelCase names with words not separated
+by underscores or hyphens.</p>
+</div>
+<div class="section" id="indentation">
+<h2>2.5. Indentation<a class="headerlink" href="#indentation" title="Permalink to this headline">¶</a></h2>
+<p>Never use tab characters. Indentation should always be applied using
+spaces. Emacs users should include the following line in their .emacs file:</p>
+<div class="highlight-common-lisp"><div class="highlight"><pre><span class="p">(</span><span class="nv">setq-default</span> <span class="nv">indent-tabs-mode</span> <span class="no">nil</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>vim users should include the following line in their .vimrc file:</p>
+<div class="highlight-python"><pre>set expandtab</pre>
+</div>
+<p>Use 2 spaces per indentation level. This applies to all constructs such as
+program, subroutine, function, if, associate, etc. Emacs users should set the
+variables f90-if-indent, f90-do-indent, f90-continuation-indent,
+f90-type-indent, f90-associate-indent, and f90-program indent to 2.</p>
+<p>Continuation lines should be indented by an extra 5 spaces. This is the default
+value of f90-continuation-indent in Emacs.</p>
+</div>
+<div class="section" id="whitespace-in-expressions">
+<h2>2.6. Whitespace in Expressions<a class="headerlink" href="#whitespace-in-expressions" title="Permalink to this headline">¶</a></h2>
+<p>Avoid extraneous whitespace in the following situations:</p>
+<ul>
+<li><p class="first">In subroutine/function calls:</p>
+<div class="highlight-python"><pre>Yes: call somesub(x, y(2), z)
+No:  call somesub( x, y( 2 ), z )</pre>
+</div>
+</li>
+<li><p class="first">In logical expressions, use one space around operators but nowhere else:</p>
+<div class="highlight-python"><pre>Yes: if (variable == 2) then
+No:  if ( variable==2 ) then</pre>
+</div>
+</li>
+</ul>
+</div>
+</div>
+
+
+      </div>
+      <div class="bottomnav">
+      
+        <p>
+        «&#160;&#160;<a href="structures.html">1. Data Structures</a>
+        &#160;&#160;::&#160;&#160;
+        <a class="uplink" href="../index.html">Contents</a>
+        &#160;&#160;::&#160;&#160;
+        <a href="workflow.html">3. Development Workflow</a>&#160;&#160;»
+        </p>
+
+      </div>
+
+
+    <div class="footer">
+        &copy; Copyright 2011-2012, Massachusetts Institute of Technology.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
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+  })();
+
+</script>
+
+  </body>
+</html>

devguide/workflow.html

@@ -0,0 +1,122 @@
+
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>3. Development Workflow &mdash; OpenMC Documentation</title>
+    
+    <link rel="stylesheet" href="../_static/haiku.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/print.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../',
+        VERSION:     '0.4.4',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="../_static/jquery.js"></script>
+    <script type="text/javascript" src="../_static/underscore.js"></script>
+    <script type="text/javascript" src="../_static/doctools.js"></script>
+    <script type="text/javascript" src="../_static/theme_extras.js"></script>
+    <link rel="top" title="OpenMC Documentation" href="../index.html" />
+    <link rel="up" title="Developer’s Guide" href="index.html" />
+    <link rel="next" title="4. xml-fortran Input Parsing" href="xml-fortran.html" />
+    <link rel="prev" title="2. Style Guide for OpenMC" href="styleguide.html" /> 
+  </head>
+  <body>
+      <div class="header">
+        <a href="../index.html">
+          <img class="logo" src="../_static/openmc.png" alt="Logo"/>
+        </a>
+      </div>
+      <div class="topnav">
+      
+        <p>
+        «&#160;&#160;<a href="styleguide.html">2. Style Guide for OpenMC</a>
+        &#160;&#160;::&#160;&#160;
+        <a class="uplink" href="../index.html">Contents</a>
+        &#160;&#160;::&#160;&#160;
+        <a href="xml-fortran.html">4. xml-fortran Input Parsing</a>&#160;&#160;»
+        </p>
+
+      </div>
+      <div class="content">
+        
+        
+  <div class="section" id="development-workflow">
+<span id="devguide-workflow"></span><h1>3. Development Workflow<a class="headerlink" href="#development-workflow" title="Permalink to this headline">¶</a></h1>
+<p>Anyone wishing to make contributions to OpenMC should be fully acquianted and
+comfortable working with <a class="reference external" href="http://git-scm.com/">git</a> and <a class="reference external" href="https://github.com/">GitHub</a>. The primary means of modifying and
+making contributions to OpenMC is through GitHub <a class="reference external" href="https://help.github.com/articles/using-pull-requests">pull requests</a>. This is
+what&#8217;s known as a fork and pull development model. The steps for this are as
+follows:</p>
+<p>1. Fork the main openmc repository from <a class="reference external" href="https://github.com/mit-crpg/openmc">mit-crpg/openmc</a>. This will create a
+repository with the same name under your personal account. As such, you can
+commit to it as you please without disrupting other developers.</p>
+<p>2. Create a branch that you want merged back to <a class="reference external" href="https://github.com/mit-crpg/openmc">mit-crpg/openmc</a> and make
+commits that you intend to go back. If you have made other changes that should
+not be merged back, those changes should be on another branch.</p>
+<ol class="arabic simple" start="3">
+<li>Issue a pull request from GitHub and select the branch you want merged.</li>
+</ol>
+<p>4. The OpenMC integration manager will review your pull request and make sure it
+conforms to the <a class="reference internal" href="styleguide.html#devguide-styleguide"><em>Style Guide for OpenMC</em></a>, compiles correctly, runs in parallel
+correctly, does not break other features in the code, etc. Any issues with the
+pull request can be discussed directly on the pull request page itself.</p>
+<p>5. After the pull request has been thoroughly vetted, it is merged back into
+<a class="reference external" href="https://github.com/mit-crpg/openmc">mit-crpg/openmc</a>.</p>
+<p>While the process above depends on the fork of the OpenMC repository being
+publicly available on GitHub, you may also wish to do development on a private
+repository for research or commercial purposes. The proper way to do this is to
+create a complete copy of the OpenMC repository (not a fork from GitHub). The
+private repository can then either be stored just locally or in conjunction with
+a private repository on Github (this requires a <a class="reference external" href="https://github.com/plans">paid plan</a>). If you want to
+merge some changes you&#8217;ve made in your private repository back to
+<a class="reference external" href="https://github.com/mit-crpg/openmc">mit-crpg/openmc</a> repository, simply follow the steps above with an extra step
+of pulling a branch from your private repository into your public fork.</p>
+</div>
+
+
+      </div>
+      <div class="bottomnav">
+      
+        <p>
+        «&#160;&#160;<a href="styleguide.html">2. Style Guide for OpenMC</a>
+        &#160;&#160;::&#160;&#160;
+        <a class="uplink" href="../index.html">Contents</a>
+        &#160;&#160;::&#160;&#160;
+        <a href="xml-fortran.html">4. xml-fortran Input Parsing</a>&#160;&#160;»
+        </p>
+
+      </div>
+
+
+    <div class="footer">
+        &copy; Copyright 2011-2012, Massachusetts Institute of Technology.
+      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
+    </div>
+<script type="text/javascript">
+
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+</html>

devguide/xml-fortran.html

@@ -8,7 +8,7 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     
-    <title>2. xml-fortran Input Parsing &mdash; OpenMC Documentation</title>
+    <title>4. xml-fortran Input Parsing &mdash; OpenMC Documentation</title>
     
     <link rel="stylesheet" href="../_static/haiku.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -29,8 +29,8 @@
     <script type="text/javascript" src="../_static/theme_extras.js"></script>
     <link rel="top" title="OpenMC Documentation" href="../index.html" />
     <link rel="up" title="Developer’s Guide" href="index.html" />
-    <link rel="next" title="3. State Point Binary File Specifications" href="statepoint.html" />
-    <link rel="prev" title="1. Data Structures" href="structures.html" /> 
+    <link rel="next" title="5. State Point Binary File Specifications" href="statepoint.html" />
+    <link rel="prev" title="3. Development Workflow" href="workflow.html" /> 
   </head>
   <body>
       <div class="header">
@@ -41,11 +41,11 @@
       <div class="topnav">
       
         <p>
-        «&#160;&#160;<a href="structures.html">1. Data Structures</a>
+        «&#160;&#160;<a href="workflow.html">3. Development Workflow</a>
         &#160;&#160;::&#160;&#160;
         <a class="uplink" href="../index.html">Contents</a>
         &#160;&#160;::&#160;&#160;
-        <a href="statepoint.html">3. State Point Binary File Specifications</a>&#160;&#160;»
+        <a href="statepoint.html">5. State Point Binary File Specifications</a>&#160;&#160;»
         </p>
 
       </div>
@@ -53,7 +53,31 @@
         
         
   <div class="section" id="xml-fortran-input-parsing">
-<span id="devguide-xml-fortran"></span><h1>2. xml-fortran Input Parsing<a class="headerlink" href="#xml-fortran-input-parsing" title="Permalink to this headline">¶</a></h1>
+<span id="devguide-xml-fortran"></span><h1>4. xml-fortran Input Parsing<a class="headerlink" href="#xml-fortran-input-parsing" title="Permalink to this headline">¶</a></h1>
+<p>OpenMC relies on the xml-fortran package for reading and intrepreting the XML
+input files for geometry, materials, settings, tallies, etc. The use of an XML
+format makes writing input files considerably more flexible than would otherwise
+be possible.</p>
+<p>With the xml-fortran package, extending the user input files to include new tags
+is fairly straightforward. A &#8220;template&#8221; file exists for each diferent type of
+input file that tells xml-fortran what to expect in a file. These template files
+can be found in the src/templates directory. The steps for modifying/adding
+input are as follows:</p>
+<p>1. Add a <tt class="docutils literal"><span class="pre">&lt;variable&gt;`</span></tt> tag to the desired template file,
+e.g. src/templates/geometry_t.xml. See the <a class="reference external" href="http://xml-fortran.sourceforge.net/documentation.html">xml-fortran documentation</a> for a
+description of the acceptable fields.</p>
+<p>2. In the input_xml module, any input given in your new tag will be read
+automatically through a call to, e.g. read_xml_file_geometry_t. Whatever
+variable name you specified should have the data available.</p>
+<p>3. Add code in the appropriate subroutine to check the variable for any possible
+errors.</p>
+<p>4. Add a variable in OpenMC to copy the temporary variable into if there are no
+errors.</p>
+<p>A set of <a class="reference external" href="http://relaxng.org/">RELAX NG</a> schemata exists that enables real-time validation of input
+files when using the GNU Emacs text editor. You should also modify the RELAX NG
+schema for the template you changed (e.g. src/templates/geometry.rnc) so that
+those who use Emacs can confirm whether their input is valid before they
+run. You will need to be familiar with RELAX NG <a class="reference external" href="http://relaxng.org/compact-tutorial-20030326.html">compact syntax</a>.</p>
 </div>
 
 
@@ -61,11 +85,11 @@
       <div class="bottomnav">
       
         <p>
-        «&#160;&#160;<a href="structures.html">1. Data Structures</a>
+        «&#160;&#160;<a href="workflow.html">3. Development Workflow</a>
         &#160;&#160;::&#160;&#160;
         <a class="uplink" href="../index.html">Contents</a>
         &#160;&#160;::&#160;&#160;
-        <a href="statepoint.html">3. State Point Binary File Specifications</a>&#160;&#160;»
+        <a href="statepoint.html">5. State Point Binary File Specifications</a>&#160;&#160;»
         </p>
 
       </div>

methods/geometry.html

@@ -93,7 +93,7 @@ material, known as &#8220;cells&#8221;.</p>
 </div><p>can be modeled in OpenMC. For example, the equation for a sphere centered at
 <img class="math" src="../_images/math/044ccf810d8b9fed4efe9df70dc0e70667c10381.png" alt="(\bar{x},\bar{y},\bar{z})"/> and of radius <img class="math" src="../_images/math/eff43e84f8a3bcf7b6965f0a3248bc4d3a9d0cd4.png" alt="R"/> can be written as</p>
 <div class="section" id="universes">
-<h3>4.1.1. Universes<a class="headerlink" href="#universes" title="Permalink to this headline">¶</a></h3>
+<span id="id1"></span><h3>4.1.1. Universes<a class="headerlink" href="#universes" title="Permalink to this headline">¶</a></h3>
 <p>OpenMC supports universe-based geometry similar to the likes of <a class="reference external" href="http://mcnp.lanl.gov">MCNP</a> and
 <a class="reference external" href="http://montecarlo.vtt.fi">Serpent</a>. This capability enables user to model any identical repeated
 structures once and then fill them in various spots in the geometry. A
@@ -391,8 +391,8 @@ w' = w - \frac{2 ( \mathbf{\Omega} \cdot \nabla f )}{|| \nabla f ||^2}
 \frac{\partial f}{\partial z}"/></p>
 </div><p>We can now use this form to develop rules for how to transform a particle&#8217;s
 direction for different types of surfaces.</p>
-<div class="section" id="id1">
-<h3>4.7.1. Plane Perpendicular to an Axis<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id2">
+<h3>4.7.1. Plane Perpendicular to an Axis<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
 <p>For a plane that is perpendicular to an axis, the rule for reflection is almost
 so simple that no derivation is needed at all. Nevertheless, we will proceed
 with the derivation to confirm that the rules of geometry agree with our
@@ -406,8 +406,8 @@ the first tell us that</p>
 </div><p>We see that reflection for a plane perpendicular to an axis only entails
 negating the directional cosine for that axis.</p>
 </div>
-<div class="section" id="id2">
-<h3>4.7.2. Generic Plane<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id3">
+<h3>4.7.2. Generic Plane<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
 <p>A generic plane has the form <img class="math" src="../_images/math/320357accceeb2f8fc933f629b9af3ab513e9468.png" alt="f(x,y,z) = Ax + By + Cz - D = 0"/>. Thus, the
 gradient to the surface is simply <img class="math" src="../_images/math/6e5e48810a5cf01884bc6dd93293920d02fa3a4e.png" alt="\nabla f = (A,B,C)"/> whose norm squared
 is <img class="math" src="../_images/math/b8314fe89d6a6080868132447c26fdf3a41466f2.png" alt="A^2 + B^2 + C^2"/>. This implies that</p>
@@ -420,8 +420,8 @@ x-component of the reflected direction will be</p>
 <div class="math" id="equation-reflection-plane">
 <p><span class="eqno">(21)</span><img src="../_images/math/823b09cef32bbcf3b6d605a8574ae69bddc480e6.png" alt="u' = u - \frac{2A(Au + Bv + Cw)}{A^2 + B^2 + C^2}"/></p>
 </div></div>
-<div class="section" id="id3">
-<h3>4.7.3. Cylinder Parallel to an Axis<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id4">
+<h3>4.7.3. Cylinder Parallel to an Axis<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h3>
 <p>A cylinder parallel to, for example, the x-axis has the form <img class="math" src="../_images/math/b815ff99327142275d747ade16d9c36e05d84274.png" alt="f(x,y,z) =
 (y - y_0)^2 + (z - z_0)^2 - R^2 = 0"/>. Thus, the gradient to the surface is</p>
 <div class="math" id="equation-reflection-cylinder-grad">
@@ -445,8 +445,8 @@ and z-components of the reflected direction will be</p>
 
 w' = w - \frac{2 ( \bar{y}v + \bar{z}w ) \bar{z}}{R^2}"/></p>
 </div></div>
-<div class="section" id="id4">
-<h3>4.7.4. Sphere<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id5">
+<h3>4.7.4. Sphere<a class="headerlink" href="#id5" title="Permalink to this headline">¶</a></h3>
 <p>The surface equation for a sphere has the form <img class="math" src="../_images/math/565a202d4c73fb023d968d521bf6059d65f51b74.png" alt="f(x,y,z) = (x - x_0)^2 +
 (y - y_0)^2 + (z - z_0)^2 - R^2 = 0"/>. Thus, the gradient to the surface is</p>
 <div class="math" id="equation-reflection-sphere-grad">

methods/index.html

@@ -99,10 +99,10 @@
 <li class="toctree-l2"><a class="reference internal" href="geometry.html#handling-surface-crossings">4.5. Handling Surface Crossings</a></li>
 <li class="toctree-l2"><a class="reference internal" href="geometry.html#building-neighbor-lists">4.6. Building Neighbor Lists</a></li>
 <li class="toctree-l2"><a class="reference internal" href="geometry.html#reflective-boundary-conditions">4.7. Reflective Boundary Conditions</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="geometry.html#id1">4.7.1. Plane Perpendicular to an Axis</a></li>
-<li class="toctree-l3"><a class="reference internal" href="geometry.html#id2">4.7.2. Generic Plane</a></li>
-<li class="toctree-l3"><a class="reference internal" href="geometry.html#id3">4.7.3. Cylinder Parallel to an Axis</a></li>
-<li class="toctree-l3"><a class="reference internal" href="geometry.html#id4">4.7.4. Sphere</a></li>
+<li class="toctree-l3"><a class="reference internal" href="geometry.html#id2">4.7.1. Plane Perpendicular to an Axis</a></li>
+<li class="toctree-l3"><a class="reference internal" href="geometry.html#id3">4.7.2. Generic Plane</a></li>
+<li class="toctree-l3"><a class="reference internal" href="geometry.html#id4">4.7.3. Cylinder Parallel to an Axis</a></li>
+<li class="toctree-l3"><a class="reference internal" href="geometry.html#id5">4.7.4. Sphere</a></li>
 </ul>
 </li>
 </ul>

publications.html

@@ -29,7 +29,7 @@
     <script type="text/javascript" src="_static/theme_extras.js"></script>
     <link rel="top" title="OpenMC Documentation" href="index.html" />
     <link rel="next" title="License Agreement" href="license.html" />
-    <link rel="prev" title="3. State Point Binary File Specifications" href="devguide/statepoint.html" /> 
+    <link rel="prev" title="5. State Point Binary File Specifications" href="devguide/statepoint.html" /> 
   </head>
   <body>
       <div class="header">
@@ -40,7 +40,7 @@
       <div class="topnav">
       
         <p>
-        «&#160;&#160;<a href="devguide/statepoint.html">3. State Point Binary File Specifications</a>
+        «&#160;&#160;<a href="devguide/statepoint.html">5. State Point Binary File Specifications</a>
         &#160;&#160;::&#160;&#160;
         <a class="uplink" href="index.html">Contents</a>
         &#160;&#160;::&#160;&#160;
@@ -55,17 +55,18 @@
 <span id="id1"></span><h1>Publications<a class="headerlink" href="#publications" title="Permalink to this headline">¶</a></h1>
 <ul class="simple">
 <li>Paul K. Romano and Benoit Forget, &#8220;Reducing Parallel Communication in Monte
-Carlo Simulations via Batch Statistics,&#8221; <em>Trans. Am. Nucl. Soc.</em>, Accepted
-(2012).</li>
+Carlo Simulations via Batch Statistics,&#8221; <em>Trans. Am. Nucl. Soc.</em>, <strong>107</strong>,
+xxx&#8211;xxx (2012).</li>
 <li>Paul K. Romano and Benoit Forget, &#8220;The OpenMC Monte Carlo Particle Transport
-Code,&#8221; <em>Annals of Nuclear Energy</em>, Accepted (2012).</li>
+Code,&#8221; <em>Ann. Nucl. Energy</em>, <strong>51</strong>, 274&#8211;281
+(2012). <a class="reference external" href="http://dx.doi.org/10.1016/j.anucene.2012.06.040">http://dx.doi.org/10.1016/j.anucene.2012.06.040</a></li>
 <li>Andrew R. Siegel, Kord Smith, Paul K. Romano, Benoit Forget, and Kyle Felker,
 &#8220;The effect of load imbalances on the performance of Monte Carlo codes in LWR
-analysis&#8221;, <em>Journal of Computational Physics</em>,
+analysis&#8221;, <em>J. Comput. Phys.</em>,
 <a class="reference external" href="http://dx.doi.org/10.1016/j.jcp.2012.06.012">http://dx.doi.org/10.1016/j.jcp.2012.06.012</a> (2012).</li>
 <li>Paul K. Romano and Benoit Forget, &#8220;Parallel Fission Bank Algorithms in Monte
-Carlo Criticality Calculations,&#8221; <em>Nuclear Science and Engineering</em>, <strong>170</strong>,
-pp. 125&#8211;135 (2012). [<a class="reference external" href="http://web.mit.edu/romano7/www/nse_v170_n2_pp125-135.pdf">PDF</a>]</li>
+Carlo Criticality Calculations,&#8221; <em>Nucl. Sci. Eng.</em>, <strong>170</strong>, 125&#8211;135
+(2012). <a class="reference external" href="http://hdl.handle.net/1721.1/73569">http://hdl.handle.net/1721.1/73569</a></li>
 </ul>
 </div>
 
@@ -74,7 +75,7 @@ pp. 125&#8211;135 (2012). [<a class="reference external" href="http://web.mit.ed
       <div class="bottomnav">
       
         <p>
-        «&#160;&#160;<a href="devguide/statepoint.html">3. State Point Binary File Specifications</a>
+        «&#160;&#160;<a href="devguide/statepoint.html">5. State Point Binary File Specifications</a>
         &#160;&#160;::&#160;&#160;
         <a class="uplink" href="index.html">Contents</a>
         &#160;&#160;::&#160;&#160;

quickinstall.html

@@ -64,7 +64,8 @@ and libraries may be needed. These include:</p>
 <li>A Fortran compiler such as <a class="reference external" href="http://gcc.gnu.org/wiki/GFortran">gfortran</a></li>
 <li><a class="reference external" href="http://git-scm.com">git</a> version control software for obtaining source code (<em>optional</em>)</li>
 <li>An MPI implementation for parallel runs (<em>optional</em>)</li>
-<li><a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5</a> Library for improved output format (<em>optional</em>)</li>
+<li><a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5</a> Library for portable binary output format (<em>optional</em>)</li>
+<li><a class="reference external" href="http://www.mcs.anl.gov/petsc/">PETSc</a> for CMFD acceleration (<em>optional</em>)</li>
 </ul>
 </div>
 <div class="section" id="obtaining-the-source">

usersguide/index.html

@@ -117,6 +117,22 @@ essential aspects of using OpenMC to perform neutronic simulations.</p>
 <li class="toctree-l3"><a class="reference internal" href="input.html#plot-element">3.6.1. <tt class="docutils literal"><span class="pre">&lt;plot&gt;</span></tt> Element</a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="input.html#cmfd-specification-cmfd-xml">3.7. CMFD Specification &#8211; cmfd.xml</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="input.html#active-flush-element">3.7.1. <tt class="docutils literal"><span class="pre">&lt;active_flush&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#begin-element">3.7.2. <tt class="docutils literal"><span class="pre">&lt;begin&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#feedback-element">3.7.3. <tt class="docutils literal"><span class="pre">&lt;feedback&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#inactive-element">3.7.4. <tt class="docutils literal"><span class="pre">&lt;inactive&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#keff-tol-element">3.7.5. <tt class="docutils literal"><span class="pre">&lt;keff_tol&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#ksp-monitor-element">3.7.6. <tt class="docutils literal"><span class="pre">&lt;ksp_monitor&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#id2">3.7.7. <tt class="docutils literal"><span class="pre">&lt;mesh&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#norm-element">3.7.8. <tt class="docutils literal"><span class="pre">&lt;norm&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#n-procs-cmfd-element">3.7.9. <tt class="docutils literal"><span class="pre">&lt;n_procs_cmfd&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#power-monitor-element">3.7.10. <tt class="docutils literal"><span class="pre">&lt;power_monitor&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#write-balance-element">3.7.11. <tt class="docutils literal"><span class="pre">&lt;write_balance&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#write-hdf5-element">3.7.12. <tt class="docutils literal"><span class="pre">&lt;write_hdf5&gt;</span></tt> Element</a></li>
+<li class="toctree-l3"><a class="reference internal" href="input.html#write-matrices-element">3.7.13. <tt class="docutils literal"><span class="pre">&lt;write_matrices&gt;</span></tt> Element</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="troubleshoot.html">4. Troubleshooting OpenMC</a><ul>

usersguide/input.html

@@ -78,16 +78,19 @@ materials, and settings for a Monte Carlo simulation.</p>
 <div class="section" id="overview-of-files">
 <h2>3.1. Overview of Files<a class="headerlink" href="#overview-of-files" title="Permalink to this headline">¶</a></h2>
 <p>To assemble a complete model for OpenMC, one needs to create separate XML files
-for the geometry, materials, and settings. Additionally, there are two optional
+for the geometry, materials, and settings. Additionally, there are three optional
 input files. The first is a tallies XML file that specifies physical quantities
 to be tallied. The second is a plots XML file that specifies regions of geometry
-which should be plotted. OpenMC expects that these files are called:</p>
+which should be plotted. The third is a CMFD XML file that specifies coarse mesh
+acceleration geometry and execution parameters. OpenMC expects that these
+files are called:</p>
 <ul class="simple">
 <li><tt class="docutils literal"><span class="pre">geometry.xml</span></tt></li>
 <li><tt class="docutils literal"><span class="pre">materials.xml</span></tt></li>
 <li><tt class="docutils literal"><span class="pre">settings.xml</span></tt></li>
 <li><tt class="docutils literal"><span class="pre">tallies.xml</span></tt></li>
 <li><tt class="docutils literal"><span class="pre">plots.xml</span></tt></li>
+<li><tt class="docutils literal"><span class="pre">cmfd.xml</span></tt></li>
 </ul>
 </div>
 <div class="section" id="settings-specification-settings-xml">
@@ -526,7 +529,7 @@ could be written as:</p>
 </pre></div>
 </div>
 <div class="section" id="surface-element">
-<h3>3.3.1. <tt class="docutils literal"><span class="pre">&lt;surface&gt;</span></tt> Element<a class="headerlink" href="#surface-element" title="Permalink to this headline">¶</a></h3>
+<span id="id1"></span><h3>3.3.1. <tt class="docutils literal"><span class="pre">&lt;surface&gt;</span></tt> Element<a class="headerlink" href="#surface-element" title="Permalink to this headline">¶</a></h3>
 <p>Each <tt class="docutils literal"><span class="pre">&lt;surface&gt;</span></tt> element can have the following attributes or sub-elements:</p>
 <blockquote>
 <div><table class="docutils field-list" frame="void" rules="none">
@@ -588,6 +591,18 @@ coefficients specified are &#8220;<img class="math" src="../_images/math/d9efe2f
 <tr class="field-even field"><th class="field-name">sphere:</th><td class="field-body">A sphere of the form <img class="math" src="../_images/math/62a745995df775198e16354b6b1ed9887e88c8a2.png" alt="(x - x_0)^2 + (y - y_0)^2 + (z - z_0)^2 =
 R^2"/>. The coefficients specified are &#8220;<img class="math" src="../_images/math/e13d971231512283e81d8480a218782f7d68b585.png" alt="x_0 \: y_0 \: z_0 \: R"/>&#8221;.</td>
 </tr>
+<tr class="field-odd field"><th class="field-name">x-cone:</th><td class="field-body">A cone parallel to the x-axis of the form <img class="math" src="../_images/math/48addcaae47a04de47d2a40f0095c771ec2ce891.png" alt="(y - y_0)^2 + (z - z_0)^2 =
+R^2 (x - x_0)^2"/>. The coefficients specified are &#8220;<img class="math" src="../_images/math/0ef6215a44c46c244ccd86bf6aadaa33b87b4e6d.png" alt="x_0 \: y_0 \: z_0
+\: R^2"/>&#8221;.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">y-cone:</th><td class="field-body">A cone parallel to the y-axis of the form <img class="math" src="../_images/math/d939cb7e10ed48f1e43b0dd6c646e423a581ab40.png" alt="(x - x_0)^2 + (z - z_0)^2 =
+R^2 (y - y_0)^2"/>. The coefficients specified are &#8220;<img class="math" src="../_images/math/0ef6215a44c46c244ccd86bf6aadaa33b87b4e6d.png" alt="x_0 \: y_0 \: z_0
+\: R^2"/>&#8221;.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">z-cone:</th><td class="field-body">A cone parallel to the x-axis of the form <img class="math" src="../_images/math/2d94d2e3228f1977c395a51961b7184af5514ca7.png" alt="(x - x_0)^2 + (y - y_0)^2 =
+R^2 (z - z_0)^2"/>. The coefficients specified are &#8220;<img class="math" src="../_images/math/0ef6215a44c46c244ccd86bf6aadaa33b87b4e6d.png" alt="x_0 \: y_0 \: z_0
+\: R^2"/>&#8221;.</td>
+</tr>
 </tbody>
 </table>
 </div></blockquote>
@@ -1058,6 +1073,175 @@ materials to plot.  This overrides any <tt class="docutils literal"><span class=
 </div></blockquote>
 </div>
 </div>
+<div class="section" id="cmfd-specification-cmfd-xml">
+<h2>3.7. CMFD Specification &#8211; cmfd.xml<a class="headerlink" href="#cmfd-specification-cmfd-xml" title="Permalink to this headline">¶</a></h2>
+<p>Coarse mesh finite difference acceleration method has been implemented in OpenMC.
+Currently, it allows users to accelerate fission source convergence during
+inactive neutron batches. To run CMFD, the <tt class="docutils literal"><span class="pre">&lt;run_cmfd&gt;</span></tt> element in
+<tt class="docutils literal"><span class="pre">settings.xml</span></tt> should be set to <tt class="docutils literal"><span class="pre">.true.</span></tt>.</p>
+<div class="section" id="active-flush-element">
+<h3>3.7.1. <tt class="docutils literal"><span class="pre">&lt;active_flush&gt;</span></tt> Element<a class="headerlink" href="#active-flush-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;active_flush&gt;</span></tt> element controls the batch where CMFD tallies should be
+reset. CMFD tallies should be reset before active batches so they are accumulated
+without bias.</p>
+<blockquote>
+<div><em>Default</em>: 0</div></blockquote>
+</div>
+<div class="section" id="begin-element">
+<h3>3.7.2. <tt class="docutils literal"><span class="pre">&lt;begin&gt;</span></tt> Element<a class="headerlink" href="#begin-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;begin&gt;</span></tt> element controls what batch CMFD calculations should begin.</p>
+<blockquote>
+<div><em>Default</em>: 1</div></blockquote>
+</div>
+<div class="section" id="feedback-element">
+<h3>3.7.3. <tt class="docutils literal"><span class="pre">&lt;feedback&gt;</span></tt> Element<a class="headerlink" href="#feedback-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;feedback&gt;</span></tt> element controls whether or not the CMFD diffusion result is
+used to adjust the weight of fission source neutrons on the next OpenMC batch.
+It can be turned on with &#8221;.true.&#8221; and off with &#8221;.false.&#8221;.</p>
+<blockquote>
+<div><em>Default</em>: .false.</div></blockquote>
+</div>
+<div class="section" id="inactive-element">
+<h3>3.7.4. <tt class="docutils literal"><span class="pre">&lt;inactive&gt;</span></tt> Element<a class="headerlink" href="#inactive-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;inactive&gt;</span></tt> element controls if cmfd tallies should be accumulated
+during inactive batches. For some applications, CMFD tallies may not be
+needed until the start of active batches. This option can be turned on
+with &#8221;.true.&#8221; and off with &#8221;.false.&#8221;</p>
+<blockquote>
+<div><em>Default</em>: .true.</div></blockquote>
+</div>
+<div class="section" id="keff-tol-element">
+<h3>3.7.5. <tt class="docutils literal"><span class="pre">&lt;keff_tol&gt;</span></tt> Element<a class="headerlink" href="#keff-tol-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;keff_tol&gt;</span></tt> element specifies acceptance criteria of a CMFD eigenvalue.
+If the CMFD eigenvalue and OpenMC batch eigenvalue are within this tolerance,
+CMFD is allowed to modify source neutron weights.</p>
+<blockquote>
+<div><em>Default</em>: 0.005</div></blockquote>
+</div>
+<div class="section" id="ksp-monitor-element">
+<h3>3.7.6. <tt class="docutils literal"><span class="pre">&lt;ksp_monitor&gt;</span></tt> Element<a class="headerlink" href="#ksp-monitor-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;ksp_monitor&gt;</span></tt> element is used to view the convergence of linear GMRES
+iterations in PETSc. This option can be turned on with &#8221;.true.&#8221; and turned off
+with &#8221;.false.&#8221;.</p>
+<blockquote>
+<div><em>Default</em>: .false.</div></blockquote>
+</div>
+<div class="section" id="id2">
+<h3>3.7.7. <tt class="docutils literal"><span class="pre">&lt;mesh&gt;</span></tt> Element<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
+<p>If a structured mesh is desired as a filter for a tally, it must be specified in
+a separate element with the tag name <tt class="docutils literal"><span class="pre">&lt;mesh&gt;</span></tt>. This element has the following
+attributes/sub-elements:</p>
+<blockquote>
+<div><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">type:</th><td class="field-body"><p class="first">The type of structured mesh. Only &#8220;rectangular&#8221; is currently supported.</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">lower_left:</th><td class="field-body"><p class="first">The lower-left corner of the structured mesh. If only two coordinate are
+given, it is assumed that the mesh is an x-y mesh.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">upper_right:</th><td class="field-body"><p class="first">The upper-right corner of the structrued mesh. If only two coordinate are
+given, it is assumed that the mesh is an x-y mesh.</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">dimension:</th><td class="field-body"><p class="first">The number of mesh cells in each direction.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">width:</th><td class="field-body"><p class="first">The width of mesh cells in each direction.</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">energy:</th><td class="field-body"><p class="first">Energy bins [in MeV], listed in ascending order (e.g. 0.0 0.625e-7 20.0)
+for CMFD tallies and acceleration. If no energy bins are listed, OpenMC
+automatically assumes a one energy group calculation over the entire
+energy range.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">albedo:</th><td class="field-body"><p class="first">Surface ratio of incoming to outgoing partial currents on global boundary
+conditions. They are listed in the following order: -x +x -y +y -z +z.</p>
+<p><em>Default</em>: 1.0 1.0 1.0 1.0 1.0 1.0</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">map:</th><td class="field-body"><p class="first">An optional acceleration map can be specified to overlay on the coarse
+mesh spatial grid. If this option is used a <tt class="docutils literal"><span class="pre">1</span></tt> is used for a
+non-accelerated region and a <tt class="docutils literal"><span class="pre">2</span></tt> is used for an accelerated region.
+For a simple 4x4 coarse mesh with a 2x2 fuel lattice surrounded by
+reflector, the map is:</p>
+<blockquote>
+<div><p><tt class="docutils literal"><span class="pre">1</span> <span class="pre">1</span> <span class="pre">1</span> <span class="pre">1</span></tt></p>
+<p><tt class="docutils literal"><span class="pre">1</span> <span class="pre">2</span> <span class="pre">2</span> <span class="pre">1</span></tt></p>
+<p><tt class="docutils literal"><span class="pre">1</span> <span class="pre">2</span> <span class="pre">2</span> <span class="pre">1</span></tt></p>
+<p><tt class="docutils literal"><span class="pre">1</span> <span class="pre">1</span> <span class="pre">1</span> <span class="pre">1</span></tt></p>
+</div></blockquote>
+<p>Therefore a 2x2 system of equations is solved rather than a 4x4. This
+is extremely important to use in reflectors as neutrons will not
+contribute to any tallies far away from fission source neutron regions.
+A <tt class="docutils literal"><span class="pre">2</span></tt> must be used to identify any fission source region.</p>
+<div class="last admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">Only two of the following three sub-elements are needed:
+<tt class="docutils literal"><span class="pre">lower_left</span></tt>, <tt class="docutils literal"><span class="pre">upper_right</span></tt> and <tt class="docutils literal"><span class="pre">width</span></tt>. Any combination
+of two of these will yield the third.</p>
+</div>
+</td>
+</tr>
+</tbody>
+</table>
+</div></blockquote>
+</div>
+<div class="section" id="norm-element">
+<h3>3.7.8. <tt class="docutils literal"><span class="pre">&lt;norm&gt;</span></tt> Element<a class="headerlink" href="#norm-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;norm&gt;</span></tt> element is used to normalize the CMFD fission source distribution
+to a particular value. For example, if a fission source is calculated for a
+17 x 17 lattice of pins, the fission source may be normalized to the number of
+fission source regions, in this case 289. This is useful when visualizing this
+distribution as the average peaking factor will be unity. This parameter will
+not impact the calculation.</p>
+<blockquote>
+<div><em>Default</em>: 1.0</div></blockquote>
+</div>
+<div class="section" id="n-procs-cmfd-element">
+<h3>3.7.9. <tt class="docutils literal"><span class="pre">&lt;n_procs_cmfd&gt;</span></tt> Element<a class="headerlink" href="#n-procs-cmfd-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;n_procs_cmfd&gt;</span></tt> element is used to set the number of processors used
+for CMFD calculation. It should be less than or equal to the number of
+processors used during OpenMC.</p>
+<blockquote>
+<div><em>Default</em>: 1</div></blockquote>
+</div>
+<div class="section" id="power-monitor-element">
+<h3>3.7.10. <tt class="docutils literal"><span class="pre">&lt;power_monitor&gt;</span></tt> Element<a class="headerlink" href="#power-monitor-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;power_monitor&gt;</span></tt> element is used to view the convergence of power iteration.
+This option can be turned on with &#8221;.true.&#8221; and turned off with &#8221;.false.&#8221;.</p>
+<blockquote>
+<div><em>Default</em>: .false.</div></blockquote>
+</div>
+<div class="section" id="write-balance-element">
+<h3>3.7.11. <tt class="docutils literal"><span class="pre">&lt;write_balance&gt;</span></tt> Element<a class="headerlink" href="#write-balance-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;write_balance&gt;</span></tt> element is used to view the balance of OpenMC tally
+residuals for every coarse mesh region and energy group. This option can be
+turned on with &#8221;.true.&#8221; and off with &#8221;.false.&#8221;.</p>
+<blockquote>
+<div><em>Default</em>: .false.</div></blockquote>
+</div>
+<div class="section" id="write-hdf5-element">
+<h3>3.7.12. <tt class="docutils literal"><span class="pre">&lt;write_hdf5&gt;</span></tt> Element<a class="headerlink" href="#write-hdf5-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;write_hdf5&gt;</span></tt> element can be turned on with &#8221;.true.&#8221; to get an
+HDF5 output file of CMFD results.</p>
+<blockquote>
+<div><em>Default</em>: .false.</div></blockquote>
+</div>
+<div class="section" id="write-matrices-element">
+<h3>3.7.13. <tt class="docutils literal"><span class="pre">&lt;write_matrices&gt;</span></tt> Element<a class="headerlink" href="#write-matrices-element" title="Permalink to this headline">¶</a></h3>
+<p>The <tt class="docutils literal"><span class="pre">&lt;write_matrices&gt;</span></tt> element is used to view the PETSc sparse matrices
+created when solving CMFD equations. These binary output files can be imported
+into MATLAB using PETSc-MATLAB utilities. This option can be
+turned on with &#8221;.true.&#8221; and off with &#8221;.false.&#8221;.</p>
+<blockquote>
+<div><em>Default</em>: .false.</div></blockquote>
+</div>
+</div>
 </div>
 
 

usersguide/install.html

@@ -76,6 +76,9 @@ sudo apt-get install openmpi-bin</pre>
 <p>To compile with support for <a class="reference external" href="http://www.hdfgroup.org/HDF5/">HDF5</a> output (highly recommended), you will need to
 have HDF5 installed on your computer. The installed version will need to have
 been compiled with the same compiler you intend to compile OpenMC with.</p>
+<p>To enable CMFD acceleration, you will need to have <a class="reference external" href="http://www.mcs.anl.gov/petsc/">PETSc</a> installed on your
+computer. The installed version will need to have been compiled with the same
+compiler you intend to compile OpenMC with.</p>
 </div>
 <div class="section" id="obtaining-the-source">
 <h2>2.2. Obtaining the Source<a class="headerlink" href="#obtaining-the-source" title="Permalink to this headline">¶</a></h2>